Note: Descriptions are shown in the official language in which they were submitted.
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VOLUME
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CONTAINING PAGES 1 TO 172
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SYSTEMS AND METHODS OF SAMPLE DEPOSITING AND TESTING
CROSS REFERENCE TO RELATED APPLICATIONS
[0001] This application claims priority to U.S. Prov. App. No. 63/066047 filed
August 14, 2020 entitled "SYSTEMS AND METHODS OF SAMPLE DEPOSITING AND
TESTING" which is incorporated by reference in its entirety.
REFERENCE TO SEQUENCE LISTING
[0002] The present application is being filed along with a Sequence Listing in
electronic format. The Sequence Listing is provided as a file entitled
ALVE0057WOSEQLIST, created August 3, 2021, which is approximately 37 Kb in
size.
The information in the electronic format of the Sequence Listing is
incorporated herein by
reference in its entirety.
FIELD
[0003] The present application is generally directed to systems, methods, and
devices
for sensing and/or identifying pathogens, genomic materials, proteins, and/or
other small
molecules or biomarkers and using historical sensing and testing results to
track a subject's
or product's wellness score or likelihood of being infected with a trackable
pathogen. More
specifically, the systems, methods, and devices described herein determine
whether the
subject or product is infected with a pathogen and/or generate a score
representative of the
subject's or product's health or wellness or consumability, where a score that
deviates from
a set threshold value, such as a higher or lower value depending on the
parameters of the
threshold set, indicates that the subject or product is healthy, well, or
suitable for
consumption, not infected with a pathogen and/or is of low risk to others in a
population or
indicates that the subject or product has compromised health, is infected with
a pathogen, not
suitable for consumption, and/or is a risk to others in the population.
BACKGROUND
[0004] Pathogens in a sample may be identified by detecting specific genomic
material (DNA or RNA). In conventional nucleic acid testing ("NAAT"), genomic
material
in a sample may first be exponentially copied using a molecular amplification
process known
as the polymerase chain reaction ("PCR") until the quantity of DNA present is
great enough
to be measurable. In the case of RNA, the genomic material of many viruses, an
additional
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step can be included to first transcribe the RNA into DNA before amplifying by
PCR. As an
alternative, loop-mediated isothermal amplification (LAMP) oilers several
advantages over
PC12. for pathogen detection purposes, including the ability to perform the
amplification
reaction at a non-cyclical and relatively low temperature. There is a lasting
need for improved
pathogen detection methods and tools, e.g., using LAMP, particularly in
geographical
regions where the use of complex laboratory equipment is not feasible.
SUMMARY
[0005] Some embodiments include an assay cartridge for containing a sample
comprising a target agent for detection by a reader device, the assay
cartridge comprising: a
sample introduction area configured to receive a sample carrier containing the
sample; a
mixing region configured to mix the sample with a reagent to generate a sample
mixture; at
least one mixing object disposed in the mixing region and configured to move
within the
mixing region to enhance mixing of the sample with the reagent in response to
a force applied
to the mixing region; a test well containing an excitation electrode and a
sensing electrode,
wherein the test well is configured to contain at least a portion of the
sample mixture
undergoing an amplification process; and a fluid path fluidically coupling the
sample
introduction area to the mixing region and the mixing region to the test well.
[0006] In some embodiments, the force applied is the result of one or more of
a
magnetic field generator, a vibration generator, a sonic generator, and
physical movement.
[0007] In some embodiments, the reagent comprises one of a dry reagent or a
liquid
reagent.
[0008] In some embodiments, the at least one mixing object comprises at least
one
magnetic bead and wherein the force is exerted by a first magnetic field
generated by a first
magnet, such as an electromagnet disposed in the reader near a first location
of the mixing
region when the assay cartridge is inserted into the reader.
[0009] In some embodiments, the force is further exerted by a second magnetic
field
generated by a second magnet, such as an electromagnet disposed in the reader
near a second
location of the mixing region when the assay cartridge is inserted into the
reader.
[0010] Some embodiments include a control circuit configured to switch between
which of the first magnet and the second magnetic is exerting the force at a
given moment.
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[0011] In some embodiments, the force is exerted by a movable force generator
disposed in the reader.
[0012] In some embodiments, one or more of the sample introduction area, the
mixing region, the test well, and the fluid path introduces an agent that
reduces effects of one
or more inhibitors that exist in the sample.
[0013] In some embodiments, the one or more of the sample introduction area,
the
mixing region, the test well, and the fluid path are coated with the agent.
[0014] In some embodiments, the reagent includes the agent that reduces
effects of
the one or more inhibitors.
[0015] In some embodiments, the one or more inhibitors that exist in the
sample
comprise one or more of lactoferrin, lysozyme, nucleases, DNAses, or RNases
and wherein
the agent is configured to improve a detection sensitivity of testing
performed with the assay
cartridge and the reader, preferably by inhibiting said one or more
inhibitors.
[0016] In some embodiments, the agent comprises one or more of an antibody,
aptamer, competitive binding protein or a proteinase and, optionally wherein
said proteinase
is inactivated by a chemical reaction, which produces heat once the proteinase
has digested
the protein in the sample.
[0017] Some embodiments also include a cap having an open configuration and a
closed configuration, wherein when the cap is in the open configuration, the
sample
introduction area is configured to receive the sample carrier, and wherein
when the cap in
the closed configuration, the sample receptacle is sealed.
[0018] Some embodiments also include a scraper inside the sample introduction
area,
the scraper configured to contact the sample carrier when the sample carrier
is position inside
the sample introduction area and facilitate collection of the sample.
[0019] Some embodiments also include a retainer inside the sample introduction
area, wherein the retainer is configured to hold the sample carrier in place
inside the sample
introduction area, and wherein at least a portion of the sample is collected
from the sample
carrier.
[0020] In some embodiments, the sample carrier comprises bristles or flock
configured to collect the sample.
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[0021] In some embodiments, the sample carrier comprises a stopper configured
to
abut an opening of the sample introduction area to prevent the sample carrier
from entering
further into the sample introduction area.
[0022] In some embodiments, the sample carrier comprises a marked section
configured to indicate a position to break or cut the sample collection device
after being
inserted into the sample receptacle.
[0023] Some embodiments also include: a first storage device storing a first
fluid; a
second storage device storing a second fluid; and wherein the first fluid or
the second fluid
or both are configured to facilitate recovery of at least a portion of the
sample from the sample
carrier or facilitate transport of at least a portion of the sample from the
sample introduction
area to the mixing region or both.
[0024] In some embodiments, the first or second fluids comprise a buffer, and
wherein the first or second fluids comprise a reagent configured to react with
at least a portion
of the biological sample, such as one or more salts e.g., magnesium.
[0025] In some embodiments, the first storage device and the second storage
device
are compressible, and wherein the first storage device and the second storage
device are
configured to release the first fluid and the second fluid, respectively, when
compressed.
[0026] Some embodiments include an assay cartridge for containing a sample
comprising a target agent for detection by a reader device, the assay
cartridge comprising: a
sample introduction area configured to receive a sample carrier containing the
sample; a
mixing region configured to mix the sample with a reagent to generate a sample
mixture; a
test well containing an excitation electrode and a sensing electrode, wherein
the test well is
configured to contain at least a portion of the sample mixture undergoing an
amplification
process; and a fluid path fluidically coupling the sample introduction area to
the mixing
region and the mixing region to the test well, wherein one or more of the
sample introduction
area, the mixing region, the test well, and the fluid path introduces an agent
that reduces
effects of one or more inhibitors that exist in the sample.
[0027] In some embodiments, the one or more of the sample introduction area,
the
mixing region, the test well, and the fluid path are coated with the agent.
[0028] In some embodiments, the reagent includes the agent that reduces
effects of
the one or more inhibitors.
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[0029] In some embodiments, the one or more inhibitors that exist in the
sample
comprise one or more of lactoferrin, lysozyme, nucleases, DNAses or RNases and
wherein
the agent is configured to improve a detection sensitivity of testing
performed with the assay
cartridge and the reader preferably by inhibiting the one or more inhibitors.
[0030] In some embodiments, the agent comprises one or more of an antibody,
aptamer, competitive binding protein or a proteinase and optionally wherein
said proteinase
is inactivated after digesting protein in the sample by a chemical reaction
that creates heat.
[0031] Some embodiments also include at least one mixing object disposed in
the
mixing region and configured to move within the mixing region to enhance
mixing of the
sample with the reagent in response to a force applied to the mixing region.
[0032] In some embodiments, the force applied is the result of one or more of
a
magnetic field generator, a vibration generator, a sonic generator, and
physical movement.
[0033] In some embodiments, the reagent comprises one of a thy reagent or a
liquid
reagent.
[0034] In some embodiments, the at least one mixing object comprises at least
one
magnetic bead and wherein the force is exerted by a first magnetic field
generated by a first
magnet such as an electromagnet disposed in the reader near a first location
of the mixing
region when the assay cartridge is inserted into the reader.
[0035] In some embodiments, the force is further exerted by a second magnetic
field
generated by a second magnet, such as an electromagnet disposed in the reader
near a second
location of the mixing region when the assay cartridge is inserted into the
reader.
[0036] Some embodiments also include a control circuit configured to switch
between which of the first magnet and the second magnetic is exerting the
force at a given
moment.
[0037] Some embodiments also include a cap having an open configuration and a
closed configuration, wherein when the cap is in the open configuration, the
sample
introduction area is configured to receive the sample carrier, and wherein
when the cap in
the closed configuration, the sample receptacle is sealed.
[0038] Some embodiments also include a scraper inside the sample instruction
area,
the scraper configured to contact the sample carrier when the sample carrier
is position inside
the sample introduction area and facilitate collection of the sample.
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[0039] Some embodiments also include a retainer inside the sample introduction
area, wherein the retainer is configured to hold the sample carrier in place
inside the sample
introduction area, and wherein at least a portion of the sample is collected
from the sample
carrier.
[0040] In some embodiments, the sample carrier comprises bristles or flock
configured to collect the sample.
[0041] In some embodiments, the sample carrier comprises a stopper configured
to
abut an opening of the sample introduction area to prevent the sample carrier
from entering
further into the sample introduction area.
[0042] In some embodiments, the sample collection device comprises a marked
section configured to indicate a position to break or cut the sample
collection device after
being inserted into the sample receptacle.
[0043] Some embodiments also include: a first storage device storing a first
fluid; a
second storage device storing a second fluid; and wherein the first fluid or
the second fluid
or both are configured to facilitate recovery of at least a portion of the
sample from the sample
carrier or facilitate transport of at least a portion of the sample from the
sample introduction
area to the mixing region or both.
[0044] In some embodiments, the first or second fluids comprise a buffer, and
wherein the first or second fluids comprise a reagent configured to react with
at least a portion
of the biological sample, such as one or more salts e.g., magnesium.
[0045] In some embodiments, the first storage device and the second storage
device
are compressible, and wherein the first storage device and the second storage
device are
configured to release the first fluid and the second fluid, respectively, when
compressed.
[0046] In some embodiments, the sample carrier comprises: a body configured to
hold the sample before depositing the sample into the assay cartridge; a tip
fluidically
coupled to the body and configured to fit into the sample introduction area of
the assay
cartridge, wherein the sample held in the body can be ejected from the sample
carrier via the
tip; and a membrane disposed between the body and the tip and configured to
prevent
molecules in the sample that exceed a threshold size from being ejected from
the body via
the tip.
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[0047] In some embodiments, the sample carrier further comprises a gel
filtration
component, resin, size exclusion matrix, membrane, or resin, or filter such as
a molecular
weight filter configured to trap salt compounds in the sample such that the
salt compounds
are not ejected from the body via the tip.
[0048] In some embodiments, the gel filtration component comprises one of a
gel
filtration bead bed or a gel filtration matrix.
[0049] In some embodiments, the sample carrier further comprises a buffer
component configured to assist in extracting the target agent from the sample.
[0050] In some embodiments, the butler component comprises one of an elution
buffer or a lysis buffer.
[0051] In some embodiments, the sample carrier further comprises a plunger
component configured to apply a force to the sample in the body and cause the
sample to
pass through the membrane and the tip and into the sample introduction area of
the assay
cartridge.
[0052] In some embodiments, the sample carrier comprises bristles or flock
configured to collect or hold the sample.
[0053] In some embodiments, the sample carrier comprises a stopper configured
to
abut an opening of the sample introduction area to prevent the sample carrier
from entering
further into the sample introduction area.
[0054] In some embodiments, the sample carrier comprises a marked section
configured to indicate a position to break or cut the sample carrier after
being inserted into
the sample introduction area.
[0055] Some embodiments include a system for detecting a target agent in a
sample
using an assay cartridge and a reader, the system comprising: the assay
cartridge, comprising:
a sample introduction area configured to receive a sample carrier containing
the sample; and
the sample carrier for depositing the sample into the assay cartridge, the
sample carrier
comprising: a body configured to hold the sample before depositing the sample
into the assay
cartridge; a tip fluidically coupled to the body and configured to fit into
the sample
introduction area of the assay cartridge, wherein the sample held in the body
can be ejected
from the sample carrier via the tip; and a membrane disposed between the body
and the tip
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and configured to prevent molecules in the sample that exceed a threshold size
from being
ejected from the body via the tip.
[0056] In some embodiments, the sample carrier further comprises a gel
filtration
component, resin, size exclusion matrix, membrane, or resin, or filter such as
a molecular
weight filter configured to trap salt compounds in the sample such that the
salt compounds
are not ejected from the body via the tip.
[0057] In some embodiments, the gel filtration component comprises one of a
gel
filtration bead bed or a gel filtration matrix.
[0058] In some embodiments, the sample carrier further comprises a buffer
component configured to assist in extracting the target agent from the sample.
[0059] In some embodiments, the buffer component comprises one of an elution
buffer or a lysis buffer.
[0060] In some embodiments, the sample carrier further comprises a plunger
component configured to apply a force to the sample in the body and cause the
sample to
pass through the membrane and the tip and into the sample introduction area of
the assay
cartridge.
[0061] In some embodiments, the assay cartridge further comprises: a mixing
region
configured to mix the sample with a reagent to generate a sample mixture; at
least one mixing
object disposed in the mixing region and configured to move within the mixing
region to
enhance mixing of the sample with the reagent in response to a force applied
to the mixing
region; a test well containing an excitation electrode and a sensing
electrode, wherein the test
well is configured to contain at least a portion of the sample mixture
undergoing an
amplification process; and a fluid path fluidically coupling the sample
introduction area to
the mixing region and the mixing region to the test well.
[0062] In some embodiments, the force applied is the result of one or more of
a
magnetic field generator, a vibration generator, a sonic generator, and
physical movement.
[0063] In some embodiments, the reagent comprises one of a dry reagent or a
liquid
reagent.
[0064] In some embodiments, the at least one mixing object comprises at least
one
magnetic bead and wherein the force is exerted by a first magnetic field
generated by a first
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magnet such as an electromagnet disposed in the reader near a first location
of the mixing
region when the assay cartridge is inserted into the reader.
[0065] In some embodiments, the force is further exerted by a second magnetic
field
generated by a second magnet such as an electromagnet disposed in the reader
near a second
location of the mixing region when the assay cartridge is inserted into the
reader.
[0066] Some embodiments also include a control circuit configured to switch
between which of the first magnet and the second magnetic is exerting the
force at a given
moment.
[0067] In some embodiments, the force is exerted by a movable force generator
disposed in the reader.
[0068] In some embodiments, one or more of the sample introduction area, the
mixing region, the test well, and the fluid path introduces an agent that
reduces effects of one
or more inhibitors that exist in the sample.
[0069] In some embodiments, the one or more of the sample introduction area,
the
mixing region, the test well, and the fluid path are coated with the agent.
[0070] In some embodiments, the reagent includes the agent that reduces
effects of
the one or more inhibitors.
[0071] In some embodiments, the inhibitors that exist in the sample comprise
one or
more of lactoferrin, lysozyme, nucleases, DNAses or kNases and wherein the
agent is
configured to improve a detection sensitivity of testing performed with the
assay cartridge
and the reader.
[0072] In some embodiments, the agent comprises one or more of an antibody,
aptamer, competitive binding protein or a proteinase and optionally wherein
said proteinase
is inactivated after digesting protein in the sample by a chemical reaction
that creates heat.
[0073] In some embodiments, the assay cartridge comprises a cap having an open
configuration and a closed configuration, wherein when the cap is in the open
configuration,
the sample introduction area is configured to receive the sample carrier, and
wherein when
the cap in the closed configuration, the sample introduction area is sealed.
[0074] In some embodiments, the assay cartridge comprises a scraper inside the
sample introduction area, the scraper configured to contact the sample carrier
when the
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sample carrier is position inside the sample introduction area and facilitate
collection of the
sample.
[0075] In some embodiments, the assay cartridge comprises a retainer inside
the
sample introduction area, wherein the retainer is configured to hold the
sample carrier in
place inside the sample introduction area, and wherein at least a portion of
the sample is
collected from the sample carrier.
[0076] In some embodiments, the sample carrier comprises bristles or flock
configured to collect the sample.
[0077] In some embodiments, the sample carrier comprises a stopper configured
to
abut an opening of the sample introduction area to prevent the sample carrier
from entering
further into the sample introduction area.
[0078] In some embodiments, the sample carrier comprises a marked section
configured to indicate a position to break or cut the sample collection device
after being
inserted into the sample receptacle.
[0079] In some embodiments, the assay cartridge further comprises: a first
storage
device storing a first fluid; a second storage device storing a second fluid;
and wherein the
first fluid or the second fluid or both are configured to facilitate recovery
of at least a portion
of the sample from the sample carrier or facilitate transport of at least a
portion of the sample
from the sample introduction area to the mixing region or both.
[0080] In some embodiments, the first or second fluids comprise a buffer, and
wherein the first or second fluids comprise a reagent configured to react with
at least a portion
of the biological sample, such as one or more salts e.g., magnesium.
[0081] In some embodiments, the first storage device and the second storage
device
are compressible, and wherein the first storage device and the second storage
device are
configured to release the first fluid and the second fluid, respectively, when
compressed.
[0082] In some embodiments, the assay cartridge further comprises: a mixing
region
configured to mix the sample with a reagent to generate a sample mixture; a
test well
containing an excitation electrode and a sensing electrode, wherein the test
well is configured
to contain at least a portion of the sample mixture undergoing an
amplification process; and
a fluid path fluidically coupling the sample introduction area to the mixing
region and the
mixing region to the test well, wherein one or more of the sample introduction
area, the
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mixing region, the test well, and the fluid path introduces an agent that
reduces effects of one
or more inhibitors that exist in the sample.
[0083] In some embodiments, the one or more of the sample introduction area,
the
mixing region, the test well, and the fluid path are coated with the agent.
[0084] In some embodiments, the reagent includes the agent that reduces
effects of
the one or more inhibitors.
[0085] In some embodiments, the inhibitors that exist in the sample comprise
one or
more of lactoferrin, lysozyme, or RNases and wherein the agent is configured
to improve a
detection sensitivity of testing performed with the assay cartridge and the
reader.
[0086] In some embodiments, the agent comprises one or more of an antibody,
aptamer, competitive binding protein or a proteinase and optionally wherein
said proteinase
is inactivated after digesting protein in the sample by a chemical reaction
that creates heat.
[0087] Some embodiments also include at least one mixing object disposed in
the
mixing region and configured to move within the mixing region to enhance
mixing of the
sample with the reagent in response to a force applied to the mixing region.
[0088] In some embodiments, the force applied is the result of one or more of
a
magnetic field generator, a vibration generator, a sonic generator, and
physical movement.
[0089] In some embodiments, the reagent comprises one of a dry reagent or a
liquid
reagent.
[0090] In some embodiments, the at least one mixing object comprises at least
one
magnetic bead and wherein the force is exerted by a first magnetic field
generated by a first
magnet such as an electromagnet disposed in the reader near a first location
of the mixing
region when the assay cartridge is inserted into the reader.
[0091] In some embodiments, the force is further exerted by a second magnetic
field
generated by a second magnet such as an electromagnet disposed in the reader
near a second
location of the mixing region when the assay cartridge is inserted into the
reader.
[0092] Some embodiments also include a control circuit configured to switch
between which of the first magnet and the second magnetic is exerting the
force at a given
moment.
[0093] In some embodiments, the assay cartridge comprises a cap having an open
configuration and a closed configuration, wherein when the cap is in the open
configuration,
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the sample introduction area is configured to receive the sample carrier, and
wherein when
the cap in the closed configuration, the sample receptacle is sealed.
[0094] In some embodiments, the assay cartridge comprises a scraper inside the
sample instruction area, the scraper configured to contact the sample carrier
when the sample
carrier is position inside the sample introduction area and facilitate
collection of the sample.
[0095] In some embodiments, the assay cartridge comprises a retainer inside
the
sample introduction area, wherein the retainer is configured to hold the
sample carrier in
place inside the sample introduction area, and wherein at least a portion of
the sample is
collected from the sample carrier.
[0096] In some embodiments, the sample carrier comprises bristles or flock
configured to collect the sample.
[0097] In some embodiments, the sample carrier comprises a stopper configured
to
abut an opening of the sample introduction area to prevent the sample carrier
from entering
further into the sample introduction area.
[0098] In some embodiments, the sample collection device comprises a marked
section configured to indicate a position to break or cut the sample
collection device after
being inserted into the sample receptacle.
[0099] In some embodiments, the sample introduction area is configured to
receive
a sample carrier.
[0100] In some embodiments, the sample carrier comprises bristles or flock
configured to collect the sample.
[0101] In some embodiments, the sample carrier comprises a stopper configured
to
abut an opening of the sample introduction area to prevent the sample carrier
from entering
further into the sample introduction area.
[0102] In some embodiments, the sample collection device comprises a marked
section configured to indicate a position to break or cut the sample
collection device after
being inserted into the sample receptacle.
[0103] In some embodiments, the assay cartridge comprises: a first storage
device
storing a first fluid; a second storage device storing a second fluid; and
wherein the first fluid
or the second fluid or both are configured to facilitate recovery of at least
a portion of the
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sample from the sample carrier or facilitate transport of at least a portion
of the sample from
the sample introduction area to the mixing region or both.
[0104] In some embodiments, the first or second fluids comprise a buffer, and
wherein the first or second fluids comprise a reagent configured to react with
at least a portion
of the biological sample, such as one or more salts e.g., magnesium.
[0105] In some embodiments, the first storage device and the second storage
device
are compressible, and wherein the first storage device and the second storage
device are
configured to release the first fluid and the second fluid, respectively, when
compressed.
[0106] Some embodiments include a system for determining a wellness score for
a
user, animal, or product, the system comprising: a database configured to
store a plurality of
user, animal, or product profiles, each user, animal, or product profile
comprising health
information for a single user, animal, or product of a plurality of users,
animals, or products
and user, animal, or product identifying information, a testing device
comprising the assay
cartridge of any of the embodiments disclosed herein, the testing device
configured to: accept
the sample from the user, animal, or product, generate test results based on
the sample, and
store the generated test results in the user, animal, or product profile for
the user, animal, or
product in the database; a computing system configured to: generate the
wellness score for
the user, animal, or product the wellness score based on the health
information stored in the
user, animal, or product profile, the health information comprising the
generated test results,
and store the wellness score in the user, animal, or product profile in the
database; a remote
computing device configured to: obtain biometric or identifying information,
such as QR
coding, RFID coding, or bar coding, for the user, animal, or product, request
the wellness
score for the user, animal, or product from the database based on the user's,
animal's, or
product's biometric or identifying information, and receive the wellness score
for the user,
animal, or product based on the computing system determining that the user's,
animal's, or
product's biometric or identifying information matches the user's, animal's,
or product's
identifier, wherein the wellness score is compared to a threshold value to
determine whether
the user, animal, or product is permitted entry to a location and optionally
providing or
displaying a visually identifiable signal or character indicating that the
wellness score is at
or exceeds the threshold value.
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[0107] In some embodiments, the health information further comprises one or
more
of health information records acquired from a medical professional, health
survey
information provided by the user, or contact tracing information.
[0108] In some embodiments, the user identifying information comprises one or
more of an identifier for the user, biometrics information for the user, and
usemame and
password information for the user.
[0109] In some embodiments, the wellness score is representative of whether
the
user, animal, or product is likely to be infected by a pathogen comprising one
or more of a
fungus, mold, bacteria, a virus, or another microbe.
[0110] In some embodiments, the testing device comprises: a cartridge
configured to
receive the biological sample, and a reader device comprising: a cavity
configured to receive
the cartridge, a memory storing at least computer-readable instructions, a
processor in
communication with the memory, and an electrode interface in communication
with the
processor and in contact with the cartridge when the cartridge is inserted
into the cavity.
[0111] In some embodiments, the cartridge comprises: an external portion; an
internal portion configured to fit within the cavity of the reader device, the
internal portion
including an electrode interface configured to establish an electrical
connection with the
electrode interface of the reader device when the cartridge is inserted into
the reader device;
and a flow path configured to sealingly enclose a biological sample within the
cartridge.
[0112] In some embodiments, the cartridge comprises: a sample receptacle; a
cap
having a closed configuration and an open configuration, wherein when the cap
is in the open
configuration, the sample receptacle is configured to receive a sample
collection device, and
wherein when the cap in the closed configuration, the sample receptacle is
sealed; and,
optionally a scraper formed inside the sample receptacle, the scraper
configured to contact
the sample collection device when the sample collection device is in the
sample receptacle
and facilitate collection of the biological sample.
[0113] In some embodiments, the cartridge comprises a retainer, wherein the
retainer
is configured to hold the sample collection device in place inside the sample
receptacle, and
wherein at least a portion of the biological sample is collected from the
sample collection
device.
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[0114] In some embodiments, the cartridge comprises: a first storage device
storing
a first fluid; a second storage device storing a second fluid; and a sample
mixing portion
fluidically coupled to the first storage device and the second storage device,
wherein the first
fluid or the second fluid or both are configured to facilitate recovery of at
least a portion of
the biological sample from the sample collection device or facilitate
transport of the
biological sample to the sample mixing portion or both.
[0115] In some embodiments, the first or second fluids comprise a buffer, and
wherein the first or second fluids comprise a reagent configured to react with
at least a portion
of the biological sample, such as one or more salts e.g., magnesium.
[0116] In some embodiments, the first storage device and the second storage
device
are compressible, and wherein the first storage device and the second storage
device are
configured to release the first fluid and the second fluid, respectively, when
compressed.
[0117] In some embodiments, the biological sample is collected using a sample
collection device, wherein the sample collection device comprises bristles or
flock
configured to collect the biological sample.
[0118] In some embodiments, the sample collection device comprises a stopper
configured to abut an opening of the sample receptacle to prevent the sample
collection
device from entering further into the sample receptacle.
[0119] In some embodiments, the sample collection device comprises a marked
section configured to indicate a position to break or cut the sample
collection device after
being inserted into the sample receptacle.
[0120] In some embodiments, the reader device further includes a communication
module configured to communicatively connect to the computing system or the
remote
computing device.
[0121] In some embodiments, the remote computing device or the computing
system
is wirelessly connected to the reader device.
[0122] In some embodiments, the testing device, the computing system, and the
remote computing device are connected by at least one of a wireless, wired, or
hybrid
network.
[0123] In some embodiments, the remote computing device comprises a biometric
input device that obtains the biometric information for the user from the
user.
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[0124] In some embodiments, the biometric information comprises one or more of
fingerprint information, facial recognition information, retinal scan
information, hand
geometry information, finger geometry information, palm vein information, ear
geometry
information, voice information, hand writing information, signature
information, typing
pattern recognition, biological sample recognition, or movement recognition.
[0125] Some embodiments also include a user device configured to: capture
location
information for the user; capture identification information for other user
devices of other
users that come within a threshold distance of the user; and store the
location information
and identification information in the user profile in the database.
[0126] Some embodiments include a system of any one of the embodiments
disclosed herein for use in detecting a target agent.
[0127] In some embodiments, the target agent indicates presents of a mold,
fungus,
bacteria, a virus, or another microbe.
[0128] In some embodiments, the biological sample is obtained from a subject,
such
as a human or an animal, a product, such as a food or beverage, or an object,
such as a high
contact surface.
[0129] Some embodiments include a method of using the system of any one of the
embodiments disclosed herein for determining the wellness score for the user,
animal, or
product.
[0130] Some embodiments include a method of determining a wellness score for a
user, animal, or product via the system of any one of the embodiments
disclosed herein, the
method comprising: creating a user, animal, or product profile for a user,
animal, or product
in a database, the user, animal, or product profile comprising health
information and user,
animal, or product identifying information; depositing a sample obtained from
the user,
animal, or product into a sample receptacle of a testing device, generating
test results based
on the sample; storing the generated test results in the user, animal, or
product profile for the
user, animal, or product; generating the wellness score for the user, animal,
or product the
wellness score based on the health information stored in the user, animal, or
product profile,
the health information comprising the generated test results, storing the
wellness score in the
user, animal, or product profile in the database; obtaining biometric or
identifying
information for the user, animal, or product; requesting the wellness score
for the user,
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animal, or product from the database based on the user's, animal's, or
product's biometric or
identifying information; receiving the wellness score for the user, animal, or
product based
on the computing system determining that the user's, animal's, or product's
biometric or
identifying information matches the user's, animal's, or product's identifier;
and comparing
the wellness score to a threshold value to determine whether the user, animal,
or product is
permitted entry to a location and optionally providing or displaying a
visually identifiable
signal or character indicating that the wellness score is at or exceeds the
threshold value.
[0131] Some embodiments include a method of collecting and testing a
biological
sample for detecting a target agent, the method comprising: inserting a sample
collection
device in a sample receptacle of a cartridge; and inserting the cartridge into
a cavity of a
reader device, the cavity configured to receive the cartridge.
[0132] Some embodiments also include breaking or cutting the sample collection
device such that a portion of the sample collection device having at least a
portion of the
biological sample remains inside the sample receptacle; and closing a cap of
the cartridge,
the cap being configured to seal the sample receptacle when in a closed
configuration.
[0133] Some embodiments also include coupling the sample collection device
with
a retainer of the sample receptacle such that the sample collection device is
held in place
inside the sample receptacle.
[0134] In some embodiments, the cartridge comprises a first storage device and
a
second storage device, wherein the method further comprises: compressing the
first storage
device prior to the inserting the sample collection device in the sample
receptacle to provide
a fluid to said sample receptacle; removing the sample collection device from
the sample
receptacle; closing a cap of the cartridge, the cap configured to seal the
sample receptacle
when in a closed configuration; and compressing the second storage device.
[0135] In a first embodiment, an assay cartridge for containing a sample
comprising
a target agent for detection by a reader device comprises a cartridge body
configured to be
received by the reader device, and a cap configured to hold the sample carrier
containing the
sample. The cartridge body includes a test well containing an excitation
electrode and a
sensing electrode, wherein the test well is configured to contain at least a
portion of the
sample comprising the target agent undergoing an amplification process; a
sample
introduction area configured to receive a sample carrier containing the
sample; and a fluid
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path fluidically coupling the sample introduction area to the test well. The
cap is further
configured to mechanically couple to the cartridge body, wherein mechanically
coupling the
cap to the cartridge body causes compression of a trapped volume of a fluid to
drive at least
a portion of the sample through the fluid path into the test well.
[0136] In some embodiments, the sample carrier comprises a capillary tube, and
the
cap comprises a retaining well having an interior diameter larger than an
exterior diameter
of the capillary tube; and a retaining structure disposed within the retaining
well and
configured to retain the capillary tube at a position spaced from a side
interior wall and a rear
interior wall of the retaining well to form at least one air channel
fluidically coupled to an
inner end of the capillary tube. In some embodiments, the cap further
comprises a plunger
disposed about at least a portion of the retaining well, and the sample
introduction area of
the cartridge body comprises a capillary tube receiving well configured to
sealingly receive
an outer end of the capillary tube to fluidically couple an inner lumen of the
capillary tube to
the fluid path when the cap is mechanically coupled to the cartridge body; and
a plunger
receiving well configured to sealingly receive the plunger when the cap is
mechanically
coupled to the cartridge body, wherein, as the cap is mechanically coupled to
the cartridge
body, the plunger compresses a volume of air within the plunger receiving
well, such that
the air flows through the air channel and forces the sample to travel into the
fluid path of the
cartridge body. In some embodiments, the cartridge body comprises a base and a
translucent
cover, the translucent cover comprising a planar surface defining one side of
at least one of
the test well and the fluid path. In some embodiments, the cartridge body
further comprise
a hollow plunger comprising an interior space fluidically coupled to the fluid
path of the
cartridge body, wherein the cap comprises a plunger receiving well configured
to sealingly
receive the hollow plunger, and, as the cap is mechanically coupled to the
cartridge body,
the plunger compresses a volume of air within the plunger receiving well, such
that the air
flows through the hollow plunger and forces the sample to travel into the
fluid path of the
cartridge body. In some embodiments, the cartridge body comprises at least a
second test
well containing an excitation electrode and a sensing electrode, and a second
fluid path
fluidically coupling the sample introduction area to the second test well,
wherein the second
test well is configured to contain at least a portion of the sample comprising
the target agent
undergoing an amplification process. In some embodiments, the cartridge body
comprises a
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base and a printed circuit board (PCB), the PCB comprising a planar surface
defining one
side of at least one of the test well and the fluid path. In some embodiments,
the PCB
comprises a heating element configured to heat the test well. In some
embodiments, the PCB
comprises the excitation electrode and the sensing electrode. In some
embodiments, the test
well is configured to mix a reagent and the sample into a substantially evenly
mixed test
fluid. In some embodiments, the reagent comprises one or more dried and/or
lyophilized
reagents stored within the test well. In some embodiments, the cartridge body
comprises a
plurality of test wells, and at least a first test well of the plurality of
test wells stores a reagent
different from a reagent stored in a second test well of the plurality of test
wells. In some
embodiments, the cartridge body comprises a plurality of test wells, and at
least two test
wells of the plurality of test wells store the same reagent. In some
embodiments, the cartridge
body further comprises a mixing chamber positioned between the sample
introduction area
and the test well along the fluid path, the mixing chamber configured to mix a
reagent and
the sample into a substantially evenly mixed test fluid. In some embodiments,
the reagent
comprises one or more dried and/or lyophilized reagents stored within the
mixing chamber.
In some embodiments, the assay cartridge further comprises a first electrode
interface
including a first contact pad leading to the excitation electrode and a second
contact pad
leading to the sensing electrode. In some embodiments, the assay cartridge
further comprises
a gas-permeable, liquid-impermeable vent fluidically coupled to the test well.
In some
embodiments, the assay cartridge further comprises a machine-readable
cartridge identifier
printed thereon, the cartridge identifier associated with one or more test
protocols. In some
embodiments, the assay cartridge is a disposable single-use assay cartridge.
In some
embodiments, the trapped volume of a fluid comprises air.
[0137] In a second embodiment, a detection system for detecting a target agent
comprises a reader device, an assay cartridge, and a power cartridge. The
reader device
includes a cavity configured to receive cartridges; a memory storing at least
computer-
readable instructions; a processor in communication with the memory; and an
electrode
interface in communication with the processor. The assay cartridge includes an
external
portion; an internal portion configured to fit within the cavity of the reader
device, the
internal portion including an electrode interface configured to establish an
electrical
connection with the electrode interface of the reader device when the assay
cartridge is
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inserted into the reader device; and a flow path configured to sealingly
enclose a fluid sample
within the assay cartridge. The power cartridge includes an internal portion
configured to fit
within the cavity; and circuitry disposed at least partially on the internal
portion and
configured to establish an electrical connection with the electrode interface
when the power
cartridge is inserted into the reader device. Inserting the power cartridge
into the cavity
causes the reader device to power off, and removing the power cartridge from
the cavity
causes the reader device to power on.
[0138] In some embodiments, the reader device further includes a communication
module configured to connect to a remote computing device executing a user
interface
application. In some embodiments, the remote computing device is wirelessly
connected to
the reader device. In some embodiments, the remote computing device is
connected to the
reader device by at least one of WEN or Bluetooth. In some embodiments, the
reader device
does not include a user interface. In some embodiments, the reader device
includes a visual
status indicator on an exterior portion of the reader device. In some
embodiments, the visual
status indicator comprises one or more light emitting diodes. In some
embodiments, the
visual status indicator comprises a plurality of differently colored light
emitting diodes. In
some embodiments, the visual status indicator comprises a plurality of
individually
controllable light emitting diodes. In some embodiments, the visual status
indicator
comprises a ring of lights at least partially surrounding the cavity of the
reader device. In
some embodiments, the visual status indicator is configured to indicate at
least one of a ready
status, a testing status, a completed testing status, an error status, and a
wireless pairing status.
[0139] In some embodiments, the assay cartridge or system is for use in
detecting a
target agent. In some embodiments, the target agent is a nucleic acid,
preferably a nucleic
acid of a pathogen. In some embodiments, the sample is a biological sample. In
some
embodiments, including any one of the embodiments disclosed herein, the
biological sample
is obtained from a subject, preferably a human or other animal, a plant, a
food, soil, or a
surface, or any combination thereof. In some embodiments, the biological
sample is obtained
by swabbing. In some embodiments, the subject is a human. In some embodiments,
the
subject is an animal. In some embodiments, the animal is a mammal, such as a
dog, cat,
rabbit, rodent, mouse, rat, hamster, guinea pig, or ferret. In some
embodiments, the animal
is not a mammal, such as a reptile, amphibian, fish, or bird. In some
embodiments, the animal
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is a livestock animal, such as a cow, pig, chicken, turkey, duck, goose,
quail, pigeon, sheep,
goat, horse, donkey, mule, alpaca, llama, buffalo, camel, or ox, or any other
animal raised
for food or products. In some embodiments, the plant is a vegetable, fruit or
legume, such as
a carrot, lettuce, cabbage, spinach, broccoli, cauliflower, cucumber,
zucchini, squash, pepper,
potato, yam, asparagus, onion, shallot, garlic, herb, apple, pear, orange,
lemon, lime,
grapefruit, peach, plum, banana, mango, strawberry, raspberry, blueberry,
kiwi, watermelon,
cantaloupe, tomato, avocado, pea, or bean, or any other plant grown for food
or products. In
some embodiments, the food is any edible substance, such as meat or plant. In
some
embodiments, soil may refer to the earthen material that plants are cultivated
in. In some
embodiments, the surface is any surface that is suspected of harboring
biological material,
including pathogens. In some embodiments, the surface is a livestock pen or
other living
area. In some embodiments, the surface is found in a hospital. In some
embodiments, the
surface is any surface that has been in contact or proximity to a subject that
has or is suspected
of having a pathogen.
[0140] In some embodiments, a method of using the assay cartridge or system
for
detecting a target agent comprises contacting a biological sample with the
assay cartridge or
system; and detecting the presence and/or amount of the target agent. In some
embodiments,
the target agent is a nucleic acid, preferably a nucleic acid of a pathogen.
In some
embodiments, the target agent is a nucleic acid and the assay cartridge or
system or method
further comprises amplifying the nucleic acid, such as by Loop-Mediated
Isothermal
Amplification (LAMP) and measuring or analyzing a modulation of an electrical
signal, such
as impedance or capacitance, which is desirably compared to a control. In some
embodiments, the LAMP is reverse transcription LAMP (RT-LAMP).
[0141] In some embodiments of the assay cartridge, system, or method, the
assay
cartridge is configured to be used in determining an impedance or a
capacitance using three-
terminal sensing or four-terminal sensing. In some embodiments of the assay
cartridge, the
test well further contains a third electrode. In some embodiments, the third
electrode is
disposed between the excitation electrode and the sensing electrode. In some
embodiments,
the test well further contains a fourth electrode. In some embodiments, the
third electrode
and the fourth electrode are disposed between the excitation electrode and the
sensing
electrode.
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[0142] In another embodiment, an assay cartridge for analyzing a sample
comprising
a target agent is described. The assay cartridge comprises a cartridge body
and a reagent
blister. The cartridge body is configured to be received by a reader device.
The cartridge
body includes at least one test well containing an excitation electrode and a
sensing electrode,
wherein the at least one test well is configured to contain at least a portion
of the sample
comprising the target agent undergoing an amplification process, a sample
introduction area
configured to receive a sample carrier containing the sample, and a fluid path
fluidically
coupling the sample introduction area to the test well. The reagent blister is
configured to
hold a reagent to be mixed with the sample prior to the amplification process.
The reagent
blister is further configured to be ruptured when the cartridge body is
inserted into the reader
device. The rupturing of the reagent blister produces a force that mixes the
reagent with the
sample and drives at least a portion of the reagent and at least the portion
of the sample
through the fluid path to the at least one test well.
[0143] In another embodiment, a detection system for detecting a target agent
is
disclosed. The detection system comprises a reader device, an assay cartridge,
and a mobile
device. The reader devices include a cavity configured to receive cartridges,
a memory
storing at least computer-readable instructions, a processor in communication
with the
memory, a communication interface, and an electrode interface in communication
with the
processor and electrodes of the cartridges. The assay cartridge includes an
external portion,
an internal portion configured to fit within the cavity of the reader device,
the internal portion
including electrodes configured to establish an electrical connection with the
electrode
interface of the reader device when the assay cartridge is inserted into the
reader device, a
flow path configured to fluidically couple a sample introduction area of the
assay cartridge
to at least one test well of the assay cartridge, and a reagent store
configured to store a reagent
for mixing with a sample prior to conveying at least a portion of a mixture of
the reagent and
the sample to the at least one test well. The mobile device includes a data
store storing at
least computer-readable instructions for the mobile device, a hardware
processor in
communication with the memory, an interface for identifying a type of assay
cartridge, and
a wireless communication interface in communication with the processor. The
mobile device
is configured to identify the type of the assay cartridge and communicate
parameters for an
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analysis of the sample by the reader device to the reader device via the
wireless
communication interface.
[0144] In another embodiment, a method for identifying a target in a sample is
described. The method comprises depositing the sample into a sample receptacle
of a
disposable cartridge, inserting the disposable cartridge into a cartridge
receptacle of an
analyzer device, and rupturing a reagent blister containing at least one
reagent. The method
further comprises generating a mixture by mixing the at least one reagent with
the sample,
conveying at least a portion of the mixture to at least one testing well
comprising at least one
dried and/or lyophilized enzyme and/or a detection agent, such as a set of,
primers, antibody
or binding fragment thereof, increasing a temperature of the at least one
testing well, and
measuring an electrical characteristic of at least the portion of the mixture
in the at least on
testing well. Insertion of the disposable cartridge into the cartridge
receptacle causes the
rupturing of the reagent blister, the generating of the mixture, and the
conveying of at least
the portion of the mixture to the at least one testing well. Preferred
additional alternatives are
set forth below.
[0145] 1. An additional alternative comprises an assay cartridge for
containing a
sample comprising a target agent for detection by a reader device, the assay
cartridge
comprising: a cartridge body configured to be received by the reader device,
the cartridge
body including: a test well containing an excitation electrode and a sensing
electrode,
wherein the test well is configured to contain at least a portion of the
sample comprising the
target agent undergoing an amplification process; a sample introduction area
configured to
receive a sample carrier containing the sample; and a fluid path fluidically
coupling the
sample introduction area to the test well; and a cap configured to hold the
sample carrier
containing the sample, the cap further configured to mechanically couple to
the cartridge
body, wherein mechanically coupling the cap to the cartridge body causes
compression of a
trapped volume of a fluid to drive at least a portion of the sample through
the fluid path into
the test well.
[0146] 2. The assay cartridge of alternative 1, wherein the sample carrier
comprises
a capillary tube, and wherein the cap comprises: a retaining well having an
interior diameter
larger than an exterior diameter of the capillary tube; and a retaining
structure disposed
within the retaining well and configured to retain the capillary tube at a
position spaced from
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a side interior wall and a rear interior wall of the retaining well to form at
least one air channel
fluidically coupled to an inner end of the capillary tube.
[0147] 3. The assay cartridge of alternative 2, wherein the cap further
comprises a
plunger disposed about at least a portion of the retaining well, and wherein
the sample
introduction area of the cartridge body comprises: a capillary tube receiving
well configured
to sealingly receive an outer end of the capillary tube to fluidically couple
an inner lumen of
the capillary tube to the fluid path when the cap is mechanically coupled to
the cartridge
body; and a plunger receiving well configured to sealingly receive the plunger
when the cap
is mechanically coupled to the cartridge body, wherein, as the cap is
mechanically coupled
to the cartridge body, the plunger compresses a volume of air within the
plunger receiving
well, such that the air flows through the air channel and forces the sample to
travel into the
fluid path of the cartridge body.
[0148] 4. The assay cartridge of any one of alternatives 1-3, wherein the
cartridge
body comprises a base and a translucent cover, the translucent cover
comprising a planar
surface defining one side of at least one of the test wells and the fluid
path.
