WO2022182837A1 - Devices and methods for rapid nucleic acid preparation and detection - Google Patents

Abstract

Disclosed herein are compositions, methods and devices for the isolation, and also for detection of a nucleic acid (e.g., a pathogen nucleic acid) in a biological sample such as a saliva sample. The compositions, method and devices isolate and detect nucleic acid (e.g., RNA of the pathogen). When used to detect a pathogen they can be used either to universally detect the pathogen or to detect variants of the pathogen. Specific pathogens for detection include viruses, such as RNA viruses, such as the SARS-CoV-2 virus. Also disclosed are compositions, methods and devices for the rapid isolation of nucleic acid (e.g., RNA) from a biological sample such as a saliva sample. Kits containing the compositions and/or devices are further disclosed for use in the methods.

Description

DEVICES AND METHODS FOR RAPID NUCLEIC ACID PREPARATION AND

DETECTION

RELATED APPLICATIONS

[0001] This application claims benefit under 35 U.S.C. § 119(e) to U.S. Provisional Application No. 63/154,327, filed February 26, 2021, the contents of which are incorporated herein by reference in their entirety.

GOVERNMENTAL SUPPORT

[0002] This invention was made with Government support under AI060354 awarded by the National Institutes of Health. The Government has certain rights in the invention.

FIELD OF THE INVENTION

[0003] The field of the invention relates to devices and methods for the preparation of nucleic acids for use in amplification reactions and for point-of-care diagnostics.

BACKGROUND

[0004] Significant progress has been made in the use of CRISPR (clustered regularly interspaced short palindromic repeats)/Cas components of adaptive microbial immunity in molecular diagnostics (1-3). Several Cas effectors have been used as highly specific nucleic acid sensors that cause detectable collateral cleavage of engineered nucleic acid probes after target binding. SHERLOCK (specific high-sensitivity enzymatic reporter unlocking) ( 4 , 5) and DETECTR (DNA endonuclease-targeted CRISPR trans reporter) ( 6 ) use Cas 13a or Cas 12a to create ultra-sensitive molecular diagnostics for a variety of targets, including infectious diseases such as Zika virus, Cytomegalovirus, BK virus, and Plasmodium species (7-9), with simplified readouts including lateral flow assays (5, 8-10).

[0005] Multiple CRISPR/Cas diagnostics have been created to target SARS-CoV-2 using varied viral purification, amplification, and detection methods (11-15). However, the vast majority of workflows still require multiple liquid-handling steps and laboratory equipment such as pipettes, centrifuges, and heating blocks, as well as the technical skills for their use. Although there are several home diagnostic tests approved for use by the US Food and Drug Administration (FDA), the vast majority of the tests involve self-collection followed by mailing to a central laboratory or are based on rapid antigen tests, which have been shown to be less accurate than nucleic acid-based testing with the potential for relatively high false negative and false positive results (16). There is only one FDA-approved at-home nucleic acid-based test for SARS-CoV-2, which costs $50.00 USD and requires a physician’s prescription (77). These diagnostic methods have contributed to ongoing efforts to make SARS-CoV-2 testing as widely available as possible. However, despite these advances, all of the tests described above only allow for the general detection of SARS-CoV-2 and not of specific strains.

[0006] There are six general categories of SARS-CoV-2 strains (75), but the relationship between specific strains and mutations and changes in virulence and viral behavior are only recently being elucidated. New variants may affect transmissibility, treatment efficacy, and the degree of immunity that is generated by both natural infection and immunization (19). Of particular concern are variants B.l.1.7 (originally discovered in the United Kingdom),