[0149] 5. The assay cartridge of alternative 1, wherein the cartridge body
further
comprise a hollow plunger comprising an interior space fluidically coupled to
the fluid path
of the cartridge body, wherein the cap comprises a plunger receiving well
configured to
sealingly receive the hollow plunger, and wherein, as the cap is mechanically
coupled to the
cartridge body, the plunger compresses a volume of air within the plunger
receiving well,
such that the air flows through the hollow plunger and forces the sample to
travel into the
fluid path of the cartridge body.
[01.50] 6. The assay cartridge of alternative 5, wherein the cartridge body
comprises
at least a second test well containing an excitation electrode and a sensing
electrode, and a
second fluid path fluidically coupling the sample introduction area to the
second test well,
wherein the second test well is configured to contain at least a portion of
the sample
comprising the target agent undergoing an amplification process.
[0151] 7. The assay cartridge of any one of alternatives 5 and 6, wherein the
cartridge
body comprises a base and a printed circuit board (PCB), the PCB comprising a
planar
surface defining one side of at least one of the test wells and the fluid
path.
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[0152] 8. The assay cartridge of alternative 7, wherein the PCB comprises a
heating
element configured to heat the test well.
[0153] 9. The assay cartridge of any one of alternatives 7 and 8, wherein the
PCB
comprises the excitation electrode and the sensing electrode.
[0154] 10. The assay cartridge of any one of alternatives 5-9, wherein the
test well is
configured to mix a reagent and the sample into a substantially evenly mixed
test fluid.
[0155] 11. The assay cartridge of alternative 10, wherein the reagent
comprises one
or more dried and/or lyophilized reagents stored within the test well.
[0156] 12. The assay cartridge of alternative 11, wherein the cartridge body
comprises a plurality of test wells, and wherein at least a first test well of
the plurality of test
wells stores a reagent different from a reagent stored in a second test well
of the plurality of
test wells.
[0157] 13. The assay cartridge of any one of alternatives 11 and 12, wherein
the
cartridge body comprises a plurality of test wells, and wherein at least two
test wells of the
plurality of test wells store the same reagent.
[0158] 14. The assay cartridge of any one of alternatives 1-13, wherein the
cartridge
body further comprises a mixing chamber positioned between the sample
introduction area
and the test well along the fluid path, the mixing chamber configured to mix a
reagent and
the sample into a substantially evenly mixed test fluid.
[0159] 15. The assay cartridge of alternative 14, wherein the reagent
comprises one
or more dried and/or lyophilized reagents stored within the mixing chamber.
[0160] 16. The assay cartridge of any one of alternatives 1-15, further
comprising a
first electrode interface including a first contact pad leading to the
excitation electrode and a
second contact pad leading to the sensing electrode.
[0161] 17. The assay cartridge of any one of alternatives 1-16, further
comprising a
gas-permeable, liquid-impermeable vent fluidically coupled to the test well.
[0162] 18. The assay cartridge of any one of alternatives 1-17, further
comprising a
machine-readable cartridge identifier printed thereon, the cartridge
identifier associated with
one or more test protocols.
[0163] 19. The assay cartridge of any one of alternatives 1-18, wherein the
assay
cartridge is a disposable single-use assay cartridge.
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[0164] 20. The assay cartridge of any one of alternatives 1-19, wherein the
trapped
volume of a fluid comprises air.
[0165] 21. A detection system for detecting a target agent, the system
comprising: a
reader device including: a cavity configured to receive cartridges; a memory
storing at least
computer-readable instructions; a processor in communication with the memory;
and an
electrode interface in communication with the processor; an assay cartridge
including: an
external portion; an internal portion configured to fit within the cavity of
the reader device,
the internal portion including an electrode interface configured to establish
an electrical
connection with the electrode interface of the reader device when the assay
cartridge is
inserted into the reader device; and a flow path configured to sealingly
enclose a fluid sample
within the assay cartridge; and a power cartridge including: an internal
portion configured to
fit within the cavity; and circuitry disposed at least partially on the
internal portion and
configured to establish an electrical connection with the electrode interface
when the power
cartridge is inserted into the reader device, wherein inserting the power
cartridge into the
cavity causes the reader device to power off, and wherein removing the power
cartridge from
the cavity causes the reader device to power on.
[0166] 22. The system of alternative 21, wherein the reader device further
includes a
communication module configured to connect to a remote computing device
executing a user
interface application.
[0167] 23. The system of alternative 22, wherein the remote computing device
is
wirelessly connected to the reader device.
[0168] 24. The system of any one of alternatives 22 and 23, wherein the remote
computing device is connected to the reader device by at least one of WiFi. or
Bluetooth.
[0169] 25. The system of any one of alternatives 21-24, wherein the reader
device
does not include a user interface.
[0170] 26. The system of any one of alternatives 21-25, wherein the reader
device
includes a visual status indicator on an exterior portion of the reader
device.
[0171] 27. The system of alternative 26, wherein the visual status indicator
comprises
one or more light emitting diodes.
[0172] 28. The system of alternative 27, wherein the visual status indicator
comprises
a plurality of differently colored light emitting diodes.
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[0173] 29. The system of any one of alternatives 26-28, wherein the visual
status
indicator comprises a plurality of individually controllable light emitting
diodes.
[0174] 30. The system of any one of alternatives 26-29, wherein the visual
status
indicator comprises a ring of lights at least partially surrounding the cavity
of the reader
device.
[0175] 31. The system of any one of alternatives 26-30, wherein the visual
status
indicator is configured to indicate at least one of a ready status, a testing
status, a completed
testing status, an error status, and a wireless pairing status.
[0176] 32. The assay cartridge or system of any one of alternatives 1-31 for
use in
detecting a target agent.
[0177] 33. The assay cartridge or system of alternative 32, wherein the target
agent
is a nucleic acid, preferably a nucleic acid of a pathogen.
[0178] 34. The assay cartridge or system of anyone of alternatives 32 or 33,
wherein
the sample is a biological sample.
[0179] 35. A method of using the assay cartridge or system of any one of
alternatives
1-31 for detecting a target agent comprising: contacting a biological sample,
with the assay
cartridge or system of any one of alternatives 1-30; and detecting the
presence and/or amount
of the target agent.
[0180] 36. The method of alternative 35, wherein the target agent is a nucleic
acid,
preferably a nucleic acid of a pathogen.
[0181] 37. The assay cartridge or system of anyone of alternatives 32-34 or
the
method of any one of alternatives 35 or 36, wherein the target agent is a
nucleic acid and the
assay cartridge or system or method further comprises amplifying the nucleic
acid, such as
by Loop-Mediated Isothermal Amplification (LAMP) and measuring or analyzing a
modulation of an electrical signal, such as impedance or capacitance, which is
desirably
compared to a control.
[0182] 38. The assay cartridge, system, or method of any one of alternatives 1-
37,
wherein the assay cartridge is configured to be used in determining an
impedance or a
capacitance using three-terminal sensing or four-terminal sensing.
[0183] 39. The assay cartridge of any one of alternatives 1-20, wherein the
test well
further contains a third electrode.
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[0184] 40. The assay cartridge of alternative 39, wherein the third electrode
is
disposed between the excitation electrode and the sensing electrode.
[0185] 41. The assay cartridge of alternative 39, wherein the test well
further contains
a fourth electrode.
[0186] 42. The assay cartridge of alternative 41, wherein the third electrode
and the
fourth electrode are disposed between the excitation electrode and the sensing
electrode.
[0187] 43. An assay cartridge for analyzing a sample comprising a target
agent, the
assay cartridge comprising: a cartridge body configured to be received by a
reader device,
the cartridge body including: at least one test well containing an excitation
electrode and a
sensing electrode, wherein the at least one test well is configured to contain
at least a portion
of the sample comprising the target agent undergoing an amplification process;
a sample
introduction area configured to receive a sample carrier containing the
sample; and a fluid
path fluidically coupling the sample introduction area to the test well; and a
reagent blister
configured to hold a reagent to be mixed with the sample prior to the
amplification process,
the reagent blister further configured to be ruptured when the cartridge body
is inserted into
the reader device, wherein the rupturing of the reagent blister produces a
force that mixes the
reagent with the sample and drives at least a portion of the reagent and at
least the portion of
the sample through the fluid path to the at least one test well.
[0188] 44. A detection system for detecting a target agent, the system
comprising: a
reader device including: a cavity configured to receive cartridges; a memory
storing at least
computer-readable instructions; a processor in communication with the memory;
a
communication interface; and an electrode interface in communication with the
processor
and electrodes of the cartridges; an assay cartridge including: an external
portion; an internal
portion configured to fit within the cavity of the reader device, the internal
portion including
electrodes configured to establish an electrical connection with the electrode
interface of the
reader device when the assay cartridge is inserted into the reader device; a
flow path
configured to fluidically couple a sample introduction area of the assay
cartridge to at least
one test well of the assay cartridge; and a reagent store configured to store
a reagent for
mixing with a sample prior to conveying at least a portion of a mixture of the
reagent and the
sample to the at least one test well; and a mobile device including: a data
store storing at least
computer-readable instructions for the mobile device; a hardware processor in
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communication with the memory; an interface for identifying a type of assay
cartridge; and
a wireless communication interface in communication with the processor,
wherein the
mobile device is configured to identify the type of the assay cartridge and
communicate
parameters for an analysis of the sample by the reader device to the reader
device via the
wireless communication interface.
[0189] 45. The system of alternative 44, wherein the reader device is further
configured to generate test results comprising a determination whether the
target agent is
present in the sample.
[0190] 46. The system of any one of alternatives 44 and 45, wherein the mobile
device is further configured to display a prompt for one or more symptoms
experienced by a
patient that provides the sample and receive the one or more symptoms
experienced by the
patient.
[0191] 47. The system of alternative 46, wherein the mobile device comprises a
user
interface configured to prompt for and receive the one or more symptoms.
[0192] 48. The system of any one of alternatives 46 and 47, wherein the one or
more
symptoms are selected from a list or entered by the user.
[0193] 49. The system of any one of alternatives 46-48, wherein the user
interface is
further configured to provide instructions for collecting the sample for
testing, loading the
sample into the assay cartridge, and inserting the assay cartridge into the
reader device.
[0194] 50. The system of any one of alternatives 46-49, wherein the mobile
device
is further configured to receive the one or more symptoms before, while, or
after the reader
device determines whether the target agent is present in the sample.
[0195] 51. The system of any one of alternatives 46-50, wherein the reader
device is
further configured to analyze the test results and the one or more symptoms to
diagnose
whether the patient is suffering from an ailment.
[0196] 52. The system of any one of alternatives 46-51, wherein each of the
one or
more symptoms has associated therewith a sliding scale value representative of
a severity of
the symptom.
[0197] 53. The system of any one of alternatives 46-52, wherein the mobile
device
is further configured to allow the user to compare previous test results for
the patient with
current test results.
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[0198] 54. The system of any one of alternatives 46-53, wherein the mobile
device
is further configured to display, to the user, information from the reader
device, the
information comprising a time remaining before the test results are generated,
an identifier
of the reader device, and an identifier of the assay cartridge.
[0199] 55. The system of any one of alternatives 44-54, wherein the mobile
device
is further configured to display, to the user, test results for the sample,
any symptoms
associated with the sample, an indication of the diagnosed ailment, and one or
more of a
recommended follow-up steps for the diagnosed ailment.
[0200] 56. The system of any one of alternatives 51-55, wherein the mobile
device
is further configured to share electronically the test results, the one or
more symptoms, or the
diagnosed ailment with another entity.
[0201] 57. The system of any one of alternatives 46-56, wherein the mobile
device
is further configured to determine that the patient is a carrier for a disease
based on test results
positive for the target agent and no reported symptoms.
[0202] 58. The system of any one of alternatives 46-57, wherein at least one
of the
one or more symptoms is weighted higher than one or more other symptoms of the
one or
more symptoms.
[0203] 59. The system of any one of alternatives 46-58, wherein a threshold
number
of the one or more symptoms, weighting of each of the one or more symptoms,
and specific
symptoms of the one or more symptoms used to diagnose the ailment is
determined based
on one or more metrics.
[0204] 60. The system of alternative 59, wherein the one or more metrics is
received
from one or more of the Center for Disease Control (CDC) or a national
organization that
monitors illnesses.
[0205] 61. The system of any one of alternatives 46-60, wherein the mobile
device
is further configured to generate a score indicator representative of a
probability that the
patient is ill.
[0206] 62. The system of any one of alternatives 46-61, wherein the score
indicator
falls within a range of 0 to 100, where 0 is a low probability that the
patient is ill and 100 is
a high probability that the patient is ill.
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[0207] 63. The system of any one of alternatives 46-62, wherein the mobile
device
is further configured to identify an illness that the patient is suffering
from based on negative
test results for the target agent and the one or more symptoms of the patient.
[0208] 64. The system of any one of alternatives 46-63, further comprising an
aggregating device that aggregates information from multiple mobile devices,
the multiple
mobile devices comprising the mobile device, and wherein the mobile device is
further
configured to determine that the patient is ill based on the test results,
symptoms, and the
aggregated information from the multiple mobile devices.
[0209] 65. The system of any one of alternatives 46-64, wherein the mobile
device
is further configured to automatically perform one or more actions based on a
determination
that the patient is ill.
[0210] 66. The system of alternative 65, wherein the one or more actions
comprises
generating and sending an alert to one or more of the patient, to the user, to
attending medical
staff, to the CDC, and to family of the patient.
[0211] 67. The system of alternative 66, wherein the alert comprises one or
more of
a phone call, a text message, an e-mail message, a push message, an audio
message, a flashing
indicator, or audible indicator.
[0212] 68. The system of alternative 64, wherein the aggregating device is
further
configured to track illnesses over a geographic area based on information
received from the
multiple mobile devices.
[0213] 69. The system of alternative 68, wherein the aggregating device is
further
configured to generate a heat map of the illnesses over the geographic area.
[0214] 70. The system of any one of alternatives 68 and 69, wherein the
aggregating
device is further configured to track quantities of available vaccines or
medications and to
compare a quantity of available vaccines or medications with a quantity of
illnesses to
determine whether sufficient vaccines or medications are available to treat or
prevent the
spread of the illnesses.
[0215] 71. The system of alternative 70, wherein the aggregating device is
further
configured to automatically generate a request to vaccine and/or medication
suppliers to
increase the quantity of available vaccines or medications when insufficient
vaccines or
medications are available.
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[0216] 72. The system of any one of alternatives 64-71, wherein the mobile
device
is further configured to display any information tracked or generated by the
aggregating
device.
[0217] 73. The system of any one of alternatives 44-72, wherein the samples
comprise a biological secretion.
[0218] 74. The system of alternative 73, wherein the biological secretion
comprises
blood, mucus, or saliva.
[0219] 75. A method for identifying a target in a sample, the method
comprising:
depositing the sample into a sample receptacle of a disposable cartridge;
inserting the
disposable cartridge into a cartridge receptacle of an analyzer device;
rupturing a reagent
blister containing at least one reagent; generating a mixture by mixing the at
least one reagent
with the sample; conveying at least a portion of the mixture to at least one
testing well
comprising at least one dried and/or lyophilized enzyme and/or a detection
agent, such as a
set of, primers, antibody or binding fragment thereof; increasing a
temperature of the at least
one testing well; and measuring an electrical characteristic of at least the
portion of the
mixture in the at least on testing well, wherein insertion of the disposable
cartridge into the
cartridge receptacle causes the rupturing of the reagent blister, the
generating of the mixture,
and the conveying of at least the portion of the mixture to the at least one
testing well.
[0220] 76. A method of detecting the presence and/or amount of a nucleic acid,
preferably a nucleic acid from a pathogen, in a biological sample, comprising:
contacting the
biological sample with an assay cartridge of a detection system; amplifying
the nucleic acid
by Loop-Mediated Isothermal Amplification (LAMP) with a primer set, wherein
the primer
set comprises any combination of: one or more F3 primers, one or more B3
primers, one or
more LF primers, one or more LB primers, one or more FIP primers, and one or
more BIP
primers, and wherein the primer set is specific for a genome region of the
pathogen;
measuring or analyzing a modulation of an electrical signal, such as impedance
or
capacitance, for the duration of the amplification with the primer set using
the detection
system, thereby detecting successful amplification of the nucleic acid with
the primer set;
and determining the presence and/or amount of the nucleic acid in the
biological sample.
[0221] 77. The method of alternative 76, further comprising determining the
biological sample as comprising the pathogen, or the genome region thereof.
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[0222] 78. The method of any one of alternatives 76 and 77, further comprising
mixing the biological sample with a reagent and the primer set in the assay
cartridge prior to
the amplifying step, wherein the reagent is used for LAMP and comprises a
strand-displacing
DNA polymerase and optionally a reverse transciiptase.
[0223] 79. The method of alternative 78, wherein the reagent or the primer
set, or
both, have been dried and/or lyophilized prior to mixing with the biological
sample.
[0224] 80. The method of any one of alternatives 75-79, wherein the detection
system
comprises a heater and the amplifying step comprises incubating the biological
sample at,
optionally a first temperature for a first time period, and one or more second
temperatures
for one or more second time periods.
[0225] 81. The method of alternative 80, wherein the first temperature is 20
C, 21 C,
22 C, 23 C, 24 C, 25 C, 26 C, 27 C, 28 C, 29 C. 30 C, 31 C, 32 C, 33 C, 34 C,
35 C,
36 C, 37 C, 38 C, 39 C, 40 C, 41 C, 42 C, 43 C, 44 C, 45 C, 46 C, 47 C, 48 C,
49 C,
50 C, 51 C, 52 C, 53 C, 54 C, or 55 C, or about 20 C, about 21 C, about 22 C,
about 23 C,
about 24 C, or about 25 C, about 26 C, about 27 C, about 28 C, about 29 C,
about 30 C,
about 31 C, about 32 C, about 33 C, about 34 C, about 35 C, about 36 C, about
37 C, about
38 C, about 39 C, about 40 C, about 41 C, about 42 C, about 43 C, about 44 C,
about 45 C,
about 46 C, about 47 C, about 48 C, about 49 C, about 50 C, about 51 C, about
52 C, about
53 C, about 54 C, or about 55 C, or any temperature within a range defined by
any two of
the aforementioned temperatures, preferably 23 C or about 23 C or 50 C or
about 50 C, and
the first time period is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15
minutes, or about 1,
about 2, about 3, about 4, about 5, about 6, about 7, about 8, about 9, about
10, about 11,
about 12, about 13, about 14, or about 15 minutes, or any time period within a
range defined
by any two of the aforementioned times, preferably 5 to 10 minutes or about 5
to about 10
minutes.
[0226] 82. The method of one of alternatives 80 or 81, wherein each of the one
or
more second temperatures is 21 C, 22 C, 23 C, 24 C, 25 C, 26 C, 27 C, 28 C, 29
C, 30 C,
31 C, 32 C, 33 C, 34 C, 35 C, 36 C, 37 C, 38 C, 39 C, 40 C, 41 C, 42 C, 43 C,
44 C,
45 C, 46 C, 47 C, 48 C, 49 C, 50 C, 51 C, 52 C, 53 C, 54 C, 55 C, 56 C, 57 C,
58 C,
59 C, 60 C, 61 C, 62 C, 63 C, 64 C, 65 C, 66 C, 67 C, 68 C, 69 C, or 70 C, or
about
21 C, about 22 C, about 23 C, about 24 C, about 25 C, about 26 C, about 27 C,
about 28 C,
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about 29 C, about 30 C, about 31 C, about 32 C, about 33 C, about 34 C, about
35 C, about
36 C, about 37 C, about 38 C, about 39 C, about 40 C, about 41 C, about 42 C,
about 43 C,
about 44 C, about 45 C, about 46 C, about 47 C, about 48 C, about 49 C, about
50 C, about
51 C, about 52 C, about 53 C, about 54 C, about 55 C, about 56 C, about 57 C,
about 58 C,
about 59 C, about 60 C, about 61 C, about 62 C, about 63 C, about 64 C, about
65 C, about
66 C, about 67 C, about 68 C, about 69 C, or about 70 C, or any temperature
within a range
defined by any two of the aforementioned temperatures, preferably 50 C or
about 50 C, and
each of the one or more second time periods is I , 2, 3, 4, 5, 6, 7, 8, 9, 10,
11, 12, 13, 14, 15,
16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34,
35, 36, 37, 38, 39, 40,
41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, or
60 minutes, or
about 1, about 2, about 3, about 4, about 5, about 6, about 7, about 8, about
9, about 10, about
11, about 12, about 13, about 14, about 15 minutes, about 16, about 17, about
18, about 19,
about 20, about 21, about 22, about 23, about 24, about 25, about 26, about
27, about 28,
about 29, about 30, about 31, about 32, about 33, about 34, about 35, about
36, about 37,
about 38, about 39, about 40, about 41, about 42, about 43, about 44, about
45, about 46,
about 47, about 48, about 49, about 50, about 51, about 52, about 53, about
54, about 55,
about 56, about 57, about 58, about 59, or about 60 minutes, or any time
period within a
range defined by any two of the aforementioned times, preferably 10 minutes or
about 10
minutes.
[0227] 83. The method of any one of alternatives 80-82, further comprising
incubating the biological sample at a third temperature for a third time
period, preferably
wherein the first temperature is performed at room temperature (e.g., 23 C or
about 23 C)
for a time period sufficient to allow the dried down reagents to rehydrate
(e.g., 10 minutes
or about 10 minutes); the second temperature is performed at 50 C or about 50
C for 10
minutes or about 10 minutes, and the amplification period is then conducted at
65 C or about
65 C.
[0228] 84. The method of alternative 83, wherein the third temperature is 60
C,
61 C, 62 C, 63 C, 64 C, 65 C, 66 C, 67 C, 68 C, 69 C, or 70 C, or about 60 C,
about
6 1 C, about 62 C, about 63 C, about 64 C, about 65 C, about 66 C, about 67 C,
about 68 C,
about 69 C, or about 70 C, or any temperature within a range defined by any
two of the
aforementioned temperatures, preferably 65 C or about 65 C, and the third time
period is 1,
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2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,
23, 24, 25, 26, 27, 28,
29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40,41, 42,43, 44,45, 46,47, 48,49,
50, 51, 52, 53,
54, 55, 56, 57, 58, 59, or 60 minutes, or about 1, about 2, about 3, about 4,
about 5, about 6,
about 7, about 8, about 9, about 10, about 11, about 12, about 13, about 14,
about 15 minutes,
about 16, about 17, about 18, about 19, about 20, about 21, about 22, about
23, about 24,
about 25, about 26, about 27, about 28, about 29, about 30, about 31, about
32, about 33,
about 34, about 35, about 36, about 37, about 38, about 39, about 40, about
41, about 42,
about 43, about 44, about 45, about 46, about 47, about 48, about 49, about
50, about 51,
about 52, about 53, about 54, about 55, about 56, about 57, about 58, about
59, or about 60
minutes, or any time period within a range defined by any two of the
aforementioned times,
preferably 30 minutes or about 30 minutes.
[0229] 85. The method of any one of alternatives 76-84, wherein the pathogen
is a
microbe, fungus, mold, virus or bacteria.
[0230] 86. The method of any one of alternatives 76-85, wherein the pathogen
is
SARS-CoV-2 and wherein: the one or more F3 primers comprise one or more
sequences
having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,
97%,
98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 1, 7, 13, 19; the
one or
more B3 primers comprise one or more sequences having at least 85%, 86%, 87%,
88%,
89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to the
sequences of SEQ ID NOs: 6, 12, 18,25; the one or more LF primers comprise one
or more
sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%,
96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 3, 9, 15,
21;
the one or more LB primers comprise one or more sequences having at least 85%,
86%, 87%,
88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology
to
the sequences of SEQ ID NOs: 5, 11, 17, 23, 24; the one or more FIP primers
comprise one
or more sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,
94%,
95%, 96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 2,8,
14,
20: and the one or more BIP primers comprise one or more sequences having at
least 85%,
86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%
homology to the sequences of SEQ ID NOs: 4, 10, 16, 22.
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[0231] 87. The method of alternative 86, wherein the primer set comprises
sequences
having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,
97%,
98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 1-6.
[0232] 88. The method of alternative 86 or 87, wherein the primer set consists
of
sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%,
96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 1-6.
[0233] 89. The method of any one of alternatives 76-85, wherein the pathogen
is
Hepatitis A Virus and wherein: the one or more F3 primers comprise one or more
sequences
having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,
97%,
98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 26, 27, 34, 35, 43;
the one
or more B3 primers comprise one or more sequences having at least 85%, 86%,
87%, 88%,
89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 1.00% homology to
the
sequences of SEQ ID NOs: 32, 33, 41, 42, 48, 49; the one or more LF primers
comprise one
or more sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,
94%,
95%, 96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 28,
36,
44; the one or more LB primers comprise one or more sequences having at least
85%, 86%,
87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%
homology to the sequences of SEQ ID NOs: 31, 39, 40, 47; the one or more FIP
primers
comprise one or more sequences having at least 85%, 86%, 87%, 88%, 89%, 90%,
91%,
92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to the sequences of
SEQ
ID NOs: 29, 37, 45; and the one or more BIP primers comprise one or more
sequences having
at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,
99%, or 100% homology to the sequences of SEQ ID NOs: 30, 38, 46.
[0234] 90. The method of alternative 89, wherein the primer set comprises
sequences
having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,
97%,
98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 26-33.
[0235] 91. The method of alternatives 89 or 90, wherein the primer set
consists of
sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%,
96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 26-33.
[0236] 92. The method of any one of alternatives 76-85, wherein the pathogen
is
Influenza A Virus Subtype H1N1 and wherein: the one or more F3 primers
comprise one or
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more sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,
94%,
95%, 96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 50,
51,
59; the one or more B3 primers comprise one or more sequences having at least
85%, 86%,
87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%
homology to the sequences of SEQ ID NOs: 52, 53, 60, 61; the one or more LF
primers
comprise one or more sequences having at least 85%, 86%, 87%, 88%, 89%, 90%,
91%,
92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to the sequences of
SEQ
ID NOs: 54, 62, 63, 64; the one or more LB primers comprise one or more
sequences having
at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,
99%, or 100% homology to the sequences of SEQ ID NOs: 55, 56, 65; the one or
more FIP
primers comprise one or more sequences having at least 85%, 86%, 87%, 88%,
89%, 90%,
91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to the sequences
of
SEQ ID NOs: 57, 66; and the one or more BIP primers comprise one or more
sequences
having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,
97%,
98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 58, 67.
[0237] 93. The method of alternative 92, wherein the primer set comprises
sequences
having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,
97%,
98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 50-58.
[0238] 94. The method of alternative 92 or 93, wherein the primer set consists
of
sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%,
96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 50-58.
[0239] 95. The method of any one of alternatives 76-85, wherein the pathogen
is
Human Immunodeficiency Virus-1 and wherein: the one or more F3 primers
comprise one
or more sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,
94%,
95%, 96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 68,
69,
77, 89, 90; the one or more B3 primers comprise one or more sequences having
at least 85%,
86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%
homology to the sequences of SEQ ID NOs: 75, 76, 87, 88,96; the one or more LF
primers
comprise one or more sequences having at least 85%, 86%, 87%, 88%, 89%, 90%,
910/,
92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to the sequences of
SEQ
ID NOs: 70, 71, 78, 79, 80, 91; the one or more LB primers comprise one or
more sequences
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having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,
97%,
98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 74, 84, 85, 86, 94,
95; the
one or more FIP primers comprise one or more sequences having at least 85%,
86%, 87%,
88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology
to
the sequences of SEQ ID NOs: 72, 81, 92; and the one or more BIP primers
comprise one
or more sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,
94%,
95%, 96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 73,
82,
83,93.
[0240] 96. The method of alternative 95, wherein the primer set comprises
sequences
having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,
97%,
98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 68-76.
[0241] 97. The method of alternative 95 or 96, wherein the primer set consists
of
sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%,
96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 68-76.
[0242] 98. The method of any one of alternatives 76-85, wherein the pathogen
is
Respiratory Syncytial Virus A and wherein: the one or more F3 primers comprise
one or
more sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,
94%,
95%, 96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 97,
98,
108; the one or more B3 primers comprise one or more sequences having at least
85%, 86%,
87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%
homology to the sequences of SEQ ID NOs: 99, 100, 109; the one or more I,F
primers
comprise one or more sequences having at least 85%, 86%, 87%, 88%, 89%, 90%,
91%,
92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to the sequences of
SEQ
ID NOs: 101, 102, 110; the one or more LB primers comprise one or more
sequences having
at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92 A), 93%, 94%, 95%, 96%, 97%,
98%,
99%, or 100% homology to the sequences of SEQ ID NOs: 103, 111; the one or
more FIP
primers comprise one or more sequences having at least 85%, 86%, 87%, 88%,
89%, 90%,
91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to the sequences
of
SEQ ID NOs: 104, 106; and the one or more BIP primers comprise one or more
sequences
having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,
97%,
98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 105, 107.
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[0243] 99. The method of alternative 98, wherein the primer set comprises
sequences
having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,
97%,
98%, 99%, or 100% homology to the sequences of SEQ 1D NOs: 97-105.
[0244] 100. The method of alternative 98 or 99, wherein the primer set
consists of
sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%,
96%, 97 A), 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 97-105.
[0245] 1.01. The method of any one of alternatives 76-85, wherein the pathogen
is
Respiratory Syncytial Virus B and wherein: the one or more F3 primers comprise
one or
more sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,
94%,
95%, 96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs:
11.2, 113,
125; the one or more B3 primers comprise one or more sequences having at least
85%, 86%,
87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%
homology to the sequences of SEQ ID NOs: 114, 126; the one or more LF primers
comprise
one or more sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%,
93%,
94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs:
115, 116, 117, 127; the one or more LB primers comprise one or more sequences
having at
least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,
99%,
or 100% homology to the sequences of SEQ ID NOs: 118, 119, 120, 128; the one
or more
FIP primers comprise one or more sequences having at least 85%, 86%, 87%, 88%,
89%,
90 A), 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to the
sequences of SEQ ID NOs: 121, 123; and the one or more BIP primers comprise
one or
more sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,
94%,
95%, 96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 122,
124.
[0246] 102. The method of alternative 101, wherein the primer set comprises
sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%,
96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 112-122.
[0247] 103. The method of alternative 101 or 102, wherein the primer set
consists of
sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%,
96%, 97 A), 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 112-
122.
[0248] 104. The method of any one of alternatives 76-85, wherein the pathogen
is
Escherichia coil, the genome region comprises at least one of Z3276, Stx 1 ,
or Stx2 genes
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and wherein: the one or more F3 primers comprise one or more sequences having
at least
85%, 86 A), 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%,
or
100% homology to the sequences of SEQ ID NOs: 129, 135, 141., 147, 153, 159;
the one or
more B3 primers comprise one or more sequences having at least 85%, 86%, 87%,
88%,
89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to the
sequences of SEQ ID NOs: 134, 140, 146, 152, 158, 164; the one or more LF
primers
comprise one or more sequences having at least 85%, 86%, 87%, 88%, 89%, 90%,
91%,
92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to the sequences of
SEQ
ID NOs: 131, 137, 143, 149, 155, 161; the one or more LB primers comprise one
or more
sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%,
96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 133, 139,
145,
151, 157, 1.63; the one or more HP primers comprise one or more sequences
having at least
85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or
1.00% homology to the sequences of SEQ ID NOs: 130, 1.36, 142, 148, 154, 160;
and the
one or more BIP primers comprise one or more sequences having at least 85%,
86%, 87%,
88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology
to
the sequences of SEQ ID NOs: 132, 138, 144, 150, 156, 162.
[0249] 105. The method of alternative 104, wherein the primer set comprises
sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%,
96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 135-140,
141-
146, 159-164.
[0250] 106. The method of alternative 104 or 105, wherein the primer set
consists of
sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%,
96%, 97 A), 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 135-
140, 141-
146, 159-164.
[0251] 107. The method of any one of alternatives 76-85, wherein the pathogen
is
Listeria monocytogenes and wherein: the one or more F3 primers comprise one or
more
sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%,
96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NO: 165; the
one or
more B3 primers comprise one or more sequences having at least 85%, 86%, 87%,
88%,
89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to the
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sequences of SEQ ID NO: 166; the one or more LF primers comprise one or more
sequences
having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,
97%,
98%, 99%, or 100% homology to the sequences of SEQ ID NO: 167; the one or more
LB
primers comprise one or more sequences having at least 85%, 86%, 87%, 88%,
89%, 90%,
91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to the sequences
of
SEQ ID NOs: 172,173; the one or more FIP primers comprise one or more
sequences having
at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,
99%, or 100% homology to the sequences of SEQ lID NOs: 168, 169; and the one
or more
BIP primers comprise one or more sequences having at least 85%, 86%, 87%, 88%,
89%,
90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to the
sequences of SEQ ID NOs: 170, 171.
[0252] 108. The method of alternative 107, wherein the primer set comprises
sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%,
96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 165-168,
170,
172.
[0253] 109. The method of alternative 107 or 108, wherein the primer set
consists of
sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%,
96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 165-168,
170,
172.
[0254] 110. The method of any one of alternatives 76-85, wherein the pathogen
is
Mycobacterium tuberculosis and wherein: the one or more F3 primers comprise
one or more
sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%,
96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 174, 180,
186;
the one or more B3 primers comprise one or more sequences having at least 85%,
86%, 87%,
88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology
to
the sequences of SEQ ID NOs: 1.75, 181, 187; the one or more LF primers
comprise one or
more sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,
94%,
95%, 96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 178,
184,
190; the one or more LB primers comprise one or more sequences having at least
85%, 86%,
87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%
homology to the sequences of SEQ ID NOs: 179, 185, 191; the one or more FIP
primers
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comprise one or more sequences having at least 85%, 86%, 87%, 88%, 89%, 90%,
91%,
92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to the sequences of
SEQ
ID NOs: 176, 1.82, 188; and the one or more SIP primers comprise one or more
sequences
having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,
97%,
98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 177, 183, 189.
[0255] 111. The method of alternative 110, wherein the primer set comprises
sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%,
96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 186-191.
[0256] 112. The method of alternative 110 or 111, wherein the primer set
consists of
sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%,
96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 186-191.
[0257] 113. The method of any one of alternatives 76-85, wherein the pathogen
is
Salmonella enterica and wherein: the one or more F3 primers comprise one or
more
sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%,
96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 192, 196;
the
one or more B3 primers comprise one or more sequences having at least 85%,
86%, 87%,
88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology
to
the sequences of SEQ ID NOs: 203, 204; the one or more LF primers comprise one
or more
sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%,
96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 194, 198,
199;
the one or more LB primers comprise one or more sequences having at least 85%,
86%, 87%,
88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology
to
the sequences of SEQ ID NOs: 201,202; the one or more F.TP primers comprise
one or more
sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%,
96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 193, 197;
and
the one or more BIP primers comprise one or more sequences having at least
85%, 86%,
87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%
homology to the sequences of SEQ ID NOs: 195, 200.
[0258] 114. The method of alternative 113, wherein the primer set comprises
sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%,
96 A, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 196-204.
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[0259] 115. The method of alternative 113 or 114, wherein the primer set
consists of
sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%,
96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 196-204.
[0260] 116. The method of any one of alternatives 76-115, wherein the
biological
sample is obtained from a subject, preferably a human or other animal, a
plant, a food, soil,
or a surface, or any combination thereof.
[0261] 117. The method of alternative 116, wherein the biological sample is
obtained
by swabbing.
[0262] 118. The method of alternative 116 or 117, wherein the animal is a
livestock
[0263] 119. The method of any one of alternatives 116-118, wherein the plant
is a
vegetable, fruit, or legume.
[0264] 120. The method of any one of alternatives 116-119, wherein the surface
is a
livestock pen or found in a hospital.
[0265] 121. The method of any one of alternatives 76-120, wherein the method
is
multiplexed to detect the presence and/or amount of more than one nucleic
acid, preferably
more than one nucleic acid from more than one pathogen, comprising amplifying
the more
than one nucleic acid with more than one primer sets, each of which is
specific for a genome
region of the more than one pathogen, and determining the presence and/or
amount of the
more than one nucleic acid in the biological sample.
[0266] 122. The F3, B3, 1,F, LB, HP, or BIP primers of any one of alternatives
86-
121.
[0267] 123. A primer comprising the sequence having at least 85%, 86%, 87%,
88%,
89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to any
one of the sequences of SEQ ffi NOs: 1-204.
[0268] 124. The primer set of any one of alternatives 87, 88, 90, 91, 93, 94,
96, 97,
99, 100, 102, 103, 105, 106, 108, 109, 111, 112, 114, or 115.
[0269] 125. The primer of alternative 123 or the primer set of alternative 124
for use
in a nucleic acid amplification, such as Loop-Mediated Isothermal
Amplification (LAMP),
preferably, in a system, wherein an electrical signal, such as impedance or
capacitance, is
evaluated to detect the presence, absence, or amount of one or more amplified
nucleic acids.
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[0270] 126. A system for determining a wellness score for a user, animal, or
product,
the system comprising: a database configured to store a plurality of user,
animal, or product
profiles, each user, animal, or product profile comprising health information
for a single user,
animal, or product of a plurality of users, animals, or products and user,
animal, or product
identifying information, a testing device configured to: accept a sample from
the user,
animal, or product, generate test results based on the sample, and store the
generated test
results in the user, animal, or product profile for the user, animal, or
product in the database;
a computing system configured to: generate the wellness score for the user,
animal, or
product the wellness score based on the health information stored in the user,
animal, or
product profile, the health information comprising the generated test results,
and store the
wellness score in the user, animal, or product profile in the database; a
remote computing
device configured to: obtain biometric or identifying information, such as QR
coding, RFID
coding, or bar coding, for the user, animal, or product, request the wellness
score for the user,
animal, or product from the database based on the user's, animal's, or
product's biometric or
identifying information, and receive the wellness score for the user, animal,
or product based
on the computing system determining that the user's, animal's, or product's
biometric or
identifying information matches the user's, animal's, or product's identifier,
wherein the
wellness score is compared to a threshold value to determine whether the user,
animal, or
product is permitted entry to a location.
[0271] 127. The system of alternative 126, wherein the health information
further
comprises one or more of health information records acquired from a medical
professional,
health survey information provided by the user, or contact tracing
information.
[0272] 128. The system of any one of alternatives 126 and 127, wherein the
user
identifying information comprises one or more of an identifier for the user,
biometrics
information for the user, and username and password information for the user.
[0273] 129. The system of any one of alternatives 126-128, wherein the
wellness
score is representative of whether the user, animal, or product is likely to
be infected by a
pathogen comprising one or more of a mold, fungus, bacteria, a virus, or
another microbe.
[0274] 130. The system of any one of alternatives 126-129, wherein the testing
device comprises: a cartridge configured to receive the biological sample, and
a reader device
comprising: a cavity configured to receive the cartridge, a memory storing at
least computer-
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readable instructions, a processor in communication with the memory, and an
electrode
interface in communication with the processor and in contact with the
cartridge when the
cartridge is inserted into the cavity.
[0275] 131. The system of alternative 130, wherein the cartridge comprises: an
external portion; an internal portion configured to fit within the cavity of
the reader device,
the internal portion including an electrode interface configured to establish
an electrical
connection with the electrode interface of the reader device when the
cartridge is inserted
into the reader device; and a flow path configured to sealingly enclose a
biological sample
within the cartridge.
[0276] 132. The system of any one of alternatives 130 and 131, wherein the
reader
device further includes a communication module configured to communicatively
connect to
the computing system or the remote computing device.
[0277] 133. The system of any one of alternatives 130-132, wherein the remote
computing device or the computing system is wirelessly connected to the reader
device.
[0278] 134. The system of any one of alternatives 126-133, wherein the testing
device, the computing system, and the remote computing device are connected by
at least
one of a wireless, wired, or hybrid network.
[0279] 135. The system of any one of alternatives 126-134, wherein the remote
computing device comprises a biometric input device that obtains the biometric
information
for the user from the user.
[0280] 136. The system of any one of alternatives 126-135, wherein the
biometric
information comprises one or more of fingerprint information, facial
recognition
information, retinal scan information, hand geometry information, finger
geometry
information, palm vein information, ear geometry information, voice
information, hand
writing information, signature information, typing pattern recognition,
biological sample
recognition, or movement recognition.
[0281] 137. The system of alternative 126, further comprising a user device
configured to: capture location information for the user; capture
identification information
for other user devices of other users that come within a threshold distance of
the user; and
store the location information and identification information in the user
profile in the
database.
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[0282] 138. The system or testing device of any one of alternatives 126-137
for use
in detecting a target agent.
[0283] 139. The system of alternatives 138, wherein the target agent indicates
presents of a mold, fungus, bacteria, a virus, or another microbe.
[0284] 140. The system any one of alternatives 126-139, wherein the biological
sample is obtained from a subject, such as a human or an animal, a product,
such as a food
or beverage, or an object, such as a high contact surface.
[0285] 141. A method of using the system of any one of alternatives 126-140
for
determining the wellness score for the user, animal, or product.
[0286] 142. A method of determining a wellness score for a user, animal, or
product
the method comprising: creating a user, animal, or product profile for a user,
animal, or
product in a database, the user, animal, or product profile comprising health
information and
user, animal, or product identifying information; depositing a sample obtained
from the user,
animal, or product into a sample receptacle of a testing device; generating
test results based
on the sample; storing the generated test results in the user, animal, or
product profile for the
user, animal, or product; generating the wellness score for the user, animal,
or product the
wellness score based on the health information stored in the user, animal, or
product profile,
the health information comprising the generated test results; storing the
wellness score in the
user, animal, or product profile in the database; obtaining biometric or
identifying
information for the user, animal, or product; requesting the wellness score
for the user,
animal, or product from the database based on the user's, animal's, or
product's biometric or
identifying information at a remote computing device; receiving the wellness
score for the
user, animal, or product based on the computing system determining that the
user's, animal's,
or product's biometric or identifying information matches the user's,
animal's, or product's
identifier; and comparing the wellness score to a threshold value to determine
whether the
user, animal, or product is permitted entry to a location and optionally
providing or
displaying a visually identifiable signal or character indicating that the
wellness score is at
or exceeds the threshold value..
[0287] 143. The method of alternative 142, wherein the health information
further
comprises one or more of health information records acquired from a medical
professional,
health survey information provided by the user, or contact tracing
information.
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[0288] 144. The method of any one of alternatives 142 and 143, wherein the
user
identifying information comprises one or more of an identifier for the user,
biometrics
information for the user, and username and password information for the user.
[0289] 145. The method of any one of alternatives 142-144, wherein the
wellness
score is representative of whether the user, animal, or product is likely to
be infected by a
pathogen comprising one or more of a mold, fungus, bacteria, a virus, or
another microbe.
[0290] 146. The method of any one of alternatives 142-145, wherein the testing
device, the computing system, and the remote computing device are connected by
at least
one of a wireless, wired, or hybrid network.
[0291] 147. The method of any one of alternatives 142-146, wherein the remote
computing device comprises a biometric input device that obtains the biometric
information
for the user from the user.
[0292] 148. The method of any one of alternatives 142-147, wherein the
biometric
information comprises one or more of fingerprint information, facial
recognition
information, retinal scan information, hand geometry information, finger
geometry
information, palm vein information, ear geometry information, voice
information, hand
writing information, signature information, typing pattern recognition,
biological sample
recognition, or movement recognition.
[0293] 149. The method of alternative 142, further comprising: capturing
location
information for the user; capturing identification information for other user
devices of other
users that come within a threshold distance of the user; and storing the
location information
and identification information in the user profile in the database.
[0294] 150. The method of any one of alternatives 142-149, further comprising
detecting a target agent.
[0295] 151. The method of alternative 150, wherein the target agent indicates
presents of a mold, fungus, bacteria, a virus, or another microbe.
[0296] 152. The method any one of alternatives 142-151, wherein the biological
sample is obtained from a subject, such as a human or an animal, a product,
such as a food
or beverage, or an object, such as a high contact surface.
[0297] 153. A system for determining a wellness score of an individual,
comprising:
a database configured to: create a data structure for a profile associated
with the individual
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and configured to store information in the data structure, the information
comprising one or
more of health information for the individual, contact tracing for the
individual, health
surveys completed by the individual, temperature measurements for the
individual,
authentication information for the individual (can include biometric
information), test results
for the individual, or a wellness score for the individual; obtain information
associated with
the individual from a source; store the obtained information in the profile
data structure;
calculate the wellness score for the individual based on an algorithm that
accounts for the
information stored in the profile data structure, wherein the algorithm
applies different
weights to the different information in the profile data structure when
calculating the
wellness score; and update the data structure based on the calculated wellness
score; a testing
device configured to test a biological sample from the individual for a
pathogen and provide
results to the test to the database for the profile associated with the
individual; and a site
device configured to: access the profile for the individual from the database;
compare the
wellness score with a threshold score; and indicate that the individual is
granted access to a
location based on the wellness score being greater than or exceeding the
threshold score and
optionally providing or displaying a visually identifiable signal or character
indicating that
the wellness score is at or exceeds the threshold value.