B.1.351 (originally discovered in South Africa), and P.l / B.1.1.28.1 (originally discovered in Brazil / Japan) (20-22). The N501 Y spike mutation is common to all three of these variants and causes a 4- to 10-fold increased affinity to the human ACE2 receptor for SARS-CoV-2 (23), which is hypothesized to contribute to the observed increase in transmissibility of B.1.1.7. The B.1.351 and P.1 variants have additional receptor binding domain (RBD) mutations, such as E484K, that show significantly reduced neutralization by antibodies generated by current vaccines and by prior natural infection presumably from non-variant SARS-CoV-2 strains (22, 24-27). These variants also have additional mutations in the spike N-terminal domain and appear to be resistant to several therapeutic monoclonal antibodies targeting that region (22). As new studies advance, it is clear that the variants and their associated mutations will have a significant impact on public health and the efficacy of SARS-CoV-2 control measures such as social restrictions, vaccinations, and therapies. While variant identification through specialized epidemiological sequencing centers is useful (19), the lack of global access to this resource and delay in result availability has hampered the tracking of and response to the spread of new SARS-CoV-2 variants. There is an urgent need for POC diagnostics for SARS-CoV-2 variants. Of particular benefit would be a system that is easy to use, simple to setup, and smartphone-integrated to enable distributed, non- centralized data collection, rapid adoption, and scaled-up deployment in response to outbreaks (19, 28).

SUMMARY

[0007] Aspect of the invention relate to a sample collection and preparation system. The system comprises a sample preparation column having a capture matrix at a base of the column, the capture matrix being configured to capture nucleic acid during heating from a sample comprising saliva (e.g., unprocessed saliva) and/or breath condensate in the column; an absorbent filter disposed below the capture matrix of the sample preparation column to cause a received sample comprising saliva and/or breath condensate to move during heating through an individual capture matrix via capillary action at a flow rate of at least about 1 min/mL; a high-heat lysis chamber in thermal connection with one or more heating mechanisms, wherein the sample preparation column is disposed within the high-heat lysis chamber.

[0008] In some embodiments, the sample collection and preparation system further comprises a saliva collection interface connected at a second end opposite the base of the sample preparation column.

[0009] In some embodiments of the sample collection and preparation system described herein, the sample preparation column is preloaded with lysis reagents comprising a reducing agent and a metal chelating agent.

[0010] In some embodiments of the sample collection and preparation system described herein the reducing agent is DTT present at a concentration to result in a final concentration of from about 10 mM to about 100 mM, and the metal chelating agent is EGTA present at a concentration to result in a final concentration of about 5mM, in an added sample.

[0011] In some embodiments of the sample collection and preparation system described herein the reducing agent is DTT present at a concentration to result in a final concentration of 10 mM DDT, and the metal chelating agent is EGTA present at a concentration to result in a final concentration from about 1 mM to about 50 mM EGTA in an added sample.

[0012] In some embodiments of the sample collection and preparation system described herein, the capture matrix is a porous membrane that can bind to nucleic acids and is compatible with in situ amplification.

[0013] In some embodiments of the sample collection and preparation system described herein, the capture matrix is a polyethersulfone (PES) membrane that contains 0.22 um pores and is optionally functionalized with a hydrophilic surface treatment.

[0014] In some embodiments of the sample collection and preparation system described herein, the capture matrix is a membrane containing pores ranging from between about 0.1 um to about 0.5 um.

[0015] In some embodiments of the sample collection and preparation system described herein the saliva sample is between about 0.2 mL and 5 mL in volume. [0016] In some embodiments of the sample collection and preparation system described herein the saliva sample is about 0.5 mL, 0.6 mL, 0.7 mL, 0.8 mL, 0.9 mL, 1.0 mL, 1.1 mL,

1.2 mL, 1.3 mL, 1.4 mL, 1.5 mL, 1.6 mL, 1.7 mL, 1.8 mL, 1.9 mL, 2.0 mL, 2.1 mL, 2.2 mL,

2.3 mL, 2.4 mL, 2.5 mL, 2.6 mL, 2.7 mL, 2.8 mL, 2.9 mL, 3.0 mL, 3.1 mL, 3.2 mL, 3.3 mL,

3.4 mL, 3.5 mL, 3.6 mL, 3.7 mL, 3.8 mL, 3.9 mL, 4.0 mL, 4.1 mL, 4.2 mL, 4.3 mL, 4.4 mL,

4.5 mL, 4.6 mL, 4.7 mL, 4.8 mL, 4.9 mL, or about 5.0 mL in volume.