[0298] 154. An assay cartridge for containing a sample comprising a target
agent for
detection by a reader device, the assay cartridge comprising: a sample
introduction area
configured to receive a sample carrier containing the sample; a mixing region
configured to
mix the sample with a reagent to generate a sample mixture; at least one
mixing object
disposed in the mixing region and configured to move within the mixing region
to enhance
mixing of the sample with the reagent in response to a force applied to the
mixing region; a
test well containing an excitation electrode and a sensing electrode, wherein
the test well is
configured to contain at least a portion of the sample mixture undergoing an
amplification
process; and a fluid path fluidically coupling the sample introduction area to
the mixing
region and the mixing region to the test well.
[0299] 155. The assay cartridge of alternative 154, wherein the force applied
is the
result of one or more of a magnetic field generator, such as an electromagnet,
a vibration
generator, a sonic generator, and physical movement.
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[0300] 156. The assay cartridge of any of alternatives 154 and 155, wherein
the
reagent comprises one of a dry reagent or a liquid reagent.
[0301] 157. The assay cartridge of any of alternatives 154-156, wherein the at
least
one mixing object comprises at least one magnetic bead and wherein the force
is exerted by
a first magnetic field generated by a first magnet, such as an electromagnet,
disposed in the
reader near a first location of the mixing region when the assay cartridge is
inserted into the
reader.
[0302] 158. The assay cartridge of alternative 157, wherein the force is
further
exerted by a second magnetic field generated by a second magnet, such as an
electromagnet
disposed in the reader near a second location of the mixing region when the
assay cartridge
is inserted into the reader.
[0303] 159. The assay cartridge of alternative 158, further comprising a
control
circuit configured to switch between which of the first magnet and the second
magnetic is
exerting the force at a given moment.
[0304] 160. The assay cartridge of any of alternatives 154-159, wherein the
force is
exerted by a movable force generator disposed in the reader.
[0305] 161. The assay cartridge of any of alternatives 154-160, wherein one or
more
of the sample introduction area, the mixing region, the test well, and the
fluid path introduces
an agent that reduces effects of one or more inhibitors that exist in the
sample.
[0306] 162. The assay cartridge of alternative 161, wherein the one or more of
the
sample introduction area, the mixing region, the test well, and the fluid path
are coated with
the agent.
[0307] 163. The assay cartridge of any of alternatives 161 and 162, wherein
the
reagent includes the agent that reduces effects of the inhibitors.
[0308] 164. The assay cartridge of any of alternatives 161-163, wherein the
one or
more inhibitors that exist in the sample comprise one or more of lactoferrin,
lysozyme,
nucleases, DNAses, or RNases and wherein the agent is configured to improve a
detection
sensitivity of testing performed with the assay cartridge and the reader by
inhibiting said
inhibitors.
[0309] 165. The assay cartridge of any of alternatives 161-164, wherein the
agent
comprises one or more of an antibody, aptamer, competitive binding protein, or
a proteinase.
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In some embodiments, a chemical reaction is used to generate heat, which
inactivates the
proteinase after it has digested proteins in the sample.
[0310] 166. An assay cartridge for containing a sample comprising a target
agent for
detection by a reader device, the assay cartridge comprising: a sample
introduction area
configured to receive a sample carrier containing the sample; a mixing region
configured to
mix the sample with a reagent to generate a sample mixture; a test well
containing an
excitation electrode and a sensing electrode, wherein the test well is
configured to contain at
least a portion of the sample mixture undergoing an amplification process; and
a fluid path
fluidically coupling the sample introduction area to the mixing region and the
mixing region
to the test well, wherein one or more of the sample introduction area, the
mixing region, the
test well, and the fluid path introduces an agent that reduces effects of one
or more inhibitors
that exist in the sample.
[0311] 167. The assay cartridge of alternative 166, wherein the one or more of
the
sample introduction area, the mixing region, the test well, and the fluid path
are coated with
the agent.
[0312] 168. The assay cartridge of any of alternatives 166 and 167, wherein
the
reagent includes the agent that reduces effects of the one or more inhibitors.
[0313] 169. The assay cartridge of any of alternatives 166-168, wherein the
one or
more inhibitors that exist in the sample comprise one or more of lactoferrin,
lysozyme,
nucleases, DNAses or RNases and wherein the agent is configured to improve a
detection
sensitivity of testing performed with the assay cartridge and the reader.
[0314] 170. The assay cartridge of any of alternatives 166-169, wherein the
agent
comprises one or more of an antibody, aptamer, competitive binding protein, or
a proteinase.
in some embodiments, a chemical reaction is used to generate heat, which
inactivates the
proteinase after it has digested proteins in the sample.
[0315] 171. The assay cartridge of any of alternatives 166-170, further
comprising at
least one mixing object disposed in the mixing region and configured to move
within the
mixing region to enhance mixing of the sample with the reagent in response to
a force applied
to the mixing region.
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[0316] 172. The assay cartridge of alternative 171, wherein the force applied
is the
result of one or more of a magnetic field generator, a vibration generator, a
sonic generator,
and physical movement.
[0317] 173. The assay cartridge of any of alternatives 171 and 172, wherein
the
reagent comprises one of a dry reagent or a liquid reagent.
[0318] 174. The assay cartridge of any of alternatives 171-173, wherein the at
least
one mixing object comprises at least one magnetic bead and wherein the force
is exerted by
a first magnetic field generated by a first magnet, such as an electromagnet
disposed in the
reader near a first location of the mixing region when the assay cartridge is
inserted into the
reader.
[0319] 175. The assay cartridge of alternative 174, wherein the force is
further
exerted by a second magnetic field generated by a second magnet, such as an
electromagnet
disposed in the reader near a second location of the mixing region when the
assay cartridge
is inserted into the reader.
[0320] 176. The assay cartridge of alternative 175, further comprising a
control
circuit configured to switch between which of the first magnet and the second
magnetic is
exerting the force at a given moment.
[0321] 177. The assay cartridge of any of alternatives 154-176, further
comprising
the sample carrier comprising: a body configured to hold the sample before
depositing the
sample into the assay cartridge; a tip fluidically coupled to the body and
configured to fit
into the sample introduction area of the assay cartridge, wherein the sample
held in the body
can be ejected from the sample carrier via the tip; and a membrane disposed
between the
body and the tip and configured to prevent molecules in the sample that exceed
a threshold
size from being ejected from the body via the tip.
[0322] 178. The assay cartridge of alternative 177, wherein the sample carrier
further
comprises a gel filtration component, a resin, size-exclusion resin, bead, or
matrix, such as a
filter or molecular weight filter, configured to trap or retain salt compounds
in the sample
such that the salt compounds are not ejected from the body via the tip.
[0323] 179. The assay cartridge of any of alternatives 177 and 178, wherein
the gel
filtration component comprises one of a gel filtration bead bed or a gel
filtration matrix or a
membrane, such as a molecular weight cut-off membrane.
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[0324] 180. The assay cartridge of any of alternatives 177-179, wherein the
sample
carrier further comprises a buffer component configured to assist in
extracting the target
agent from the sample.
[0325] 181. The assay cartridge of alternative 180, wherein the buffer
component
comprises one of an elution buffer or a lysis buffer.
[0326] 182. The assay cartridge of any of alternatives 177-181, wherein the
sample
carrier further comprises a plunger component configured to apply a force to
the sample in
the body and cause the sample to pass through the membrane and the tip and
into the sample
introduction area of the assay cartridge.
[0327] 183. A system for detecting a target agent in a sample using an assay
cartridge
and a reader, the system comprising: the assay cartridge, comprising: a sample
introduction
area configured to receive a sample carrier containing the sample; and the
sample carrier for
depositing the sample into the assay cartridge, the sample carrier comprising:
a body
configured to hold the sample before depositing the sample into the assay
cartridge; a tip
fluidically coupled to the body and configured to fit into the sample
introduction area of the
assay cartridge, wherein the sample held in the body can be ejected from the
sample carrier
via the tip; and a membrane disposed between the body and the tip and
configured to prevent
molecules in the sample that exceed a threshold size from being ejected from
the body via
the tip.
[0328] 184. The system of alternative 183, wherein the sample carrier further
comprises a gel filtration component, a resin, size-exclusion resin, bead, or
matrix, such as a
filter or size-exclusion filter configured to trap or retain salt compounds in
the sample such
that the salt compounds are not ejected from the body via the tip.
[0329] 185. The system of any of alternatives 183 and 184, wherein the gel
filtration
component comprises one of a gel filtration bead bed or a gel filtration
matrix or a membrane,
such as a molecular weight cut-off membrane.
[0330] 186. The system of any of alternatives 183-185, wherein the sample
carrier
further comprises a buffer component configured to assist in extracting the
target agent from
the sample.
[0331] 187. The system of any of alternatives 183-186, wherein the buffer
component comprises one of an elution buffer or a lysis buffer.
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[0332] 188. The system of any of alternatives 183-187, wherein the sample
carrier
further comprises a plunger component configured to apply a force to the
sample in the body
and cause the sample to pass through the membrane and the tip and into the
sample
introduction area of the assay cartridge.
[0333] 189. The system of any of alternatives 183-188, wherein the assay
cartridge
further comprises: a mixing region configured to mix the sample with a reagent
to generate
a sample mixture; at least one mixing object disposed in the mixing region and
configured
to move within the mixing region to enhance mixing of the sample with the
reagent in
response to a force applied to the mixing region; a test well containing an
excitation electrode
and a sensing electrode, wherein the test well is configured to contain at
least a portion of
the sample mixture undergoing an amplification process; and a fluid path
fluidically coupling
the sample introduction area to the mixing region and the mixing region to the
test well.
[0334] 190. The system of alternative 189, wherein the force applied is the
result of
one or more of a magnetic field generator, a vibration generator, a sonic
generator, and
physical movement.
[0335] 191. The system of any of alternatives 189 and 190, wherein the reagent
comprises one of a dry reagent or a liquid reagent.
[0336] 192. The system of any of alternatives 189-191, wherein the at least
one
mixing object comprises at least one magnetic bead and wherein the force is
exerted by a
first magnetic field generated by a first magnet, such as an electromagnet
disposed in the
reader near a first location of the mixing region when the assay cartridge is
inserted into the
reader.
[0337] 193. The system of alternative 192, wherein the force is further
exerted by a
second magnetic field generated by a second magnet, such as an electromagnet
disposed in
the reader near a second location of the mixing region when the assay
cartridge is inserted
into the reader.
[0338] 194. The system of alternative 193, further comprising a control
circuit
configured to switch between which of the first magnet and the second magnetic
is exerting
the force at a given moment.
[0339] 195. The system of any of alternatives 189-194, wherein the force is
exerted
by a movable force generator disposed in the reader.
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[0340] 196. The system of any of alternatives 189-195, wherein one or more of
the
sample introduction area, the mixing region, the test well, and the fluid path
introduces an
agent that reduces effects of one or more inhibitors that exist in the sample.
[0341] 197. The system of alternative 196, wherein the one or more of the
sample
introduction area, the mixing region, the test well, and the fluid path are
coated with the
agent.
[0342] 198. The system of any of alternatives 196 and 197, wherein the reagent
includes the agent that reduces effects of the one or more inhibitors.
[0343] 199. The system of any of alternatives 196-198, wherein the one or more
inhibitors that exist in the sample comprise one or more of lactoferrin,
lysozyme, nucleases,
DNAses or RNases and wherein the agent is configured to improve a detection
sensitivity of
testing performed with the assay cartridge and the reader.
[0344] 200. The system of any of alternatives 196-199, wherein the agent
comprises
one or more of an antibody or a proteinase. In some embodiments, a chemical
reaction is
used to generate heat, which inactivates the proteinase after it has digested
proteins in the
sample.
[0345] 201. The system of any of alternatives 183-188, wherein the assay
cartridge
further comprises: a mixing region configured to mix the sample with a reagent
to generate
a sample mixture; a test well containing an excitation electrode and a sensing
electrode,
wherein the test well is configured to contain at least a portion of the
sample mixture
undergoing an amplification process; and a fluid path fluidically coupling the
sample
introduction area to the mixing region and the mixing region to the test well,
wherein one or
more of the sample introduction area, the mixing region, the test well, and
the fluid path
introduces an agent that reduces effects of one or more inhibitors that exist
in the sample.
[0346] 202. The system of alternative 201, wherein the one or more of the
sample
introduction area, the mixing region, the test well, and the fluid path are
coated with the
agent.
[0347] 203. The system of any of alternatives 201 and 202, wherein the reagent
includes the agent that reduces effects of the one or more inhibitors.
[0348] 204. The system of any of alternatives 201-203, wherein the inhibitors
that
exist in the sample comprise one or more of lactoferrin, lysozyme, nucleases,
DNAses or
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RNases and wherein the agent is configured to improve a detection sensitivity
of testing
performed with the assay cartridge and the reader.
[0349] 205. The system of any of alternatives 201-204, wherein the agent
comprises
one or more of an antibody or a proteinase. In some embodiments, a chemical
reaction is
used to generate heat, which inactivates the proteinase after it has digested
proteins in the
sample.
[0350] 206. The system of any of alternatives 201-205, further comprising at
least
one mixing object disposed in the mixing region and configured to move within
the mixing
region to enhance mixing of the sample with the reagent in response to a force
applied to the
mixing region.
[0351] 207. The system of alternative 206, wherein the force applied is the
result of
one or more of a magnetic field generator, a vibration generator, a sonic
generator, and
physical movement.
[0352] 208. The system of any of alternatives 206 and 207, wherein the reagent
comprises one of a dry reagent or a liquid reagent.
[0353] 209. The system of any of alternatives 206-208, wherein the at least
one
mixing object comprises at least one magnetic bead and wherein the force is
exerted by a
first magnetic field generated by a first magnet, such as an electromagnet
disposed in the
reader near a first location of the mixing region when the assay cartridge is
inserted into the
reader.
[0354] 210. The system of alternative 209, wherein the force is further
exerted by a
second magnetic field generated by a second magnet, such as an electromagnet
disposed in
the reader near a second location of the mixing region when the assay
cartridge is inserted
into the reader.
[0355] 211. The system of alternative 210, further comprising a control
circuit
configured to switch between which of the first magnet and the second magnetic
is exerting
the force at a given moment.
[0356] 212. A system for determining a wellness score for a user, animal, or
product,
the system comprising: a database configured to store a plurality of user,
animal, or product
profiles, each user, animal, or product profile comprising health information
for a single user,
animal, or product of a plurality of users, animals, or products and user,
animal, or product
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identifying information, a testing device comprising the assay cartridge of
any of alternatives
153482, the testing device configured to: accept the sample from the user,
animal, or
product, generate test results based on the sample, and store the generated
test results in the
user, animal, or product profile for the user, animal, or product in the
database; a computing
system configured to: generate the wellness score for the user, animal, or
product the
wellness score based on the health information stored in the user, animal, or
product profile,
the health information comprising the generated test results, and store the
wellness score in
the user, animal, or product profile in the database; a remote computing
device configured
to: obtain biometric or identifying information, such as QR coding, RFID
coding, or bar
coding, for the user, animal, or product, request the wellness score for the
user, animal, or
product from the database based on the user's, animal's, or product's
biometric or identifying
information, and receive the wellness score for the user, animal, or product
based on the
computing system determining that the user's, animal's, or product's biometric
or identifying
information matches the user's, animal's, or product's identifier, wherein the
wellness score
is compared to a threshold value to determine whether the user, animal, or
product is
permitted entry to a location and optionally providing or displaying a
visually identifiable
signal or character indicating that the wellness score is at or exceeds the
threshold value..
[0357] 213. The system of alternative 212, wherein the health information
further
comprises one or more of health information records acquired from a medical
professional,
health survey information provided by the user, or contact tracing
information.
[0358] 214. The system of any one of alternatives 212 and 213, wherein the
user
identifying information comprises one or more of an identifier for the user,
biometrics
information for the user, and username and password information for the user.
[0359] 215. The system of any one of alternatives 212-214, wherein the
wellness
score is representative of whether the user, animal, or product is likely to
be infected by a
pathogen comprising one or more of a mold, fungus, bacteria, a virus, or
another microbe.
[0360] 216. The system of any one of alternatives 212-215, wherein the testing
device comprises: a cartridge configured to receive the biological sample, and
a reader device
comprising: a cavity configured to receive the cartridge, a memory storing at
least computer-
readable instructions, a processor in communication with the memory, and an
electrode
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interface in communication with the processor and in contact with the
cartridge when the
cartridge is inserted into the cavity.
[0361] 217. The system of alternative 216, wherein the cartridge comprises: an
external portion; an internal portion configured to fit within the cavity of
the reader device,
the internal portion including an electrode interface configured to establish
an electrical
connection with the electrode interface of the reader device when the
cartridge is inserted
into the reader device; and a flow path configured to sealingly enclose a
biological sample
within the cartridge.
[0362] 218. The system of any one of alternatives 216 and 217, wherein the
reader
device further includes a communication module configured to communicatively
connect to
the computing system or the remote computing device.
[0363] 219. The system of any one of alternatives 216-218, wherein the remote
computing device or the computing system is wirelessly connected to the reader
device.
[0364] 220. The system of any one of alternatives 212-219, wherein the testing
device, the computing system, and the remote computing device are connected by
at least
one of a wireless, wired, or hybrid network.
[0365] 221. The system of any one of alternatives 212-220, wherein the remote
computing device comprises a biometric input device that obtains the biometric
information
for the user from the user.
[0366] 222. The system of any one of alternatives 212-221, wherein the
biometric
information comprises one or more of fingerprint information, facial
recognition
information, retinal scan information, hand geometry information, finger
geometry
information, palm vein information, ear geometry information, voice
information, hand
writing information, signature information, typing pattern recognition,
biological sample
recognition, or movement recognition.
[0367] 223. The system of any one of alternatives 212-222, further comprising
a user
device configured to: capture location information for the user; capture
identification
information for other user devices of other users that come within a threshold
distance of the
user; and store the location information and identification information in the
user profile in
the database.
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[0368] 224. The system of any one of alternatives 212-223 for use in detecting
a
target agent.
[0369] 225. The system of alternative 224, wherein the target agent indicates
presents
of a mold, fungus, bacteria, a virus, or another microbe.
[0370] 226. The system any one of alternatives 212-225, wherein the biological
sample is obtained from a subject, such as a human or an animal, a product,
such as a food
or beverage, or an object, such as a high contact surface.
[0371] 227. A method of using the system of any one of alternatives 212-226
for
determining the wellness score for the user, animal, or product.
[0372] 228. A method of determining a wellness score for a user, animal, or
product
the method comprising: creating a user, animal, or product profile for a user,
animal, or
product in a database, the user, animal, or product profile comprising health
information and
user, animal, or product identifying information; depositing a sample obtained
from the user,
animal, or product into a sample receptacle of a testing device comprising the
assay cartridge
of any of alternatives 154-182; generating test results based on the sample;
storing the
generated test results in the user, animal, or product profile for the user,
animal, or product;
generating the wellness score for the user, animal, or product the wellness
score based on the
health information stored in the user, animal, or product profile, the health
information
comprising the generated test results; storing the wellness score in the user,
animal, or
product profile in the database; obtaining biometric or identifying
information for the user,
animal, or product; requesting the wellness score for the user, animal, or
product from the
database based on the user's, animal's, or product's biometric or identifying
information;
receiving the wellness score for the user, animal, or product based on the
computing system
determining that the user's, animal's, or product's biometric or identifying
information
matches the user's, animal's, or product's identifier; and comparing the
wellness score to a
threshold value to determine whether the user, animal, or product is permitted
entry to a
location and optionally providing or displaying a visually identifiable signal
or character
indicating that the wellness score is at or exceeds the threshold value..
[0373] 229. A system for determining a wellness score of an individual,
comprising:
a database configured to: create a data structure for a profile associated
with the individual
and configured to store information in the data structure, the information
comprising one or
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more of health information for the individual, contact tracing for the
individual, health
surveys completed by the individual, temperature measurements for the
individual,
authentication information for the individual (can include biometric
information), test results
for the individual, or a wellness score for the individual; obtain information
associated with
the individual from a source; store the obtained information in the profile
data structure;
calculate the wellness score for the individual based on an algorithm that
accounts for the
information stored in the profile data structure, wherein the algorithm
applies different
weights to the different information in the profile data structure when
calculating the
wellness score; and update the data structure based on the calculated wellness
score; a testing
device comprising the assay cartridge of any of alternatives 154-82 and
configured to test a
biological sample from the individual for a pathogen and provide results to
the test to the
database for the profile associated with the individual; and a site device
configured to: access
the profile for the individual from the database; compare the wellness score
with a threshold
score; and indicate that the individual is granted access to a location based
on the wellness
score being greater than or exceeding the threshold score and optionally
providing or
displaying a visually identifiable signal or character indicating that the
wellness score is at
or exceeds the threshold value..
[0374] 230. A method of determining a wellness score for a user, animal, or
product
via the system of any one of alternatives 193-211, the method comprising:
creating a user,
animal, or product profile for a user, animal, or product in a database, the
user, animal, or
product profile comprising health information and user, animal, or product
identifying
information; depositing a sample obtained from the user, animal, or product
into a sample
receptacle of a testing device; generating test results based on the sample;
storing the
generated test results in the user, animal, or product profile for the user,
animal, or product;
generating the wellness score for the user, animal, or product the wellness
score based on the
health information stored in the user, animal, or product profile, the health
information
comprising the generated test results; storing the wellness score in the user,
animal, or
product profile in the database; obtaining biometric or identifying
information for the user,
animal, or product; requesting the wellness score for the user, animal, or
product from the
database based on the user's, animal's, or product's biometric or identifying
information;
receiving the wellness score for the user, animal, or product based on the
computing system
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determining that the user's, animal's, or product's biometric or identifying
information
matches the user's, animal's, or product's identifier; and comparing the
wellness score to a
threshold value to determine whether the user, animal, or product is permitted
entry to a
location and optionally providing or displaying a visually identifiable signal
or character
indicating that the wellness score is at or exceeds the threshold value..
[0375] 231. A method of improving a limit of detection of a nucleic acid by
Loop-
Mediated Isothermal Amplification (LAMP) with a primer set, comprising:
amplifying a
nucleic acid by LAMP with a primer set at a first temperature of between 23 C
and 55 C,
and then at a second temperature of 60 C to 70 C, wherein the primer set is
specific for a
genomic region of a pathogen; and measuring or analyzing a modulation of an
electrical
signal, such as impedance or capacitance, for the duration of the
amplification with the
primer set using a detection system, thereby detecting successful
amplification of the nucleic
acid with the primer set; and determining the presence of the nucleic acid in
the biological
sample, wherein a limit of detection of the nucleic acid is improved compared
to performing
LAMP only at the second temperature.
[0376] 232. A method of improving a limit of detection of a nucleic acid by
Loop-
Mediated Isothermal Amplification (LAMP) with a primer set, comprising:
amplifying a
nucleic acid by LAMP with a primer set at a first temperature of between 23 C
and 55 C,
preferably 50 C, and then at a second temperature of 60 C to 70 C, preferably
65 C,
optionally wherein the amplification at the first temperature is for 5, 6, 7,
8, 9, 10, 11, 12, 13,
14, or 15 minutes.
[0377] 233. A method of improving a limit of detection of a nucleic acid by
Loop-
Mediated Isothermal Amplification (LAMP) with a primer set, comprising
amplifying a
nucleic acid by LAMP with a primer set at more than one temperature.
[0378] 234. The method of any one of alternatives 231 to 233, wherein the
primer set
is the primer set of any alternative described above.
[0379] 235. The method of any one of alternatives 231 to 234, wherein the
nucleic
acid is from a pathogen selected from the group consisting of SARS-CoV-2,
hepatitis A
virus, Influenza A virus subtype H1N1, human immunodeficiency virus-1,
respiratory
syncytial virus A, respiratory syncytial virus B, laccherichia coil, Listeria
monocytogenes,
Mycobacterium tuberculosis, and Salmonella enterica, or any combination
thereof.
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[0380] Additional embodiments disclosed herein are methods of detecting the
presence and/or amount of a nucleic acid in a biological sample. In some
embodiments, the
nucleic acid is a nucleic acid from a pathogen, such as the DNA or RNA genome,
or a
fragment or derivative thereof, of the pathogen. The methods may include
contacting the
biological sample with any one of the assay cartridges or detection systems
disclosed herein,
amplifying the nucleic acid by loop-mediated isothermal amplification (LAMP)
with a
primer set, measuring or analyzing a modulation of an electrical signal for
the duration of
the amplification with the primer set using the assay cartridge or detection
system disclosed
herein, thereby detecting successful amplification of the nucleic acid with
the primer set, and
determining the presence and/or amount of the nucleic acid in the biological
sample. In some
embodiments, the biological sample is contacted with an assay cartridge that
is part of a
detection system. In some embodiments, the primer set comprises one or more F3
primers,
one or more B3 primers, one or more LF primers, one or more LB primers, one or
more FIP
primers, and one or more BIP primers used for LAMP. In some embodiments, the
primer set,
and/or the constituent primers, are specific for a genome region of the
pathogen. In some
embodiments, the electrical signal that is measured or analyzed is impedance
or capacitance.
In some embodiments, the presence and/or amount of the nucleic acid in the
biological
sample allows for determination of the presence and/or amount of the pathogen,
or the
genome region thereof, in the biological sample. In some embodiments, the
nucleic acid is
RNA, and the LAMP is reverse transcription LAMP (RT-LAMP). In some
embodiments,
the subject is a mammal. In some embodiments, the subject is a human.
[0381] In some embodiments, any one of the assay cartridges or detection
systems
disclosed herein comprises a heater. The heater can be used to keep any one of
the biological
samples, primers, and reagents at a constant temperature during the
amplification by LAMP.
In some embodiments, the amplifying step comprises incubating the biological
sample at,
optionally a first temperature for a first time period, and at least a second
temperature for a
second time period. In some embodiments, the amplifying step further comprises
incubating
the biological sample at a third temperature for a third time period. In some
embodiments,
the amplifying step comprises incubating the biological sample at, optionally
a first
temperature for a first time period, and one or more additional temperatures
for one or more
additional time periods (e.g., a second temperature, a third temperature, a
fourth temperature,
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a fifth temperature, and/or a sixth temperature or more for a second, third,
fourth, fifth, sixth,
and/or more time periods). The incubation at these temperatures for these time
periods
enables robust and rapid reverse transcription of RNA and/or LAMP
amplification of the
nucleic acid in the biological sample with the primer sets described herein.
[0382] In some embodiments, the primer sets, and the one or more F3 primers,
one
or more B3 primers, one or more LF primers, one or more LB primers, one or
more FIP
primers, and one or more BIP primers, are designed, configured or selected to
be not only
specific towards a genome region of a pathogen but also to amplify said
specific genome
region more efficiently than other primer sets (e.g., more rapidly, exhibiting
a faster time to
detection of a positive amplification and/or with greater specificity). In
some embodiments,
the pathogen is a virus or bacteria. In some embodiments, the pathogen is SARS-
CoV-2,
hepatitis A virus, Influenza A virus subtype H1 NI, human immunodeficiency
virus-1,
respiratory syncytial virus A, respiratory syncytial virus B, Escherichia
coli, Listeria
monocytogenesõWcobacterium tuberculosis, Salmonella enterica, or any
combination
thereof. In some embodiments, the primer sets comprise a functional set of
LAMP primers
(e.g. one or more of each of an F3 primer, a B3 primer, LF primer, LB primer,
FIP primer,
and BIP primer) selected from sequences having at least 85%, 86%, 87%, 88%,
89%, 90%,
91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology of SEQ ID NOs: 1-
204. In some embodiments, the primers specific for SARS-CoV-2 comprise
sequences
selected from sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%,
92%, 93%,
94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to SEQ ID NOs: 1-25. In a non-
limiting embodiment, a primer set specific for SARS-CoV-2 comprises, consists
essentially
of, or consists of sequences having at least 85%, 86%, 87%, 88%, 89%, 90%,
91%, 92%,
93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to SEQ ID NOs: 1-6. In
some
embodiments, the primers specific for hepatitis A virus comprise sequences
selected from
sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%,
96%, 97%, 98%, 99%, or 100% homology to SEQ ID NOs: 26-49. In a non-limiting
embodiment, a primer set specific for hepatitis A virus comprises, consists
essentially of, or
consists of sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%,
93%,
94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to SEQ ID NOs: 26-33. In some
embodiments, the primers specific for influenza A virus subtype H1N1 comprise
sequences
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selected from sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%,
92%, 93%,
94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to SEQ ID NOs: 50-67. In a non-
limiting embodiment, a primer set specific for influenza A virus subtype Hi NI
comprises,
consists essentially of, or consists of sequences having at least 85%, 86%,
87%, 88%, 89%,
90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to SEQ. ID
NOs: 50-58. In some embodiments, the primers specific for HIV-1 comprise
sequences
selected from sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%,
92%, 93%,
94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to SEQ ID NOs: 68-96. In a non-
limiting embodiment, a primer set specific for HIV-1 comprises, consists
essentially of, or
consists of sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%,
93%,
94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to SEQ ID NOs: 68-76. In some
embodiments, the primers specific for respiratory syncytial virus A comprise
sequences
selected from sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%,
92%, 93%,
94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to SEQ ID NOs: 97-111. In a non-
limiting embodiment, a primer set specific for respiratory syncytial virus A
comprises,
consists essentially of, or consists of sequences having at least 85%, 86%,
87%, 88%, 89%,
90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 1.00% homology to SEQ ID
NOs: 97-105. In some embodiments, the primers specific for respiratory
syncytial virus B
comprise sequences selected from sequences having at least 85%, 86%, 87%, 88%,
89%,
90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to SEQ ID
NOs: 112-128. In a non-limiting embodiment, a primer set specific for
respiratory syncytial
virus B comprises, consists essentially of, or consists of sequences having at
least 85%, 86%,
87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%
homology to SEQ ID NOs: 112-122. In some embodiments, the primers specific for
E. colt
(i.e. the pathogenic genes Z3276, Stx1 A, or Stx1 B) comprise sequences
selected from
sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%,
96%, 97%, 98%, 99%, or 100% homology to SEQ ID NOs: 129464. In a non-limiting
embodiment, a primer set specific for E. coli comprises, consists essentially
of, or consists
of sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%,
96%, 97%, 98%, 99%, or 100% homology to SEQ M NOs: 135-1.40, 141-146, 159-164.
In
some embodiments, the primers specific for L. monocytogenes comprise sequences
selected
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from sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,
94%,
95%, 96%, 97%, 98%, 99%, or 100% homology to SEQ ID NOs: 165-173. In a non-
limiting
embodiment, a primer set specific for L. monocytogenes comprises, consists
essentially of,
or consists of sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%,
92%, 93%,
94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to SEQ ID NOs: 165-168, 170,
172.
In some embodiments, the primers specific forM tuberculosis comprise sequences
selected
from sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,
94%,
95%, 96%, 97%, 98%, 99%, or 100% homology to SEQ ID NOs: 174-191. In a non-
limiting
embodiment, a primer set specific for M tuberculosis comprises, consists
essentially of, or
consists of sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%,
93%,
94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to SEQ ID NOs: 186-191. In some
embodiments, the primers specific for S. enterica comprise sequences selected
from
sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%,
96%, 97%, 98%, 99%, or 1.00% homology to SEQ ID NOs: 192-204. In a non-
limiting
embodiment, a primer set specific for S. enterica comprises, consists
essentially of, or
consists of sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%,
93%,
94%, 95%, 96%, 97%, 98%, 99%, or 1.00% homology to SEQ ID NOs: 196-204.
[0383] Also disclosed in some embodiments are the primers and/or primer sets,
or
compositions thereof, provided herein with sequences having at least 85%, 86%,
87%, 88%,
89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to SEQ
ID NOs: 1-204. These primer sets can be used in a nucleic acid amplification,
such as Loop-
Mediated Isothermal Amplification (LAMP), preferably, in a system, wherein an
electrical
signal, such as impedance or capacitance, is evaluated to detect the presence,
absence, or
amount of one or more amplified nucleic acids.
[0384] Additional embodiments disclosed herein comprise assay cartridges for
containing a sample comprising a target agent for detection by a reader
device. The assay
cartridges comprise a sample introduction area configured to receive a sample
carrier
containing the sample, a mixing region configured to mix the sample with a
reagent to
generate a sample mixture, at least one mixing object disposed in the mixing
region and
configured to move within the mixing region to enhance mixing of the sample
with the
reagent in response to a force applied to the mixing region, a test well
containing an excitation
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electrode and a sensing electrode, wherein the test well is configured to
contain at least a
portion of the sample mixture undergoing an amplification process, and a fluid
path
fluidically coupling the sample introduction area to the mixing region and the
mixing region
to the test well.
[0385] In some embodiments, the force applied is the result of one or more of
a
magnetic field generator (for example, a magnet or electromagnet), a vibration
generator, a
sonic generator, and physical movement. In some embodiments, the reagent
comprises one
of a dry reagent or a liquid reagent. In some embodiments, the at least one
mixing object
comprises at least one magnetic bead and wherein the force is exerted by a
first magnetic
field generated by a first magnet, such as an electromagnet disposed in the
reader near a first
location of the mixing region when the assay cartridge is inserted into the
reader. In some
embodiments, the force is further exerted by a second magnetic field generated
by a second
magnet, such as an electromagnet disposed in the reader near a second location
of the mixing
region when the assay cartridge is inserted into the reader. In some
embodiments, the assay
cartridges further comprise a control circuit configured to switch between
which of the first
magnet and the second magnetic is exerting the force at a given moment. In
some
embodiments, the force is exerted by a movable force generator disposed in the
reader. In
some embodiments, one or more of the sample introduction area, the mixing
region, the test
well, and the fluid path introduces an agent that reduces effects of one or
more inhibitors that
exist in the sample. In some embodiments, the one or more of the sample
introduction area,
the mixing region, the test well, and the fluid path are coated with the
agent. In some
embodiments, the reagent includes the agent that reduces effects of the one or
more
inhibitors. In some embodiments, the one or more inhibitors that exist in the
sample
comprise one or more of lactoferrin, lysozyme, nuclease, DNAse or RNases and
wherein the
agent is configured to improve a detection sensitivity of testing performed
with the assay
cartridge and the reader. In some embodiments, the agent comprises one or more
of an
antibody or a proteinase. In some embodiments, a chemical reaction is used to
generate heat,
which inactivates the proteinase after it has digested proteins in the sample.
[0386] Additional embodiments disclosed herein comprise assay cartridges for
containing a sample comprising a target agent for detection by a reader
device. The assay
cartridges comprise: a sample introduction area configured to receive a sample
carrier
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containing the sample; a mixing region configured to mix the sample with a
reagent to
generate a sample mixture; a test well containing an excitation electrode and
a sensing
electrode, wherein the test well is configured to contain at least a portion
of the sample
mixture undergoing an amplification process; and a fluid path fluidically
coupling the sample
introduction area to the mixing region and the mixing region to the test well,
wherein one or
more of the sample introduction area, the mixing region, the test well, and
the fluid path
introduces an agent that reduces effects of one or more inhibitors that exist
in the sample.
[0387] In some embodiments, the one or more of the sample introduction area,
the
mixing region, the test well, and the fluid path are coated with the agent. In
some
embodiments, the reagent includes the agent that reduces effects of the one or
more
inhibitors. In some embodiments, the inhibitors that exist in the sample
comprise one or
more of lactoferrin, lysozyme, nucleases, DNAses or RNases and wherein the
agent is
configured to improve a detection sensitivity of testing performed with the
assay cartridge
and the reader by inhibiting these inhibitors. In some embodiments, the agent
comprises one
or more of an antibody, aptamer, competitive binding protein or a proteinase.
In some
embodiments, a chemical reaction is used to generate heat, which inactivates
the proteinase
after it has digested proteins in the sample. In some embodiments, the assay
cartridges
further comprise at least one mixing object disposed in the mixing region and
configured to
move within the mixing region to enhance mixing of the sample with the reagent
in response
to a force applied to the mixing region. In some embodiments, the force
applied is the result
of one or more of a magnetic field generator, a vibration generator, a sonic
generator, and
physical movement. In some embodiments, the reagent comprises one of a dry
reagent or a
liquid reagent. In some embodiments, the at least one mixing object comprises
at least one
magnetic bead and wherein the force is exerted by a first magnetic field
generated by a first
magnet, such as an electromagnet disposed in the reader near a first location
of the mixing
region when the assay cartridge is inserted into the reader. In some
embodiments, the force
is further exerted by a second magnetic field generated by a second magnet,
such as an
electromagnet disposed in the reader near a second location of the mixing
region when the
assay cartridge is inserted into the reader. In some embodiments, the assay
cartridges further
comprise a control circuit configured to switch between which of the first
magnet and the
second magnetic is exerting the force at a given moment. In some embodiments,
the assay
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cartridges further comprise the sample carrier comprising: a body configured
to hold the
sample before depositing the sample into the assay cartridge; a tip
fluidically coupled to the
body and configured to fit into the sample introduction area of the assay
cartridge, wherein
the sample held in the body can be ejected from the sample carrier via the
tip; and a
membrane disposed between the body and the tip and configured to prevent
molecules in the
sample that exceed a threshold size from being ejected from the body via the
tip. In some
embodiments, the sample carrier further comprises a gel filtration component,
resin, size-
exclusion resin, membrane, or filter, such as a size exclusion filter
configured to trap or retain
salt compounds in the sample such that the salt compounds are not ejected from
the body via
the tip. In some embodiments, the gel filtration component comprises one of a
gel filtration
bead bed or a gel filtration matrix. In some embodiments, the sample carrier
further
comprises a buffer component configured to assist in extracting the target
agent from the
sample. In some embodiments, the buffer component comprises one of an elution
buffer or
a lysis buffer. In some embodiments, the sample carrier further comprises a
plunger
component configured to apply a force to the sample in the body and cause the
sample to
pass through the membrane and the tip and into the sample introduction area of
the assay
cartridge.
[0388] Additional embodiments disclosed herein comprise systems for detecting
a
target agent in a sample using an assay cartridge and a reader. The systems
comprise the
assay cartridge, comprising: a sample introduction area configured to receive
a sample carrier
containing the sample; and the sample carrier for depositing the sample into
the assay
cartridge, the sample carrier comprising: a body configured to hold the sample
before
depositing the sample into the assay cartridge; a tip fluidically coupled to
the body and
configured to fit into the sample introduction area of the assay cartridge,
wherein the sample
held in the body can be ejected from the sample carrier via the tip; and a
membrane disposed
between the body and the tip and configured to prevent molecules in the sample
that exceed
a threshold size from being ejected from the body via the tip.
[0389] In some embodiments, the sample carrier further comprises a gel
filtration,
resin, or membrane component configured to trap or retain salt compounds in
the sample
such that the salt compounds are not ejected from the body via the tip. In
some embodiments,
the gel filtration component comprises one of a gel filtration bead bed or a
gel filtration
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matrix. In some embodiments, the sample carrier further comprises a buffer
component
configured to assist in extracting the target agent from the sample. In some
embodiments,
the buffer component comprises one of an elution buffer or a lysis buffer. In
some
embodiments, the sample carrier further comprises a plunger component
configured to apply
a force to the sample in the body and cause the sample to pass through the
membrane and
the tip and into the sample introduction area of the assay cartridge. In some
embodiments,
the assay cartridge further comprises: a mixing region configured to mix the
sample with a
reagent to generate a sample mixture; at least one mixing object disposed in
the mixing region
and configured to move within the mixing region to enhance mixing of the
sample with the
reagent in response to a force applied to the mixing region; a test well
containing an
excitation electrode and a sensing electrode, wherein the test well is
configured to contain at
least a portion of the sample mixture undergoing an amplification process; and
a fluid path
fluidically coupling the sample introduction area to the mixing region and the
mixing region
to the test well. In some embodiments, the force applied is the result of one
or more of a
magnetic field generator, a vibration generator, a sonic generator, and
physical movement.
In some embodiments, the reagent comprises one of a dry reagent or a liquid
reagent. In
some embodiments, the at least one mixing object comprises at least one
magnetic bead and
wherein the force is exerted by a first magnetic field generated by a first
magnet, such as an
electromagnet disposed in the reader near a first location of the mixing
region when the assay
cartridge is inserted into the reader. In some embodiments, the force is
further exerted by a
second magnetic field generated by a second magnet, such as an electromagnet
disposed in
the reader near a second location of the mixing region when the assay
cartridge is inserted
into the reader. In some embodiments, the assay cartridges further comprise a
control circuit
configured to switch between which of the first magnet and the second magnetic
is exerting
the force at a given moment. In some embodiments, the force is exerted by a
movable force
generator disposed in the reader. In some embodiments, one or more of the
sample
introduction area, the mixing region, the test well, and the fluid path
introduces an agent that
reduces effects of one or more inhibitors that exist in the sample. In some
embodiments, the
one or more of the sample introduction area, the mixing region, the test well,
and the fluid
path are coated with the agent. In some embodiments, the reagent includes the
agent that
reduces effects of the one or more inhibitors. In some embodiments, the one or
more
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inhibitors that exist in the sample comprise one or more of lactoferrin,
lysozyme, Nucleases,
DNAses or RNases and wherein the agent is configured to improve a detection
sensitivity of
testing performed with the assay cartridge and the reader. In some
embodiments, the agent
comprises one or more of an antibody, aptamer, competitive binding protein or
a proteinase.
In some embodiments, a chemical reaction is used to generate heat, which
inactivates the
proteinase after it has digested proteins in the sample. In some embodiments,
the assay
cartridge further comprises: a mixing region configured to mix the sample with
a reagent to
generate a sample mixture; a test well containing an excitation electrode and
a sensing
electrode, wherein the test well is configured to contain at least a portion
of the sample
mixture undergoing an amplification process; and a fluid path fluidically
coupling the sample
introduction area to the mixing region and the mixing region to the test well,
wherein one or
more of the sample introduction area, the mixing region, the test well, and
the fluid path
introduces an agent that reduces effects of one or more inhibitors that exist
in the sample. In
some embodiments, the one or more of the sample introduction area, the mixing
region, the
test well, and the fluid path are coated with the agent. In some embodiments,
the reagent
includes the agent that reduces effects of the one or more inhibitors. In some
embodiments,
the one or more inhibitors that exist in the sample comprise one or more of
lactoferrin,
lysozyme, Nucleases, DNAses, or RNases and wherein the agent is configured to
improve a
detection sensitivity of testing performed with the assay cartridge and the
reader. In some
embodiments, the agent comprises one or more of an antibody, aptamer,
competitive binding
protein or a proteinase. In some embodiments, a chemical reaction is used to
generate heat,
which inactivates the proteinase after it has digested proteins in the sample.
In some
embodiments, the assay cartridges further comprise at least one mixing object
disposed in
the mixing region and configured to move within the mixing region to enhance
mixing of the
sample with the reagent in response to a force applied to the mixing region.
In some
embodiments, the force applied is the result of one or more of a magnetic
field generator, a
vibration generator, a sonic generator, and physical movement. In some
embodiments, the
reagent comprises one of a dry reagent or a liquid reagent. In some
embodiments, the at least
one mixing object comprises at least one magnetic bead and wherein the force
is exerted by
a first magnetic field generated by a first magnet, such as an electromagnet
disposed in the
reader near a first location of the mixing region when the assay cartridge is
inserted into the
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reader. In some embodiments, the force is further exerted by a second magnetic
field
generated by a second magnet, such as an electromagnet disposed in the reader
near a second
location of the mixing region when the assay cartridge is inserted into the
reader. In some
embodiments, the assay cartridges further comprise a control circuit
configured to switch
between which of the first magnet and the second magnetic is exerting the
force at a given
moment.
[0390] Additional embodiments disclosed herein comprise a system for
determining
a wellness score for a user, animal, or product. The systems comprise: a
database configured
to store a plurality of user, animal, or product profiles, each user, animal,
or product profile
comprising health information for a single user, animal, or product of a
plurality of users,
animals, or products and user, animal, or product identifying information, a
testing device
comprising the assay cartridge described herein, the testing device configured
to: accept the
sample from the user, animal, or product, generate test results based on the
sample, and store
the generated test results in the user, animal, or product profile for the
user, animal, or product
in the database; a computing system configured to: generate the wellness score
for the user,
animal, or product the wellness score based on the health information stored
in the user,
animal, or product profile, the health information comprising the generated
test results, and
store the wellness score in the user, animal, or product profile in the
database; a remote
computing device configured to: obtain biometric or identifying information,
such as QR
coding, RFID coding, or bar coding, for the user, animal, or product, request
the wellness
score for the user, animal, or product from the database based on the user's,
animal's, or
product's biometic or identifying information, and receive the wellness score
for the user,
animal, or product based on the computing system determining that the user's,
animal's, or
product's biometic or identifying information matches the user's, animal's, or
product's
identifier, wherein the wellness score is compared to a threshold value to
determine whether
the user, animal, or product is permitted entry to a location.