[0017] In some embodiments of the sample collection and preparation system described herein the sample preparation column is reversibly disposed within the high-heat lysis chamber and/or the absorbent filter is reversibly disposed below the capture matrix.

[0018] In some embodiments of the sample collection and preparation system described herein it further comprises a cap that securely attaches to the base of the sample preparation column containing the capture matrix, upon removal of the absorbent filter, to cover and protect the capture matrix.

[0019] In some embodiments of the sample collection and preparation system described herein is for use within an integrated diagnostic testing device.

[0020] Other aspects of the invention relate to an integrated diagnostic testing device comprising one or more heating mechanisms, a high-heat lysis chamber in thermal connection with the one or more heating mechanisms, a low-heat reaction chamber adjoining the lysis chamber and in thermal connection with the one or more heating mechanisms, the low-heat reaction chamber including one or more individual reaction sub chambers for sample analysis, the low-heat reaction chamber including an exterior transilluminator filter, a saliva collection interface connected to one or more sample preparation columns disposed within the high-heat lysis chamber, the one or more sample preparation columns having a capture matrix at a base of the columns configured to capture nucleic acid during heating from a saliva sample in the one or more sample preparation columns, an absorbent filter disposed in the high-heat lysis chamber below the capture matrix of the one or more sample preparation columns to cause a received saliva sample to move during heating through an individual capture matrix via capillary action at a flow rate at least about 1 min/mL, an extraction mechanism for transferring the individual capture matrix to the individual reaction sub-chamber within the low-heat chamber, and a light source positioned to illuminate an interior of the low-heat reaction chamber to allow a visual florescence determination of the saliva sample in the individual capture matrix through the transilluminator filter. [0021] In some embodiments of the device described herein the one or more heating mechanisms are configured to heat the high-heat lysis chamber to a temperature that extract RNA molecules and inactivates nucleases.

[0022] In some embodiments of the device described herein the one or more heating mechanisms are configured to heat the low-heat reaction chamber to a temperature that regulates amplification and detection reactions.

[0023] In some embodiments of the system or device described herein the absorbent filter is disposed immediately below the capture matrix.

[0024] In some embodiments of the system or device described herein the saliva sample moves during heating through the capture matrix at a flow rate of about 1.5 min/mL.

[0025] In some embodiments of the device described herein low-heat reaction chamber further includes one or more sealed water reservoirs for reaction mixture hydrating.

[0026] In some embodiments of the device described herein the extraction mechanism is a plunger for insertion into the sample preparation column to release the water from the sealed reservoir.

[0027] In some embodiments of the device described herein the sample preparation column is removable from the high heat lysis chamber into the low-heat reaction chamber for transfer of the individual capture matrix to the individual reaction sub-chambers.

[0028] In some embodiments of the system or device described herein the sample preparation column is preloaded with lysis reagents to thereby result in a final concentration of 10 mM DTT and 5 mM EGTA in the saliva sample.

[0029] In some embodiments of the system or device described herein the capture matrix is a porous membrane that can bind to nucleic acids and is compatible with in situ amplification. [0030] In some embodiments of the device described herein the extraction mechanism is a plunger for insertion into the sample preparation column to dislodge the capture matrix from the column and deposit the capture matrix and the water into the reaction sub-chamber.

[0031] In some embodiments of the device described herein one or more of the high heat lysis chamber, the low-heat reaction chamber, the sample preparation column, and the extraction mechanism are modular, optionally disposable, and wherein the heating mechanisms, and optionally the light source are housed in a modular, reusable portion of the device.

[0032] In some embodiments of the device described herein the reaction sub-chamber comprises one or more components of a reaction mixture necessary for one-pot SHERLOCK detection of target nucleic acid. [0033] In some embodiments of the device described herein the one or more components comprises RPA primers and/or guide RNA specific for universal detection of SARS-CoV-2 nucleic acid.

[0034] In some embodiments of the device described herein the RPA primers and guide RNAs detect regions of SARS-CoV-2 nucleic acid conserved across most variants (e.g., the N gene).