[0391] In some embodiments, the health information further comprises one or
more
of health information records acquired from a medical professional, health
survey
information provided by the user, or contact tracing information. In some
embodiments, the
user identifying information comprises one or more of an identifier for the
user, biometrics
information for the user, and username and password information for the user.
In some
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embodiments, the wellness score is representative of whether the user, animal,
or product is
likely to be infected by a pathogen comprising one or more of a mold, fungus,
bacteria, a
virus, or another microbe. In some embodiments, the testing device comprises:
a cartridge
configured to receive the biological sample, and a reader device comprising: a
cavity
configured to receive the cartridge, a memory storing at least computer-
readable instructions,
a processor in communication with the memory, and an electrode interface in
communication
with the processor and in contact with the cartridge when the cartridge is
inserted into the
cavity. In some embodiments, the cartridge comprises: an external portion; an
internal
portion configured to fit within the cavity of the reader device, the internal
portion including
an electrode interface configured to establish an electrical connection with
the electrode
interface of the reader device when the cartridge is inserted into the reader
device; and a flow
path configured to sealingly enclose a biological sample within the cartridge.
In some
embodiments, the reader device further includes a communication module
configured to
communicatively connect to the computing system or the remote computing
device. In some
embodiments, the remote computing device or the computing system is wirelessly
connected
to the reader device. In some embodiments, the testing device, the computing
system, and
the remote computing device are connected by at least one of a wireless,
wired, or hybrid
network. In some embodiments, the remote computing device comprises a
biometric input
device that obtains the biometric information for the user from the user. In
some
embodiments, the biometric information comprises one or more of fingerprint
information,
facial recognition information, retinal scan information, hand geometry
information, finger
geometry information, palm vein information, ear geometry information, voice
information,
hand writing information, signature information, typing pattern recognition,
biological
sample recognition, or movement recognition. In some embodiments, the assay
cartridges
further comprise a user device configured to: capture location information for
the user;
capture identification information for other user devices of other users that
come within a
threshold distance of the user; and store the location information and
identification
information in the user profile in the database. In some embodiments, the
assay cartridges
detect a target agent. In some embodiments, the target agent indicates
presents of a mold,
fungus, bacteria, a virus, or another microbe. In some embodiments, the
biological sample
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is obtained from a subject, such as a human or an animal, a product, such as a
food or
beverage, or an object, such as a high contact surface.
[0392] Additional embodiments disclosed herein comprise methods of using the
system of the assay cartridges for determining the wellness score for the
user, animal, or
product.
[0393] Additional embodiments disclosed herein comprise methods of determining
a wellness score for a user, animal, or product. The methods comprise:
creating a user,
animal, or product profile for a user, animal, or product in a database, the
user, animal, or
product profile comprising health information and user, animal, or product
identifying
information; depositing a sample obtained from the user, animal, or product
into a sample
receptacle of a testing device comprising the assay cartridge; generating test
results based on
the sample; storing the generated test results in the user, animal, or product
profile for the
user, animal, or product; generating the wellness score for the user, animal,
or product the
wellness score based on the health information stored in the user, animal, or
product profile,
the health information comprising the generated test results; storing the
wellness score in the
user, animal, or product profile in the database; obtaining biometric or
identifying
information for the user, animal, or product; requesting the wellness score
for the user,
animal, or product from the database based on the user's, animal's, or
product's biometric or
identifying information; receiving the wellness score for the user, animal, or
product based
on the computing system determining that the user's, animal's, or product's
biometric or
identifying information matches the user's, animal's, or product's identifier;
and comparing
the wellness score to a threshold value to determine whether the user, animal,
or product is
permitted entry to a location.
[0394] Additional embodiments disclosed herein comprise systems for
determining
a wellness score of an individual. The systems comprise: a database configured
to: create a
data structure for a profile associated with the individual and configured to
store information
in the data structure, the information comprising one or more of health
information for the
individual, contact tracing for the individual, health surveys completed by
the individual,
temperature measurements for the individual, authentication information for
the individual
(can include biometric information), test results for the individual, or a
wellness score for the
individual; obtain information associated with the individual from a source;
store the
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obtained information in the profile data structure; calculate the wellness
score for the
individual based on an algorithm that accounts for the information stored in
the profile data
structure, wherein the algorithm applies different weights to the different
information in the
profile data structure when calculating the wellness score; and update the
data structure based
on the calculated wellness score; a testing device comprising the assay
cartridges described
above and configured to test a biological sample from the individual for a
pathogen and
provide results to the test to the database for the profile associated with
the individual; and a
site device configured to: access the profile for the individual from the
database; compare
the wellness score with a threshold score; and indicate that the individual is
granted access
to a location based on the wellness score being greater than or exceeding the
threshold score.
[0395] Additional embodiments disclosed herein comprise methods of determining
a wellness score for a user, animal, or product via the systems described
above. The methods
comprise: creating a user, animal, or product profile for a user, animal, or
product in a
database, the user, animal, or product profile comprising health information
and user, animal,
or product identifying information; depositing a sample obtained from the
user, animal, or
product into a sample receptacle of a testing device; generating test results
based on the
sample; storing the generated test results in the user, animal, or product
profile for the user,
animal, or product; generating the wellness score for the user, animal, or
product the wellness
score based on the health information stored in the user, animal, or product
profile, the health
information comprising the generated test results; storing the wellness score
in the user,
animal, or product profile in the database; obtaining biometric or identifying
information for
the user, animal, or product; requesting the wellness score for the user,
animal, or product
from the database based on the user's, animal's, or product's biometric or
identifying
information; receiving the wellness score for the user, animal, or product
based on the
computing system determining that the user's, animal's, or product's biometric
or identifying
information matches the user's, animal's, or product's identifier; and
comparing the wellness
score to a threshold value to determine whether the user, animal, or product
is permitted entry
to a location.
[0396] In an additional embodiment, a method of determining a wellness score
for a
user, animal, or product is disclosed herein. The method comprises creating a
user, animal,
or product profile for a user, animal, or product in a database, the user,
animal, or product
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profile comprising health information and user, animal, or product identifying
information;
depositing a sample obtained from the user, animal, or product into a sample
receptacle of a
testing device comprising the assay cartridge; amplifying a nucleic acid from
a pathogen,
such as a mold, fungus, bacteria, virus, or other microbe in the sample by
Loop-Mediated
Isothermal Amplification (LAMP) with a primer set, wherein the primer set
comprises any
combination of: one or more F3 primers, one or more B3 primers, one or more LF
primers,
one or more LB primers, one or more FIP primers, and one or more BIP primers,
wherein
the primer set is specific for a genome region of the pathogen, such as
including a primer
comprising the sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%,
92%, 93%,
94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to any one of the sequences of
SEQ
ID NOs: 1-204, and wherein the nucleic acid is amplified with the primer set
at least a first
temperature of between 23 C and 55 C, and then at a second temperature of 60 C
to 70 C,
preferably wherein the first temperature is performed at room temperature
(e.g., 23 C or
about 23 C) for a time period sufficient to allow any dried down reagents to
rehydrate (e.g.,
minutes or about 10 minutes); the second temperature is performed at 50 C or
about 50 C
for 10 minutes or about 10 minutes, and a third temperature is performed at 65
C or about
65 C; measuring or analyzing a modulation of an electrical signal, such as
impedance or
capacitance, for the duration of the amplification with the primer set using
the testing device,
thereby detecting successful amplification of the nucleic acid with the primer
set;
determining the presence and/or amount of the nucleic acid in the sample,
wherein a limit of
detection of the nucleic acid is improved compared to performing LAMP only at
the second
temperature; generating test results based on the sample and the determined
presence and/or
amount of the nucleic acid in the sample; storing the generated test results
in the user, animal,
or product profile for the user, animal, or product; generating the wellness
score for the user,
animal, or product the wellness score based on the health information stored
in the user,
animal, or product profile, the health information comprising the generated
test results;
storing the wellness score in the user, animal, or product profile in the
database; obtaining
biometric or identifying information for the user, animal, or product;
requesting the wellness
score for the user, animal, or product from the database based on the user's,
animal's, or
product's biometric or identifying information; receiving the wellness score
for the user,
animal, or product based on the computing system determining that the user's,
animal's, or
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product's biometric or identifying information matches the user's, animal's,
or product's
identifier; and comparing the wellness score to a threshold value to determine
whether the
user, animal, or product is permitted entry to a location and optionally
providing or
displaying a visually identifiable signal or character indicating that the
wellness score is at
or exceeds the threshold value.
[0397] In other embodiments, a system for determining a wellness score of an
individual is described. The system comprises a database configured to: create
a data
structure for a profile associated with the individual and configured to store
information in
the data structure, the information comprising one or more of health
information for the
individual, contact tracing for the individual, health surveys completed by
the individual,
temperature measurements for the individual, authentication information for
the individual
(can include biometric information), test results for the individual, or a
wellness score for the
individual; obtain information associated with the individual from a source;
store the
obtained information in the profile data structure; calculate the wellness
score for the
individual based on an algorithm that accounts for the information stored in
the profile data
structure, wherein the algorithm applies different weights to the different
information in the
profile data structure when calculating the wellness score; and update the
data structure based
on the calculated wellness score. The system also comprises a testing device
comprising the
assay cartridge and configured to test a biological sample from the individual
for a pathogen
and provide results to the test to the database for the profile associated
with the individual,
wherein the testing device is configured to: amplify a nucleic acid from a
pathogen, such as
a microbe, fungus, mold, bacteria, or virus in the sample by Loop-Mediated
Isothermal
Amplification (LAMP) with a primer set, wherein the primer set comprises any
combination
of: one or more F3 primers, one or more B3 primers, one or more LF primers,
one or more
LB primers, one or more FIP primers, and one or more B1P primers, wherein the
primer set
is specific for a genome region of the pathogen, such as including a primer
comprising the
sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%,
96%, 97%, 98%, 99%, or 100% homology to any one of the sequences of SEQ Ill
NOs: 1-
204 and, wherein the nucleic acid is amplified with the primer set at at least
a first
temperature of between 23 C and 55 C, and then at a second temperature of 60 C
to 70 C,
preferably wherein the first temperature is performed at room temperature
(e.g., 23 C or
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about 23 C) for a time period sufficient to allow any dried down reagents to
rehydrate (e.g.,
minutes or about 10 minutes); the second temperature is performed at 50 C or
about 50 C
for 10 minutes or about 10 minutes, and a third temperature is performed at 65
C or about
65 C, determine the presence and/or amount of the nucleic acid in the sample,
wherein a
limit of detection of the nucleic acid is improved compared to performing LAMP
only at the
second temperature, and generate the results based on the sample and the
determined
presence and/or amount of the nucleic acid in the sample. The system also
comprises a site
device configured to: access the profile for the individual from the database;
compare the
wellness score with a threshold score; and indicate that the individual is
granted access to a
location based on the wellness score being greater than or exceeding the
threshold score.
BRIEF DESCRIPTION OF THE DRAWINGS
[0398] FIGs. 1A-1C depict an example handheld system for detection of a
target.
[0399] FIGs. 2A-2F depict an example cartridge for detection of a target that
can be
used in the handheld system of FIGs. 1A-1C.
[0400] FIGs. 3A-3E depict a mechanical fluid transfer mechanism of the example
cartridge of FIGs. 2A-2F.
[0401] FIGs. 4A-4G depict various examples of electrodes that can be used in a
test
well of the cartridges of FIGs. 1A-2F or in the test well or channel of
another suitable target
detection cartridge as described herein.
[0402] FIGs. 4H-4N depict further examples of electrodes that can be used to
implement three-terminal sensing and/or four-terminal sensing in a test well
of the cartridges
of FIGs. 1A-2F or in the test well or channel of another suitable target
detection cartridge as
described herein.
[0403] FIG. 5A depicts a first electrode or excitation electrode and a second
electrode
or signal electrode that may be spaced apart from one another within a test
well of the
cartridges of FIGs. 1A-2F or in the test well or channel of another suitable
target detection
cartridge as described herein.
[0404] FIG. 5B depicts an example signal that can be extracted from the signal
electrode of FIG. 5A.
[0405] FIG. 5C depicts the resistance and reactance components extracted from
a
signal as shown in FIG 5B generated based on an example positive test.
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[0406] FIG. 5D depicts the resistance and reactance components extracted from
signals as shown in FIG 5B from example tests of positive and negative
controls.
[0407] FIG. 5E depicts the resistance and reactance components extracted from
a
signal as shown in FIG 5B generated based on another example positive test.
[0408] FIG. 6 depicts a schematic block diagram of an example reader device
that
can be used with the cartridges described herein.
[0409] FIG. 7A depicts a flowchart of an example process for operating a
reader
device during a test as described herein.
[0410] FIG. 7B depicts a flowchart of an example process for analyzing test
data to
detect a target as described herein.
[0411] FIGs. 8A-8D depict an example user interface of a user device
implementing
an example testing process in communication with a reader device as described
herein.
[0412] FIGs. 9A and 9B depict an example handheld system for detection of a
target.
[0413] FIGs. 10A-10K depict an example cartridge for detection of a target
that can
be used in the handheld system of FIGs. 9A and 9B.
[0414] FIGs. 11A-11D depict a mechanical fluid transfer mechanism of the
example
cartridge of FIGs. 10A-10K .
[0415] FIGs. 12A-12I depict an example cartridge for detection of a target
that can
be used in conjunction with the handheld systems disclosed herein.
[0416] FIGs. 13A-13E depict an example of another type or format of cartridge
configured to detect a target that can be used in conjunction with a handheld
system disclosed
herein.
[0417] FIGs. 13F-13.1 schematically depict an example process of collecting
and
testing a sample.
[0418] FIGs. 13K-13L depict an example cartridge with an example retainer that
can
hold a swab in place inside a swab receptacle.
[0419] FIGs. 14A and 14B depict an example of another handheld system
disclosed
herein.
[0420] FIGs. 15A-15P depict screenshots of an example graphical user interface
hosted on an external computing device and configured to receive input,
provide instructions,
testing control, and/or monitoring of the handheld system disclosed herein.
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[0421] FIG. 16A depicts SARS-CoV-2-specific primer sequences for LAMP (SEQ
ID NOs: 1-25). One selected and three alternative primer sets are depicted.
F3, B3, LF, LB,
FIP, and RIP primers are denoted accordingly in respective primer names.
Primer sequences
are shown 5' to 3'.
[0422] FIG. 16B depicts the time to detection of a positive amplification, or
lack
thereof, at different copy numbers of SARS-CoV-2 RNA genomes using the primer
sets of
FIG. 16A. 0, 10, 100, 1000, and 10000 copies of the SARS-CoV-2 RNA genome were
tested
in each reaction. Time points at "60 min" denote unsuccessful amplifications.
[0423] FIG. 17A depicts Hepatitis A Virus-specific primer sequences for LAMP
(SEQ ID NOs: 26-49). One selected and two alternative primer sets are
depicted. F3, B3,
LF, LB, HP, and BIP primers are denoted accordingly in respective primer
names. Primer
sequences are shown 5' to 3'.
[0424] FIG. 17B depicts the time to detection of a positive amplification, or
lack
thereof, of samples with either 0 or 8890 x (50% Tissue Culture Infectious
Dose [TCID50])
virus titer using the primer sets of FIG. 17A. Time points at "60 min" denote
unsuccessful
amplifications.
[0425] FIG. 18A depicts Influenza A Virus Subtype H1N1-specific primer
sequences
for LAMP (SEQ ID NOs: 50-67). One selected and one alternative primer sets are
depicted.
F3, B3, LF, LB, FIP, and BIP primers are denoted accordingly in respective
primer names.
Primer sequences are shown 5' to 3'.
[0426] FIG. 18B depicts the time to detection of a positive amplification, or
lack
thereof, of samples containing synthetic DNA copies of Influenza A H1N1
strains
Brisbane/59/07, CA/07/09, MI/45/15, NewCa1/20/99, NY/18/09, or SI/03/06, or
non-
template control (NTC), at 1 million copies per reaction using the primer sets
of FIG. 18A.
Time points at "60 min" denote unsuccessful amplifications.
[0427] FIG. 19A depicts Human Immunodeficiency Virus-1 Subtype B (HIV-1B)-
specific primer sequences for LAMP (SEQ ID NOs: 68-96). One selected and two
alternative primer sets are depicted. F3, B3, LF, LB, FIP, and BIP primers are
denoted
accordingly in respective primer names. Primer sequences are shown 5' to 3'.
[0428] FIG. 19B depicts the time to detection of a positive amplification, or
lack
thereof, of samples containing 0 (null), 100 (low), 1000 (medium), or 100000
(high) copies
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of HIV-1 genomic template per reaction using the primer sets of FIG. 19A. Time
points at
"60 mm" denote unsuccessful amplifications.
[0429] FIG. 20A depicts Respiratory Syncytial Virus A (RSV A)-specific primer
sequences for LAMP (SEQ ID NOs: 97-111). One selected and one alternative
primer sets
are depicted. F3, B3, 1,F, LB, HP, and BIP primers are denoted accordingly in
respective
primer names. Primer sequences are shown 5' to 3'.
[0430] FIG. 20B depicts the time to detection of a positive amplification, or
lack
thereof, of either RSV A patient-derived swab samples (Swab1-5), or purified
RSV A virus
(100, 1000, or 10000 copies for Virus 1, and 0.1, 1, or 10 PFU for Virus 2 and
Virus 3 per
sample) using the primer sets of FIG. 20A. Time points at "60 min" denote
unsuccessful
amplifications.
[0431] FIG. 21A depicts Respiratory Syncytial Virus B (RSV B)-specific primer
sequences for LAMP (SEQ ID NOs: 112-128). One selected and one alternative
primer sets
are depicted. F3, B3, 1,F, LB, FIP, and BIP primers are denoted accordingly in
respective
primer names. Primer sequences are shown 5' to 3'.
[0432] FIG. 21B depicts the time to detection of a positive amplification, or
lack
thereof, of either RSV B patient-derived swab samples (Swab1-8), or purified
RSV B virus
(0.1 or 1 PFU for Virus 1-4 per sample) using the primer sets of FIG. 21A.
Time points at
"60 min" denote unsuccessful amplifications.
[0433] FIG. 22A depicts Escherichia coil-specific primer sequences for LAMP
(SEQ ID NOs: 129-164). One selected and seven alternative primer sets obtained
from the
combination of primer sets Z3276 A, Z3276 B, Stxl A, Stxl B, Stx2 A, and Stx2
B are
depicted. F3, B3, I,F, LB, FIP, and BIP primers are denoted accordingly in
respective primer
names. Primer sequences are shown 5' to 3'.
[0434] FIG. 22B depicts the time to detection of a positive amplification, or
lack
thereof, of the Stxl, Stx2, or Z3276 gene of pathogenic E. coli genomes, or
non-template
control (NTC) using the primer sets of FIG. 22A. One million copies of E. colt
genome were
used per reaction. Time points at "60 min" denote unsuccessful amplifications.
[0435] FIG. 23A depicts Listeria monocytogeties-specific primer sequences for
LAMP (SEQ ID NOs: 165-173). One selected and two alternative primer sets are
depicted.
F3, B3, LF, LB, FIP, and BIP primers are denoted accordingly in respective
primer names.
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Primer sequences are shown 5' to 3'. Primers listed as "All Sets" were used in
all three primer
sets.
[0436] FIG. 23B depicts the time to detection of a positive amplification, or
lack
thereof, of L. monocytogenes genome at 0, 1 million, or 10000 copies of genome
per reaction
using the primer sets of FIG. 23A. Time points at "60 min" denote unsuccessful
amplifications.
[0437] FIG. 24A depicts Mycobacterium tuberculosis-specific primer sequences
for
LAMP (SEQ ID NOs: 174-191). One selected and two alternative primer sets are
depicted.
F3, B3, LF, LB, FIP, and B1P primers are denoted accordingly in respective
primer names.
Primer sequences are shown 5' to 3'.
[0438] FIG. 24B depicts the time to detection of a positive amplification, or
lack
thereof, of M. tuberculosis genome at 1 million copies per reaction, or non-
template control
(NTC) using the primer sets of FIG. 24A. Time points at "60 min" denote
unsuccessful
amplifications.
[0439] FIG. 25A depicts Salmonella enterica-specific primer sequences for LAMP
(SEQ ID NOs: 192-204). One selected and one alternative primer sets are
depicted. F3, B3,
LE, LB, HP, and B I P primers are denoted accordingly in respective primer
names. Primer
sequences are shown 5' to 3'. Primers listed as "Both" were used in both
Selected and
Alternative primer sets.
[0440] FIG. 25B depicts the time to detection of a positive amplification, or
lack
thereof, of S. enterica genome at 0, 1 million, or 10000 copies per reaction
using the primer
sets of FIG. 25A. Time points at "60 min" denote unsuccessful amplifications.
[0441] FIG. 26 depicts an example network diagram of a networked system for
tracking infection potential.
[0442] FIG. 27 is a flow diagram showing example interactions between
components
of the networked system of FIG. 26.
[0443] FIG. 28 depicts a general architecture of a computing device
implementing
one or more of the components of the system of FIG. 26.
[0444] FIG. 29 depicts a comparison of LAMP amplification of SARS-CoV-2
gamma-inactivated virus using a one-step protocol comprising heating the
sample for 40 min
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at 65 C, and a two-step protocol comprising heating the sample for 10 min at
50 C, then for
40 min at 65 C. Each point represents data from one well. Points at 40 min did
not amplify.
[0445] FIG. 30 depicts a comparison of the two-step protocol performed at 0,
2, 5,
and 10 min at 50 C. Each point represents data from one well. Points at 40 min
did not
amplify.
[0446] FIG. 31 depicts a comparison of the two-step protocol performed at 0,
2, 5,
and 10 min at 50 C using a low concentration of genomic viral RNA. Each point
represents
data from one well. Points at 40 min did not amplify.
[0447] FIG. 32 depicts a comparison of the two-step protocols at 50 C, 55 C,
and
60 C using two different RNAse inhibitors. Each point represents data from one
well. Points
at 40 min did not amplify.
[0448] FIG. 33 depicts the sample insertion device that can deposit the
purified
sample into the test cartridge.
[0449] FIGs. 34A-34C are flow diagrams representing example processes of
collecting and testing a sample.
DETAILED DESCRIPTION
[0450] Aspects of the disclosure herein concern the use of amplification and
contactless electrical sensing to detect the presence and/or amount of a
target in a sample.
Such a diagnostic platform may replace the complex optical systems and
expensive
fluorescent labels used for optical detection and the electrodes and
electroactive agents used
in existing electrochemical and FET techniques with common electronic
components. In
some aspects, the amplification can be isothermal. In some embodiments, the
amplification
is loop-mediated isothermal amplification (LAMP). In some embodiments, the
amplification
is reverse transcription loop-mediated isothermal amplification (RT-LAMP). The
platform
described herein is inexpensive, robust, portable, and consumes less power
than traditional
diagnostic systems. In some aspects, the diagnostic platform is small enough
to fit in the
palm of a consumer's hand and capable of performing in the field, for example,
a diagnosis
in a doctor's office, in the home, in a location remote from a medical
facility.
[0451] Many commercially available nucleic acid detection platforms utilize
traditional PCR, thereby requiring temperature cycling, fluorescent labels and
optical
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detection instrumentation. These factors result in expensive, lab-based
instrumentation
which employ delicate, vibration sensitive detectors, costly fluorescent
markers, and have a
large footprint. The equipment requires operation, and frequent calibration,
by highly trained
personnel.
[0452] These large, unwieldy platforms make routine use of conventional NAAT
challenging to use in the clinic, much less in the home. NAAT remains a costly
and slow
strategy closely tied to centralized laboratory facilities. The presently
disclosed technology,
in contrast, avoids these challenges.
[0453] A hurdle to point of care ("POC") testing is the potential inhibition
of
amplification by interferents often encountered in crude, unprocessed clinical
samples such
as whole blood, saliva, mucus, or any other bodily fluid or biological
component. The
mitigation of amplification inhibitors may challenge the direct detection of
target nucleic
acids from clinically relevant biologic samples. As described herein, a sample
may comprise
one or more of blood, saliva, mucus, or any other bodily fluid or biological
secretion or
component.
[0454] Traditional detection strategies commonly rely on fluorescence
detection
techniques. Such techniques may be complex, more expensive, and require
precision optical
systems. The present disclosure however, generally relies on electrical
detection systems.
Such electrical detection systems may leverage microelectronics that consume
relatively low
power and can be manufactured at a reduced cost due to high volume
manufacturing. Thus,
electrical detection of genomic material may transfer the advances of the
computer industry
to bioassay sensing.
[0455] Existing electronic methods for monitoring amplification may require
the
binding of an electrochemically active label or the selective binding of the
amplified material
to a surface. However, when used in real world clinical applications, these
techniques often
suffer from slow response times, biofouling of the electrode or binding
surfaces resulting in
poor signal to noise ratios, and limitations on the lifetime and reliability
of the device. While
potentially enabling great sensitivity, the use of electrochemical or field
effect transistor
"FET" detection adds a layer of complexity to the detection. This can result
in more
expensive and less robust strategies than POC and other consumer applications
typically
dictate. Accordingly, the need for additional diagnostic devices is manifest.
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[0456] The platform disclosed herein relies on measurement of the change in
electrical conductivity that occurs during nucleic acid amplification. In sum,
during
biochemical synthesis of DNA from nucleotide triphosphates, the number and the
mobility
of electrically charged molecules are altered. This, in turn, results in a
change in the solution
conductivity as amplification progresses. This change in solution electrical
conductivity may
be sensed using frequency-dependent capacitively coupled contactless
conductivity
detection ("jC4D").
[0457] In some implementations, jC41) uses a pair of electrodes in close
proximity
to, but not in contact with, a fluid disposed in an amplification chamber to
measure the
solution's electrical properties. The ability to measure the properties of the
solution in this
way, without direct contact, avoids the challenges of surface fouling common
to other
electrical measurement methods.
[0458] In some implementations, utilizing /C4D, a high frequency alternating
current
("AC") signal is applied to the excitation electrode. This signal is
capacitively coupled
through the solution where it is detected at the signal electrode. By
comparing the excitation
signal with the signal at the signal electrode, the solution's conductivity
can be determined.
[0459] Informed by high-resolution finite element models and empirical
studies,
specific tolerances ofICD based technology may achieve the optimal detection
sensitivity
and dynamic sensing range for particular implementations of the platform. Such
calculated
and empirically determined parameters of microfluidic dimensions, capacitive
coupling
characteristics, and the applied frequency can enable the determination of the
effective
parameters for detecting solution conductivity changes. In
some embodiments, the
parameters corresponding to optimal detection can be interdependent variables.
According
to the following equation, the measured impedance is a function of the
solution resistance,
capacitance and the applied frequency:
Z = R (1/pi *f*C)*j
[0460] As the thickness of the electrode passivation layer increases, a
parasitic
capacitance due to this layer consequently increases. The optimal AC frequency
with which
to measure solution conductivity by jC4D therefore can be chosen with respect
to the
capacitance of the passivation layer.
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[0461] Some embodiments provided herein include aspects disclosed in WO
2020/132008; WO 2016/057422; WO 2018/057647; WO 2020/132042; WO 2020/132042;
WO 2020/132005; WO 2020/132010; WO 2020/132008; U.S. 2016/0097740; U.S.
2016/0097741; U.S. 2016/0097739; U.S. 2016/0097742; and U.S. 2016/0130639
which are
each incorporated by reference in its entirety for all purposes.
Overview of Example Cartridges, Readers, and Signal Processing
[0462] In some aspects, a system for detecting a target in a sample includes a
removable fluidics cartridge that is couplable to a companion reader device. A
user can apply
a sample to the cartridge and then insert it into the reader device. The
reader device is
configured for performing the testing procedures using the cartridge and
analyzing the test
data to determine the presence, absence, or quantity of a target in the
sample. For example,
the cartridge can be provided with the desired agents, proteins, or other
chemical matter for
an amplification process by which a target initially present in the sample is
amplified.
Specifically, some cartridges can be provided with the desired chemical matter
for nucleic
acid testing, wherein genomic material in the sample is exponentially copied
using a
molecular amplification process, as described herein. The cartridge can also
include a test
well for containing the amplification process, where a test well refers to a
well, chamber,
channel, or other geometry configured for containing (or substantially
containing) test fluid
and constituents of the amplification process. The reader device may maintain
a desired
temperature or other test environment parameters for the cartridge to
facilitate the
amplification process, and can electronically monitor a test well of the
cartridge throughout
some or all of the amplification process. The reader device can thus gather
signal data
representing the impedance of the test well over time during the amplification
process, and
can analyze the impedance as described herein to ascertain the presence,
absence, or quantity
of the target in the sample. As an example, the amplification process can
range from five
minutes to sixty minutes, with some examples ranging from ten minutes to
thirty minutes.
Preferably, in some embodiments, the amplification products are detected while
being
suspended in the fluid within the wells such that the amplification products
are not attached
or sequestered to the wells or fixed or bound to probes, which are bound to
the wells. In
other embodiments, the amplification products are detected as they are
attached or
sequestered to the wells e.g., fixed or bound to probes, which are bound to
the wells.
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[0463] Such systems can beneficially provide target detection performable in a
clinical setting or even the home of a user, rather than requiring the sample
to be sent to a
laboratory for amplification and analysis. In the clinical setting, this can
avoid the delays of
conventional nucleic acid testing thereby enabling clinicians to determine
diagnoses within
the typical timeframe of a patient's office visit. A.s such, the disclosed
systems enable
clinicians to develop treatment plans for patients during their initial office
visit, rather than
requiring the clinician to wait for hours or even days to receive test results
back from a
laboratory. For example, when a patient visits a clinic a nurse or other
healthcare practitioner
can collect a sample from the patient and begin testing using the described
system. The
system can provide the test result by the time the patient consults with their
doctor or clinician
to determine a treatment plan. Particularly when used to diagnose pathologies
that progress
quickly, the disclosed systems can avoid the delays associated with laboratory
testing that
can negatively impact the treatment and outcome of the patient.
[0464] As another benefit, the disclosed systems can be used outside of the
clinical
setting (e.g., in the field, in rural settings without easy access to an
established healthcare
clinic) to detect health conditions such as contagious diseases (e.g., Ebola),
thus enabling the
appropriate personnel to take immediate action to prevent or mitigate the
spread of a
contagious disease. Similarly, the disclosed systems can be used in the field
or at the site of
a suspected hazardous contaminant (e.g., anthrax) to quickly determine whether
a sample
contains the hazardous contaminant, thus enabling the appropriate personnel to
take
immediate action to prevent or mitigate human exposure to the contaminant.
Additionally,
the disclosed systems can be used to detect contaminants in the blood or
plasma supply or in
the food industry. It will be appreciated that the disclosed systems can
provide similar
benefits in other scenarios in which real-time detection of a target enables
more effective
action than delayed detection through sending a sample to an off-site
laboratory.
[0465] Another benefit of such systems is their use of low-cost, disposable
single use
cartridges together with a reusable reader device that can be used many times
with different
cartridges and/or for tests with different targets. In some embodiments
disclosed herein, a
single use cartridge includes a cartridge body and a cap which, when
mechanically coupled
together, create pressurized air that propels a collected sample from the cap
into a mixing
well and a test well of the cartridge body, reducing a necessary level of
skill required to
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operate the reader device and reducing the complexity of both the cartridge
and the reader
device.
[0466] FIGs. 1A-1C depict an example handheld detection system 100 for
detection
of a target. The system 100 includes a reader device 110 and a cartridge 120
configured to
fit within a cavity 112 of the reader device 110. The cartridge 120 generally
includes an
external section 122 and an internal section 124. When the cartridge 120 is
inserted within
the reader device 110, some or all of the internal section 124 is contained
within the reader
device 110. The external section 122 is sized and shaped to be gripped by a
user and may
include one or more three-dimensional surface features such as an indentation
126 to
facilitate insertion and/or removal of the cartridge 120 from the reader
device 110.
[0467] As shown in FIGs. 1B and IC, the reader device 110 and the cartridge
120
are sized and shaped such that one or more interchangeable cartridges 120 can
be inserted
and/or removed by hand at the cavity 112. As will be described in greater
detail, the reader
device 110 can include one or more heating components configured to heat at
least a portion
of the internal section 124 of the cartridge 120. The reader device 110 can
further include
circuitry configured to connect with circuitry of the cartridge 120 to detect
one or more
electrical properties of a sample contained within the cartridge.
[0468] In some embodiments, some of the cartridges 120 can be power
cartridges.
The reader device 110 can be powered on and powered off by a power cartridge
120, instead
of or in addition to a conventional power switch or button on the exterior of
the reader device
110. A power cartridge 120 may have a size and shape similar to other
cartridges for use
with the reader device 110. In operation, the power cartridge 120 may be kept
engaged
within the cavity 112 when the reader device 110 is powered off Circuitry of
the power
cartridge 120 can be in contact with internal circuitry of the reader device
110 such that
removal of the power cartridge 120 from the reader device 110 causes the
reader device 110
to power on for testing. After completion of one or more tests, or at any
other time when the
reader device 110 is to be powered off, the power cartridge 120 is inserted
into the cavity
112. As the power cartridge 120 is inserted, the circuitry of the power
cartridge 120 again
comes into contact with the internal circuitry of the reader device 110 such
that insertion of
the power cartridge 120 causes the reader device 110 to power off Power
cartridge
applications are discussed in greater detail with reference to FIG. 6.
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[0469] In some embodiments, one or more external status indicators can be
provided
on an exterior portion of the reader device 110 to provide status indications
to a user. For
example, in one particular implementation the status indicator may include a
light ring 114
disposed about the cavity 112. In other implementations, the optional status
indicators may
be located at any suitable location on the reader device 110. The light ring
114 or other status
indicator may include one or more light sources, such as light emitting diodes
(LEDs) or the
like. The light ring may also be configured to indicate e.g., when the device
is in use or not
in use, or when different stages of the detection method using the device have
been reached,
completed, or are being performed, such as sample being received by the device
or in the
well(s), amplification being performed, detection of aggregates in the
well(s), or transmission
of the results to a receiver. Different colored lights can be used to indicate
different stages
of the detection method using the device such as those mentioned above.
[0470] In some embodiments, a plurality of differently colored LEDs may be
provided within the light ring 114 or other status indicator in order to
display a variety of
status indications. For example, light ring 114 may include a combination of
two or more
colors (e.g., white, blue, and red), each of which may be independently
activated. Each light
source may be operated in a number of modes, such as a "solid" mode
characterized by
continuous activation of the light source (e.g., a steady "on" state), a
"blinking" mode
characterized by repeated activation and deactivation of the light source, a
"flash" mode
characterized by a single activation and deactivation of the light source, a
"breathing" mode
characterized by repeated gradual brightening and dimming of the light source,
etc.
[0471] Combinations of colors and activation modes may be used to indicate the
status of the reader device 100. For example, in some embodiments, the light
ring 114 or
other status indicator may display a first indication such as a solid white
light when the reader
device 100 is powered up and ready to receive an assay cartridge 120 (e.g.,
when a power
cartridge is removed). Other examples of device status that may be indicated
by the status
indicator include, for example, a cartridge 120 is inserted into the reader
device 110, a test
has been started and is running, a test is complete, a cartridge is removed
after completion of
a test, an error (e.g., a test malfunction, premature removal of the cartridge
120, etc.),
Bluetooth pairing, or any other status of the reader device 110. In one non-
limiting example,
a solid white light ring 114 indicates that a power cartridge has been removed
and the device
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is powered up or that a test cartridge has been removed after completion of a
test, a solid blue
light ring 114 indicates that a test cartridge has been inserted into the
reader device 110, a
breathing blue light ring 114 indicates that a test has been started and is
running, a breathing
white light ring 114 indicates that a test is completed and the cartridge may
be removed, a
solid, breathing, or blinking red light ring indicates an enror, a flash of
blue and red at the
light ring 114 indicates Bluetooth pairing in progress, and a steady,
flashing, or blinking blue
light ring 114 indicates Bluetooth pairing complete. It will be understood
that other
implementations may include any combination or subcombination of the status
indicator
modes listed above, and/or may include further status indications, light
colors, operation
modes, or the like.
[0472] FIGs. 2A-2F depict an example cartridge 200 configured for detection of
a
target. As described herein, the target may be a viral target, bacterial
target, antigen target,
parasite target, microRNA target, or agricultural analyte. Some embodiments of
the cartridge
200 can be configured for testing for a single target, while some embodiments
of the cartridge
200 can be configured for testing for multiple targets. The cartridge 200
includes a cartridge
body 210 and a cap 240 configured to be mechanically coupled to the cartridge
body 210.
When the cartridge body 210 and the cap 240 are coupled together, the
cartridge body 210
forms the internal section 204 of the cartridge 200 and a portion of the
external section 202.
The cap 240 forms a remaining portion of the external section 202.
[0473] FIGs. 2A and 2B depict a complete cartridge 200 including the cartridge
body
210 and the cap 240 coupled together. In use, the cap 240 and cartridge body
210 can operate
to seal a provided sample within the cartridge 200, thereby preventing
exposure of test
operators to the sample and preventing any liquid from escaping into the
electronics of an
associated reader device. The cartridge body 210 and the cap 240 may be
coupled by a
friction fit, a snap fit, and/or one or more mechanical or chemical securing
means. Coupling
of the cartridge body 210 and the cap 240 is discussed in greater detail with
reference to
FIGs. 3A-3E.
[0474] The cartridge body 210 and the cap 240 can be formed from suitable
fluid-
impermeable materials such as plastic, metals, or the like, and may be opaque,
translucent,
or transparent. The cartridge body 210 can also include a translucent or
transparent cover
212 partially defining a fluid path within the cartridge body 210, and one or
more electrode
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interfaces 214. The cover 212, fluid paths, and electrode interfaces 214 are
discussed in
greater detail with reference to FIGs. 2C and 2D. The cartridge body 210
and/or the cap 240
can further include a cartridge identifier 215. The cartridge identifier 215
may include
human-readable and/or machine-readable information, such as text, a barcode, a
QR code,
or the like. The cartridge identifier 215 can include any suitable information
associated with
the cartridge, such as information specifying a type of test, a target agent,
a sample type, a
cartridge serial number or other individual cartridge identifier, etc. In
addition to serving as
an identifier for a user of the type of test associated with the cartridge
200, the cartridge
identifier 215 may also be scanned by a user (e.g., using a user interface
device in
communication with a reader device) to communicate one or more test protocols
to the reader
device. The cartridge body 210 and/or the cap 240 can include ergonomic
features such as
an indentation 216 to facilitate handling of the cartridge 200.
[0475] FIGs. 2C and 2D depict the cartridge body 210 component of the
cartridge
200 of FIGS. 2A and 2B. The cartridge body 210 includes a base 211 and a cover
212. The
base 211 can be formed from a fluid-impermeable material, for example
injection molded or
milled acrylic or plastic. The base 211 includes a receiving well 218 and
components of a
cartridge body flow path, including a first segment 222, a mixing well 224, a
second segment
226, a test well 228, a third segment 230, and a vent 232. It will be
appreciated that the
particular geometric configurations or relative arrangements of these features
may be varied
in other embodiments. As used herein, fluidic communication refers to the
capability to
transfer fluids (e.g., liquid or gas). The cover 212 can be formed from a
fluid-impermeable
material. In some embodiments, the cover 212 is a translucent or transparent
material, such
as glass, plastic, or the like. The cover 212 is sealed to the base 211 to
form the cartridge
body 210 and to serve as a boundary confining fluids within the cartridge body
flow path
components described above. In some embodiments, a translucent or transparent
cover 212
advantageously allows for visual inspection of a fluid within the cartridge
body flow path
(e.g., to verify that the test well is full prior to testing, etc.). One or
more conductive
components of an electrode interface 214 are disposed on the cover 212. Mating
features
238 are sized and shaped to receive corresponding mating features of the cap
240. The
receiving well 218 optionally includes a chamfer 220 to facilitate coupling of
the cap 240 to
the cartridge body 210.
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[0476] The cartridge body flow path includes segments 222, 226, and 230, as
well as
an inlet (FIG. 3C) fluidically coupling the receiving well 218 to the first
segment 222, the
mixing well 224, and the test well 228. The first segment 222 of the cartridge
body flow
path leads from the inlet to the mixing well 224. The second segment 226 of
the cartridge
body flow path leads from the mixing well 224 to the test well 228. The third
segment 230
is a test well outlet path leading from the test well 228 to a vent 232 that
allows gas to escape
from the test well 228 and out of the cartridge 200.
[0477] The mixing well 224 may include one or more reagents in a dry form
(e.g., a
powder). Powdered reagents and/or other dry reagents may be hydrated by a
fluid sample
when the fluid sample enters the mixing well 224. The reagents provided in the
mixing well
224 can be selected based on one or more protocols of the intended test
associated with the
cartridge 200. Even or homogenous mixing of the reagents with the fluid sample
can yield
more accurate test results in some embodiments. As such, the mixing well 224
is configured
to promote even mixing of the reagent with the fluid sample, for example by
including curved
regions and/or a cross-sectional shape that promote turbulent flow rather than
laminar flow
of the liquids within the mixing well 224. Turbulent flow is a flow regime in
fluid dynamics
characterized by chaotic changes in pressure and flow velocity of a fluid.
Turbulent flow is
in contrast to laminar flow, which occurs when fluid flows in parallel layers,
with no
disruption between those layers.
[0478] The segments 222, 226, and 230 of the cartridge body flow path, the
mixing
well 224, and/or the test well 228 can be entirely encased within the material
of the base 211,
or can have three surfaces formed from the material of the base 211 with the
cover 212
forming an upper surface that seals these channels.
[0479] The internal section 204 or test region of the cartridge body 210
includes the
segments 226, 230 of the cartridge body flow path, the test well 228, the
valve 232, electrodes
213, 215, and an electrode interface 214. The electrode interface 214 includes
a plurality of
contact pads 2141-2145. Although five contact pads 2141-2145 are depicted, the
cartridge
body 210 may equally include more or fewer than five contact pads. A first
contact pad 2141
is electrically connected to a first electrode 213 of the test well 228, and a
second contact pad
2145 is electrically connected to a second electrode 215 of the test well 228.
One of the
contact pads 214i, 2145 is configured for coupling an excitation electrode of
a test well with
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a voltage or current source of a reader device and the other of the contact
pads 2141, 2145 is
configured for electrically coupling a signal electrode of the test well with
a signal reading
conductor of the test device. Additional ones of the contact pads 2141-2145
may serve other
purposes in conjunction with the reader device. For example, one or more of
the contact
pads 2141-2145 may couple to circuitry of the electrode interface of the
reader device to
indicate one or more test protocols to the reader. In another example, a power
cartridge, as
described above with reference to FIGs. 1A-1C, may include a similar set of
contact pads
2141-2145 configured to connect to circuitry of the reader device's electrode
interface to
activate a power circuit of the reader device.
[0480] The mixing well 224 can be provided with solid dried and/or lyophilized
constituents for the testing process, for example primers and proteins. The
particular
selection and chemistry of these dried and/or lyophilized constituents can be
tailored to a
particular target or targets for which the cartridge 200 is designed to test.
These dried and/or
lyophilized constituents can be hydrated with the liquid e.g., a buffer or
liquid sample that
flows into the test well (e.g., the fluid sample within the cartridge 200) and
thus activated for
the test procedure. Beneficially, providing the dried and/or lyophilized solid
constituents in
the mixing well 224 enables the cartridge 200 to be stored before use
containing the
components needed for the amplification process, while also delaying
initiation of
amplification until after the sample has been applied.
[0481] The test well 224 is depicted as a generally cylindrical well formed as
a
circular opening in the material of the base 211 and bounded by the planar
surface of the
cover 212. The test well 224 contains two electrodes 213, 215, with one
electrode being an
excitation electrode configured to apply current to the sample in the test
well 224 and the
other electrode being a signal electrode configured to detect current flowing
from the
excitation electrode through the liquid sample. In some embodiments, one or
more test wells
can be provided with a thermistor in place of the electrodes in order to
provide for monitoring
of the temperature of the fluid within the cartridge 100.
[0482] In some embodiments, gas bubbles within the test well 224, particularly
if
positioned along the current path between the electrodes 213, 215, can create
noise in the
signal picked up by the signal electrode. This noise can reduce the accuracy
of test results
determined based on the signal from the signal electrode. A desired high-
quality signal may
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be obtained when only liquid is present along the current path or when minimal
gas bubbles
are present along the current path. As described above, any air initially
present in the fluid
flowing along the cartridge body flow path can be pushed out through the vent
232. In
addition, the electrodes 213, 215 and/or test well 224 can be shaped to
mitigate or prevent
nucleation of the liquid sample in which air or gas bubbles form in the fluid
sample and
collect along the electrodes 213, 215.
[0483] For example, the electrodes 213, 21.5 may be positioned at the bottom
of the
test well 224 in some embodiments. This can allow any air or gas to rise to
the top of the
fluid in the test well and away from the path between the electrodes. As used
herein, the
bottom of the test well 224 refers to the portion of the test well in which
heavier liquid settles
due to gravity, and the top of the test well refers to the portion of the test
well in which lighter
gas rises above the heavier liquids. Further, the electrodes 213, 215 are
positioned away
from the perimeter or edges of the test well 224 which is a location at which
bubble
nucleation typically occurs.
[0484] Further, the electrodes 213, 215 can be formed from a thin, flat layer
of
material that has minimal height relative to the underlying circuit board
layer that forms the
bottom of the test well 224. In some embodiments, the electrodes 213, 215 can
be formed
using electrodeposition and patterning to form a thin layer of metal film, for
example around
300 nrn in height. This minimal height can help prevent or mitigate air
bubbles from
becoming trapped along the interface between the electrode and the underlying
layer. In
some embodiments, a layer of conductive material can be deposited on top of
each electrodes
to create a smoother transition between the edge of the electrode and the
bottom of the test
well. For example, a thin polymid layer (e.g., around 5 microns in height) can
be deposited
on top of the electrode or the circuit board can be butter coated.
Additionally or alternatively,
the electrodes can be positioned in grooves in the underlying layer with the
grooves having
a depth approximately equal to the height of the electrode. These and other
suitable methods
can achieve an electrode that is approximately flat or flush with the bottom
surface of the
well.
[0485] Beneficially, the above-described features can help to keep the
electrodes 213,
215 surrounded by liquid and prevent or reduce gas bubbles from becoming
positioned along
the current path between the electrodes 213, 215.
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[0486] FIGs. 2E and 2F depict the cap 240 component of the cartridge 200. FIG.
2F
is a cross-sectional view taken about the line 2F-2F in FIG. 2E to illustrate
internal structures
of the cap 240. The cap 240 is sized and shaped to mate with or otherwise
mechanically
couple to the cartridge body 210 to form a complete cartridge 200. The cap 240
includes
mating features 242 configured to interlock with corresponding mating features
238 of the
cartridge body when the cartridge 200 is assembled. The cap further includes a
plunger 244
disposed about a retaining well 250 for retaining a capillary tube therein.
[0487] The plunger 244 is sized and shaped to sealingly engage with the
receiving
well 218 of the cartridge body 210 (FIGs. 2C-2D). The plunger 244 optionally
includes a
groove 246 configured to receive an 0-ring or other gasket to eve and/or
enhance the seal
between the plunger 244 and the receiving well 218. An optional chamfer 248 at
a distal end
of the plunger 244 may facilitate the engagement of the plunger 244 with the
receiving well
218, alone or in combination with the chamfer 200 of the receiving well 218
(FIGs. 2C-2D).
As will be described in greater detail with reference to FIGs. 3A-3E, the
plunger 244 thus
sealingly engages with the receiving well 218 to propel a fluid sample into
the cartridge body
210.
[0488] The retaining well 250 is configured to partially surround a capillary
tube
containing a fluid sample for testing. The retaining well 250 preferably has
an interior
diameter larger than the exterior diameter of the capillary tube to be
inserted. A plurality of
retaining structures 252 extend inward from the interior walls of the
retaining well 250 to
hold the capillary tube at a central location within the retaining well 250.
Preferably, the
distance between opposing retaining structures 252 is approximately equal to
or slightly
larger than the exterior diameter of the capillary tube. As shown in FIG. 2F,
a rear portion
254 of each retaining structure 252 extends further inward relative to the
remaining portion
of the retaining structure 252. The distance between opposing rear portions
254 is small
enough that the capillary tube cannot fit between the rear portions 254.
Accordingly, the rear
portions 254 of the retaining structures 252 block the movement of the
capillary tube along
the retaining well 250 and maintain a space between the capillary tube and the
rear wall of
the retaining well 250. As will be described in greater detail with reference
to FIGs. 3A-3E,
this spaced location of the capillary tube within the cap 240 allows air or
other fluid to flow
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into the retaining well 250 around the sides of a capillary tube between the
retaining
structures and into the rear of the capillary tube.
[0489] The cartridge 200 of FIGs. 2A-2F provides a self-contained, easy to use
device for performing an amplification-based test for a target, for example
nucleic acid
testing wherein genomic material in the sample is exponentially copied using a
molecular
amplification process. Beneficially, the user only needs to apply the sample
and insert the
cartridge 200 into a reader device in order to ascertain the result of the
test in some
embodiments, as the solid constituents of the amplification process are pre-
provided within
the cartridge and automatically mixed with the sample. In some embodiments,
one or both
of the cartridge or reader may include a heater and a controller configured to
operate the
heater to maintain the cartridge at the desired temperature for amplification.
In some
embodiments, one or both of the cartridge or reader may include a motor to
impart vibrations
to or otherwise agitate the cartridge to cause any trapped gas to rise to the
top of the liquid
and vent from the test wells.
[0490] FIGs. 3A-3E illustrate mechanical fluid transfer aspects of the
cartridges 120,
200 described herein. As will be described in greater detail, the cartridge
body 210 and cap
240 are configured to create air pressure when coupled together, such that the
air pressure
propels a fluid sample through the fluid path of the cartridge body 210. In
some
embodiments, the fluid sample may be driven through the fluid path of the
cartridge body
210 by capillary action or wicking, instead of or in addition to fluid
pressure. FIGs. 3A-3E
illustrate the cap 240 with translucency to reveal interior features of the
cap 240. The
cartridge body 210 is illustrated in a cutaway view in FIGs. 3C-3E to reveal
interior features
of the cartridge body 210.
[0491] With reference to FIGs. 3A and 3B, a fluid sample may be received in a
capillary tube 300, for example, within an inner lumen 305 of the capillary
tube 300. The
cap 240 is sized and shaped to receive the capillary tube 300 as described
above with
reference to FIGs. 2E and 2F. The fluid sample may be introduced into the
capillary tube
300 while the capillary tube 300 is within the cap 240, or the capillary tube
300 may contain
the fluid sample when it is placed into the cap 240.
[0492] FIG. 3A is a front view of the cap 240 of the cartridge 200. While the
capillary
tube 300 is disposed within the retaining well 250 of the cap 240, the
retaining structures 252
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hold the capillary tube 300 in a position spaced from the walls of the
retaining well 250.
Thus, a plurality of air channels 310 are formed between the interior of the
retaining well
250 and the exterior of the capillary tube 300.
[0493] FIG. 3B is a top view of the cap 240 of FIG. 3A. A rear portion 310 of
some
or all of the retaining structures 310 (e.g., the rear portions 254 of FIG.
2F) cause the capillary
tube 300 to remain spaced from the rear of the retaining well 250. This
arrangement forms
a cap fluid path 315 such that air or other fluids can flow into the retaining
well 250 through
the air channels 310, around the rear of the capillary tube 300, and out of
the retaining well
250 through the inner lumen 305 of the capillary tube 300. Accordingly,
application of a
relatively high pressure at the air channels 310 can cause a fluid within the
inner lumen 305
to flow out of the capillary tube 300 along the cap fluid path 315.
[0494] FIGS. 3C-3E illustrate various stages in a process of coupling the cap
240 to
the cartridge body 210, together with associated fluid paths for effecting
sample movement
into the test well 228 and other components of a cartridge body flow path 325.
FIG. 3C
depicts the cap 240 adjacent but not coupled to the cartridge body 210, FIG.
3D depicts the
cap 240 being coupled to the cartridge body 210, and FIG. 3E depicts the cap
240 fully
coupled with the cartridge body 210.
[0495] As shown in FIG. 3C, the plunger 244, retaining well 250, and capillary
tube
300 are aligned with the receiving well 218 of the cartridge body 210. The
plunger 244 is
sized and shaped to sealingly engage the receiving well 218. An 0-ring or
other seal (not
shown) can be positioned in the groove 246 of the plunger 244 to achieve
and/or enhance the
seal between the plunger 244 and the receiving well 218. The receiving well
218 is
fluidically coupled to the mixing well 224 by an inlet 221 sized and shaped to
sealingly
receive an end of the capillary tube 300. When the cap 240 is aligned with the
cartridge body
210, the process continues to the configuration of FIG. 3D.
[0496] As shown in FIG. 3D, the plunger 244 engages the walls of the receiving
well
218. As the plunger 244 (and/or an 0-ring disposed on the plunger 244) engages
the walls
of the receiving well 218, a volume of ambient air is trapped within the
receiving well 218.
This trapped air 320 has a volume defined by the portion of the receiving well
218 not
occupied by the plunger 244. As the cap 240 is pressed further onto the
cartridge body 210,
an outer end of the capillary tube 300 enters and sealingly engages with the
inlet 221. Thus,
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as cap 240 and the cartridge body 210 are pressed further together, the
trapped air 320 is
compressed within the shrinking volume of the portion of the receiving well
218 not occupied
by the plunger 214. Because the inlet 221 is blocked by the capillary tube
300, the
compression of the trapped air 320 causes the trapped air 320 to flow along
the cap flow path
315 of FIG. 3B.
[0497] Referring now to FIG. 3E, the fluid transfer effected by coupling the
cap 240
and the cartridge body 210 will be described. FIG. 3E illustrates the flow
along the cap flow
path 315 and the cartridge body flow path 325 with encircled numbers shown as
labels for
certain points along the fluid path. The encircled numbers are discussed below
as example
steps of a progression of trapped air 320 and a fluid sample as they travel
through the cap
flow path 315 and the cartridge body flow path 325 within the cartridge 200,
with each step
including a directional arrow showing the direction of fluid travel at that
step. For clarity
and simplicity of FIG. 3E, some components labeled with reference numbers in
FIGs.
3D are not labeled in FIG. 3E.
[0498] Prior to step (1), a user provides a fluid sample within a capillary
tube 300.
Also prior to step (1), the capillary tube 300 is placed within the retaining
well 250 of the
cap 240 between the retaining structures 252 to form the cap flow path 315.
[0499] At step (1), as the plunger 244 compresses the trapped air 320, the
trapped air
320 is forced into the air channels 310. The trapped air 320 flows along the
cap flow path
315 through the air channels 310 between the retaining structures 252 and
along the exterior
of the capillary tube 300.
[0500] At step (2), the trapped air 320 reaches the rear of the retaining well
218. The
trapped air 320 continues along the cap flow path 315 into the inner lumen 305
of the
capillary tube 300. Upon entering the inner lumen 305, the trapped air 320
contacts and
exerts a pressure upon the fluid sample contained within the capillary tube
300. The pressure
is directed along the length of the capillary tube 300 toward the cartridge
body 210.
[0501] At step (3), the fluid sample flows out of the capillary tube 300 and
into the
inlet 221 of the cartridge body 210. The fluid sample is propelled into the
inlet 221 by the
pressured exerted at the opposite end of the capillary tube 300 by the trapped
air 320.
Capillary action or wicking may also propel the fluid sample into the inlet
221, for example,
where the inlet and fluidically connected segments along the cartridge body
flow path 325
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are suitably narrow to cause wicking. At step (4), the fluid sample travels
through the first
segment 222 of the cartridge body flow path 325.
[0502] At step (5), the fluid sample enters the mixing well 224. The mixing
well
may include one or more reagents. Agitation caused by the flow of the fluid
sample within
the relatively larger space of the mixing well 224 causes the reagent and the
sample to be
mixed. In some embodiments, the reagent and the fluid sample are mixed into a
homogeneous solution in which the reagent is evenly distributed throughout the
fluid sample.
The depth, width, and/or cross-sectional profile of the mixing well 224 may be
selected to
facilitate mixing of the reagent and the fluid sample.
[0503] At step (6), the mixed reagent and fluid sample (referred to as the
"test fluid")
leave the mixing well 224 and travel along the second segment 226 of the
cartridge body
flow path 325 into the test well 228.
[0504] At step (7), a portion of the test fluid continues along the third
segment 230
of the cartridge body flow path 325 to fill any remaining open volume within
the cartridge
body flow path 325. The path of step (7) shows the optional flow of a gas
(e.g., a gas portion
of the test fluid or ambient air present within the cartridge body 210)
through the valve 232.
In some embodiments, the valve 232 can include a liquid-impermeable, gas-
permeable filter
to allow any gas present in the test fluid or within the cartridge body 210 to
vent through the
valve 232 as the test fluid fills the space within the cartridge body flow
path 325. The valve
232 may further minimize the occurrence of air bubbles within the test well
228. In some
embodiments the valve 232 may not present and/or may not be configured to vent
gas.
[0505] Following the completion of steps (1)-(7), the cartridge 200 is sealed
and
contains the test fluid within the cartridge body 210 and the cap 240. The
sealed cartridge
200 may then be placed into a reader device such as the reader devices 110,
600 described
herein, for testing to detect one or more target agents within the test fluid.
In various
embodiments, the size of the fluid sample and/or the quantity of the reagent
may preferably
be selected to provide sufficient test fluid to substantially fill the fluid
space enclosed within
the cartridge 200 along the cap flow path 315 and the cartridge body flow path
325. The
volume of the receiving well 218, and the corresponding size of the plunger
244, may
preferably be selected so that the receiving well 218 contains sufficient air
for transporting
the fluid sample along the length of the fluid path and into the test well
328. It will be
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understood that the propulsion of the fluid sample through the capillary tube
300 into and
along the cartridge body flow path 325, as described above with reference to
FIGs. 3A-3E,
may occur due to capillary action or wicking, fluid pressure due to the
compression of a
trapped liquid or gas (e.g., air) within the receiving well 218, or both.
[0506] FIGs. 4A-4N depict various examples of electrode configurations that
can be
used in a test well of the cartridges of FIGs. 2A-3E or in the test well or
channel of another
suitable target detection cartridge as described herein. The test wells shown
in FIGs. 4A-4N
are depicted as circular, however the electrodes can be used in test wells of
other geometries
in other examples. Unless otherwise noted, the solid circles in FIGs. 4A-4N
represent
contacts between the disclosed electrodes and conductors leading to or from
the electrode.
"Width" as used below refers to a dimension along the horizontal direction of
the pages of
FIGs. 4A-4N, and "height" as used below refers to a dimension along the
vertical direction
of the pages of FIGs. 4A-4N. Though depicted in a particular orientation, the
illustrated
electrodes of FIGs. 4A-4N can be rotated in other implementations. Further,
the disclosed
example dimensions represent certain potential implementations of the
electrode
configurations 400A-400G, and variations can have different dimensions that
follow the
same ratios between the provided example dimensions. The electrodes shown in
FIGs. 4A-
4N can be made from suitable materials including platinum, gold, steel, or
tin. In
experimental testing, tin and platinum performed similarly and suitably for
certain test setups
and test targets.
[0507] FIG. 4A depicts a first electrode configuration 400A wherein the first
and
second electrodes 405A, 405B are each formed as a semicircular perimeter. The
straight
edge of the first electrode 405A is positioned adjacent to the straight edge
of the second
electrode 405B and separated by a gap along the width of the configuration
400A. The gap
is larger than the radius of the semicircle of the electrodes. Thus, the first
and second
electrodes 405A, 405B are positioned as mirrored semicircular perimeters. In
one example
of the first electrode configuration 400A, the gap between the closest
portions of the first and
second electrodes 405A, 405B spans approximately 26.369 mm, the height (along
the
straight edge) of each of the electrodes 405A, 405B is approximately 25.399
mm, and the
radius of the semicircle of each of the electrodes 405A, 405B is approximately
12.703 mm.
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[0508] FIG. 4B depicts a second electrode configuration 400B. Similar to the
first
electrode configuration 400A, the first and second electrodes 410A, 410B of
the second
electrode configuration 400B are each formed as a semicircular perimeter and
are positioned
as mirrored semicircles with their straight edges facing one another. The
first and second
electrodes 410A, 410B of the second electrode configuration 400B can be the
same size as
the first and second electrodes 405A, 405B of the first configuration 400A. In
the second
electrode configuration 400B, the gap along the width of the configuration
400B between the
first and second electrodes 410A, 410B is smaller than in the first
configuration 400A, and
the gap is smaller than the radius of the semicircle of the electrodes 410A,
410B. In one
example of the second electrode configuration 400B, the gap between the
closest portions of
the first and second electrodes 410A, 410B spans approximately 10.158 mm, the
height
(along the straight edge) of each of the electrodes 410A, 410B is
approximately 25.399 mm,
and the radius of the semicircle of each of the electrodes 410A, 410B is
approximately 12.703
mm.
[0509] FIG. 4C depicts a third electrode configuration 400C having first and
second
linear electrodes 415A, 415B separated by a gap along the width of the
configuration 400C,
where the gap is approximately equal to the height of the electrodes 415A,
415B. The width
of the electrodes 415A, 415B is approximately one half to one third of the
height of the
electrodes. In one example of the third electrode configuration 400C, the gap
between the
closest portions of the first and second electrodes 415A, 415B spans
approximately 25.399
mm, the height of each of the electrodes 415A., 415B is also approximately
25.399 mm, and
the width of each of the electrodes 415A, 415B is approximately 10.158 mm. The
ends of
the first and second electrodes 415A, 415B can be radiused, for example having
a radius of
around 5.078 mm.
[0510] FIG. 4D depicts a fourth electrode configuration 400D having first and
second
rectangular electrodes 420A, 420B separated by a gap along the width of the
configuration
400D, where the gap is approximately equal to the width of the electrodes
420A, 420B. In
one example of the fourth electrode configuration 400D, the gap between the
closest portions
of the first and second electrodes 420A, 420B spans approximately 20.325 mm,
the height
of each of the electrodes 420A, 420B is also approximately 23.496 mm, and the
width of
each of the electrodes 420A, 420B is approximately 17.777 mm.
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[0511] FIG. 4E depicts a fifth electrode configuration 400E having first and
second
linear electrodes 425A, 425B separated by a gap along the width of the
configuration 400E,
where the gap is approximately equal to the height of the electrodes 425A,
425B. The fifth
electrode configuration 400E is similar to the third electrode configuration
400C, with the
width of the electrodes 425A, 425B reduced to around one half to two thirds of
the width of
the electrodes 415A, 415B while having the same height. In one example of the
fifth
electrode configuration 400E, the gap between the closest portions of the
first and second
electrodes 425A, 425B spans approximately 25.399 mm, the height of each of the
electrodes
425A, 425B is also approximately 25.399 mm, and the width of each of the
electrodes 425A,
425B is approximately 5.078 mm. The ends of the first and second electrodes
425A, 425B
can be radiused, for example having a radius of around 2.542 mm.
[0512] FIG. 4F depicts a sixth electrode configuration 400F having concentric
annular electrodes 430A, 430B. The sixth electrode configuration 400F is the
configuration
shown in the test well 228 of FIGs. 2A, 2C, and 21). The inner electrode 430B
can be a disc
or circular-shaped electrode and can be positioned in the center of the test
well. The outer
electrode 430A can be a semicircular electrode formed concentrically around
the inner
electrode 430B and separated from the inner electrode 430B by a gap. In the
sixth electrode
configuration 400F, the gap is approximately equal to the radius of the inner
electrode 430B.
A break in the semicircle of the outer electrode 430A occurs where a
conductive lead
connects the inner electrode 430B to the current providing conductor. In one
example of the
sixth electrode configuration 400F, the gap between the inner edge of the
annular first
electrode 430A and the outer perimeter of the circular second electrode 430B
spans
approximately 11.430 mm, the radius of the circular second electrode 430B is
approximately
17.777 mm, and the thickness of the annulus of the annular first electrode
430A is
approximately 5.080 mm. The ends of the first electrode 430A can be radiused,
for example
having a radius of around 2.555 mm, and the gap between the open ends of the
annulus of
the first electrode 435A can be around 28.886 mm from vertex to vertex.
[0513] FIG. 4G depicts a seventh electrode configuration 400G having
concentric
annular electrodes 435A, 435B. Similar to the embodiment of FIG. 4F, the inner
electrode
435B can be a disc or circular-shaped electrode having the same radius as
inner electrode
430B and can be positioned in the center of the test well. The outer electrode
435A can be a
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semicircular electrode formed concentrically around the inner electrode 435A
and separated
from the inner electrode 435A by a gap. In the seventh electrode configuration
400G, the
gap is greater than the radius of the inner electrode 435B, for example two to
three times
greater. Correspondingly, the outer electrode 435B has a larger radius than
the outer
electrode 430B. In one example of the seventh electrode configuration 400G,
the gap
between the inner edge of the annular first electrode 435A and the outer
perimeter of the
circular second electrode 435B spans approximately 24.131 mm, the radius of
the circular
second electrode 435B is approximately 17.777 mm, and the thickness of the
annulus of the
annular first electrode 435A is approximately 5.080 mm. The ends of the first
electrode
435A can be radiused, for example having a radius of around 2.555 mm, and the
gap between
the open ends of the annulus of the first electrode 435A can be around 46.846
mm from
vertex to vertex.
[0514] In the embodiments of FIGs. 4A-4E, either electrode can be used as the
excitation electrode and the other electrode can be used as the signal
electrode. In the
embodiments of FIGs. 4F and 4G, the inner electrode 430B, 435B is configured
to be used
as the excitation electrode (e.g., coupled to a current source) and the outer
electrode 430A,
435A is configured to be used as the signal electrode (e.g., provides its
signal to a memory
or processor). In some example tests, the sixth electrode configuration 400F
exhibited the
best performance of the configurations shown in FIGs. 4A-4G.
[0515] FIGs. 4H-4N depict further examples of electrode configurations
suitable for
implementing three-terminal sensing and/or four-terminal sensing. In some
embodiments,
three-terminal sensing (e.g., potentiostat-type or 3-wire measurement) or four-
terminal
sensing (e.g., Kelvin-type or 4-wire measurement) may improve the accuracy of
impedance
measurements in the systems and methods described herein. For example, the
excitation
electrode and the signal electrode may themselves carry some charge.
Additionally, there
may be some additional impedance related to surface effects at the electrode-
fluid interface.
Accordingly, a third electrode or a third and fourth electrode (e.g., a second
electrode pair)
may further be disposed within the test well. The third and/or fourth
electrodes can carry a
substantially smaller or negligible current relative to the current carried by
the excitation and
signal electrodes. The third and/or fourth electrodes may thus be used to
accurately
determine a voltage (e.g., a voltage between the third and fourth electrodes,
or a voltage
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between the third electrode and the excitation or signal electrode). This
precisely measured
voltage may be used to determine an impedance measurement having enhanced
accuracy. It
will be understood that the configurations of three or four electrodes
illustrated in FIGs. 4H-
4N are merely examples of a number of three- or four-terminal configurations
that may be
provided within the test wells of the present disclosure.
[0516] FIG. 4H depicts an electrode configuration similar to the electrode
configuration of FIG. 4A, with the addition of a third electrode 440A and a
fourth electrode
440B disposed between the first electrode 405A and the second electrode 405B.
Either or
both of the third electrode 440A and the fourth electrode 440B may be used to
implement
three- or four-terminal sensing.
[0517] FIG. 41 depicts an electrode configuration similar to the electrode
configuration of FIG. 4B, with the addition of a third electrode 440A disposed
between the
first electrode 410A and the second electrode 410B. The third electrode 440A
may be used
to implement three-terminal sensing.
[0518] FIG. 4J depicts an electrode configuration similar to the electrode
configuration of FIG. 4C, with the addition of a third electrode 440A and a
fourth electrode
440B disposed between the first electrode 415A and the second electrode 415B.
Either or
both of the third electrode 440A and the fourth electrode 440B may be used to
implement
three- or four-terminal sensing.
[0519] FIG. 4K depicts an electrode configuration similar to the electrode
configuration of FIG. 4D, with the addition of a third electrode 440A disposed
between the
first electrode 420A and the second electrode 420B. The third electrode 440A
may be used
to implement three-terminal sensing.
[0520] FIG. 4L depicts an electrode configuration similar to the electrode
configuration of FIG. 4E, with the addition of a third electrode 440A disposed
between the
first electrode 425A and the second electrode 425B. The third electrode 440A
may be used
to implement three-terminal sensing.
[0521] FIG. 4M depicts an electrode configuration similar to the electrode
configuration of FIG. 4F, with the addition of a third electrode 440A disposed
between the
outer electrode 430A and the inner electrode 430B. The third electrode 440A
may be used
to implement three-terminal sensing.
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[0522] FIG. 4N depicts an electrode configuration similar to the electrode
configuration of FIG. 4G, with the addition of a third electrode 440A and a
fourth electrode
440B disposed between the outer electrode 435A and the inner electrode 435B.
Either or
both of the third electrode 440A and the fourth electrode 440B may be used to
implement
three- or four-terminal sensing.
[0523] FIG. 5A schematically depicts a first electrode or excitation electrode
and a
second electrode or signal electrode that may be spaced apart from one another
within a test
well of the cartridges of FIGs. 2A-3E or in the test well or channel of
another suitable target
detection cartridge as described herein.
[0524] The formation of an aggregate, nucleic acid complex, or polymer, for
example
during an amplification process in the test wells of cartridges of FIGs. 2A-
3E, can affect
waveform characteristics of one or more electrical signals that are sent
through a channel.
As shown in FIG. 5A, a first electrode or excitation electrode 510A is spaced
apart from a
second electrode or sensing electrode 510B within test well 505. The test well
505 can
contain a test solution undergoing an amplification process. During some of
all of that
process, an excitation voltage 515 can be provided to the excitation electrode
510A, from
which the excitation voltage 515 is transmitted into the fluid (preferably all
or substantially
all liquid) within the well 505.
[0525] After passage through and attenuation by the liquid sample (represented
schematically by the resistance R and reactance X), the attenuated excitation
voltage is
sensed or detected at the sensing electrode 510B. The fluid acts as a resistor
R in series with
the excitation electrode 510A and the sensing electrode 510B. The fluid also
acts as in series
capacitor(s), shown by the reactance X. The raw sensed signal during some or
all of the
duration of a test can be represented over time as a sinusoidal curve with
varying amplitudes,
similar to that shown in plot 520.
[0526] The excitation voltage 515 can be an alternating current at a
predetermined
drive frequency. The particular frequency selected can depend for example upon
the
particular target sought to be detected, the medium of the test sample, the
chemical makeup
of the amplification process constituents, the temperature of the
amplification process, and/or
the excitation voltage. In some embodiments of the cartridges of FIGs. 2A-3E,
the excitation
drive frequency can be between 1 kHz and 10 kHz at as low an excitation
voltage as possible.
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As one example, in tests performed to identify a target of H. influenzae (106
copies/reaction)
spiked into 5% whole blood, excitation sensor drive frequency was varied from
100 Hz to
100,000 Hz at 0.15 Volts. These tests revealed that the desired "signal
cliff," an artifact in a
portion of the signal indicative of a positive test sample described in more
detail below,
becomes more easily detectable below 100 Hz and is most easily detectable
between 1 kHz
and 10 kHz. Further, with frequencies in the range between 1 kHz and 10 kHz,
the signal
cliff advantageously could be identified before 12 minutes of test time had
elapsed.
Beneficially, faster identification of the signal cliff can result in shorter
test times, in turn
resulting in quicker provision of test results and the ability to perform more
tests per day. At
frequencies lower than 1 kHz, the reactance component of the signal (in which
the signal
cliff may be found in a positive sample) decreased monotonically. The sensor
drive
frequency can be similarly fine-tuned for other tests to optimize performance,
that is, to
optimize the detectability of a signal cliff. Detectability of a signal cliff
refers to the ability
to consistently differentiate between a positive sample and a negative sample.
[0527] FIG. 5B depicts an example plot 525 showing an impedance signal 530
that
can be extracted from the raw signal 520 provided by the sensing electrode
510B. The
impedance signal 530 represents the electrical impedance Z of the test well
over time. The
impedance Z can be represented by a Cartesian complex number equation as
follows:
= R. + jX
where R represents the resistance of the test well and is the real part of the
above equation and
the X represents the reactance of the test well and is the imaginary part of
the above equation
(denoted by j). Thus, the impedance of the test well can be parsed into two
components, the
resistance R and the reactance X.
[0528] Initially, the value of the resistance R can be determined by taking a
baseline
measurement of the test well prior to or at the outset of the amplification
process. Although
the resistance of the test fluid can drift away from this baseline value
throughout the duration
of the test, the current sensed by the sensing electrode 510B due to the
resistance of the test
fluid can be in phase with the signal provided through the excitation
electrode 510A. Thus,
changes or drift in the resistance can be identified by values of the in-phase
component of
the signal 520 over time. The reactance can arise from the effect of
inductance in the test
fluid, capacitance in the test fluid, or both; this effect can cause the fluid
to retain current
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(e.g., electrons provided by excitation electrode 510A) temporarily. After
some time, this
retained current flows out of the test fluid into the sensing electrode 510B.
Due to this delay,
the current sensed by the sensing electrode 510B due to the reactance of the
test fluid can be
out of phase with the current sensed from the resistance of the test fluid.
Thus, values of the
reactance of the test fluid can be identified by values of the out of phase
component of the
signal 520 over time. The reactance can fluctuate throughout the duration of
the test based
on changes to the chemical constituents of the test fluid due to the
amplification process.
The signal cliff (e.g., a rise or drop in the reactance at or greater than a
threshold rate or
magnitude and/or during a predetermined window of time) indicative of a
positive sample
can be found in the reactance X.
[0529] During a test, the excitation electrode 510A can be sinusoidally
excited with
some amplitude and voltage. The excitation electrode 510A is in series with
the test liquid
in the well, which can be considered as a resistor R. The resistor (e.g., the
test fluid) and
electrode form a voltage divider, which has a voltage determined by the ratio
of the resistor
and electrode chemistry/impedances. The resulting voltage waveform sensed at
the sensing
electrode 510B represents the complex impedance signal 530. In some
embodiments, a curve
such as the impedance signal 530 may not be generated, but rather the raw
sensed signal 520
can be parsed into its resistance and reactance components as described
herein. The
impedance signal 530 is provided as an example representation of a combined
curve
representing both the resistance of the test fluid and the reactance of the
test fluid over time.
The complex impedance signal 530 can be interpreted as a quadrature-modulated
waveform
(e.g., a combination of an in-phase waveform resulting from the resistance of
the test fluid
and an out-of-phase waveform, resulting from the reactance of the test fluid),
where the in-
phase and out-of-phase components change on a timescale much greater than the
modulation
frequency. The in-phase waveform is in-phase with the composite waveform of
the complex
impedance. Some implementations can use a synchronous detector, for example
having
multipliers and low pass filters implemented in a field programmable gate
array (FPGA), to
extract the in-phase and out-of-phase components from the raw signal 520 and
compute their
amplitude and phase.
[0530] In order to parse the impedance signal 530 (or the raw sensed signal
520) into
its constituent resistance and reactance components, the voltage waveform 520
at the sensing
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electrode 510B is sampled faster than its Nyquist frequency (e.g., two times
the highest
frequency of the excitation voltage) and then decomposed into an in-phase
component
(resistance) and an out-of-phase component (reactance). The in-phase and out-
of-phase
voltage components can be computed using the known series resistance (e.g.,
the value of R)
to calculate the real component of the impedance (the resistance) and the
imaginary
component of the impedance (the reactance).
[0531] FIG. 5C depicts a plot 541 of the resistance 540A and reactance
components
540B over time (t = 3 minutes to t = 45 minutes) extracted from a raw signal
520 generated
based on an example positive test. As illustrated, the signal cliff 545
represents a change AR
in the reactance 540B during a particular window of time Tw. The signal cliff
545 indicates
a positive sample. At times occurring prior to the signal cliff 545, the
reactance curve 540B
is relatively flat or stable, and again after the signal cliff 545 the
reactance curve 540B is
relatively flat or stable. Thus, in this embodiment the signal cliff 545 for
the particular test
parameters represented by the plot 541 occurs as a drop of AR in the expected
region 535.
[0532] The magnitude of the change AR in the reactance that corresponds to a
positive
sample signal cliff 545, as well as the position and/or duration of the
particular window of
time Tw at which the signal cliff 545 is expected to occur, can vary depending
on a number
of parameters of the test. These parameters include the particular target of
the test (e.g., the
rate at which that target amplifies), the frequency of the excitation voltage,
the configuration
of the excitation and sensor electrodes (e.g., their individual shapes and
dimensions, the gap
separating the electrodes, and the material of the electrodes), the sampling
rate, the quantity
of amplification agents provided at the start of the test, the temperature of
the amplification
process, and the amount of target present in the sample. In some embodiments,
the expected
characteristics of a signal cliff of a positive sample, predetermined for
example through
experimentation, can be used for differentiating between positive samples and
negative
samples. In some embodiments, the expected characteristics of a signal cliff
can be used for
determining the severity or progress of a medical condition, for example via
correlations
between particular signal cliff characteristics and particular initial
quantities of the target in
the sample. The predetermined expected characteristics can be provided to,
stored by, and
then accessed during test result determination by a reader device configured
to receive
signals from the sensing electrode(s) of a test cartridge.
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[0533] For a given test, the expected magnitude of the change AR in the
reactance
and the expected window of time Tw of a signal cliff 545 for a positive sample
can be
determined experimentally based on monitoring and analyzing the reactance
curves
generated by positive control samples (and optionally negative control
samples). In some
embodiments, the test parameters influencing the signal cliff can be varied
and fine-tuned to
identify the parameters that correspond to an accurately distinguishable
signal cliff. A reader
and cartridge as described herein can be configured to match the tested
configuration and
provided with expected signal cliff characteristics for that test.
[0534] For example, in a set of experimental tests for H. influenzae, the test
fluid
initially included amplification primers and 1,000,000 added target copies,
the excitation
voltage was 200 mV P2P, the test parameters included a 10 kHz sweep start and
a 10 MHz
sweep stop for the frequency of the excitation current, and close and far
electrode gaps were
configured at 2.55 mm and 5 mm respectively. The amplification temperature was
set to
65.5 degrees Celsius, and the two electrode setups (one for each of the close
and far gaps)
included platinum electrodes. At low frequencies (10 kHz-100kHz), detectable
signal cliffs
were identified beginning around 23 minutes into amplification around 10 kHz
and around
30 minutes around 100 kHz using the 5 mm gap electrode configuration, with the
magnitude
of change in reactance being around 3.5-4 Ohms at 10 kHz and dropping to
around 3.25-3.5
Ohms at 100 kHz. At low frequencies (10 kHz-100kHz), detectable signal cliffs
were
identified beginning around 25 minutes into amplification around 10 kHz and
around 30
minutes around 100 kHz using the 2.5 mm gap electrode configuration, with the
magnitude
of change in reactance being around 3.5-4 Ohms. At higher frequencies, the
drop in
reactance of the signal cliff decreased, and the time at which these smaller
signal cliffs were
identified was shifted to later in the amplification process. Accordingly, in
this example a
test well in a test cartridge may be configured with the 5 mm gap electrodes
and a reader
device may be configured to provide 10 kHz excitation current to the test
cartridge during
amplification. The reader device can be provided with instructions to provide
this current
and monitor the resulting reactance of the test well throughout amplification
or for a window
of time around the expected signal cliff time (here, 23 minutes), for example
between 20 and
35 minutes. The reader device can also be provided with instructions to
identify a positive
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sample based on the reactance exhibiting around a 3.5-4 Ohm change around 23
minutes into
amplification, or within the window of time around the expected signal cliff
time.
[0535] Once identified, the values for AR and Tw can be provided to reader
devices
for use in distinguishing between positive and negative samples for that
particular test. In
some examples, such devices can determine whether the reactance curve 540B has
the
required value and/or slope at the identified window of time Tw to correspond
to the signal
cliff In other embodiments, the reader device can analyze the shape of the
reactance curve
over time to determine whether it contains a signal cliff In some embodiments,
a reader can
modify its testing procedures based on the identified window of time Tw at
which the signal
cliff 545 is expected to occur, for example by only providing the excitation
voltage and
monitoring the resultant signal within this window, advantageously conserving
power and
processing resources compared to continuous monitoring during an entire test
time.
[0536] FIG. 5D depicts a plot 551 of the resistance and reactance components
extracted from the raw sensor data of a sensing electrode 510B dining example
tests of
positive and negative controls. Specifically, the plot 551 shows a curve 550A
of the
resistance of the positive sample, a curve 550B of the reactance of the
positive sample, a
curve 550C of the resistance of the positive sample, and a curve 550D of the
reactance of the
positive sample over the 35 minute duration of the test. As shown by FIG. 5D,
the positive
sample signal cliff occurs around 17 minutes into the test, with a relatively
flat and stable
reactance curve 550B leading up to the signal cliff In contrast, at this same
time the negative
sample reactance curve 550D exhibits no signal cliff but rather maintains a
quadratic
curvature from around t = 8 minutes through the end of the test.
[0537] FIG. 5E depicts a plot 561 of the resistance 560A and reactance
components
560B over time (t = 0 minutes to t = 60 minutes since the start of
amplification) extracted
from a raw signal 520 generated based on an example positive test. As
illustrated, the signal
cliff 565 represents a change AR in the reactance 560B during a particular
window of time
Tw. The signal cliff 565 indicates a positive sample. At times occurring prior
to the signal
cliff 565, the reactance curve 560B is relatively flat or stable, and again
after the signal cliff
565 the reactance curve 560B is relatively flat or stable with slight
concavity. The signal
cliff 565 for the particular test parameters represented by the plot 561
occurs as a peak, spike,
or bell curve in the expected region 535, during which the reactance values
rise and fall by
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the AR value in an approximately parabolic curve. As described herein, varying
of certain
test parameters (e.g., test well configuration, chemistry and initial quantity
of amplification
constituents, target, and excitation current characteristics) can vary the
geometry of the signal
cliff yielded from a positive sample. Thus, in some embodiments the geometry
of a "signal
cliff" in the reactance values vs time curve can vary from test to test,
though for a particular
test the curve geometry and/or timing signal cliff remains consistent within
reactance change
and/or timing parameters across positive samples for that test.
[0538] FIG. 6 depicts a schematic block diagram of an example reader device
600
that can be used with the cartridges described herein, for example the
cartridges 120 or 200.
The schematically illustrated reader device 600 may be, for example, the
reader device 110
of FIGs. 1A-1C. The reader device 600 includes a memory 605, processor 610,
communications module 61.5, heater 625, electrode interface 630, voltage
source 635, and a
cavity 660 into which a cartridge can be inserted. The reader device 600 may
further include
a status indicator 640. The reader device 600 is in communication with a user
interface 620,
which may include a user interface of a remote computing device such as a
smartphone,
tablet, or other device having a testing control application executing
thereon.
[0539] When test cartridge 120, 200 is inserted into the cavity 660 of the
reader
device 600, the electrode interface 214 of the cartridge couples with the
electrode interface
630 of the reader device 600. This can allow the reader device 600 to detect
that a cartridge
is inserted, for example by testing whether a communication path is
established. In some
embodiments, the optional power cartridges described above with reference to
FIGS. 1B and
1C may activate a power supply circuit of the reader device 600 when the
electrode interface
214 of the cartridge couples with the electrode interface 630 of the reader
device 600.
Further, such communications can enable the reader device 600 to identify a
particular
inserted test cartridge 120,200 and access corresponding testing protocols.
Testing protocols
can include the duration of the test, the temperature of the test, the
characteristics of a positive
sample impedance curve, and the information to output to the user based on
various
determined test results. In other embodiments, the reader device 600 can
receive an
indication via user interface 620 that a cartridge is inserted (e.g., by a
user inputting a "begin
testing" command and optionally a test cartridge identifier).
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[0540] The memory 605 includes one or more physical electronic storage devices
configured for storing computer-executable instructions for controlling
operations of the
reader device 600 and data generated during use of the reader device 600. For
example, the
memory 605 can receive and store data from sensing electrodes coupled to the
electrode
interface 630.
[0541] The processor 610 includes one or more hardware processors that execute
the
computer-executable instructions to control operations of the reader device
600 during a test,
for example by controlling the heater 625, controlling the communications
module 615 to
interact with the user interface 620, and activating the voltage source 635.
One example of
testing operations is described with respect to FIG. 7A below. The processor
610 can be also
be configured by the instructions to determine test results based on data
received from the
excitation electrodes of an inserted test cartridge, for example by performing
the process of
FIG. 7B described below.
[0542] The communications module 61.5 includes network-enabled hardware
components, for example wired or wireless networking components, for providing
networked communications between the reader device 600 and remote computing
devices.
Suitable networking components include Wi Fi, Bluetooth, cellular modems,
Ethernet ports,
or USB ports, and the like. Beneficially, networking capabilities can enable
the reader device
600 to interact with and be controlled by remote computing devices such as one
or more
additional handheld computing devices (e.g., smartphones, tablets, etc.). In
some
embodiments, remote devices may be in communication additional remote
computing
systems such as hospital information systems and/or laboratory information
systems that
store electronic medical records, national health agency databases, and the
computing
devices of clinicians or other designated personnel. In addition, the
networking capabilities
can enable the reader device 600 to receive information over the network from
remote
computing devices, for example updated signal cliff parameters for existing
test, new signal
cliff parameters for new tests, and updated or new testing protocols.
[0543] The user interface 620 can be implemented within a remote device
connected
to the communications module 615 via WiFi, or Bluetooth, or the like. The
remote device
may have a testing control application installed thereon to provide a testing
system user
interface, for providing control options and/or presenting test results and
other test
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information to users, on a display of the remote device. Further details of
the user interface
620 are described with reference to FIGs. 8A-8D and FIGs. 15A-15P.
[0544] The heater 625 can be positioned adjacent to the cavity 660 for heating
an
inserted cartridge to the desired temperature for an amplification process.
Though depicted
on a single side of the cavity 660, in some embodiments the heater 625 can
surround the
cavity.
[0545] As described herein, the voltage source 635 can provide an excitation
signal
at a predetermined voltage and frequency to the excitation electrode of an
inserted test
cartridge.
[0546] The status indicator 640 may include any suitable notification device,
such as
one or more lights, sound generators, or the like. Operation of a light-based
status indicator
is described in greater detail with reference to FIGS. 1A-1C.
[0547] FIG. 7A depicts a flowchart of an example process 700 for operating a
reader
device during a test as described herein. The process 700 can be performed by
the reader
device 600 described above.
[0548] At block 705, the reader device 600 can detect that a power cartridge
has been
removed from the reader device 600. In some embodiments, the detection of
block 705 can
occur based on the disconnection of a signal path between the electrode
interface 630 of the
reader device 600 and one or more contact pads 2141-2145 (FIG. 2D) of the
power cartridge.
[0549] At block 710, the reader device 600 automatically powers on in response
to
detecting the removal of the power cartridge at block 705. In some
embodiments, the reader
device may transmit a notification to a user interface 620 device and/or
illuminate one or
more status lights of a status indicator 640 to indicate that the reader
device 600 is powered
on and ready to receive an assay cartridge 120, 200.
[0550] At block 715, the reader device 600 can detect that an assay cartridge
120,
200, has been inserted, for example in response to user input or in response
to establishing a
signal path with the inserted cartridge. In some embodiments, the cartridge
120, 200 can
include an information element that identifies the particular test(s) to be
performed to the
reader device 600 and optionally includes test protocol information.
[0551] At block 720, the reader device 600 can heat the cartridge 120, 200 to
a
specified temperature for amplification. For example, the temperature can be
provided by
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information stored on the cartridge 120, 200 or accessed in the internal
memory of the reader
device 600 in response to identification of the cartridge 120, 200.
[0552] At decision block 725, the reader device 600 can determine whether the
test
is still within its specified test duration. For example, where the expected
window of time in
which a signal cliff should appear in a positive sample is known, the duration
of the test may
end at or some predetermined period of time after the end of the window. If
so, the process
700 transitions to optional decision block 730 or, in embodiments omitting
block 730, to
block 735.
[0553] At optional decision block 730, the reader device 600 determines
whether to
monitor the test well amplification by logging data from the test well sensing
electrode. For
example, the reader 600 may be provided with instructions to only monitor the
impedance of
the test well during a particular window or windows of a test. If the reader
device 600
determines not to monitor the test well amplification, the process 700 loops
back to decision
block 725.
[0554] If the reader device 600 determines to monitor the test well
amplification, the
process 700 transitions to block 735. At block 735, the reader device 600
provides an
excitation signal to the excitation electrode of the test well(s) of the
inserted cartridge. As
described above, this can be an alternating current at a particular frequency
and voltage.
[0555] At block 740, the reader device 600 detects and logs data from the
sensing
electrode of the test well(s) of the inserted cartridge. In some embodiments,
this data can be
stored for later analysis, for example after completion of the test. In some
embodiments, the
reader device 600 can analyze this data in real time (e.g., as the test is
still occurring) and
may stop the test once a positive sample signal cliff is identified.