[0035] In some embodiments of the device described herein the one or more components comprises RPA primers and guide RNA for detection of human RNaseP for use as a control. [0036] In some embodiments of the device described herein the RPA primers and guide RNAs are for specific detection of single nucleotide polymorphisms unique to specific SARS-CoV-2 variants.

[0037] In some embodiments of the device described herein the single nucleotide polymorphisms are in the spike protein gene.

[0038] In some embodiments of the device described herein use of the device in a method for detecting a pathogen results in greater than or equal to about 96% sensitivity and greater than or equal to about 95% specificity for the detection of a pathogen in saliva samples across a range of viral loads (e.g., SARS-CoV-2 in clinical saliva samples).

[0039] In some embodiments of the device described herein the pathogen is a RNA containing pathogen, such as SARS-CoV-2.

[0040] In some embodiments of the device described herein the device further comprises a smartphone device comprising an embedded camera for receiving illumination projected through the transilluminator filter, and one or more processors configured to implement a color segmentation algorithm stored in memory for detecting and quantifying florescence of the received illumination, wherein quantifying florescence includes quantifying the number of pixels corresponding to a predetermined florescence color to determine a result for the rehydrated nucleic acid samples.

[0041] In some embodiments of the system or device described herein one or more of the heating mechanisms includes a temperature sensitive circuit linked to a polyimide heater and a temperature sensor.

[0042] In some embodiments of the device described herein, the light source includes one or more LEDs.

[0043] Other aspects of the invention relate to a high-heat lysis chamber, a low-heat reaction chamber, an extraction mechanism, and/or a base structure housing one or more heating mechanisms for use within the device described herein. [0044] Other aspects of the invention relate to a method for detecting a pathogen in a subject comprising providing an embodiment of the integrated diagnostic testing device described herein, wherein the device comprises a reaction mixture comprising dried components necessary for SHERLOCK detection of pathogen specific nucleic acid in the individual reaction sub-chamber using a fluorescent label readout, depositing unprocessed saliva of the subject into the saliva collection interface and activating the heating mechanism to heat the high-heat lysis chamber for a period sufficient to lyse pathogen, inactivate nucleases and allow for deposition of pathogen nucleic acids onto the capture matrix, transferring the individual capture matrix and water from the sealed water reservoir to the individual reaction sub-chamber using the extraction mechanism, and activating the heating mechanism to heat the low-heat reaction chamber for a period sufficient to promote sample analysis, detecting visual florescence through the transilluminator filter to thereby determine presence or absence of the pathogen.

[0045] Other aspects of the invention relate to a method for preparing RNA, comprising depositing an unprocessed saliva sample into a composition comprising i) DTT present at a concentration from about 10 mM to about 500 mM; and ii) EGTA present at a concentration from about 5 mM to about 50mM; heating the composition with saliva sample to about 70⁰ to 99° C for a period sufficient to lyse a pathogen present within the saliva and inactivate nucleases, and concentrating RNA present in the heated composition on a capture matrix by flowing the heated composition through the capture matrix to thereby deposit the RNA onto the capture matrix.

[0046] In some embodiments of the methods described herein heating is to about 95⁰ C. [0047] Other aspects of the invention relate to a method for preparing RNA, comprising depositing an unprocessed saliva sample into a sample preparation column comprising i) 10 mM DTT and 5 mM EGTA final concentration; ii) a capture matrix at a base of the columns for capturing nucleic acid during heating; iii) an absorbent filter disposed immediately below the capture matrix of the one or more sample preparation columns to cause the saliva sample to move during heating through the capture matrix at a flow rate of at least about 1 minute/mL, heating the column containing the saliva sample to about 70⁰ to 99° C for a period sufficient to lyse a pathogen present within the saliva and inactivate nucleases and allow for deposition RNA onto the capture matrix, and flowing the sample through the capture matrix to thereby deposit the RNA onto the capture matrix. [0048] Other aspects of the invention relate to a kit for RNA preparation from a saliva sample, comprising the sample collection and preparation system described herein, and instructions for use.