[0556] When the reader device 600 determines at block 725 that the test is not
still
within its specified duration, the process 700 moves to block 745 to analyze
the test data and
output the test result. The test result can include an indication that the
sample tested positive
or negative for the target, or can more specifically indicate an estimated
quantity of the target
in the tested sample. Following the conclusion of the test, further tests may
be performed by
returning to block 715 for a new assay cartridge. Alternatively, the reader
device 600 may
detect insertion of a power cartridge and power off in response.
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[0557] FIG. 7B depicts a flowchart of an example process 750 for analyzing
test data
to detect a target as described herein that can be performed by the reader
device 600 as block
745 of FIG. 7A.
[0558] At block 755, the reader device 600 can access logged signal data
received
from the electrode of a well.
[0559] At block 760, the reader device 600 can decompose the signal into
resistance
and reactance components across some or all of the different time points of
the test. For
example, as described above, at each time point the reader device 600 can
determine in phase
and out of phase components of the raw sampled voltage waveform and can then
deconvolute
these components using known series resistance of the electrode circuit to
calculate the in-
phase (resistance) and out-of-phase (reactance) portions of the impedance of
the test well.
[0560] At block 765, the reader device 600 can generate a curve of the
reactance
values over time. Also, at block 765, the reader device 600 can optionally
generate a curve
of the resistance values over time.
[0561] At block 770, the reader device 600 can analyze the reactance curve to
identify a signal change indicative of a positive test. As described above
with respect to the
signal cliff of FIG. 5C, the reader device 600 can look for greater than a
threshold change in
reactance, can look for such a change within a predetermined window of time,
can analyze
the slope of the reactance curve at a predetermined time, or can analyze the
overall shape of
the reactance curve in order to determine whether a signal cliff (e.g., a rise
or drop in the
signal preceded and followed by relatively more stable values) is present.
[0562] At decision block 775, based on the analysis performed at block 770,
the
reader device 600 can determine whether the sought-after signal change was
identified in the
reactance curve. If so, the process 750 transitions to block 780 to output an
indication of a
positive test result to the user. If not, the process 750 transitions to block
785 to output an
indication of a negative test result to the user. The result can be output
locally, for example
on the display of the device, or output over a network to a designated remote
computing
device.
[0563] FIGs. 8A-8D depict screens of an example graphical user interface 800
of a
user device implementing an example testing process in communication with a
reader device
as described herein. The user interface 800 may be, for example, the user
interface 620
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illustrated in connection with the reader device 600 of FIG. 6. The user
interface 800 may
be implemented with any of the reader devices 110, 600 and/or assay cartridges
120, 200
described herein. The screens depicted in FIGs. 8A-8D may be displayed, for
example, by
an application executing on a smartphone or other user interface device paired
to the reader
device 110, 600 (e.g., by WEN, Bluetooth, or the like) so as to allow a user
to control and/or
monitor the reader device 110, 600 from the user interface device.
[0564] FIG. 8A depicts an initial pre-test screen which may be displayed after
an
inserted assay cartridge 120, 200 has been detected. In one example, a user
scans a cartridge
identifier (e.g., cartridge identifier 215 of FIG. 2B) of a cartridge before
inserting the
cartridge into the reader device. When the device is inserted, the paired
reader device detects
the inserted cartridge and sends a message to the user interface device that
the cartridge has
been inserted. The application then displays the initial pre-test screen
depicted in FIG. 8A.
[0565] The initial pre-test screen includes a status indication area 805, a
test
identifying area 810, a progress indication area 815 including a numeric
progress indication
817 and a graphical progress indication 819, and an input area 820. The status
indication
area 805 may include an instruction, such as a request for the user to confirm
the information
in the test identifying area 810. The test identifying area 810 includes
information associated
with the test to be performed, such as a name or other identifier of a test
subject, a condition
or target agent to be detected, or the like. In the initial pre-test screen of
FIG. 8A, the input
area 820 includes user-selectable "cancel" and "start test" options to allow
the user to cancel
the test or confirm the details and start the test.
[0566] FIG. 8B depicts a mid-test screen that may be displayed while the
reader
device is conducting the test on the fluid sample within the cartridge. The
status indication
area 805 indicates that the test is in progress. As the test progresses, the
numeric progress
indication 817 and the graphical progress indication 819 are updated to
display the current
progress of the test. A user-selectable option to cancel the test is provided
in the input area
to allow a user to stop the test if desired.
[0567] FIG. 8C depicts an initial test completion screen that may be displayed
when
the reader device has completed the test and has analyzed the logged test data
to determine a
test result. The status indication area 805, numerical progress indication
817, and/or the
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graphical progress indication 819 may indicate that the test is complete. In
the input area
820, a user-selectable option to view the test results is provided.
[0568] FIG. 8D depicts a test result display screen for communicating the
results of
the test to a user. The test identifying area 810 may still display some or
all of the originally
displayed test identifying information. The test identifying area 810 may
additionally di splay
an outcome 812, such as positive or negative, or other condition associated
with the test
results. The input area 820 may provide a user-selectable option to continue
(e.g., to conduct
additional tests, transmit results, etc.).
[0569] FIGs. 9A and 9B depict a further example of a handheld detection system
900
for detection of a target. Similar to the system 100 of FIGs. 1A-1C, the
system 900 may be
implemented in conjunction with any of the target detection processes,
systems, and devices
described herein. The system 900 includes a reader device 910 and a cartridge
920
configured to fit within a cavity 912 of the reader device 910. The cartridge
920 is sized and
shaped to be gripped by a user to facilitate insertion and/or removal of the
cartridge 920 from
the reader device 910. The reader device 910 may further include a light ring
914 disposed
about the cavity 912. The light ring 914 may include any or all of the light
sources, colors,
operation modes, etc., described above with reference to the light ring 114 of
FIGs. 1A-1C.
[0570] FIGs. 10A-10K depict an example cartridge 1000 configured for detection
of
a target. As described herein, the target may be a viral target, bacterial
target, antigen target,
parasite target, microRNA target, or agricultural analyte. Some embodiments of
the cartridge
1000 can be configured for testing for a single target, while some embodiments
of the
cartridge 1000 can be configured for testing for multiple targets. The
cartridge 1000 includes
a cartridge body 1010 and a cap 1050 configured to be mechanically coupled to
the cartridge
body 1010. The cartridge body 1010 and the cap 1050, when coupled together,
can form an
assembled cartridge 1000 for insertion into a reader device such as the reader
device 910 of
FIGs. 9A and 9B. As will be described in greater detail below, the cartridge
body 1010 may
include a plurality of test wells therein, such that a single cartridge 1000
can be configured
for testing a single sample for multiple targets.
[0571] FIGs. 10A and 10B depict a complete cartridge 1000 including the
cartridge
body 1010 and the cap 1050 coupled together. In use, the cap 1050 and the
cartridge body
1010 can operate to seal a provided sample within the cartridge 1000, thereby
preventing
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exposure of test operators to the sample and preventing any liquid from
escaping into the
electronics of an associated reader device. The cartridge body 1010 and the
cap 1050 may
be coupled by a friction fit, a snap fit, and/or one or more mechanical or
chemical securing
means. Coupling of the cartridge body 1010 and the cap 1050 is discussed in
greater detail
with reference to FIGs. 11A-11D.
[0572] The cartridge body 1010 and the cap 1050 can be formed from suitable
fluid-
impermeable materials such as plastic, metals, or the like, and may be opaque,
translucent,
or transparent. The cartridge body 1010 can also include a transparent,
translucent, or opaque
cover surface such as a printed circuit board (PCB) 1014 or other surface
partially defining
a fluid path within the cartridge body 1010. The PCB 1014 and fluid paths are
discussed in
greater detail with reference to FIGs. 10E-10K. The cartridge body 1010 and/or
the cap 1050
can further include a cartridge identifier 1011. The cartridge identifier 1011
may include
human-readable and/or machine-readable information, such as text, a barcode, a
QR code,
or the like. The cartridge identifier 1011 can include any suitable
information associated
with the cartridge, such as information specifying a type of test, a target
agent, a sample type,
a cartridge serial number or other individual cartridge identifier, etc. In
addition to serving
as an identifier for a user of the type of test associated with the cartridge
1000, the cartridge
identifier 1011 may also be scanned by a user (e.g., using a user interface
device in
communication with a reader device) to communicate one or more test protocols
to the reader
device.
[0573] The cartridge body 1010 and/or the cap 1050 can include ergonomic
features
such as an indentation or the like to facilitate handling of the cartridge
1000. In the example
cartridge 1000 depicted, the cartridge body 1010 further includes an alignment
groove 1012
located to align with an alignment groove 1052 of the cap 1050. The alignment
groove 1052
of the cap 1050 terminates at a stop 1054 configured to engage a protrusion
within a
corresponding reader device (e.g., the reader device 910 of FIGs. 9A and 9B)
to define a
fully inserted position of the cartridge 1000 within the reader device. The
cap 1050 can
further include a sample receiving area cap 1056 sized and shaped to sealingly
close an
opening in the cap 1050 for receiving a swab or other sample carrying holding
a sample to
be analyzed.
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[0574] FIGs. 10C and 10D depict the cap 1050 component of the cartridge 1000
of
FIGs. 10A and 10B. The cap 1050 comprises an elongate body which is at least
partially
hollow to receive a sample carrier such as a swab or the like. An opening in
the cap 1050
for receiving the sample carrier may be sealed by the sample receiving area
cap 1056, which
may include one or more 0-rings or other resilient structures to sealingly
block the opening
in the cap 1050.
[0575] The cap 1050 further includes a collar 1058 protruding from the cap
1050.
The collar 1058 is sized and shaped to facilitate coupling with the cartridge
body 1010. The
collar 1058 generally comprises a hollow cylindrical body defining a plunger
receiving well
1060 through which the fluid sample may pass from the cap 1050 into the
cartridge body
1010. The collar 1058 includes interlocking fins 1062 extending radially
outward from an
exterior surface of the collar 1058, and receiving channels 1064 within an
interior surface of
the collar 1058. Each receiving channel 1064 terminates in a widened section
1065 such that
the receiving channels 1064 are configured to receive and retain one or more
snap-fit
connectors of the cartridge body 1010, as will be described with reference to
FIGs. 11A-11D.
[0576] The cap 1050 may further include one or more liquid constituents
therein to
be mixed with a received sample. For example, liquid constituents may include
one or more
amplification reagents, buffer solutions, water, mucin mitigating agents, or
other desired
liquid constituents for the testing process. The particular selection and
chemistry of these
liquids can be tailored to a particular target or targets for which the
cartridge 1000 is designed
to test. In some embodiments, the liquid constituents may be contained within
a blister pack
within the cap 1050. The blister pack may be punctured by, for example,
insertion of a
sample carrier, coupling of the cap 1050 to the cartridge body 1010, etc.
[0577] FIGs. 10E-10K depict the cartridge body 1010 component of the cartridge
1000 of FIGs. 10A and 10B. FIGs. 10E-10G are exterior views of the cartridge
body 1010.
FIGs. 10H-10.1 depict the cartridge body 1010 with partial translucency to
illustrate fluid
paths integrally formed therein. FIG. 10K is an enlarged view depicting the
PCB 1014 of
the cartridge body 1010. Referring to FIGs. 10E-10G, the cartridge body 1010
includes a
base 1016 and a hollow plunger 1018 rotatably coupled within a receiving well
1026 of the
base such that the plunger 1018 can rotate about its longitudinal axis while
being retained
within the receiving well 1026.
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[0578] The plunger 1018 comprises a generally cylindrical body sized and
shaped to
fit within the plunger receiving well 1060 of the cap 1050 (FIGs. 10C and
10D). A sealing
portion 1020 of the plunger 1018 is disposed at a distal end of the plunger
1.018 and may
include one or more resilient structures (e.g., one or more 0-rings,
integrally formed
elastomeric structures, etc.) having an appropriate diameter to sealingly
engage with the
interior walls of the plunger receiving well 1060 of the cap 1050. A
sacrificial seal 1024
such as a layer of a metallic foil or other thin material may be provided to
prevent exposure
of the interior of the cartridge body 1010 to the atmosphere prior to use. The
plunger 1018
additionally includes one or more snap-fit clips 1022 extending along the
exterior of the
plunger 1018 parallel to the longitudinal axis of the plunger. The snap-fit
clips 1022 are
sized and shaped to engage within and be retained by the receiving channels
1064 of the
plunger receiving well 1060 of the cap 1050. A plunger baseplate 1019 is
rotationally fixed
to the plunger 1018 (e.g., may be integrally formed with the plunger 1018).
The diameter of
the plunger baseplate 1019 may be substantially equal to or slightly larger
than the outer
diameter of the collar 1058 of the cap 1050.
[0579] In some embodiments, one or more liquid constituents may be included
within the plunger 1018, instead of or in addition to liquid constituents
included within the
cap 1050. For example, the sacrificial seal 1024 may contain the liquid
constituents within
the plunger 1018 and/or the liquid constituents may be contained within a
blister pack within
the plunger 1018. Liquid constituents contained within the plunger may include
one or more
amplification reagents, buffer solutions, water, mucin mitigating agents, or
other desired
liquid constituents for the testing process. The particular selection and
chemistry of these
liquids can be tailored to a particular target or targets for which the
cartridge 1000 is designed
to test. The blister pack may be punctured by, for example, insertion of a
sample carrier,
coupling of the cap 1050 to the cartridge body 1010, etc.
[0580] The receiving well 1026 is coaxial with the plunger 1018 and has a
generally
cylindrical profile with a diameter substantially equal to or slightly larger
than the plunger
baseplate 1019 and/or the collar 1058 of the cap 1050. The receiving well 1026
further
includes cutouts 1028 sized to receive the interlocking fins 1062 of the cap
1050. Stops 1030
within the cutouts 1028 are disposed within the cutouts 1028 to block
longitudinal motion of
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the interlocking fins 1062 in certain rotational positions, as will be
described in greater detail
with reference to FIGs. 11A-11D.
[0581] FIGs. 10H-10J depict additional views of the cartridge body 1010 in
which
the base 1016 is illustrated with transparency to show the fluid paths
contained therein. The
base 101.6 may comprise any suitable liquid-impermeable material, such as
plastic or metal.
The base 1016 may be formed by one or more processes such as injection
molding, die
casting, milling, or the like, such that the depicted fluid paths can be
integrally formed
therein.
[0582] The base 1016 of FIGs. 10H-10J includes eight substantially identical
fluid
paths, each fluid path including a test well 1040. Various embodiments may
include fewer
than eight or more than eight fluid paths and test wells 1040 without
departing from the scope
of the present disclosure. For example, a base 1016 may include 1, 2, 3, 4, 5,
6, 7, 9, 10, 11,
12, or more fluid paths. Multiple identical or similar fluid paths within the
base may
accommodate simultaneous testing for a plurality of different targets and/or a
plurality of
simultaneous tests for the same target (e.g., to improve reliability of
results).
[0583] Each fluid path includes an inlet channel 1042, a lateral channel 1044,
a test
well 1040, and an outlet channel 1046. Each inlet channel 1042 extends
vertically through
the base 1016 to fluidically connect a first end adjacent to the plunger
baseplate 1019 to an
opposite end adjacent to the PCB 1014. Each lateral channel 1044 fluidically
connects an
inlet channel 1042 to the corresponding test well 1040. Each outlet channel
1046 extends
vertically from a test well 1040 to fluidically connect the test well 1040 to
the bottom of the
plunger baseplate 1019. In the cartridge body 1010 of FIGs. 10H-10J, the PCB
1014 forms
a boundary partially defining each lateral channel 1044 and each test well
1040. In this
example embodiment, the PCB 1014 may be oriented with the electrodes 1036,
1038 on the
side adjacent to the cartridge body 1010 such that the electrodes 1036, 1038
are in contact
with the interior of the test wells 1040.
[0584] As shown in FIG. 10J, each inlet channel 1042 is disposed radially
outward
from the longitudinal axis of the plunger baseplate 1019 at substantially the
same distance as
an array of sample inlets 1041 of the plunger baseplate 1019. Similarly, each
outlet channel
1046 is disposed radially outward from the longitudinal axis of the plunger
baseplate 1019
at substantially the same distance as the outer ends of an array of J-shaped
sample outlets
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1048 of the plunger baseplate 1019. The sample inlets 1041 and the inner ends
of the
shaped sample outlets 1048 are fluidically connected through the plunger
baseplate 1019 to
one or more interior spaces within the plunger 1018. Accordingly, when the
plunger
baseplate 1019 is rotated to an engaged position, as will be described with
reference to FIGs.
11B and 11C, the sample inlets 1041 align with the inlet channels 1042, and
the sample
outlets 1048 align with the outlet channels 1046, such that a fluid sample
within the plunger
1018 can flow into and fill the fluid paths within the base 1016 of the
cartridge body 1010.
[0585] FIG. 10K illustrates components of the PCB 1014, which may be disposed
along a surface of the cartridge body 1010 opposite the receiving well 1026 as
shown in
FIGs. 10E-10K. In some embodiments, the PCB 1014 may perform heating and/or
electrode
interface functions, and may further serve as a boundary for one or more fluid
paths within
the cartridge body 1010. Although the example PCB 1014 depicted herein
includes heating
and electrode interface functionality, these functions may equally be
performed by two or
more discrete elements in the cartridge body 1010. In some embodiments,
heating may be
achieved by heating elements located within a corresponding reader device
instead of or in
addition to heating elements disposed on or in the cartridge 1000.
[0586] The PCB 1014 comprises a generally planar surface having one or more
traces
disposed thereon in one or more layers. For example, the PCB 1014 may include
one or
more flex circuits, rigid printed circuit boards, or any other suitable
circuitry including one
or more current paths disposed on a generally planar substrate. One or more
heating traces
1032 electrically connect test well heating elements 1033 to heating current
pads 1034. The
heating current pads 1034 may come into contact with contacts of a current
source of a reader
device when the cartridge 1000 is inserted into the reader device, such that a
current may be
provided to the test well heating elements 1033 to heat fluid samples in one
or more test
wells of the cartridge body 1010.
[0587] The PCB 1014 further comprises a pair of electrodes 1036, 1038 (e.g.,
an
excitation electrode and a sensor electrode) corresponding to each test well.
In some
embodiments, the electrodes 1036, 1038 may be in direct contact with the fluid
sample in
each test well if the PCB 1014 serves as a boundary for the test wells. Each
electrode 1036,
1038 is electrically connected to an electrode interface pad 1035 by electrode
traces 1037,
1039 of the PCB 1014.
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[0588] In various embodiments, the PCB 1014 may include one or more layers.
For
example, in some embodiments the PCB is a flex circuit comprising an electrode
layer and a
heating layer separated from the electrode layer. The electrode layer may
include the
electrodes 1036, 1038 as well as the electrode traces 1037, 1039 and/or the
electrode interface
pads 1035. The heating layer may include the heating elements 1033, heating
traces 1032,
and/or heating current pads 1034. In some aspects, the electrode layer and the
heating layer
may be disposed on opposite sides of a common substrate, or may be provided on
separate
substrates. Preferably, the PCB 1014 may be disposed such that the electrode
layer including
the electrodes 1036, 1038 is adjacent to the cartridge body 1010 and the
electrodes 1036,
1038 are fluidically connected to the test wells 1040.
[0589] FIGs. 11A-11D illustrate mechanical fluid transfer aspects of the
cartridges
920, 1000 described herein. Similar to the fluid transfer aspects described
with reference to
FIGs. 3A-3E, the cartridge body 1010 and cap 1050 are configured to create air
pressure
when coupled together, such that the air pressure propels a fluid sample
through the fluid
paths of the cartridge body 1010. The cap 1050 is illustrated with
translucency in FIGs. 11A-
11D, and the cartridge body 1010 is illustrated with translucency in FIGs. 11C
and 11D, to
reveal interior features of the cap 1050 and cartridge body 1010. The
cartridge body 1010 is
depicted with the PCB 1014 removed in FIG. 11C.
[0590] With reference to FIG. 11A, a fluid sample may be received within the
cap
1050. For example, a swab or other sample carrier may be inserted into an
opening of the
cap 1050 opposite the cartridge body 1010, and the opening may then be sealed
by the sample
receiving area cap 1056 to contain the sample within the cap (e.g., within the
plunger
receiving well 1060 or other internal space within the cap 1050. When the
fluid sample has
been sealed within the cap 1050, the process of FIGs. 11A-11D may be used to
mechanically
couple the cartridge body 1010 to the cap 1050 and move the fluid sample into
the cartridge
body 1010.
[0591] As shown in FIG. 11A, the mechanical coupling of the cartridge body
1010
and the cap 1050 begins by inserting the plunger 1018 of the cartridge body
1010 into the
plunger receiving well 1060 of the cap 1050. The sealing portion 1020 of the
plunger 1018
can sealingly engage with the interior of the plunger receiving well 1060 to
trap and begin
compressing a volume of air within the plunger receiving well 1060. As the
plunger 1018
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slides into the plunger receiving well 1060, the snap-fit clips 1022 slide
within the receiving
channels 1064 until they pass into the widened sections 1065 of the receiving
channels 1064,
where they are longitudinally retained. Retention of the snap-fit clips 1022
within the
receiving channels 1064 prevents removal of the cap 1050 from the cartridge
body 1010, and
further locks the cap 1050 rotationally with the plunger 1018, thereby
allowing a user to
rotate the plunger 1018 and plunger baseplate 1019 by rotating the cap 1050,
which may be
relatively large and easy to manipulate manually. The cap 1050 and cartridge
body 101.0
may slide together until the collar 1058 of the cap 1050 is partially within
the receiving well
1026 of the cartridge body 1010 and the interlocking fins 1062 of the collar
1058 contact the
stops 1030 (FIG. 10F) within the cutouts 1028.
[0592] As shown in FIG. 11B, the cap 1050, plunger 1018, and plunger baseplate
1019 may then be rotated about the longitudinal axis. Because the snap-fit
clips 1022
rotationally fix the plunger 1018 to the cap 1050, rotation of the plunger
1018 and plunger
baseplate 101.9 may be achieved by rotating the cap 1050. The cap 1050 may
rotate until the
interlocking fins 1062 are blocked by a lateral side of the cutouts 1028 of
the receiving well
1026. In the example cartridge 1000, the cutouts 1028 and interlocking fins
1062 are sized
to allow a total rotation of approximately 22.5 while the interlocking fins
1062 are within
the cutouts 1028. However, other example cartridges may function with a
different range of
rotational motion, such as between approximately 5 and approximately 90 ,
between
approximately 10 and approximately 45 , between approximately 15 and
approximately
30', between approximately 20 and approximately 25', or any angle or subrange
of angles
therebetween. In some embodiments in which liquid constituents are contained
in a blister
pack within the cap 1050 and/or the plunger 101.8, the rotation of components
in FIG. 11B
may cause the blister pack to be punctured so as to release the liquid
constituents to mix with
the sample.
[0593] With reference to FIG. 11C, the cap 1050 may be moved downward along
the
longitudinal axis, such that the collar 1058 moves further into the receiving
well 1026.
Because the stops 1030 only extend along a portion of the cutouts 1028, the
rotational motion
described with reference to FIG. 11B moves the interlocking fins 1062 clear of
the stops
1030 such that the interlocking fins 1062 can move to an interior portion 1029
of the cutouts
1028. As shown in FIG. 11C, the rotated position of the plunger baseplate 1019
substantially
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aligns the inlet channels 1042 and the outlet channels 1046 with the sample
inlets 1041 and
the sample outlets 1048, respectively. When the cap 1050 is pressed further
onto the
cartridge body 1010 to the position of FIG. 11C, the sample carrier and/or one
or more
internal structures within the cap 1050 may mechanically contact and rupture a
seal on or
within the plunger 1018 (e.g., the sacrificial seal 1024 of FIG. 10F), thereby
allowing the
trapped air compressed by the plunger 1018 to flow into the interior of the
plunger and propel
the fluid sample through the plunger baseplate 1019 and into the fluid paths
of the cartridge
body 1010. In some embodiments in which liquid constituents are contained in a
blister pack
within the cap 1050 and/or the plunger 1018, the longitudinal motion of
components in FIG.
1 IC may cause the blister pack to be punctured so as to release the liquid
constituents to mix
with the sample.
[0594] The flow of the fluid sample through the fluid paths of the cartridge
body
1010 will now be described with continued reference to FIG. 11C. FIG. 11C
illustrates the
flow of a portion of a fluid sample through a single example fluid path 1105
within the
cartridge body 1010 with encircled numbers shown as labels for certain points
along the fluid
path. The encircled numbers are discussed below as example steps of a
progression of a fluid
sample as it travels through the flow path 1105. within the cartridge body
1010, with each
step including a directional arrow showing the direction of fluid travel at
that step.
[0595] At step (1), as the compressed air is allowed to flow into the plunger
1018,
the fluid sample is forced through the sample inlet 1041 into the inlet
channel 1042. The
fluid sample travels along the inlet channel 1042 toward the lateral channel
1044.
[0596] At step (2), the fluid sample reaches the PCB 1014 boundary of the
fluid path,
and begins traveling parallel to the PCB 1014 within the lateral channel 1044.
At step (3),
the fluid sample continues through the curved lateral channel 1044 toward the
test well 1040.
[0597] At step (4), the fluid sample enters the test well 1040. The test well
1040 may
contain one or more reagents. Agitation caused by the turbulent flow of the
fluid sample
within the relatively larger space of the test well 1040 causes the reagent
and the sample to
be mixed. In some embodiments, the reagent and the fluid sample are mixed into
a
homogeneous solution in which the reagent is evenly distributed throughout the
fluid sample.
The depth, width, shape, and/or cross-sectional profile of the test well 1040
may be selected
to facilitate mixing of the reagent and the fluid sample.
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[0598] At step (5), any excess fluid sample is pushed from the test well 1040
into the
outlet channel 1046 and enters the outer end of the J-shaped sample outlet
1048. As the
excess fluid sample reaches the inner end the sample outlet 1048, it passes
through a
corresponding opening in the plunger baseplate 1019 at step (6) and is vented
into the plunger
1018. In some embodiments, the interior volume of the plunger 1018 and/or the
cap 1050 is
separated from the interior volume that is fluidically connected to the sample
inlet 1041, so
as to create a directional flow of fluid sample along the fluid path 1105.
[0599] After the cap 1050 is pressed fully onto the cartridge body 1010 as
shown in
FIG. 11C, initiating the flow of the fluid sample through the fluid path
within the cartridge
body, the cartridge 1000 may reach a pressure equilibrium as the compressed
air forces the
fluid sample into the fluid path 1105, the fluid path 1105 is filled with the
fluid sample, and
a portion of the sample is vented back into the plunger 1018 and/or the cap
1050. The
pressure equilibrium may be reached relatively quickly, for example, within 10
seconds, 5
seconds, 2 seconds, 1 second, or less.
[0600] Referring now to FIG. 11D, when the fluid path 1105 is filled, the cap
1050,
plunger 1018, and plunger baseplate 1019 may again be rotated relative to the
cartridge body
1010. in the example process of FIGs. 11A-11D, the above components are
rotated by the
same angular displacement, but in the opposite direction, relative to the
rotation of FIG. 11B.
Thus, as shown in FIG. 11D, the plunger baseplate 1019 rotates relative to the
fluid path
1105 such that the inlet channels 1042 and outlet channels 1046 are no longer
aligned with
the sample inlets 1041 and sample outlets 1048, thereby sealing the fluid path
1105 and
retaining the fluid sample within the test wells 1040 for testing. This final
rotation step
additionally causes the interlocking fins 1062 of the cap 1050 to be retained
under the stops
1030 within the interior portion 1029 of the receiving well cutouts 1028,
completing and
securing the mechanical coupling of the cartridge body 1010 and cap 1050.
Moreover, the
final rotation step substantially aligns the exterior profiles of the
cartridge body 1010 and the
cap 1050 such that the assembled cartridge 1000 can be inserted into a reader
device to
perform one or more tests on the fluid sample contained therein.
[0601] FIGs. 12A-12I illustrate a further embodiment of a cartridge 1200
configured
for detection of a target. As described herein, the target may be a viral
target, bacterial target,
antigen target, parasite target, microRNA target, or agricultural analyte.
Some embodiments
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of the cartridge 1.200 can be configured for testing a single target, while
some embodiments
of the cartridge can be configured for testing for multiple targets. The
cartridge 1200
includes a cartridge body 1202 and a swab assembly 1220 configured to be
mechanically
coupled to the cartridge body 1202 at a swab assembly insertion point 1208.
[0602] The cartridge body 1.202 includes a thin film testing assembly 1204 and
an
ergonomic frame 1206 configured to be grasped by a user. The thin film testing
assembly
1204 generally includes a plurality of test wells 1258, pinch valves 121.4 for
isolating fluid
within the test wells 1258, a gas permeable filter 1212 such as a membrane or
the like, and
an electrode interface 1210 for electrically connecting electrodes at the test
wells to circuitry
of a reader device. The cartridge further includes a fluidic piston 1218 and a
transition point
1216 for introducing a fluid sample from the swab assembly 1220 into the thin
film testing
assembly 1204. The features of the thin film testing assembly 1204 are
discussed in greater
detail with reference to FIGs. 12H and 121.
[0603] Referring now to FIGs. 12C-12G, the swab assembly 1220 includes a tube
1222, a slider 1224, and a cap 1234 configured to fit together to form a
substantially sealed
swab assembly 1220. The tube 1222 includes a tube channel 1226 sized and
shaped to
receive a shaft 1236 of the cap 1234. The tube channel 1226 may be sealed,
such as with a
foil seal or the like, to contain one or more liquid reagents, buffers, etc.,
during shipping
and/or prior to use of the swab assembly 1220. The tube channel 1226 may have
an hourglass
profile, a dual lobe profile, or other shape configured to facilitate mixing
of fluids therein.
In some embodiments, the tube channel 1226 may further include interior
threading or other
protruding features further configured to facilitate mixing of fluids within
the tube channel
1226. The slider 1224 comprises a hollow structure configured to fit around an
engagement
end 1223 of the tube 1222. The tube 1222 further includes one or more snap-fit
clips 1232
configured to interlock with first and second snap-fit openings 1228 and 1230
of the slider
1224. As shown in FIG. 12A, the cartridge body 1202 includes an overhand that
keeps the
tube 1222 centered in a width of the cartridge body 1202.
[0604] FIGS. 12E and 12F illustrate the cap 1234. FIG. 12E is a perspective
view of
the cap. FIG. 12F is a cross-sectional view of the cap illustrating internal
components
thereof. The cap 1.234 comprises a hollow shall 1236 surrounding a cap channel
1238, and
a hollow upper section 1244 surrounding a metered volume 1240. The upper
section 1244
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may further include a sealing portion 1242 comprising a resilient material
(e.g., rubber, a
resilient plastic, or other elastomeric material) sized and shaped to
sealingly engage the
interior of the slider 1224. A foil seal 1246 may seal one or more liquid,
dried and/or
lyophilized reagents within the cap 1234. A vent 1248 may be fluidically
connected to the
metered volume 1240 to allow any gas trapped within the cap 1234 to be vented.
The shaft
1236 terminates at a cap inlet 1250 fluidically connected to the cap channel
1238, which may
include one or more sections of a filter 1252 configured to allow fluid flow
into the cap
channel 1238. In some embodiments, an additional seal may be provided over the
cap inlet
1250 to seal any liquid, dried and/or lyophilized reagents within the cap 1234
prior to use.
[0605] Referring jointly to FIGs. 12C-12G, and particularly with reference to
FIG.
12G, an example process of introducing a sample to the swab assembly 1220 will
now be
described. Prior to introduction of the sample, the cap 1234 is separate from
the tube 1222
and the slider 1224. The tube 1222 includes a liquid comprising one or more
liquid reagents,
buffers, or the like, sealed within the tube 1222 by a seal at the engagement
end 1223 of the
tube 1222. The cap 1234 includes one or more additional liquid reagents,
buffers, or the like,
sealed within the cap 1234 by the foil seal 1246. In the initial
configuration, the snap-fit
clips 1232 are engaged in first snap-fit openings 1228.
[0606] A sample (e.g., a nasal swab or other swab-collected sample) may be
received
on a swab. Prior to inserting the swab into the swab assembly 1220, the slider
1224 is moved
along a first direction 1254 relative to the tube 1222 such that the snap-fit
clips 1232 of the
tube 1222 engage with the second snap-fit openings 1230. This motion may cause
an internal
structure 1231 of the slider 1224 to break the foil seal at the opening of the
tube to expose
the liquid reagents or buffers contained within the tube channel 1226.
[0607] When the tube channel 1226 is exposed, the swab may be introduced into
the
tube channel 1226 such that the sample on the swab mixes with the liquid
reagents within
the tube channel 1226. The interior profile and/or other mixing features of
the tube channel
1226 may facilitate mixing of the sample with the liquid reagents to form a
test fluid. In
some embodiments, the swab may be broken off from a handle such that the
portion of the
swab containing the sample remains within the tube channel 1226.
[0608] After the sample has been introduced to the tube channel 1226 to form
the test
fluid, the cap 1234 may be mechanically coupled to the tube 1222 and slider
1224 to complete
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the swab assembly 1220. If a seal is provided around the cap inlet 1250, the
seal may be
removed. The shaft 1236 of the cap is inserted through the slider 1224, and
the cap 1234 is
pushed into the slider 1224 and the tube channel 1222 such that the sealing
portion 1242
sealingly engages with the interior of the slider 1242. As the cap 1234
continues to move
along the direction 1254, air and fluid are compressed within the tube channel
1222 to drive
the mixed test fluid through the cap inlet 1250 and the cap channel 1238 into
the metered
volume 1240. Any gas, such as air, present within the metered volume 1240 may
be vented
externally through the vent 1248. The filter 1252 at the cap inlet 1250
prevents solids, such
as solids within the swab sample or pieces of the swab itself, from entering
the cap 1234.
The location of the cap inlet 1250 at an end of the tube channel 1226 distal
from the metered
volume 1240 may advantageously cause the inlet 1250 to receive an optimal
portion of the
test fluid in the event that the test fluid has not quite achieved a
homogeneous mixture. When
the cap 1234 has been sealingly inserted into the tube 1222 and slider 1224,
the swab
assembly 1220 is fully assembled, and any liquid therein is retained within
the swab
assembly 1220 by the foil seal 1246 of the cap 1234. The swab assembly 1220
may then be
placed into the swab assembly insertion point 1208 of the cartridge 1200 to
introduce the test
fluid to the thin film testing assembly 1204.
[0609] Referring now to FIGs. 12B, 12H, and 121, the thin film testing
assembly
1204 includes a substrate 1207 surrounding a plurality of test wells 1258. One
boundary of
the test wells 1258 is formed by a cover film 1205 including a plurality of
pinch valves 1214
which form a portion of a fluid flow path into the thin film testing assembly
1204. A pair of
electrodes 1260, which may be formed consistent with any of the electrodes
described
elsewhere herein, are provided within each test well 1258 and electrically
connected to
electrode connection pads 1211 of the electrode interface 1210 for connection
to a reader
device.
[0610] When the swab assembly 1220 is inserted into the swab assembly
insertion
point 1208 of the cartridge 1200, the fluid within the metered volume 1240 of
the swab
assembly 1220 flows through the transition point 1216 and along a fluid path
within the thin
film testing assembly 1204 to fill the test wells 1258. Any gas such as air
within the thin
film testing assembly 1204 may be displaced from the test wells 1258 and
vented at a vent
1262 and/or at the gas permeable filter 1212.
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[0611] The cartridge 1200 may then be inserted into a reader device sized and
shaped
to receive the cartridge 1200. As the cartridge 1200 is inserted into the
reader device (in a
direction of the arrow in FIG. 12A), electrical contacts within the reader
device come into
contact with the electrode connection pads 1211 of the cartridge 1200. In
addition, the
opening within the reader device for receiving the cartridge 1200 has a width
selected such
that an interior surface of the reader device compresses and/or crushes the
pinch valves 1214,
preventing fluid flow therethrough after the cartridge 1200 has been inserted
into the reader
device. In some embodiments, the pinch valves 1214 may comprise a thermoformed
plastic
or other material selected such that the pinch valves 1214 can be compressed
and closed off
without breaking and allowing the test fluid to escape. When the pinch valves
1214 are
compressed and/or crushed, the test fluid within each test well 1258 is
fluidically isolated
within the test well 1258 for testing. Heating and testing of the test fluids
in the test wells
1258 may then proceed as described above with reference to the cartridges 200,
1000. In
some embodiments, the test wells 1258 may be pre-loaded with one or more
primers (e.g.,
spot-dried, lyophilized, powdered, or other non-liquid primers) or other
reagents
corresponding to the tests to be performed and/or target agents to be detected
in each test
well 1258. Some or all of the test wells 1258 may include the same or
different primers as
the primers present in the other test wells 1258, depending on the individual
test to be
performed and/or target agents to be detected in each test well 1258.
[0612] FIGs. 13A-13E depict an example of another type or format of cartridge
1300
configured to detect a target, such as a nucleic acid e.g., a desired DNA or
RNA sequence,
which can be used in conjunction with one or more of the handheld systems
disclosed herein.
In some embodiments, the target may be a viral target, bacterial target,
antigen target, parasite
target, microRNA target, or agricultural analyte. Preferably, such targets are
selected viral,
bacterial, parasite, microRNA, or agricultural DNA or RNA sequences e.g.,
sequences
complementary to selected primers designed to identify the presence or absence
and/or
amount of such targets. Some embodiments of the cartridge 1300 can be
configured for
testing for the presence or absence and/or amount of a single target, while
some embodiments
of the cartridge 1300 can be configured for testing for multiple targets,
optionally
simultaneously or within a short time after the first identified result. In
some embodiments,
the cartridge 1300 may be configured to test for enzymes (for example, in the
evaluating
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and/or analyzing for enzyme replacement therapy). In some embodiments, the
cartridge
1300 may be configured to test for environmental contaminants such as
pesticide residues
(e.g., glyphosate, and so forth), heavy metals, benzene residues, and so
forth. In some
embodiments, the cartridge 1300 may be configured to test for or identify
pathogens,
genomic materials, proteins, and/or other small molecules or biomarkers. In
some
embodiments, the cartridge 1300 may be configured to test for and/or identify
elevated
prostate-specific antigen (PSA) levels, elevated cells counts, low cell
counts, tumor cells,
and so forth, for use in oncology applications. In some embodiments, the
cartridge 1300 may
be configured to identify and/or test for microRNA or used to test for
infections, diseases,
and so forth often of concern with respect to food safety and/or plasma and/or
blood
screenings. In some embodiments, the cartridge 1300 may be further configured
to identify
and/or test for rare infectious diseases, tick and/or mosquito borne (or other
insect, plant,
and/or animal vector borne) diseases. In some embodiments, the cartridge 1300
may be
configured to test for and/or identify norovirus and/or rotavirus, for example
in water quality
applications. In some embodiments, the cartridge 1300 is configured to test
for anything any
of the other cartridges described herein test for, and vice versa. The
cartridge 1300 includes,
among other components, a cartridge body 1302, a cover 1314, electrodes 1304,
and a cap
1310. These components will be described in further detail below.
[0613] Referring now to FIGs. 13A-13E, the cartridge body 1302 may be
thermoformed from a polyethylene or similar plastic material. The cartridge
body 1302 may
house various components and/or features of the cartridge 1300. For example,
the cartridge
body 1302 may house at least a portion of the electrodes 1304, a swab
receptacle 1342, a
sample mixing and microfiltration region 1.330 (described further below), a
reagent stored in
a reagent blister 1340, and an integrated reagent blister rupture feature
1344, a distribution
tree 1328 for a sample/reagent mixture from the sample mixing and
microfiltration region
1330, an exhaust port 1326 to vent gases, a degassing gas-permeable membrane
1320, and a
plurality of reaction wells 1322 configured to allow the electrodes 1304 to
generate signals
based on the sample/reagent mixture. The cartridge body 1.302 also includes a
thumb detent
configured to be grasped by a user to facilitate removal of the cartridge 1300
from the
analyzer, described in further detail below. The cartridge body 1302 also,
optionally includes
an isolation cap 1310 or a locking isolation cap 1310 configured to isolate,
close, or protect
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the swab receptacle 1342 from external variables. The cover 1314 of the
cartridge body 1302
may be thermoformed from a plastic or similar material and includes an exhaust
port crush
valve 1306 and well isolations crush valves 1312.
[0614] The well isolations crush valves 1312 may isolate fluid within the
plurality of
reaction wells 1322. In some embodiments, the reaction wells 1322 may function
similarly
to the test wells 1258 described above. The electrodes 1304 may electrically
connect
electrodes at the reaction wells 1322 to circuitry of a reader device
described further below.
The electrodes 1304 may function similarly to the electrode interface 1210
described above.
[0615] In some embodiments, the swab receptacle 1342 includes a tapering,
tubular
portion 1348, a scraper portion 1350, dispensing portion 1352, and the
isolation cap 1310 or
the locking isolation cap 1310. The isolation cap 1310 or the locking
isolation cap 1310 and
the swab receptacle 1342 are configured to fit together to form a sealed or
substantially sealed
swab assembly. The tapering, tubular portion 1348 includes a tapering tube
channel sized
and shaped to receive a swab including mucus or another sample and to be
sealed or
substantially sealed by the isolation cap 1310 or locking isolation cap 1310.
The reagent
blister 1340 may contain one or more reagents (for example, a liquid reagent,
a buffer, etc.)
during shipping and handling before the cartridge 1300 is inserted into the
corresponding
analyzer. In some embodiments, the reagent blister 1340 includes only reagents
in a liquid
form. In some embodiments, the reagent blister may comprise a sealed
compartment, for
example sealed with a foil seal or the like, similar to the sealed channel
1226 described above.
The sample mixing and macrofiltration region 1330 may be configured and
operate to
facilitate mixing of fluids and so forth therein (for example, the sample with
the reagent). In
some embodiments, the tapering, tubular portion 1348 may further include the
scraper 1350
configured to facilitate acquisition of the sample from the swab inserted into
the swab
receptacle 1342. Further details are provided below. The cartridge body 1302
includes snap-
fit clips 1346 that may lock and/or engage with snap-fit openings to interlock
and hold the
cartridge body 1302 together, similar to the snap-fit clips 1232 and snap-fit
openings 1228
described above.
[0616] The cartridge 1300 may be a disposable cartridge that is fully
integrated,
enables detection of one or more pathogens, and includes no moving parts,
improving
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reliability of the cartridge 1300. In many instances, the cartridge 1300
operates similarly to
the cartridge 1200 described above.
[0617] The cartridge 1.300 may be used in conjunction with an analyzer,
similar to
the analyzer or reader device (for example, reader device 110, 600, or 910)
described above
with reference to the cartridges described above (for example, cartridge 120,
200, 1000, and
1200). In some embodiments, the analyzer (also referred to herein as the
"reader device")
may be handheld and battery operated and enable wireless communication with an
application operating, for example, on a user's mobile phone or other mobile
device. In some
embodiments, the application may provide the operator or patient with a view
of the results
from the analysis of the cartridge as well as an option for the patient to
input particular
symptoms being suffered. In some embodiments, the application may communicate
with a
cloud storage system (or similar storage) to store data from the application
that is received
from or via the analyzer. In some embodiments, the analyzer, application, and
cloud storage
may enable secure communications and may aggregate information from various
cartridge
samples to enable treatment decisions (for example, identify that a sample
being tested with
a cartridge indicates a particular sickness, etc., based on a comparison of
the analysis results
from the analyzer with results from a historical database of analyses and
corresponding
sickness, etc., determinations. For example, if the cartridge analyzed by the
analyzer
indicates influenza, as compared to similar results in the cloud-based
historical database, the
application may identify appropriate treatments or therapies for influenza and
present them
to the operator of the application (e.g., to the patient, physician, or health
care practitioner,
etc.). In some embodiments, the data stored in the cloud may be analyzed in
real time to
identify outbreaks of diseases, and so forth. Additionally, such information
may be used to
update manufacturers of vaccines and medications in response to the outbreaks,
etc., to
ensure sufficient stockpiles of vaccines and/or medications are available.
[0618] FIGs. 14A and 14B depict an example of the other handheld analyzer
system
1400 disclosed herein. The analyzer 1400 includes the features described above
of other
analyzers, including a slot for insertion of the cartridge, for example the
cartridge 1300. In
some embodiments, the analyzer 1400 comprises a printed circuit board (PCB)
1402 on
which various electrical components are disposed and electrically connected.
The PCB 1402
includes a communication or charging port, such as a USB (or similar) port
1404. The PCB
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1402 further includes a microprocessor 1406 and a digital signal processor
(DSP) 1408. The
PCB 1402 further comprises an analog sub-section 1410 and cartridge mating
connectors
1412 to electronically couple to the cartridge 1300. The PCB 1402 further
comprises a
cryptographic processor 1414, a battery controller 1416, and storage 1418. The
PCB 1402
may also include one or more mounting holes or devices 1.420.
[0619] Operation of the cartridge 1300 with the analyzer 1400 is now
described.
[0620] Before operating the cartridge and the analyzer 1400, the application
may be
used to select a particular cartridge 1300 that will be used with the analyzer
1400. In some
embodiments, the selection may comprise indicating one or more parameters
associated with
the particular cartridge 1.300 to the analyzer 1400. A swab may be used to
collect a fluid
sample (for example, a nasal fluid or sputum sample). The swab with the fluid
sample from
the patient may be pressed into the swab receptacle 1342 until the swab stops
moving into
the swab receptacle 1342. As described above, the swab receptacle 1342 tapers
down in
diameter to a shape/size that compresses the bristles or other material of the
swab against the
walls of the swab receptacle 1342. In some embodiments, the swab receptacle
1342
comprises one or more walls (or other surfaces) molded with a specifically
selected surface
finish. The surface finish enables wetting the fluid sample to the walls. As
the swab
continues to its fully compressed position as it is pushed into the swab
receptacle 1342, the
fluid that has been wetted to the walls is forced further in front of the swab
because of the
decreasing cross-section profile of the swab receptacle 1342. As the swab is
removed, the
fluid that is forced ahead of the swab is drawn back with the swab being
removed, trailing
behind the swab. At the point in which the bristles or material of the swab
have separated
far enough from the walls of the swab receptacle 1342, a surface tension of
the fluid sample
that is wetted to the walls is sufficient to retain at least a portion of the
fluid sample in the
swab receptacle 1342 (for example, a reservoir portion of the swab receptacle
1342). Thus,
the fluid sample to be analyzed by the analyzer is removed from the fluid
sample initially
collected on the swab and remains in place as the cap 1310 is closed, sealing
or substantially
sealing the swab receptacle 1.342 and the cartridge 1300.
[0621] In some embodiments, a user may insert a swab 1360 into the swab
receptacle
1342 of the cartridge 1300 as shown in, for example, FIG. 13G. Once inserted
into the swab
receptacle 1342, the swab 1360 may be broken or cut, for example, at 1, 2, 3,
4, 5, 6, 7, 8, 9,
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or 10rnm or within a range defined by any two of the aforementioned sizes
below a swab
stopper 1362 or the cartridge interface, such that two separate pieces are
generated one being
a portion of the swab 1.360 including mucus or another type of sample (for
example, a first
portion), which remains inside the swab receptacle 1342 and a portion of the
swab 1360
without the mucus or another type of sample (for example, a second portion),
which is
separated from the first portion and discarded. FIG. 13H schematically
illustrates a location
1370 where swab 1360 can be broken or cut (for example, snapped) into two
separate pieces.
As shown in FIG. 131, the cap 1310 can be moved to close (for example, seal)
the swab
receptacle 1342 of the cartridge 1300, leaving the first portion of the swab
(for example, a
portion with mucus or another type of sample) positioned inside the swab
receptacle 1342.
After the swab receptacle 1342 of the cartridge 1300 is closed via the cap
1310, a user (for
example, a patient, a care provider, an operator of the analyzer 1400 and the
cartridge 1300)
can insert the sealed cartridge 1300 into the analyzer 1400 as shown in FIG.
13J to test the
collected sample.
[0622] In some embodiments, as shown in FIG. 13F, a swab 1360 can include a
stopper 1362. The stopper 1362 can be a radial protrusion from a shaft of the
swab 1360 that
can cover an opening of the swab receptacle 1342 when the swab 1360 is
inserted into the
swab receptacle 1342. As such, when the swab 1360 is inserted into the swab
receptacle
1342, the stopper 1.362 can prevent the swab 1360 from being inserted into the
swab
receptacle 1342 further, for example, than a predetermined distance.
[0623] The stopper 1362 can indicate where to break or cut the swab 1360 after
inserting the swab 1360 into the swab receptacle 1342. In some embodiments,
the swab 1360
has a perforated or marked section 1364, which indicates a position to break
or cut the swab
1360. When the stopper 1362 covers the opening of the swab receptacle 1342, a
user can
break or cut a shaft of the swab 1360, for example, proximal to or against the
opening of the
swab receptacle 1342 using the stopper 1362 as a lever or guide for the cut In
some examples,
the stopper 1362 can remain with, for example, a portion of the swab 1360 with
the bristles
or flock. In other examples, the stopper 1362 may break off from the portion
of the swab
1360 with the bristles or flock and be discarded.
[0624] In some embodiments, the location of the stopper 1362 can be such that
the
bristles or flock (or a portion of the swab 1360 having mucus or another type
of sample) of
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the swab 1360 are positioned near or adjacent to the scraper 1.350 when the
stopper 1362
stops the swab 1360 from entering further into the swab receptacle 1342.
Alternatively, the
location of the stopper 1362 can be such that the swab 1360 is in its fully
compressed or
substantially fully compressed position in the swab receptacle 1342 when the
stopper 1362
stops the swab 1360 from moving further into the swab receptacle 1342.
Alternatively, the
location of the stopper 1362 can be such that, for example, the bristles or
flock (or a portion
of the swab 1360 having mucus or another type of sample) affix swab are
positioned further
down into the swab receptacle 1342 past the scraper 1350. The stopper 1362 can
desirably
indicate to users how far the swab 1360 is preferably inserted into the swab
receptacle 1342
to allow the cartridge 1300 via the scraper 1350 to collect mucus or other
types of sample
from the swab 1360.
[0625] In some embodiments, the swab receptacle 1342 can include, for example,
a
retainer 1380 that can hold a swab once it is inserted into the swab
receptacle 1342. For
example, the retainer 1380 can include fingers 1382 that can function as a
clamp for the swab
1360. After the swab 1360 is inserted into the swab receptacle 1342, the swab
1360, for
example, pressed against the retainer 1380 such that the swab 1360 can be
positioned
between the fingers 1382 and held in place in the swab receptacle 1342. Once
the swab is
held in place in the swab receptacle 1342, a user (for example, a patient, a
care provider, an
operator of the analyzer 1400 and the cartridge 1300) can insert the cartridge
1300 into the
analyzer 1400 to test the sample from the swab. Other designs of the retainer
1380 suitable
to hold, for example, the shaft of the swab 1360 may be used in conjunction
with the swab
receptacle 1342. Having the retainer 1380 to hold the swab 1360 in place
inside the swab
receptacle 1342 can desirably eliminate the need to break the swab and closing
the cap 1310
to keep the swab in place inside the swab receptacle 1342 during testing.
[0626] The reagent blister 1340 and the integrated rupture feature 1344 of the
cartridge 1300 can be used to improve testing of collected samples. Prior to
receiving
samples (for example, mucus or other types of samples), the integrated rupture
feature 1344
may be pressed. When the integrated rupture feature 1344 is pressed, it may
rupture and
release solution or solutions stored inside (that is, inside the integrated
rupture feature 1344)
e.g., 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 microliters of solution or an
amount of solution
that is within a range defined by any two of the aforementioned volumes, which
then enters
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the swab receptacle also referred to as the sample port1342. Once sample is
collected via the
swab receptacle 1342, the cap 1310 can be closed to seal the swab receptacle
1342. Once the
cap 1310 is closed, the reagent blister 1340 may be pressed. The pressing of
the reagent
blister 1340 can desirably mix the solution (for example, a buffer) released
from the rupture
feature 1344 with solution (for example, reagent) previously stored in the
reagent blister
1340. Additionally, the pressing of the reagent blister 1340 can cause the
mixed solution to
flow towards, for example, the sample mixing and macrofiltration region 1330
of the
cartridge 1300. The mixing of the solutions from the integrated rupture
feature 1344 and the
reagent blister 1340 can provide improved recovery of sample from the swab
1360, improved
reaction rate between the collected sample and the reagent, and improved test
results (for
example, decreased rate of false-positive). In some embodiments, after the
solution from the
integrated rupture feature 1344 is provided to the swab receptacle 1342, the
swab 1360 is
inserted into the swab receptacle 1342 and is twisted or rotated a plurality
of times e.g., 1, 2,
3, 4, 5, 6, 7, 8, 9, or 10 times or an amount that is within a range defined
by any two of the
aforementioned times.
[0627] After the swab receptacle 1342 of the cartridge 1300 is closed via the
cap
1310, the patient or operator of the analyzer and cartridge may be prompted to
insert the now
sealed cartridge 1300 into the analyzer 1400. The process of inserting the
cartridge 1300
into the analyzer 1400 may actuate multiple features on the cartridge 1300
using static and/or
passive components. For example, the singular action of inserting the
cartridge 1300 into
the analyzer 1400, as performed by the patient or operator, can have its
functionality divided
into 3 major phases, with some overlap amongst them, as described below.
[0628] The first major phase involves inserting the cartridge 1300 into the
analyzer
1400. As the cartridge 1300 is first inserted into the analyzer 1400, a static
platform located
on the bottom mating surface of the cartridge/analyzer interface in the
analyzer 1400
depresses a living hinge via interference (for example, mechanical
interference). Thus, the
static platform translates a linear motion of the cartridge 1300 as it is
inserted into the
analyzer 1.400 into an angular displacement of a lever mechanically coupled to
and engaged
with the living hinge. The displacement of the lever/living hinge may result
in the rupture
of the reagent blister 1340. In some embodiments, the lever and/or living
hinge may
correspond to the integrated rupture feature 1344, introduced above. The lever
coupled to
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the living hinge may continue to rotate about the living hinge and flex along
a length of the
lever to depress the reagent blister 1340, thereby distributing the reagents
into the cartridge
1300 (for example, into the sample mixing and macrofiltration region 1330 of
the cartridge
1300). In some embodiments, forces associated with this distribution action
may cause the
sample in from the swab receptacle 1342 to mix with and be diluted by the
reagents from the
ruptured reagent blister 1340 in the sample mixing and macrofiltration region
1330. The
forces may further distribute the mixed sample and reagent to the reaction
wells 1322,
rehydrating dried and/or lyophilized reagents disposed in the reaction wells
1322. The flow
of the mixed sample and reagent may terminate at the exhaust gas-permeable
membrane
1324 located at the exit of each reaction well 1322, thereby ensuring uniform
filling in each
well. All of these processes may occur before the cartridge 1300 is inserted
into the analyzer
1400.
[0629] As a second of the three major phases, the reaction wells 1322 are
isolated.
As the mixed sample and reagent is distributed through the cartridge 1300 as
described
above, a path through with the mixed sample and reagent flows transitions from
the
distribution tree 1328 of the injection molded cartridge body 1302 (for
example, the portions
of the cartridge 1300 not including and below the thermoformed cover 1314)
into small
channels 1315 formed in the thermoformed cover 1314. In some embodiments, the
thermoformed cover 1314 is attached to the cartridge body 1302 via pressure-
sensitive
adhesive (PSA) above the plane of the injection molded cartridge body 1302. In
some
embodiments, the thermoformed cover 131.4 also serves as a housing for or
includes other
fluidic channel components for the cartridge body 1302. In some embodiments,
these other
fluidic channel components, for example, the well isolation crush valves 1312,
act as
isolation valves for each individual reaction well 1322. As the cartridge 1300
nears the end
of its insertion into the analyzer 1400, after each of the reaction wells 1322
has been filled
with the mixed sample and reagent, passive features located on the upper
mating surface of
the analyzer 1400 "crush" the isolation crush valves 1312 (which may comprise
thin
channels) down against the PSA bonding the thermoformed cover 1312 or a film
to the
injection molded cartridge body 1302. Because of the nature of the PSA, the
PSA conforms
to the deformed shape of the thin film channel in the cartridge body 1302,
serving to isolate
the reaction well 1322 fluidically from the channels that join the reaction
wells 1322 together
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fluidically. This isolation may prevent crosstalk and diffusion from reaction
well 1322 to
reaction well 1322. Additionally, this isolation may serve to isolate the
reagents and the
byproducts of the reaction from the analyzer 1400 and user.
[0630] While the cartridge 1302 is being inserted into the analyzer 1400, the
third
phase occurs. As described above, the well-isolation crush valves 1312 may
protrude from
an upper surface of the thermoformed cover 1314 on the cartridge body 1302 so
that they are
crushed when the cartridge 1302 is inserted into the analyzer 1400. This
orientation
combined with a dual sided heating design for the cartridge 1300 in the
analyzer 1400
necessitated a method of removing a heater surface out of the way of the
exhaust crush valve
1306. In order to passively accomplish this, an upper heater is mounted to an
integrated
crossbar and leaf spring of the analyzer 1400. In some embodiments, two cam
runners are
positioned in a cartridge receptacle of the analyzer 1400 such that when the
cartridge 1300
begins to be inserted, the cam runners push the upper heater up and out of the
way of the
crush valves (for example, the well isolation crush valves 1312 and/or the
exhaust port crush
valve 1306) disposed on the thermoformed cover 1312. The cam runners continue
to pass
along an upper edge of the cartridge body 1302 until the cam runners arrive at
a molded drop
in the upper edge of the cartridge body 1302. The molded drop in the upper
edge of the
cartridge body 1302 may be timed or positioned in such a way so as to allow
the upper heater
to press back down against the cartridge body 1302 while not interfering with
the
thermoformed valves on the thermoformed cover 1312. In some embodiments, the
cam
runners dropping into the molded drop of the cartridge body 1302 may also
double as a
retention feature for the cartridge 1300 in the analyzer 1400. As such, the
user may displace
a leaf spring that moves the upper heater up and out of the way of the crush
valves and
displacing the cam runners from the molded drop in order to extract the
cartridge 1300 after
the testing is completed in the analyzer 1400.
[0631] After these three major phases are completed, the cartridge 1300 is
fully
inserted into the analyzer 1400, the mixed sample and reagent are distributed
to the reaction
wells 1322 and isolated in each reaction well 1322. The upper heater in the
analyzer 1400
may uniformly contact the upper surface of the cartridge body 1302,
sandwiching the
cartridge body 1302 against a lower heater in the analyzer 1400. Upon full
insertion, the
cartridge 1300 may also establish an electrical connection to the analyzer
1400 via the
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flexible electrode layer 1304, thereby enabling the analyzer 1.400 to begin a
test of the mixed
sample and reagent in the reaction wells 1322.
[0632] In some embodiments, the method for using the cartridge 1300 with the
analyzer 1400 to detect a target involves first collecting a sample fluid from
a patient or user.
In some embodiments, the sample fluid may be collected using a swab or other
similar
sample collecting method or means. Once the sample fluid is collected, the
sample fluid is
introduced into the cartridge 1300. For example, when the sample fluid is
collected using
the swab, the swab is inserted into the cartridge 1300 via the swab receptacle
1342. The
optional cartridge cap 1310 may be closed and the cartridge 1300 may be
inserted into the
analyzer 1400. The insertion of the cartridge 1300 may cause a reagent blister
1340 to
rupture and mix the reagents contained therein with the sample fluid. In some
embodiments,
the mixture of the reagents and the sample fluid is conveyed to the reaction
wells 1322. The
reaction wells 1322 may each have a volume of approximately 25 microliters
(ilL). In some
embodiments, the reaction wells 1322 has a volume, size, and/or shape that is
based on the
overall volume of liquid which will fill the reaction wells 1322 as well as a
favorable
geometry above the sensing electrode. For example, in some embodiments the
reaction wells
1322 are circular, triangular, or rectangular, or any other polygonal shape.
In some
embodiments, when the reaction wells 1322 comprise a plurality of reaction
wells (for
example, eight (8) reaction wells), the electrodes 1304 (or corresponding
circuitry and/or
circuit board components/parameters) of the cartridge 1300 may enable the
analyzer 1400 to
simultaneously test each of the reaction wells 1322 (for example, each
representing a
different channel) at a plurality of frequencies (for example, three (3)
frequencies). In some
embodiments, each reaction well 1322 has a depth or height of approximately 1
millimeter
(mm). In some embodiments, the reaction wells 1322 may have a shape such that
the volume
of each reaction well 1322 is or is approximately 25 }IL when each reaction
well 1322 has a
depth or height of 1 mm. In some embodiments, the reaction wells 1322 contain
dried and/or
lyophilized enzymes and primers. The primers and enzymes may be spotted into
the reaction
wells 1322 as liquids and dried and/or lyophilized (for example, in two spots
per well). Thus,
the reaction wells 1322 may include dried and/or lyophilized primers and
enzymes while the
reagent blister 1340 may include the wet or liquid reagents. In some
embodiments, the
reagent blister 1340 and/or the reaction wells 1322 may contain liquid
reagents and/or
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primers and enzymes, respectively, configured to allow for the testing of one
or more of a
viral target, a bacterial target, an antigen target, a parasite target, a
microRNA target, an
agricultural analyte, an enzyme, an environmental contaminant, pathogens,
genomic
materials, proteins, PSA levels, elevated or reduced cell counts, specific
cells and/or cell
types, infections and/or diseases associated with a particular industry or
environment,
infectious diseases, vector borne diseases, norovirus, rotavims, and/or any
other small
molecules or biomarkers. In some embodiments, the dried and/or lyophilized
enzymes and
primers are contained in the reagent blister 1.340 or elsewhere in the
cartridge 1300. Once
the mixture of the reagents and the sample fluid is introduced to the reaction
wells 1322, one
or more heating elements in the analyzer 1400 are activated to increase a
temperature of the
mixture in the reaction wells 1322 and impedance sensors begin tracking data
in real time.
The analyzer 1400 then conducts a test through an isothermal nucleic acid
amplification
process, and any results are communicated to an application and/or a database
for further
analysis.
[0633] In some embodiments, each of the reader devices 110, 600, 910, and 1400
may incorporate any of the functions and/or components of the other reader
devices. For
example, the components (and corresponding functions) of the reader device 600
in FIG. 6
may be integrated into the reader devices 110, 910, and 1400. Similarly, each
of the reader
devices 110, 600, and 910 may include the functionality and features of the
reader device
1400. Similarly, the reader device 1400 may include in the functionality and
features of the
readers devices 110 and 910 to process any cartridge inserted into the reader
device 1400.
[0634] Similarly, each of the cartridges 120, 200, 1000, 1200, and 1300 may
incorporate any of the functions and/or components of the other cartridges.
For example, the
components and corresponding functions of the cartridge 1300 in FIGs. 13A-13E
may be
integrated into the cartridges 120, 200, 1000, and 1200. Similarly, the
cartridge 1300 may
include in the functionality and features of one or more of the cartridges
120, 200, 1000, and
1200 and may be processed by any reader device described herein.
[0635] The various components of the handheld detection systems 100 and 900
(for
example, the analyzers or reader devices 110, 600, 910, and 1400 and
cartridges 120, 200,
1000, 1200, and 1300, described herein) may be integrated with an external
computing
device. The external computing device, for example a mobile phone, a computer,
a tablet, a
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laptop, or similar device, may communicate with the reader devices 110, 600,
910, and/or
1400 using a communication interface, for example the communications module
615. The
external computing device may comprise a testing monitoring and/or control
application
installed thereon to provide a user options and abilities to monitor and/or
control one or more
of the cartridge and the reader device. Further details of the functionality
of the testing
control application (including providing a testing system user interface for
controlling
options and/or presenting test results and other test information to users, on
a display of the
remote device) are provided below with reference to FIGs. 15A-15P.
[0636] FIGs. 15A-15P depict screenshots of an example graphical user interface
1500 hosted on an external computing device and configured to provide testing
control
and/or monitoring of the handheld system disclosed herein. The graphical user
interface
1500 may include one or more of the features of the graphical user interface
800 described
with reference to FIGs. 8A-8D above.
[0637] The user interface 1500 may be, for example, the user interface 620
illustrated
in connection with the reader device 600 of FIG. 6 or the user interface 800.
The user
interface 1500 may be implemented with any of the reader devices 110, 600,
910, and/or
1400 and/or assay cartridges 120, 200, 1000, 1200, and 1300 described herein.
The screens
depicted in FIGs. 15A-15P may be displayed, for example, by an application
executing on
the external computing device paired to the reader device 110, 600, 910, 1.400
(e.g., by WiFi,
Bluetooth, or the like). The screens may allow a user of the external
computing device to
control and/or monitor the reader device 110, 600, 910, 1400 from the external
computing
device.
[0638] FIG. 15A depicts an initial user screen 1505 which may be displayed
when
the application is activated or run. In one example, a user selects the
application from a home
screen or the application is launched automatically when the external
computing device is
paired with the reader device. In some embodiments, the application may run in
the
background of the external computing device and automatically open or prompt
the user
when the application detects that the reader is paired to the external
computing device or
when a cartridge is inserted into the reader device. The user screen 1505
optionally includes
a header portion that may be generic to all or a majority of screenshots for
the application.
The header portion may include a title portion and a menu portion. The title
portion may
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provide a title for the screen being viewed (for example, the title portion
for the user screen
1505 includes "Who is Sick?", prompting the user of the application to select
or add a person
for whom a test has been run, is being run, or will be run. The menu portion
optionally may
comprise a "hamburger" button that, when clicked, presents the user with
available options
from a current screen (for example, the screen from which the user accesses
the hamburger
button.
[0639] The user screen 1.505 allows the user to identify a patient for which
test results
are being generated by the reader device, test results are being reviewed, or
a profile is being
created, revised, or reviewed. The user may be one of the patients identified
on the screen
1505 or may be associated with one of the patients identified. The user screen
1505 identifies
a single patient's profile, "Benjamin Franklin", but includes a button to add
new patients or
people to the application. By including an ability for multiple patients to be
associated with
the application (for example, have test information stored in or by the
application), the user
interface can link and reference tests associated with corresponding patients
in a simplified
and secure manner. Accessing a patient's account may require a password or
biometric (or
other) authentication to ensure privacy of test results and corresponding
data.
[0640] When the user logs into the application (and provides any necessary
authorization information), the application may provide the user with the
option to edit an
existing profile (for example, the Benjamin Franklin profile) or add a new
profile. When the
user edits the existing profile(s), the user may edit one or more of the name,
birthdate, and
representative image or photo. In some embodiments, editing the existing
profile comprises
removing or deleting the existing profile, which may delete the profile along
with any
associated information (for example, associated test information). In some
embodiments,
when a profile is deleted, the user has the option to save or export
corresponding test
information and other information. When the user adds a new profile, the user
may create a
new profile including the name, birthdate, and/or representative image or
photo for the new
profile. Adding a new profile may require the user to authenticate (for
example, via e-mail
authentication) some information associated with the new profile.
[0641] In some embodiments, when the user selects the menu button on any of
the
screens (for example, screen 1505 of FIG. 1.5A, the menu may provide the user
with many
options. The options include: (1) closing the menu; (2) transitioning to a
home page; (3)
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transitioning to a page to manage connected devices; (4) transitioning to a
page for ordering
supplies; (5) transitioning to a page with information about the application;
(6) transitioning
to a page to contact a vendor of the application; (7) transitioning to a page
for a user manual;
and (8) logging out of and exiting the application. Option (1) may close the
menu and return
the user to the previously visible screen. Option (2) may take the user to the
home page of
the application, which may be the "Who is Sick?" page where the patient is
selected. Option
(3) may transition to a page where connected devices (for example, one or more
of the reader
devices 110, 600, 910, and/or 1400) are managed. Option (4) transitions to a
page where the
user can order supplies, for example additional cartridges 120, 200, 1000,
1200, and/or 1300
or reader devices 110, 600, 910, and/or 1400, swabs, or similar items. Option
(5) may display
details of the application (for example, copyright date, version information,
application
identifier, and so forth). Option (6) may allow the user to contact the vendor
of one or more
of the application, the reader devices 110, 600, 910, and/or 1400, and the
cartridges 120, 200,
1000, 1200, and/or 1300. Option (7) opens a digital user manual for one or
more of the
application, the reader devices 110, 600, 910, and/or 1400, and the cartridges
120, 200, 1000,
1200, and/or 1300. Option (8) causes the user to sign out (for example, de-
authenticate) and
exit the application.
[0642] Option (3) from the menu may transition the application to the user
screen
1510 of FIG. 15B, having the title portion "Devices". The screen 1510 shows
devices that
are added to and/or associated with the application, such as the Reader #1 and
the Reader #2,
and an option to add a new device. When the user selects to add the new
device, the
application transitions to a pairing reader screen 1515 that requests the user
to input
information to enable the application to communicate with the new device(s),
such as a new
reader. For example, the pairing reader screen 1515 may prompt the user to
pair the new
reader with the application over Bluetooth, Wi-Fi, or another communication
medium. The
pairing reader screen 151 may include a video prompt to show the user how to
add the new
reader and generally include instructions for pairing the new reader with the
application. In
some embodiments, the pairing reader screen 1515 may prompt the user to scan
or enter a
barcode on or associated with the new reader. Once the new reader is added to
or associated
with the application, the application may return to the screen 1510, where the
added reader
(e.g., Reader #2) is shown with a note of "Device added!".
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[0643] When the user selects one of the added devices (for example, the Reader
#1),
the application transitions to a user screen 1520 of FIG. 15D. The user screen
1520 may
provide various information and options to the user. For example, the user
screen 1520
provides an option to change the name of the Reader #1, to forget the Reader
#1, and to
connect to the Reader #1. If the Reader #1 is currently connected to the
application, then the
user screen 1520 may provide an option to disconnect from the Reader #1. The
user screen
1520 also displays identifying information for the Reader #1 and may include a
connection
status indicator, indicating a status of the connection between the Reader #1
and the
application. In some embodiments, the user screen 1520 also includes
information regarding
current status of the Reader #1. For example, the screen 1520 can indicate
whether the
Reader #1 is performing a test, analyzing a cartridge, waiting for a
cartridge, and so forth, or
a recently completed action. Though not shown in FIG. 15D, the screen 1520 may
provide
one or more commands or controls to the Reader #1.
[0644] As described herein, the reader devices and the cartridges provide
testing for
target agents. The application on the external computing device may facilitate
the
performance, control, and review of the test and the review and/or
communication of the test
results. For example, user screen 1525 of FIG. 15E shows results for the user
Benjamin
Franklin for two previous tests or provides the user the option to start a new
test. The screen
1525 shows the two previous test results: a positive test result for Influenza
A/B on April 28,
2019 and a negative test result for Influenza AJB on April 28, 2019. The user
of the external
computing device may select one of the previously completed positive and
negative test
results and review details of the test, the test results, and any symptoms
reported for the
patient at the time that the selected test was performed. Additionally, the
user can review
identifiers for the cartridge from each test and/or the reader device from
each test. When the
user selects to start a new test, the user interface 1500 may prompt the user
to connect to a
reader device (for example, one of reader devices 110, 600, 910, and/or 1400,
if not already
connected). The user interface may also request the user to identify a
cartridge (for example,
one of cartridges 120, 200, 1000, 1200, and/or 1300) to be used in the test.
[0645] When the user selects to start a new test from the screen 1525, the
user
interface 1500 transitions to and through the screens described above that the
user accesses
when selecting to add the new reader from the screen 1510. As such, the
pairing and
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connecting of the reader device with the external computing device and user
interface 1500
may be completed as described above. When the reader device is paired with the
external
computing device and the user interface 1500, the user interface 1500 may
prompt the user
to identify the cartridge being used with the paired reader device at a user
screen 1530 of
FIG. 15F. The screen 1530 provides the user with a video and/or instructions
for identifying,
to the application, the cartridge being used. In some embodiments, as
described herein,
different cartridges may be used for different tests. For example, an
influenza test uses a first
cartridge while a bronchitis test uses a second cartridge. Because the
different tests may use
different cartridges, identifying the cartridge to being used for the test may
be essential to
the test providing a reliable result when analyzed by the reader device. For
example, the
reader device may receive specific instructions and/or set points, etc., for
use in the test based
on the identified cartridge. Thus, the instructions provided by the screen
1530 may include
scanning a barcode or taking a picture of the cartridge being used or manually
entering
information identifying the cartridge.
[0646] Once the user provides the details of the cartridge being used for the
requested
test, the user interface 1500 provides instructions to the user for using the
cartridge, at a
screen 1535 of FIG. 15G. The instructions comprise obtaining a swab and
removing a
cartridge that matches the identified cartridge for use in the test. The
screen 1535 also shows
the test that corresponds to the selected and identified cartridge, in this
case the influenza
A/B test. The screen 1535 may provide any additional instructions or notes to
assist the user
in preparing to conduct the test.
[0647] FIGs. 15H-15J show the user screens 1540-1550, which include
instructions
provided to the user via the external computing device. The instructions
provided to the user
screens 1540-1545 include instructions for getting the sample, loading the
sample into the
cartridge, and getting the cartridge into the reader device. For example, the
user interface
1500 instructs the user to get the sample by swabbing the patient's nose such
that mucus
covers a tip of the swab. The instructions tell the user to then put the tip
of the swab into the
cartridge and then retract or extract the swab, which causes the cartridge to
scrape the mucus
into the cartridge. The instructions further teach the user to insert the
cartridge into the reader
until the user hears a click, which may cause the test to begin. The click may
be the result
of a mechanical coupling of the reader device to the cartridge. In some
embodiments, the
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user interface 1500 may provide additional instructions to the user. The
screens 1540-1550
also include navigation buttons to navigate between screens. The screen 1550
may indicate
to the user that the corresponding test has begun. Specifically, the screen
1550 provides the
user with a summary of the patient or subject (for example, Benjamin Franklin)
along with
some information about the patient (for example, date of birth). The screen
1550 also
provides details on the test being run, here the Influenza A/B test, and an
identifier for the
cartridge being used to run the test and the reader running the test. In some
embodiments,
the screen 1550 also includes a timer or countdown indicating how much time is
remaining
in the current test, if any.
[0648] FIGs. 15K-15M show examples of user screens 1565-1565 through which the
user can provide symptoms that the patient is experiencing. In some
embodiments, the user
can provide the symptoms before the test is run, while the test is run, and/or
after the test is
run. In some embodiments, the reader or the user interface (herein referred to
also as the
"application") may use the symptoms in conjunction with the test results to
make a
determination as to whether the patient is suffering from an ailment
(otherwise referred to
herein as a sickness or illness) associated with the test. For example, as
shown in FIGs. 15K
and 15L, the user can input or select symptoms such as fever, chills, muscle
aches, sore
throat, headache, congested or runny nose, cough, difficulty breathing,
decreased appetite,
or decreased activity, and so forth. The user may input a symptom that is not
shown in FIGs.
15K and 15L. In some embodiments, the user interface 1500 allows the user to
select severity
levels associated with one or more indicated symptoms, as shown on the screen
1560. For
example, if the patient reports having a fever, the user can enter the
patient's temperature
when the swab collected the sample of the patient's mucus. Similarly, other
symptoms may
have sliding scale values to provide associated values (for example, a sliding
scale for
severity of muscle aches or congestion, and so forth. Additionally, screens
1555-1565
include a timer or countdown regarding the test being run as well as the
patient name and the
test name. On the screen 1565 of FIG. 15M, the user interface 1500 shows when
the test is
complete and shows any symptoms that the user identifies for the patient. The
screen 1565
also gives the user options to view the results of the completed test. The
results may include
any target agent levels or associated information.
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[0649] The screen 1570 of FIG. 15N shows a list of completed tests, similar to
the
screen 1525 of FIG. 15E, described above. However, the screen 1570 includes an
additional
test as compared to the screen 1525, the additional test being the influenza
A/B test
completed in screen 1565. The new test is shown as being positive for
influenza A/B and
includes the date on which the new test was completed. In some embodiments,
though not
shown in the figures, the user interface 1500 can show the status of the
reader device being
disconnected and unable to show test results. In some embodiments, if the
reader device
becomes disconnected from the user interface 1500 and the external computing
device during
a test, then the user interface 1500 may provide the user with an alert and/or
steps to take to
reconnect with the reader device. In some embodiments, if the reader device is
disconnected
from the user interface 1500 and the external computing device, then the user
interface 1500
may track and/or display information from when the reader device was last
connected to the
user interface 1500 and the external computing device. Selecting the new test
on the screen
1570 causes the user interface 1500 to present the screen 1575 of FIG. 150,
which includes
details of the positive influenza A/B test, symptoms reported along with the
test by the user,
and details of the cartridge used in the test and potentially the reader
device used in the test.
In some embodiments, the screen 1575 of FIG. 150 may also include an indicator
(not shown
in the figures) of a diagnosed ailment and/or one or more recommended steps to
follow-up
on the test results and/or the indicated ailment. Screen 1580 of FIG. 15P
provides the user
with options for sharing the test results, for example via text message, e-
mail, printing, and
so forth. In some embodiments, the user establishes a default sharing plan for
all test results,
symptoms, and other data for a particular patient. For example, the user can
set up the sharing
plan to e-mail or message all results, symptoms, and other data to the
patient's doctor or
parents automatically upon completion of a test or entry of new data, or both.
[0650] In some embodiments, as described above with reference to FIGs. 8A-8D,
the
external computing device and the user interface 1.500 are used to scan a
cartridge identifier
(e.g., cartridge identifier 215 of FIG. 2B) of a cartridge before inserting
the cartridge into the
reader device. When the cartridge is inserted, the paired reader device
detects the inserted
cartridge and sends a message to the user interface that the cartridge has
been inserted. The
user interface 1500 may then display one of the screens described above, with
reference to
FIGs. 15A-15P. In some embodiments, one or more of the screens of the FIGs.
15A-15P
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include one or more of the indications, buttons, input fields, areas, and so
forth of the FIGs.
8A-8D.
[0651] In some embodiments, the user interface (for example, the user
interface 1500
or the user interface 800) works with the reader device (for example, one of
the reader devices
110, 600, 910, and/or 1400) to determine whether a patient is suffering from a
particular
illness. For example, the reader device may perform a test using one of the
cartridges 120,
200, 1000, 1200, and/or 1300 and determine that a particular target agent is
present in the
patient's mucus. However, merely the presence and/or amount of the target
agent may be
insufficient to determine that the patient is suffering from an illness or
ailment. For example,
if the patient is merely a carrier of an illness, the patient test results may
indicate presence
and/or amount of the virus but the patient may not be suffering from an
associated illness.
Thus, the user interface may receive symptoms that the patient is experiencing
and combine
these symptoms with the test results from the reader device to determine
whether the patient
is suffering from an illness or ailment corresponding to the target agent. For
example, if the
test result from the reader device indicates the presence and/or amount of the
influenza A/B
virus in the patient's mucus but the patient is not experiencing or reporting
any symptoms,
then the user interface may determine that the patient is not suffering from
the influenza virus
but is instead a carrier for the virus. On the other hand, when the test
result indicates the
presence and/or amount of the influenza A/B virus and the patient reports
symptoms known
to coincide with the influenza A/B virus in someone suffering from the
influenza illness, then
the user interface may determine that the patient is infected with the
influenza illness. Such
a determination may be based on a threshold number of symptoms or specific
being met
while the target agent is detected (for example, one or two symptoms being
suffered while
the influenza A/13 virus is present). The symptoms may be weighted differently
depending
on the target agent in the test and/or the corresponding illness. For example,
when the target
agent is influenza A/B, then symptoms such as fever, chills, muscle aches may
be more
highly weighted than symptoms such as headache or cough. Thus, symptoms
associated
with a corresponding illness for the target agent may have higher weights and
be more
indicative that the patient carrying the virus is suffering the corresponding
illness. In some
embodiments, the threshold number of symptoms, weighting of symptoms, or
specific
symptoms to be met to determine that the patient is ill is determined based on
one or more
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metrics. A standard setting or national organization, such as the Center for
Disease Control
(CDC) or similar organization or entity, may establish the one or more
metrics. Thus, the
user interface may use the test results from the reader device and the symptom
information
provided by the user to determine whether the patient is (1) ill or sick or
(2) a carrier for the
target agent. In some embodiments, the user interface offloads one or more of
the
determinations described herein to one or more external systems with which the
user
interface (and the corresponding external computing device) interacts.
[0652] In some embodiments, the user interface may generate a score or similar
indicator to indicate a probability that the patient is ill or sick. A higher
score may correspond
to a higher probability that the patient is ill while a lower score may
correspond to a higher
probability that the patient is not ill. For example, the user interface may
use details from
the test results from the reader device along with the user provided symptom
information to
generate the score indicating the probability of sickness of the patient.
[0653] The reader device may provide test results that include a range of
values,
where the range of values correspond to a range of possible detection levels
of the target
agent. For example, the test results may include one or more of a likelihood
that the mucus
sample included the target agent (for example, between 0 and 100% probability)
and a
quantity of the target agent determined to have been included in the mucus
sample. The
probability that the mucus sample included the target agent may be associated
with the
quantity of the target agent determined to have been included in the mucus.
The range of
possible detection levels may refer to different likelihoods or probabilities
that the patient
has a particular virus or infection. For example, if the reader device
provides test results
indicating that the patient does have the virus or infection with 100%
certainty or that a
quantity of the target agent above a first threshold was present, then the
score (or probability)
may be assigned a minimum value, for example 50 out of a 0 to 100 range. Then,
if the
patient is experiencing any symptoms associated with the illness associated
with the virus or
infection, then the value of the score (indicating that the patient is
suffering from the
corresponding illness) may be increased. For example, for each symptom that
the patient
experiences that is associated with the illness, the value may increase by a
threshold value
(for example, 10 points). Thus, the combination of the target agent detection
and the
symptoms can increase or decrease the score or probability of the patient
being sick.
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Alternatively, if the reader device indicates that the patient has the virus
or infection with
50% certainty (or that a quantity of the target agent below the first
threshold but above a
second threshold was present), then the score may be assigned a different
minimum value,
for example 25 out of the 0 to 100 range. Accordingly, when the test results
indicate a lower
probability of the presence of the target agent, more symptoms suffered by the
patient are
needed to increase the score to the same value as compared to when the test
results indicate
a high probability of sickness. If the reader device indicates that the
patient does not have
the virus or infection (or that a quantity of the target agent below the
second threshold was
present), then the score may be assigned a zero value, for example 0 out of
the 0 to 100 range.
When the score starts at a zero-value based on the test results, no quantity
of symptoms may
be sufficient to raise the score because the virus or target agent is not
present to make the
patient ill. Thus, the user interface and the reader device may together
generate the score
that represents the probability of the patient being sick based on the test
results of the target
agent and the symptoms suffered by the patient.
[0654] In some embodiments, the user interface may review the test results and
the
provided symptoms to determine whether the patient is suffering from a
particular illness not
associated with the target agent for which the test was run. For example, if
the patient's test
results are negative for influenza A/13 but the patient is experiencing a
fever with chills and
a sore throat, the user interface may determine that the patient is suffering
from a cold or
respiratory syncytial virus (RSV). Thus, the user interface may identify an
illness that the
patient is suffering from or is likely suffering from based on a positive or
negative test results
and the symptoms experienced. As such, the user interface may use knowledge
(for example,
databases) of similarities and differences in symptoms of different illnesses
but differences
in test results and so forth in illness determinations.
[0655] In some embodiments, the user interface generates a score value that
indicates
a probability that the patient is sick or ill, based on the test results and
the symptom
information. The user interface may further aggregate external information
into the score
value, regardless of what the test results and symptoms by themselves would
otherwise
indicate. The external information may include one or more of test results
from other patients
that used the same reader device, test results from other reader devices that
interfaced with
the user interface and the external computing device, test results and other
diagnostic
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information for patients in a hospital or a geographic region, and so forth.
For example, the
user interface may use test results and/or symptom information from other
patients tested by
the reader device to inform further the score values. For example, many other
patients tested
with the reader device coupled to the user interface have positive test
results for the same
target agent and report one or more similar symptoms. The user interface may
use this
information to increase a score or probability that the patient is ill or
sick, even if the patient's
test results and/or symptoms may alone not indicate that the patient is iH.
Similarly, the test
results and the symptom information for the patient may indicate that the
patient is ill but
other patients having similar test results and symptoms report that they are
not ill. The user
interface then may decrease the score or probability that the patient is ill,
regardless of what
the patient's test results and/or symptom information otherwise indicate. If
the test results
and the symptoms for the patient are different from those of other patients
that report as not
being sick (for example, by a threshold amount), then the user interface may
increase the
score or probability that the patient is sick. On the other hand, if the test
results and
symptoms are different from those of other patients that report as being sick
(for example,
by the threshold amount), then the user interface may decrease the score or
probability that
the patient is sick, regardless of the test results and symptoms.
[0656] In some embodiments, the user interface performs one or more actions
based
on the score or probability values. The user interface may communicate
information to one
or more of the user, the patient, attending medical staff, the CDC, or similar
entities.
Alternatively, or additionally, the user interface may generate an alert to
the one or more of
the user, the patient, attending medical personnel, the CDC, or similar
entities. The alert may
comprise one or more of a phone call, a text message, an e-mail message, a
push message,
an audio message, a flashing indicator, or audible indicator, or any other
communication
used to communicate information. For example, the user interface may
automatically
generate and transmit an alert to the user based on the results of the test or
the indicated
symptoms, a combination of the two, or the test results or symptoms in
aggregate with
information from other patients. For example, if the test results and the
indicated symptoms
suggest that the patient is suffering from a rare illness, then the user
interface may generate
and communicate an alert to the patient or user suggesting a follow-up visit
to a specialist.
Similarly, if the test results and the indicated symptoms suggest that the
patient is suffering
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from highly contagious illness, then the user interface may generate and
communicate the
alert to the patient or user requesting that the patient restrict interaction
with others to
minimize risk of communication of the illness to others. If the test results
and the indicated
symptoms suggest that the patient is suffering from a highly contagious, rare,
and difficult to
treat illness, then the user interface may generate and communicate the alert
to the patient or
user but also to local, regional, or national medical staff or disease
monitoring agencies. As
such, the reader device, cartridge, and user interface on the external
computing device may
generate information used to help detect an outbreak of a virus or disease.
[0657] For example, the user interface and the external computing device may
communicate and/or interact with a system that tracks illnesses over a
geographic area, for
example a city, county, state, or nation, or a specific portion of the
population. Thus, the
user interface and the external computing device may enable tracking of
diseases and/or
infections by the system for a number of patients in various geographic areas.
In some
embodiments, the system performs the tracking based on one or both of the test
results and
the identified symptoms. In some embodiments, the system performs the tracking
based on
the scores or probabilities generated by the user interface. The system may
aggregate and
use the information from multiple user interfaces and external computing
devices to generate
a geographic heat map. The heat map may show levels of one or more illnesses
and/or
corresponding rates of infection or healing as different colors or levels on
the map, where
different colors correspond to different levels (for example, numbers) of
reported injections
or rates of infection. Thus, the heat map may visually show how numbers of ill
patients vary
in the geographic area. In some embodiments, the system may use such heat maps
to identify
pockets of specific illnesses or infections and/or an epidemic that is
occurring based on
aggregated test results and symptoms provided from multiple user interfaces
and
corresponding external computing devices. The heat map may show different
quantities of
illnesses or different rates of illness detection in different colors. The
heat map may enable
an entity to review quickly the geographic area to identify relational
information (for
example, information for portions of the geographic area relative to one
another) and specific
information (for example, detailed information for individual portions of the
geographic
area).
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[0658] In some embodiments, the user interface and the external computing
device
may be integrated with a system (for example, the system that generates the
heat map) used
to track and/or determine need for vaccines or other medications. The system
may receive
the test results, symptoms, and/or scores from a number of user interfaces and
corresponding
external computing devices. The system may track that information to ensure
that a
particular geographic region is supplied with appropriate vaccines or
medications to handle
the identified quantity of illnesses. If the system identifies that a
difference in identified
illnesses and an expected level of supplies exceeds a determined threshold,
then the system
may automatically request vaccine and/or medication suppliers to increase
production to
meet an expected demand based on the illnesses tracked by the system. For
example, the
system determines that test results, symptoms, and/or scores received from a
city in
California indicate that 50,000 people out of a population of 500,000 are
suffering from
influenza A/B. The city is expected to have vaccine and medication supplies
for 10,000
people to treat and prevent the spread of the influenza AM virus (for example,
only 10,000
units of medication and/or vaccines). The system may determine that the
difference of
40,000 people exceeds the threshold amount and may automatically request that
influenza
A/B vaccine and medication manufacturers and/or suppliers increase production
and provide
an increased supply to the city. Such automatic detection of supply need and
request for
additional supplies may improve response times in times of outbreaks and help
prevent
and/or reduce the spread of communicable diseases.
[0659] Similarly, such aggregate tracking of test results, symptoms, and/or
scores
may allow the system to provide recommendations. Such recommendations may
include
increased education, advertisement, and so forth. For example, if the system
determines an
increase in numbers of people infected with a communicable disease that
presents itself as
or shares symptoms with another disease, then the system may recommend
increased
education of the different diseases and advertisements to inform people of the
potential
confusion and to help them seek treatment. For example, certain sexually
transmitted
diseases may exhibit cold- or flu-like symptoms. For example, hepatitis and/or
gonorrhea
may have similar symptoms to the common cold or influenza. Thus, some people
experiencing the cold-like or flu-like symptoms may not get tested for any
infection,
assuming they just have the cold or flu. Thus, the system may determine that
an unusually
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large number of people in a town have test results, symptoms, and scores that
indicate
infection with hepatitis during a period when a large number of patients are
reporting cold or
flu infections. The system may then determine that education regarding safer
sex practices
and differences between the diseases should be provided to the town. The
system may also
recommend increased advertisement about the spike in infections to encourage
the safer
practices and lead to increased detection and treatment for the appropriate
illness.