[0049] Other aspects of the invention relate to a kit for detecting a pathogen in a subject, comprising the integrated diagnostic testing device described herein, and instructions for use. [0050] In some embodiments of the kits described herein, they further comprise water and/or a composition comprising a reducing agent and a metal chelating agent in aqueous suspension.

[0051] In some embodiments of the kits described herein the reducing agent is DTT present at a concentration to result in a final concentration of from about 10 mm to about 100 mM, and the reducing agent is EGTA present at a concentration to result in a final concentration of about 5mM, in an added saliva sample.

[0052] In some embodiments of the kits described herein, the kit does not contain any nuclease inhibitors.

[0053] In some embodiments of the kits described herein, the kit further comprises one or more of a) a reaction mixture comprising one or more components necessary for SHERLOCK detection of target nucleic acid; b) RPA primers and/or guide RNA specific for universal detection of SARS-CoV-2 nucleic acid; and/or c) RPA primers and/or guide RNAs for specific detection of single nucleotide polymorphisms unique to specific SARS-CoV-2 variants.

[0054] In some embodiments of the kits described herein the single nucleotide polymorphisms are in the spike protein gene.

[0055] In some embodiments of the kits described herein or the methods described herein the pathogen is SARS-CoV-2.

[0056] Definitions

[0057] The term “saliva sample” as used herein refers to a sample containing unprocessed saliva obtained from a subject. In some embodiments, the saliva sample further contains biological fluids obtained from the nose or mouth, such as breath condensate. The saliva sample may further include small amounts of additives for lysis and nuclease inactivation.

For example, without limitation, the unprocessed saliva may be diluted no more than 2%

(e.g., about 0.5%, 0.6%, 0.7%, 0.8%, 0.9%, 1.0%, 1.1%, 1.2%, 1.3%, 1.4%, 1.5%, 1.6%,

1.7%, 1.8%, 1.9%, or about 2%) or no more than 6% (e.g., 2%, 2.5%, 3%, 2.5%, 4%, 4.5%, 5%, 5.5%, or about 6%), or no more than 11% (e.g., 6.5%, 7%, 7.5%, 8%, 8.5%, 9%, 9.5%, 10%, 10.5%, or about 11%) such as with additives for lysis and/or nuclease inactivation. In one embodiment, the saliva sample further contains biological fluids obtained from the nose or mouth, such as breath condensate.

[0058] The term "biological sample" as used herein refers to a cell or population of cells or a quantity of tissue or fluid from a subject. Often, a "biological sample" will contain cells from an animal or subject, but the term can also refer to non-cellular biological material, such as non-cellular fractions of blood, saliva, or urine, that can be used to prepare nucleic acids using the methods and compositions described herein. Biological samples include, but are not limited to, whole blood, plasma, serum, saliva, sputum, breath condensate, nasopharyngeal swab, oropharyngeal swab, urine, cell culture, tissue biopsies, scrapes ( e.g buccal scrapes), or cerebrospinal fluid. When a biological sample is intended for point-of- care diagnostics, it is preferred that the sample be easily and non-invasibly obtained, for example, blood, serum, saliva, breath condensate, sputum, nasopharyngeal swab, oropharyngeal swab, or urine. A biological sample or tissue sample can refer to a sample of tissue or fluid isolated from an individual including, but not limited to, blood, plasma, serum, breath condensate, tumor biopsy, urine, stool, sputum, spinal fluid, pleural fluid, nipple aspirates, lymph fluid, the external sections of the skin, respiratory, intestinal, and genitourinary tracts, tears, saliva, milk, cells (including, but not limited to, blood cells), tumors, organs, and also samples of in vitro cell culture constituent.

[0059] As used herein, the term “nucleic acid sample preparation” refers to a method of preparing nucleic acids (e.g. pathogen nucleic acids such as RNA) such that they can be used in a downstream reaction, such as an amplification and/or detection reaction, without the need for additional isolation or purifucation steps.