[0660] In some embodiments, the user interface may also generate an indicator
to
indicate whether the patient is becoming sicker or healthier. For example, if
the user
performs multiple tests for the patient, then the user interface may determine
that different
combinations of symptoms suffered by the patient or different quantities of
the target agent
in the test sample indicate whether the patient is sicker than a previous test
or healthier than
a previous test.
[0661] In some embodiments, the indicator may comprise an arrow or
representation
of a face, or similar indicator.
Overview of Example Devices
[0662] Some embodiments of the methods, systems and compositions provided
herein include devices comprising an excitation electrode and a sensor
electrode. In some
embodiments, the excitation electrode and the sensor electrode measure
electrical properties
of a sample. In some embodiments, the electrical properties comprise complex
admittance,
impedance, conductivity, resistivity, resistance, and/or a dielectric
constant.
[0663] In some embodiments, the electrical properties are measured on a sample
having electrical properties that do not change during the measurement. In
some
embodiments, the electrical properties are measured on a sample having dynamic
electrical
properties. In some such embodiments, the dynamic electrical properties are
measured in
real-time.
[0664] In some embodiments, an excitation signal is applied to the excitation
electrode. The excitation signal can include direct current or voltage, and/or
alternating
current or voltage. In some embodiments, the excitation signal is capacitively
coupled
to/through a sample. In some embodiments, the excitation electrode and/or the
sensor
electrode is passivated to prevent direct contact between the sample and the
electrode.
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[0665] In some embodiments, parameters are optimized for the electric
properties of
a sample. In some such embodiments, parameters can include the applied
voltage, applied
frequency, and/or electrode configuration with respect to the sample volume
size and/or
geometry.
[0666] In some embodiments, the voltage and the frequency of the excitation
voltage
may be fixed or varied during the measurement. For example, measurement may
involve
sweeping voltages and frequencies during detection, or selecting a specific
voltage and
frequency which may be optimized for each sample. In some embodiments, the
excitation
voltage induces a current on the signal electrode that is can vary with the
admittance of the
device and/or sample characteristics.
[0667] In some embodiments, the detection parameters are optimized by modeling
the admittance, device and sample by the lumped-parameter equivalent circuit
consisting of
electrode-sample coupling impedances, sample impedance, and inter-electrode
parasitic
impedance. Parameters of the lumped-parameter equivalent circuit is determined
by
measuring the admittance of the electrode-sample system at one or many
excitation
frequencies for a device. In some embodiments, the complex (number having both
real and
imaginary components) admittance of the electrode-sample system is measured
using both
magnitude- and phase-sensitive detection techniques. In some embodiments, the
detection
parameters are optimized by determining the frequencies corresponding to the
transitions
between the frequency regions by measuring the admittance across a wide range
of
frequencies. In some embodiments, the detection parameters are optimized by
determining
the frequencies corresponding to the transitions between the frequency regions
by computing
from the values given lumped-parameter model.
[0668] In some embodiments, the admittance of a capacitively-coupled electrode-
sample system comprises three frequency regions: a low frequency region
dominated by the
electrode-sample coupling impedance, a mid-frequency region dominated by the
sample
impedance, and a high frequency region dominated by parasitic inter-electrode
impedance.
The admittance in the electrode-sample coupling region is capacitive in nature
and is
characterized by a magnitude that increases linearly with frequency, whose
phase is ninety
degrees. The admittance in the sample region is conductive in nature and is
characterized by
an admittance that does not vary significantly with respect to frequency,
whose phase is
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approximately zero degrees. The admittance inter-electrode region is
capacitive in nature and
is characterized by a magnitude that increases linearly with frequency and a
phase of ninety
degrees.
[0669] In some embodiments, an induced current at the pick-up electrode is
related
to the excitation voltage and complex admittance by the relation:
current = (complex admittance) X (voltage)
[0670] In some embodiments, the device measures both the excitation voltage
magnitude and induced current magnitude to determine the magnitude of the
complex
admittance. In some embodiments, the device is calibrated to known excitation
voltages and
measure the magnitude of the induced current. In order to determine the phase
of complex
admittance, the device may measure the relative phase difference between the
excitation
voltage and the induced current.
[0671] In some embodiments, the magnitude and phase are measured directly.
[0672] In some embodiments, the magnitude and phase are measured indirectly
e.g.,
by using both synchronous and asynchronous detection. The synchronous detector
gives the
in-phase component of the induced current. The asynchronous detector gives the
quadrature
component of the induced current. Both components can be combined to determine
the
complex admittance.
[0673] In some embodiments, the electrodes are not passivated.
[0674] In some embodiments, the excitation and/or detection electrodes are
passivated. The excitation and/or detection electrodes may be passivated to
prevent e.g.,
undesirable adhesion, fouling, adsorption or other detrimental physical
interactions between
the electrode with the sample or components therein. In some embodiments, the
passivation
layer comprises a dielectric material. In some embodiments, passivation
enables efficient
capacitive coupling from the electrodes to the sample. The efficiency of the
coupling is
determined by measuring the characteristics of the electrode/sample system,
for example,
which may include: the dielectric properties of the passivation layer, the
thickness of the
passivation layer, the area of the passivation/sample interface, the
passivation surface
roughness, the electric double layer at the sample/passivation interface,
temperature, applied
voltage and applied frequency, the electrical properties of the sample, the
electric and/or
chemical properties of the electrode materials.
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[0675] In some embodiments, the electrode configuration and fabrication are
optimized to mitigate undesirable parasitic coupling between electrodes. This
may be
accomplished through electric field shielding, the use of a varying dielectric
constant
electrode substrate, layout optimization, and/or grounding layers.
[0676] In some embodiments, the electrode configuration and fabrication are
not
optimized to mitigate undesirable parasitic coupling between electrodes.
Implementing Systems and Terminology
[0677] Implementations disclosed herein provide systems, methods and apparatus
for
detection of the presence and/or quantity of a target analyte. One skilled in
the art will
recognize that these embodiments may be implemented in hardware or a
combination of
hardware and software and/or firmware.
[0678] The signal processing and reader device control functions described
herein
may be stored as one or more instructions on a processor-readable or computer-
readable
medium. The term "computer-readable medium" refers to any available medium
that can be
accessed by a computer or processor. By way of example, and not limitation,
such a medium
may comprise RAM, ROM, EEPROM, flash memory, CD-ROM or other optical disk
storage, magnetic disk storage or other magnetic storage devices, or any other
medium that
can be used to store desired program code in the form of instructions or data
structures and
that can be accessed by a computer. It should be noted that a computer-
readable medium
may be tangible and non-transitory. The term "computer-program product" refers
to a
computing device or processor in combination with code or instructions (e.g.,
a "program")
that may be executed, processed or computed by the computing device or
processor. As used
herein, the term "code" may refer to software, instructions, code or data that
is/are executable
by a computing device or processor.
[0679] The various illustrative logical blocks and modules described in
connection
with the embodiments disclosed herein can be implemented or performed by a
machine, such
as a general purpose processor, a digital signal processor (DSP), an
application specific
integrated circuit (ASIC), a field programmable gate array (FPGA) or other
programmable
logic device, discrete gate or transistor logic, discrete hardware components,
or any
combination thereof designed to perform the functions described herein. A
general purpose
processor can be a microprocessor, but in the alternative, the processor can
be a controller,
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microcontroller, combinations of the same, or the like. A processor can also
he implemented
as a combination of computing devices, e.g., a combination of a DSP and a
microprocessor,
a plurality of microprocessors, one or more microprocessors in conjunction
with a DSP core,
or any other such configuration. Although described herein primarily with
respect to digital
technology, a processor may also include primarily analog components. For
example, any
of the signal processing algorithms described herein may be implemented in
analog circuitry.
A computing environment can include any type of computer system, including,
but not
limited to, a computer system based on a microprocessor, a mainframe computer,
a digital
signal processor, a portable computing device, a personal organizer, a device
controller, and
a computational engine within an appliance, to name a few.
Additional Definitions
[0680] The practice of the present disclosure will employ, unless indicated
specifically to the contrary, conventional methods of molecular biology and
recombinant
DNA techniques within the skill of the art, many of which are described below
for the
purpose of illustration. Such techniques are explained fully in the
literature. See, e.g. ,
Sambrook, el al, Molecular Cloning: A Laboratory Manual (3rd Edition, 2000);
DNA
Cloning: A Practical Approach, vol. 1 & 11 (D. Glover, ed.); Oligonucleotide
Synthesis (N.
Gait, ed., 1984); Oligonucleotide Synthesis: Methods and Applications (P.
Herdewijn, ed.,
2004); Nucleic Acid Hybridization (B. Flames & S. Higgins, eds., 1985);
Nucleic Acid
Hybridization: Modern Applications (Buzdin and Lukyanov, eds., 2009);
Transcription and
Translation B. Hames & S. Higgins, eds., 1984); Animal Cell Culture (R.
Freshney, ed.,
1986); Freshney, R.I. (2005) Culture of Animal Cells, a Manual of Basic
Technique, 5th Ed.
Hoboken NJ, John Wiley & Sons; B. Perbal, A Practical Guide to Molecular
Cloning (3rd
Edition 2010); Farrell, R., RNA Methodologies: A Laboratory Guide for
Isolation and
Characterization (3rd Edition 2005).
[0681] The terms "function" and "functional" as used herein refer to a
biological,
enzymatic, or therapeutic function.
[0682] The term "isolated" as used herein refers to material that is
substantially or
essentially free from components that normally accompany it in its native
state. For example,
an "isolated cell," as used herein, includes a cell that has been purified
from the milieu or
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organisms in its naturally occurring state, a cell that has been removed from
a subject or from
a culture, for example, it is not significantly associated with in vivo or in
vitro substances.
[0683] The terms "nucleic acid" or "nucleic acid molecule" as used herein
refers to
polynucleotides, such as deoxyribonucleic acid (DNA) or ribonucleic acid
(RNA),
oligonucleotides, fragments generated by the polymerase chain reaction (PCR),
and
fragments generated by any of ligation, scission, endonuclease action, and
exonuclease
action. Nucleic acid molecules can be composed of monomers that are naturally-
occurring
nucleotides (such as DNA and RNA), or analogs of naturally-occurring
nucleotides (e.g.,
enantiomeric forms of naturally-occurring nucleotides), or a combination of
both. Modified
nucleotides can have alterations in sugar moieties and/or in pyrimidine or
purine base
moieties. Sugar modifications include, for example, replacement of one or more
hydroxyl
groups with halogens, alkyl groups, amines, and azido groups, or sugars can be
functionalized as ethers or esters. Moreover, the entire sugar moiety can be
replaced with
sterically and electronically similar structures, such as aza-sugars and
carbocyclic sugar
analogs. Examples of modifications in a base moiety include alkylated purines
and
pyrimidines, acylated purines or pyrimidines, or other well-known heterocyclic
substitutes.
Nucleic acid monomers can be linked by phosphodiester bonds or analogs of such
linkages.
Analogs of phosphodiester linkages include phosphorothioate,
phosphorodithioate,
phosphoroselenoate, phosphorodiselenoate, phosphoroanilothioate,
phosphoranilidate, or
phosphoramidate. The term "nucleic acid molecule" also includes so-called
"peptide nucleic
acids," which comprise naturally-occurring or modified nucleic acid bases
attached to a
polyamide backbone. Nucleic acids can be either single stranded or double
stranded.
"Oligonucleotide" can be used interchangeable with nucleic acid and can refer
to either
double stranded or single stranded DNA or RNA. A nucleic acid or nucleic acids
can be
contained in a nucleic acid vector or nucleic acid construct (e.g. plasmid,
virus,
bacteriophage, cosmid, fosmid, phagemid, bacterial artificial chromosome
(BAC), yeast
artificial chromosome (YAC), or human artificial chromosome (HAC)) that can be
used for
amplification and/or expression of the nucleic acid or nucleic acids in
various biological
systems. Typically, the vector or construct will also contain elements
including but not
limited to promoters, enhancers, terminators, inducers, ribosome binding
sites, translation
initiation sites, start codons, stop codons, polyadenylation signals, origins
of replication,
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cloning sites, multiple cloning sites, restriction enzyme sites, epitopes,
reporter genes,
selection markers, antibiotic selection markers, targeting sequences, peptide
purification
tags, or accessory genes, or any combination thereof.
[0684] A nucleic acid or nucleic acid molecule can comprise one or more
sequences
encoding different peptides, polypeptides, or proteins. These one or more
sequences can be
joined in the same nucleic acid or nucleic acid molecule adjacently, or with
extra nucleic
acids in between, e.g. linkers, repeats or restriction enzyme sites, or any
other sequence that
is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25,
30, 35, 40, 45, 50, 55,
60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, or 300 bases long, or any
length in a range
defined by any two of the aforementioned lengths. The term "downstream" on a
nucleic acid
as used herein refers to a sequence being after the 3' -end of a previous
sequence, on the
strand containing the encoding sequence (sense strand) if the nucleic acid is
double stranded.
The term "upstream" on a nucleic acid as used herein refers to a sequence
being before the
5'-end of a subsequent sequence, on the strand containing the encoding
sequence (sense
strand) if the nucleic acid is double stranded. The term "grouped" on a
nucleic acid as used
herein refers to two or more sequences that occur in proximity either directly
or with extra
nucleic acids in between, e.g. linkers, repeats, or restriction enzyme sites,
or any other
sequence that is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,
18, 19, 20, 25, 30, 35,
40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, or 300 bases
long, or any length
in a range defined by any two of the aforementioned lengths, but generally not
with a
sequence in between that encodes for a functioning or catalytic polypeptide,
protein, or
protein domain.
[0685] The terms "peptide", "polypeptide", and "protein" as used herein refers
to
macromolecules comprised of amino acids linked by peptide bonds. The numerous
functions
of peptides, polypeptides, and proteins are known in the art, and include but
are not limited
to enzymes, structure, transport, defense, hormones, or signaling. Peptides,
polypeptides, and
proteins are often, but not always, produced biologically by a ribosomal
complex using a
nucleic acid template, although chemical syntheses are also available. By
manipulating the
nucleic acid template, peptide, polypeptide, and protein mutations such as
substitutions,
deletions, truncations, additions, duplications, or fusions of more than one
peptide,
polypeptide, or protein can be performed. These fusions of more than one
peptide,
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polypeptide, or protein can be joined in the same molecule adjacently, or with
extra amino
acids in between, e.g. linkers, repeats, epitopes, or tags, or any other
sequence that is 1, 2, 3,
4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35,
40,45, 50, 55, 60, 65, 70,
75, 80, 85, 90, 95, 100, 150, 200, or 300 bases long, or any length in a range
defined by any
two of the aforementioned lengths.
[0686] The term "% w/w" or "% wt/wt" as used herein has its ordinary meaning
as
understood in light of the specification and refers to a percentage expressed
in terms of the
weight of the ingredient or agent over the total weight of the composition
multiplied by 100.
The term "% v/v" or "% vol/vol" as used herein has its ordinary meaning as
understood in
the light of the specification and refers to a percentage expressed in terms
of the liquid
volume of the compound, substance, ingredient, or agent over the total liquid
volume of the
composition multiplied by 100.
[0687] The term "loop-mediated isothermal amplification (LAMP)" as used herein
has its plain and ordinary meaning as understood in light of the specification
and refers to a
method of nucleic acid amplification that is performed isothermally, or
without the repeating
cycles of temperatures as seen in PCR. LAMP oilers a robust way to amplify and
detect
nucleic acid material from samples such as those derived from patients rapidly
and cost-
effectively. Methods of LAMP are well established in the art. Amplification is
generally done
with a DNA template and a strand-displacing DNA polymerase; inclusion of a
reverse
transcriptase either added to the amplification solution in a one-pot method,
or used to
prepare complementary DNA (cDNA) prior to the amplification enables the
detection of
RNA. Amplification is typically carried out at elevated temperatures (but not
near-boiling
temperatures as seen with PCR) anywhere within a range between 50 C-70 C that
is
optimized for the thermotolerant Bst DNA polymerase. However, other
temperatures and
DNA polymerases can be used with minimal optimization required. LAMP involves
at least
4 primers designed for a short region of interest of the nucleic acid target
(e.g. a pathogenicity
island of a pathogenic bacteria genome). According to conventional primer
nomenclature,
the 4 primers include two inner primers, forward inner primer (F1P) and
backward inner
primer (BIP), and two outer primers, F3 and B3. Amplification of the target
nucleic acid
with the 4 primers results in a characteristic stem-loop containing "dumb-
bell" shaped
template. Progressive strand synthesis with the inner primers results in the
formation of large
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stem-loop structures from this original template. A later improvement to this
original LAMP
technique involves the inclusion of 2 loop primers, LF and LB, which hybridize
to loop
regions of the amplicons and serve as additional points of DNA elongation,
significantly
improving the speed of complete amplification. The LAMP process can be
quantified by
several different approaches. Traditional methods include colorimetric
detection (e.g.
observation of solution turbidity due to the formation of insoluble magnesium
pyrophosphate, or with DNA-specific colorimetric dyes), electrophoresis, or
antibody-based
immunoassays. As disclosed herein in embodiments of detection systems and
methods of
measuring or analyzing modulations of electrical signals (e.g. impedance or
capacitance),
LAMP amplification may also be electrochemically detected (e.g. magnesium
pyrophosphate accumulation, or the buildup of protons as a result of DNA
polymerase
activity). Additional information about LAMP can be found in Notomi T et al.
"Loop-
mediated isothermal amplification of DNA" Nucleic Acids Res. (2000);
28(12):e63 and
Nagamine K et al. "Accelerated reaction by loop-mediated isothermal
amplification using
loop primers" Mol Cell Probes (2002); 16(3):223-229, each of which is hereby
expressly
incorporated by reference in its entirety.
[0688] Disclosed herein are methods of detecting the presence and/or amount of
a
nucleic acid in a biological sample. In some embodiments, the biological
sample is obtained
from a subject, preferably a human or other animal, a plant, a food, soil, or
a surface, or any
combination thereof. In some embodiments, the biological sample is obtained by
swabbing.
In some embodiments, the biological sample is or is derived from saliva, nasal
wash, nasal
swab, nasal nasopharyngeal swab, oropharyngeal swab, mucus, lavage fluid,
blood, plasma,
urine, stool, serum, cerebral spinal fluid, or any material comprising a
pathogen such as one
or more of a microbe, virus, bacteria, mold, or fungus. In some embodiments,
the subject is
a human. In some embodiments, the subject is a mammal. The methods comprise
contacting
the biological sample with an assay cartridge or a detection system,
amplifying the nucleic
acid by loop-mediated isothermal amplification (LAMP) with a primer set,
measuring or
analyzing a modulation of an electrical signal for the duration of the
amplification with the
primer set using the detection system, thereby detecting successful
amplification of the
nucleic acid with the primer set, and determining the presence and/or amount
of the nucleic
acid in the biological sample. In some embodiments, the nucleic acid is a
nucleic acid from
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a pathogen. In some embodiments, the primer set comprises, consists
essentially of, or
consists of one or more F3 primers, one or more B3 primers, one or more FIP
primers, and
one or more BIP primers. In some embodiments, the primer set comprises,
consists
essentially of, or consists of one or more F3 primers, one or more B3 primers,
one or more
LF primers, one or more LB primers, one or more FIP primers, or one or more
BIP primers,
or any combination thereof. In some embodiments, the primer set comprises,
consists
essentially of, or consist of one or more F3 primers, one or more B3 primers,
one or more
LF primers, one or more LB primers, one or more FIP primers, and one or more
BIP primers.
Each of the F3 primers, B3 primers, LF primers, LB primers, FIP primers and
BIP primers
are used for LAMP. The HP primers and BIP primers are required for the LAMP
process,
whereas the F3 primers, B3 primers, LF primers and/or LB primers strongly
enhance the
amplification but optionally may be excluded for high concentration targets.
In some
embodiments, each of the one or more F3 primers, one or more B3 primers, one
or more LF
primers, one or more LB primers, one or more FIP primers, or one or more BIP
primers
comprise 1, 2,3, 4, 5, 6, 7, 8, 9, or 10 primers. In some embodiments, the
pathogen comprises
more than one population obtained from different sources that may exhibit
variations in their
genes or genome regions (e.g., serotypes, strains, mutants, isolates, species,
variants, types,
subtypes, or clones) and the inclusion of more than one primer may increase
amplification
of the pathogen comprising more than one population. In some embodiments, the
primer set
is specific for a gene or a genome region of the pathogen. In some
embodiments, the gene or
the genome region is associated with the pathogenicity of the pathogen. In
some
embodiments, the nucleic acid is DNA, RNA, both, or a fragment or hybrid
thereof. In some
embodiments, where the nucleic acid is RNA, the nucleic acid is reverse
transcribed to
complementary DNA (cDNA) during the amplifying step. In other embodiments,
where the
nucleic acid is RNA, the nucleic acid is reverse transcribed to cDNA prior to
the amplifying
step. In some embodiments, the subject is a mammal. In some embodiments, the
subject is a
human.
[0689] Any one of the methods disclosed herein that employ an assay cartridge
or
detection system for LAMP may be applied to any one of the assay cartridges or
detection
systems, or both, disclosed herein or those that are previously known in the
art. In some
embodiments, the assay cartridges or detection systems, or both, comprise
elements that
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permit detection of the electrical signal during the amplifying step. In some
embodiments,
the electrical signal is impedance or capacitance, or both. In some
embodiments, the
electrical signal is measured or analyzed compared to a pre-determined control
value. In
some embodiments, the methods further comprise determining the biological
sample as
comprising the pathogen, or the gene or genome region thereof
[0690] Any one of the methods disclosed herein may further comprise mixing the
biological sample with a reagent and the primer set in the assay cartridge or
detection system,
or both, prior to the amplifying step. In some embodiments, the reagent is
used for LAMP.
In some embodiments, the reagent comprises a strand-displacing DNA polymerase
and
optionally a reverse transcriptase. Some non-limiting examples of strand-
displacing DNA
polymerases include but are not limited to Klenow fragment, phi29 DNA
polymerase, Bsm
DNA polymerase, or Bst DNA polymerase, or any combination thereof, or any
strand-
displacing DNA polymerase known in the art. Some non-limiting examples of
reverse
transcriptases include but are not limited to M-MLV reverse transcriptase,
reverse
transcription xenopolymerase (RTX), or variants thereof, or any combination
thereof, or any
reverse transcriptase known in the art. In some embodiments, the reagent or
the primer set,
or both, have been dried and/or lyophilized prior to mixing with the
biological sample. In
some embodiments, the biological sample is aqueous and dissolves the dried
and/or
lyophilized reagent or primer set, or both.
[0691] Any one of the methods disclosed herein may comprise an assay cartridge
or
detection system, or both, that comprises a heater. In some embodiments, the
amplifying step
comprises incubating the biological sample at, optionally a first temperature
for a first time
period, and at least a second temperature for a second time period. In some
embodiments,
the amplifying step comprises incubating the biological sample at, optionally
a first
temperature for a first time period, and one or more second temperatures for
one or more
second time periods (e.g., a second temperature, a third temperature, a fourth
temperature, a
fifth temperature, and/or a sixth temperature or more for a second, third,
fourth, fifth, sixth,
and/or more time periods). In some embodiments, the first temperature is 20 C,
21 C, 22 C,
23 C, 24 C, 25 C, 26 C, 27 C, 28 C, 29 C, 30 C, 31 C, 32 C, 33 C, 34 C, 35 C,
36 C,
37 C, 38 C, 39 C, 40 C, 41 C, 42 C, 43 C, 44 C. 45 C, 46 C, 47 C, 48 C, 49 C,
50 C,
51 C, 52 C, 53 C, 54 C, or 55 C, or about 20 C, about 21 C, about 22 C, about
23 C,
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about 24 C, about 25 C, about 26 C, about 27 C, about 28 C, about 29 C, about
30 C, about
31 C, about 32 C, about 33 C, about 34 C, about 35 C, about 36 C, about 37 C,
about 38 C,
about 39 C, about 40 C, about 41 C, about 42 C, about 43 C, about 44 C, about
45 C, about
46 C, about 47 C, about 48 C, about 49 C, about 50 C, about 51 C, about 52 C,
about 53 C,
about 54 C, or about 55"C, or any temperature within a range defined by any
two of the
aforementioned temperatures, preferably 23 C or about 23 C or 50 C or about 50
C, and the
first time period is 1., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15
minutes, or about 1, about
2, about 3, about 4, about 5, about 6, about 7, about 8, about 9, about 10,
about 11, about 12,
about 13, about 14, or about 15 minutes, or any time period within a range
defined by any
two of the aforementioned times, preferably 5 to 10 minutes or about 5 to
about 10 minutes.
In some embodiments, the second temperature or each of the one or more second
temperatures (e.g., second, third, fourth, fifth, sixth, and/or more
temperatures) is 21 C,
22 C, 23 C, 24 C, 25 C, 26 C, 27 C, 28 C, 29 C, 30 C, 31 C, 32 C, 33 C, 34 C,
35 C,
36 C, 37 C, 38 C, 39 C, 40 C, 41 C, 42 C, 43 C, 44 C, 45 C, 46 C, 47 C, 48 C,
49 C,
50 C, 51 C, 52 C, 53 C, 54 C, or 55 C, 56 C, 57 C, 58 C, 59 C, 60 C, 61 C, 62
C, 63 C,
64 C, 65 C, 66 C, 67 C, 68 C, 69 C, or 70 C, or about 21 C, about 22 C, about
23 C, about
24 C, about 25 C, about 26 C, about 27 C, about 28 C, about 29 C, about 30 C,
about 31 C,
about 32 C, about 33 C, about 34 C, about 35 C, about 36 C, about 37 C, about
38 C, about
39 C, about 40 C, about 41 C, about 42 C, about 43 C, about 44 C, about 45 C,
about 46 C,
about 47 C, about 48 C, about 49 C, about 50 C, about 51 C, about 52 C, about
53 C, about
54 C, or about 55 C, about 56 C, about 57 C, about 58 C, about 59 C, about 60
C, about
61 C, about 62 C, about 63 C, about 64 C, about 65 C, about 66 C, about 67 C,
about 68 C,
about 69 C, or about 70 C, or any temperature within a range defined by any
two of the
aforementioned temperatures, preferably 50 C or about 50 C, and each of the
one or more
second time periods (e.g., a second temperature, a third temperature, a fourth
temperature, a
fifth temperature, and/or a six temperature or more for a second, third,
fourth, fifth, sixth,
and/or more time periods) is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,
15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39,
40, 41, 42, 43, 44,45,
46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60 minutes, or
about 1, about 2, about
3, about 4, about 5, about 6, about 7, about 8, about 9, about 10, about 11,
about 12, about
13, about 14, about 15 minutes, about 16, about 17, about 18, about 19, about
20, about 21,
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about 22, about 23, about 24, about 25, about 26, about 27, about 28, about
29, about 30,
about 31, about 32, about 33, about 34, about 35, about 36, about 37, about
38, about 39,
about 40, about 41, about 42, about 43, about 44, about 45, about 46, about
47, about 48,
about 49, about 50, about 51, about 52, about 53, about 54, about 55, about
56, about 57,
about 58, about 59, or about 60 minutes, or any time period within a range
defined by any
two of the aforementioned times, preferably 10 minutes or about 10 minutes.
[0692] In one embodiment, the first step is performed at or about at 50 C, and
the
second step is performed at or about at 65 C. in another embodiment, the first
step is
performed for about 10 minutes or 10 minutes.
[0693] In some embodiments, the amplifying step further comprises incubating
the
biological sample at a third temperature for a third time period. In some
embodiments, the
third temperature is 60 C, 61"C, 62 C, 63 C, 64 C, 65 C, 66 C, 67 C, 68 C. 69
C, or 70 C,
or about 60 C, about 61 C, about 62 C, about 63 C, about 64 C, about 65 C,
about 66 C,
about 67 C, about 68 C, about 69 C, or about 70 C, or any temperature within a
range
defined by any two of the aforementioned temperatures, preferably 65 C or
about 65 C, and
the third time period is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
16, 17, 18, 19, 20, 21,
22, 23, 24, 25, 26, 27, 28, 29, 30, 31., 32, 33, 34, 35, 36, 37, 38, 39, 40,
41, 42, 43, 44, 45, 46,
47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60 minutes, or about 1,
about 2, about 3,
about 4, about 5, about 6, about 7, about 8, about 9, about 1.0, about 1.1,
about 1.2, about 1.3,
about 14, about 15 minutes, about 16, about 17, about 18, about 19, about 20,
about 21, about
22, about 23, about 24, about 25, about 26, about 27, about 28, about 29,
about 30, about 31,
about 32, about 33, about 34, about 35, about 36, about 37, about 38, about
39, about 40,
about 41, about 42, about 43, about 44, about 45, about 46, about 47, about
48, about 49,
about 50, about 51, about 52, about 53, about 54, about 55, about 56, about
57, about 58,
about 59, or about 60 minutes, or any time period within a range defined by
any two of the
aforementioned times, preferably 30 minutes or about 30 minutes. In some
embodiments, the
first temperature is performed at room temperature (e.g., 23 C or about 23 C)
for a time
period sufficient to allow the dried down reagents to rehydrate (e.g., 10
minutes or about 10
minutes); the second temperature is performed at 50 C or about 50 C for 10
minutes or about
minutes, and the amplification period is then conducted at 65 C or about 65 C.
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[0694] Examples 1 and 2 (FIGs. 29 and 30) show that by using the primers
described
herein and a SARS-CoV-2 template, that enhancement of LAMP occurs when a two-
step
incubation is used, and that the two-step protocol surprisingly resulted in a
lower limit of
detection (LOD), than the one-step protocol, with the most consistent
detection occurring at
the 10 minute time point. Example 3 (FIG. 31) shows that the two-step protocol
resulted in
improved detection of low concentration of SARS-CoV-2 genomic RNA compared to
the
one-step protocol. Lastly, Example 4 (FIG. 32) shows that 50 C appears to be
the optimal
temperature for the two-step protocol.
[0695] The ramping protocols for LAMP amplification set forth herein (e.g.,
the two-
step protocol) is suitable for use with any primer directed to any viral or
bacterial pathogen
nucleic acid template, preferably using the primers described herein, and is
not limited to
SARS-CoV-2. While it is preferred that the ramping protocols for LAMP
amplification set
forth herein (e.g., the two-step protocol) are utilized in one or more of the
systems described
herein (e.g., a be.well cartridge), it is also evident that the ramping
protocols for LAMP
amplification set forth herein (e.g., the two-step protocol) will improve the
level of detection
in other assays that utilize LAMP amplification. Accordingly, more generally,
use of a
starting temperature that is lower than the amplification temperature of 65 C
for a pre-
amplification time period is contemplated to improve the level of detection in
LAMP
amplification, preferably in one or more of the systems described herein
(e.g., a be.well
cartridge) but also in other detection systems that utilize e.g., optical or
radioactivity
detection. That is, a method of improving a limit of detection of a nucleic
acid using LAMP
amplification with a primer set at more than one temperature is contemplated.
[0696] Any one of the methods disclosed herein may be applied to the detection
of a
nucleic acid of a pathogen, or a genome region thereof. In some embodiments,
the pathogen
is a human pathogen. In some embodiments, the primer sets, or the one or more
F3 primers,
one or more B3 primers, one or more LF primers, one or more LB primers, one or
more FIP
primers, or one or more BIP primers, or any combination thereof, are designed,
configured
or selected to be not only specific towards a genome region of a pathogen but
also to amplify
said specific genome region more efficiently than other primer sets (e.g.,
more rapidly,
exhibiting faster time to detection of a positive amplification and/or with
greater specificity).
In some embodiments, the pathogen is a virus or a bacterium. In some
embodiments, the
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pathogen is SARS-CoV-2, hepatitis A virus, Influenza A virus subtype H1N1,
human
immunodeficiency virus-1, respiratory syncytial virus A, respiratory syncytial
virus B,
.Escherichia coli, Listeria monocytogenes, Mycobacterium tuberculosis,
Salmonella
enterica, or any combination thereof.
[0697] In some embodiments, the primers of any of the methods disclosed herein
are
provided for LAMP at defined concentrations.
[0698] In some embodiments, each of the one or more F3 primers are provided at
a
concentration of 100 nM, 200 nM, 300 nM, 400 nM, 500 nM, 600 nM, 700 nM, 800
nM,
900 nM, 1000 nM, 1100 nM, 1200 nM, 1300 nM, 1400 nM, 1500 nM, 1600 nM, 1700
nM,
1800 nM, 1900 nM, or 2000 nM or about 100 nM, about 200 nM, about 300 nM,
about 400
nM, about 500 nM, about 600 nM, about 700 nM, about 800 nM, about 900 nM,
about 1000
nM, about 1100 nM, about 1200 nM, about 1300 nM, about 1.400 nM, about 1500
nM, about
1600 nM, about 1700 nM, about 1800 nM, about 1900 nM, or about 2000 nM per
amplifying
reaction, or any concentration within a range defined by any two of the
aforementioned
concentrations, preferably 200 nM or about 200 nM.
[0699] In some embodiments, each of the one or more B3 primers are provided at
a
concentration of 100 nM, 200 nM, 300 nM, 400 nM, 500 nM, 600 nM, 700 nM, 800
nM,
900 nM, 1000 nM, 1100 nM, 1200 nM, 1300 nM, 1400 nM, 1500 nM, 1600 nM, 1700
nM,
1800 nM, 1.900 nM, or 2000 nM, or about 100 nM, about 200 nM, about 300 nM,
about 400
nM, about 500 nM, about 600 nM, about 700 nM, about 800 nM, about 900 nM,
about 1000
nM, about 1100 nM, about 1200 nM, about 1300 nM, about 1400 nM, about 1500 nM,
about
1600 nM, about 1700 nM, about 1800 nM, about 1900 nM, or about 2000 nM per
amplifying
reaction, or any concentration within a range defined by any two of the
aforementioned
concentrations, preferably 200 nM or about 200 nM.
[0700] In some embodiments, each of the one or more LF primers are provided at
a
concentration of 100 nM, 200 nM, 300 nM, 400 nM, 500 nM, 600 nM, 700 nM, 800
nM,
900 nM, 1000 nM, 1100 nM, 1200 nM, 1300 nM, 1400 nM, 1500 nM, 1600 nM, 1700
nM,
1800 nM, 1.900 nM, or 2000 nM, or about 100 nM, about 200 nM, about 300 nM,
about 400
nM, about 500 nM, about 600 nM, about 700 nM, about 800 nM, about 900 nM,
about 1000
nM, about 1100 nM, about 1200 nM, about 1300 nM, about 1400 nM, about 1500 nM,
about
1600 nM, about 1700 nM, about 1800 nM, about 1900 nM, or about 2000 nM per
reaction,
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or any concentration within a range defined by any two of the aforementioned
concentrations,
preferably 400 nM, about 400 nM, 1000 nM or about 1000 nM.
[0701] In some embodiments, each of the one or more LB primers are provided at
a
concentration of 100 nM, 200 nM, 300 nM, 400 nM, 500 nM, 600 nM, 700 nM, 800
nM,
900 nM, 1.000 nM, 1.100 nM, 1200 nM, 1300 nM, 1400 nM, 1500 nM, 1600 nM, 1700
nM,
1800 nM, 1900 nM, or 2000 nM, or about 100 nM, about 200 nM, about 300 nM,
about 400
nM, about 500 nM, about 600 nM, about 700 nM, about 800 nM, about 900 nM,
about 1000
nM, about 1100 nM, about 1200 nM, about 1300 nM, about 1400 nM, about 1.500
nM, about
1600 nM, about 1700 nM, about 1800 nM, about 1900 nM, or about 2000 nM per
amplifying
reaction, or any concentration within a range defined by any two of the
aforementioned
concentrations, preferably 400 nM, about 400 nM, 1000 nM or about 1000 nM.
[0702] In some embodiments, each of the one or more FIP primers are provided
at a
concentration of 100 nM, 200 nM, 300 nM, 400 nM, 500 nM, 600 nM, 700 nM, 800
nM,
900 nM, 1000 nM, 1100 nM, 1200 nM, 1300 nM, 1400 nM, 1500 nM, 1600 nM, 1700
nM,
1800 nM, 1900 nM, or 2000 nM, or about 100 nM, about 200 nM, about 300 nM,
about 400
nM, about 500 nM, about 600 nM, about 700 nM, about 800 nM, about 900 nM,
about 1000
nM, about 1100 nM, about 1200 nM, about 1300 nM, about 1400 nM, about 1.500
nM, about
1600 nM, about 1700 nM, about 1800 nM, about 1900 nM, or about 2000 nM per
amplifying
reaction, or any concentration within a range defined by any two of the
aforementioned
concentrations, preferably 1600 nM or about 1600 nM.
[0703] In some embodiments, each of the one or more BIP primers are provided
at a
concentration of 100 nM, 200 nM, 300 nM, 400 nM, 500 nM, 600 nM, 700 nM, 800
nM,
900 nM, 1000 nM, 1100 nM, 1200 nM, 1300 nM, 1400 nM, 1500 nM, 1600 nM, 1700
nM,
1800 nM, 1900 nM, or 2000 nM, or about 100 nM, about 200 nM, about 300 nM,
about 400
nM, about 500 nM, about 600 nM, about 700 nM, about 800 nM, about 900 nM,
about 1000
nM, about 1100 nM, about 1200 nM, about 1300 nM, about 1400 nM, about 1.500
nM, about
1600 nM, about 1700 nM, about 1800 nM, about 1900 nM, or about 2000 nM per
amplifying
reaction, or any concentration within a range defined by any two of the
aforementioned
concentrations, preferably 1600 nM or about 1600 nM.
[0704] In some embodiments of any of the methods disclosed herein, the
pathogen
is SARS-CoV-2. In some embodiments, the one or more F3 primers comprise one or
more
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sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%,
96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 1,7, 13,
19. In
some embodiments, the one or more B3 primers comprise one or more sequences
having at
least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,
99%,
or 100% homology to the sequences of SEQ ID NOs: 6, 12, 18, 25. In some
embodiments,
the one or more LF primers comprise one or more sequences having at least 85%,
86%, 87%,
88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology
to
the sequences of SEQ ID NOs: 3, 9, 15, 21. In some embodiments, the one or
more LB
primers comprise one or more sequences having at least 85%, 86%, 87%, 88%,
89%, 90%,
91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to the sequences
of
SEQ ID NOs: 5, 11, 17, 23, 24. In some embodiments, the one or more F1P
primers comprise
one or more sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%,
93%,
94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs:
2,
8, 14, 20. In some embodiments, the one or more BIP primers comprise one or
more
sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%,
96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 4, 10,
16, 22.
In some embodiments, the primer set comprises, consists essentially of, or
consists of
sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%,
96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 1-6.
[0705] In some embodiments of any of the methods disclosed herein, the
pathogen
is hepatitis A virus. In some embodiments, the one or more F3 primers comprise
one or more
sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%,
96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 26, 27,
34, 35,
43. In some embodiments, the one or more B3 primers comprise one or more
sequences
having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,
97%,
98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 32, 33, 41, 42, 48,
49. In
some embodiments, the one or more LF primers comprise one or more sequences
having at
least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,
99%,
or 100% homology to the sequences of SEQ ID NOs: 28, 36, 44. In some
embodiments, the
one or more LB primers comprise one or more sequences having at least 85%,
86%, 87%,
88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology
to
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the sequences of SEQ ID NOs: 31, 39, 40, 47. In some embodiments, the one or
more HP
primers comprise one or more sequences having at least 85%, 86%, 87%, 88%,
89%, 90%,
91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to the sequences
of
SEQ ID NOs: 29, 37, 45. In some embodiments, the one or more BIP primers
comprise one
or more sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,
94%,
95%, 96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 30,
38,
46. In some embodiments, the primer set comprises, consists essentially of, or
consists of
sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%,
96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 26-33.
[0706] In some embodiments of any of the methods disclosed herein, the
pathogen
is influenza A virus subtype HIM. In some embodiments, the one or more F3
primers
comprise one or more sequences having at least 85%, 86%, 87%, 88%, 89%, 90%,
91%,
92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to the sequences of
SEQ
ID NOs: 50, 51, 59. In some embodiments, the one or more B3 primers comprise
one or
more sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,
94%,
95%, 96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 52,
53,
60, 61. In some embodiments, the one or more LF primers comprise one or more
sequences
having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,
97%,
98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 54, 62, 63, 64. In
some
embodiments, the one or more LB primers comprise one or more sequences having
at least
85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or
100% homology to the sequences of SEQ ID NOs: 55, 56, 65. In some embodiments,
the
one or more HP primers comprise one or more sequences having at least 85%,
86%, 87%,
88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology
to
the sequences of SEQ ID NOs: 57, 66. In some embodiments, the one or more BIP
primers
comprise one or more sequences having at least 85%, 86%, 87%, 88%, 89%, 90%,
91%,
92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to the sequences of
SEQ
ID NOs: 58, 67. In some embodiments, the primer set comprises, consists
essentially of, or
consists of sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%,
93%,
94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs:
50-
58.
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[0707] In some embodiments of any of the methods disclosed herein, the
pathogen
is human immunodeficiency virus-1. In some embodiments, the one or more F3
primers
comprise one or more sequences having at least 85%, 86%, 87%, 88%, 89%, 90%,
91%,
92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to the sequences of
SEQ
ID NOs: 68, 69, 77, 89, 90. In some embodiments, the one or more B3 primers
comprise one
or more sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,
94%,
95%, 96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 75,
76,
87, 88, 96. In some embodiments, the one or more LF primers comprise one or
more
sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%,
96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 70, 71,
78, 79,
80, 91. In some embodiments, the one or more LB primers comprise one or more
sequences
having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,
97%,
98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 74, 84, 85, 86, 94,
95. In
some embodiments, the one or more FIP primers comprise one or more sequences
having at
least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,
99%,
or 100% homology to the sequences of SEQ ID NOs: 72, 81, 92. In some
embodiments, the
one or more B1P primers comprise one or more sequences having at least 85%,
86%, 87%,
88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology
to
the sequences of SEQ ID NOs: 73, 82, 83, 93. In some embodiments, the primer
set
comprises, consists essentially of, or consists of sequences having at least
85%, 86%, 87%,
88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology
to
the sequences of SEQ ID NOs: 68-76.
[0708] In some embodiments of any of the methods disclosed herein, the
pathogen
is respiratory syncytial virus A. In some embodiments, the one or more F3
primers comprise
one or more sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%,
93%,
94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs:
97,
98, 108. In some embodiments, the one or more B3 primers comprise one or more
sequences
having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,
97%,
98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 99, 100, 109. In
some
embodiments, the one or more LF primers comprise one or more sequences having
at least
85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or
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100% homology to the sequences of SEQ ID NOs: 101, 1.02, 11Ø In some
embodiments,
the one or more LB primers comprise one or more sequences having at least 85%,
86%, 87%,
88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology
to
the sequences of SEQ ID NOs: 103, 111. In some embodiments, the one or more
FIP primers
comprise one or more sequences having at least 85%, 86%, 87%, 88%, 89%, 90%,
91%,
92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to the sequences of
SEQ
ID NOs: 104, 106. In some embodiments, the one or more BIP primers comprise
one or
more sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,
94%,
95%, 96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 105,
107.
In some embodiments, the primer set comprises, consists essentially of, or
consists of
sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%,
96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 97-105.
[0709] In some embodiments of any of the methods disclosed herein, the
pathogen
is respiratory syncytial virus B. In some embodiments, the one or more F3
primers comprise
one or more sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%,
93%,
94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs:
11.2, 1.13, 125. In some embodiments, the one or more B3 primers comprise one
or more
sequences having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%,
96%, 97%, 98%, 99%, or 100% homology to the sequences of SEQ ID NOs: 114, 126.
In
some embodiments, the one or more LF primers comprise one or more sequences
having at
least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,
99%,
or 100% homology to the sequences of SEQ ID NOs: 115, 116, 117, 127. In some
embodiments, the one or more LB primers comprise one or more sequences having
at least
85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or
100% homology to the sequences of SEQ ID NOs: 118, 119, 120, 128. In some
embodiments, the one or more HP primers comprise one or more sequences having
at least
85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or
100% homology to the sequences of SEQ ID NOs: 121, 123. In some embodiments,
the one
or more BIP primers comprise one or more sequences having at least 85%, 86%,
87%, 88%,
89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% homology to the
sequences of SEQ ID NOs: 122, 124. In some embodiments, the primer set
comprises,
-1.72-
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