[0060] The term “isothermal amplification reaction” refers to a nucleic acid amplification method that does not require thermal cycling to permit amplification. The term distinguishes amplification methods, such as the polymerase chain reaction (PCR), that use cycles of thermal denaturation of nucleic acid by incubation at a temperature above the melting temperature (T_m), annealing of nucleic acid primers by incubation at another temperature generally below the Tm, and most often, incubation at another temperature optimal for a polymerase enzyme to extend the annealed primers. An isothermal amplification reaction, by contrast, can be performed at a single temperature, and generally relies upon, for example, DNA binding and strand-displacing enzyme factors to permit target nucleic acid amplification. In one embodiment, the temperature of the isothermal amplification reaction does not deviate by more than 10° C in either direction (e.g., deviates by less than 5° C, by less than 2° C, by less than 1°C) or is performed at a single temperature with no temperature deviation required for amplification.

[0061] As used herein, the terms “amplify”, “amplification”, “amplification reaction”, or “amplifying” refer to any in vitro process for multiplying the copies of a target nucleic acid using an isothermal amplification method. Amplification can refer to an “exponential” increase in target nucleic acid. However, “amplifying” can also refer to linear increases in the numbers of a target nucleic acid, but is different than a one-time, single primer extension step.

[0062] As used herein, the term “capture matrix” refers to a porous membrane or matrix that can bind to nucleic acids non-specifically and is compatible with in situ amplification. The matrix may be solid or semisolid. Exemplary solid supports include membranes made from a polymeric material, such as cellulose and cellulose ester membranes, glass fiber, nitrocellulose, nylon, polytetrafluoroethylene (PTFE), polypropylene, polyvinylidene fluoride (PVDF) or polycarbonate membranes, and polyethersulfone membrane. The membrane may be further functionalized with a hydrophilic surface treatment to facilitae nucleic acid capture. Pore size of the membrane can be further varied, such as to modify capture and/or flow rate through the membrane. In one embodiment, the capture matrix is polyethersulfone (PES) membrane that contains 0.22 um pores (e.g., functionalized with a hydrophilic surface treatment). Membrane thickness (diameter) will also affect flow rate, and will be selected by the skilled practitioner to achieve the desired flow rate (e.g., 0.5 min/ml or slower; 0.5 min/ml to 5 min/ml). In some embodiments, thickness is about 160, to about 185 pm. In some embodiments, thickness is about 0.1mm to about 1 mm. In some embodiments, thickness is about 2 mm to about 10mm. In some embodiments, porosity of the membrane is about 60% to about 80%. The methods and devices described herein may also be further adapted for use of other capture matrixes, such as magnetic beads (e.g., micron-sized magnetic beads), Sepharose beads, agarose beads, column chromatography matrices, etc.

[0063] As used herein, the term “universal detection” when used in the context of detection of a pathogen by the methods compositions and devices described herein, refers to detection of all or a large subset (e.g., the majority) of variants/strains/serotypes of the pathogen. Without limitation, universal detection is accomplished, for example, by detection of a highly conserved portion of a specific pathogen nucleic acid, or a portion thereof. For example, a portion of the N-gene of SARS-CoV-2 as described herein may be used for universal detection of the SARS-CoV-2 pathogen. The skilled artisan will recognize that as a pathogen evolves, sufficient genetic variation may arise that prevent detection of all such pathogens by detection of a single nucleic acid. However, as long as a portion of a nucleic acid is conserved across the majority of variants/serotypes/strains, or at miminum a usefull proportion of variants/serotypes/strains, universal detection, as the term is used herein, may be accomplished.

[0064] As used herein, the term “specific detection” when used in the context of detection of a pathogen by the methods, compositions and devices described herein, refers to detection of a variant/serotype/strain, or a subset of variants/serotypes/strains of a pathogen, by detection of one or more single nucleotide polymorphisms (SNPs) unique to that variant/serotype/strain or subset. For example, specific SNPs present in nucleic acid encoding the spike protein of SARS-CoV-2 as described herein, may be used for specific detection of one or more SARS- CoV-2 pathogen variants. The skilled artisan will recognize that different variants/serotypes/strains of a pathogen may share some SNPs, and it may be necessary to detect a specific combination of SNPs unique to a target pathogen variant in order to delineate some variants/serotypes/strains. Such detection is still considered specific detection as the term is used herein.

[0065] As used herein, the term “target pathogen” refers to the pathogen to be identified by the methods, compositions, and/or devices of the invention, either by universal detection or by specific detection. The term “target variant” or “target pathogen variant” may also be used when referring to specific detection.

[0066] As used herein, the term “target nucleic acid” refers to the nucleic acid used in the methods, compositions, and/or devices of the invention, to identify the target pathogen.

[0067] As used herein, the term “comprising” means that other elements can also be present in addition to the defined elements presented. The use of “comprising” indicates inclusion rather than limitation.

[0068] As used herein the term "consisting essentially of refers to those elements required for a given embodiment. The term permits the presence of additional elements that do not materially affect the basic and novel or functional characteristic(s) of that embodiment of the invention.

[0069] The term "consisting of' refers to compositions, methods, and respective components thereof as described herein, which are exclusive of any element not recited in that description of the embodiment.

[0070] Further, unless otherwise required by context, singular terms shall include pluralities and plural terms shall include the singular. [0071] Other than in the operating examples, or where otherwise indicated, all numbers expressing quantities of ingredients or reaction conditions used herein should be understood as modified in all instances by the term “about.” The term “about” when used in connection with percentages can mean ±1% or ±5%.

BRIEF DESCRIPTION OF THE DRAWINGS [0072] The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.

[0073]

[0074] FIGS. 1A and IB are illustrations of exemplary embodiments. (A) illustrates a cross-sectional view of an exemplary integrated diagnostic testing device, according to some implementations of the present disclosure. (B) illustrates a cross-sectional view of an exemplary sample collection and preparation system, according to some implementations of the present disclosure.

[0075] FIG. 2 illustrates a cross-sectional view of an exemplary reaction sub-chamber, according to some implementations of the present disclosure.

[0076] FIG. 3 illustrates an exploded perspective view of an exemplary integrated diagnostic testing device, according to some implementations of the present disclosure.

[0077] FIG. 4 illustrates an oblique view of an exemplary integrated diagnostic testing device prior to diagnostic testing, according to some implementations of the present disclosure.

[0078] FIGS. 5A and 5B illustrates an exemplary integrated diagnostic testing device during the sample preparation and reaction stages, according to some implementations of the present disclosure.

[0079] FIGS. 6 illustrates the exemplary integrated diagnostic testing device from FIGS. 5A and 5B during the illumination and reaction reading stages, according to some implementations of the present disclosure.

[0080] FIG. 7A-7B is a series of illustrations of the overall miSHERLOCK workflow and SARS-CoV-2 target regions, related to the exemplary integrated testing device and reaction sub-chamber of FIGS. 1 and 2. (A) Schematic of miSHERLOCK, which integrates instrument-free viral RNA extraction and concentration from unprocessed saliva, one-pot SHERLOCK reactions that detect SARS-CoV-2 and variants, fluorescent output, and accessory mobile phone app for automated result interpretation. Step 1, the user turns on the device and introduces 4mL of saliva into the flow column (alsoreferred to ehrein as the sample preparation column), disposal within the sample preparation chamber (also referred to herein as high-heat lysis chamber) (2 mL per filter), and adds 40pL of 1M DTT and 500mM EGTA lysis buffer. Saliva flows by gravity and capillary action through a PES membrane which accumulates and concentrates viral RNA. Step 2, the user transfers the flow columns into the reaction chamber and depresses the plunger cover to release the PES membrane and sealed stored water into sample tubes containing freeze-dried, one-pot SHERLOCK reaction pellets. Step 3, the user returns after 55 minutes and visualizes the assay directly or using a smartphone app that quantifies fluorescent output and automates result interpretation. The app may also be used for distributed remote result reporting. (B) SARS-CoV-2 genomic map indicating regions that are targeted in this study. The N gene target is used for a universal SARS-CoV-2 assay. SARS-CoV-2 variants are detected by targeting key mutations in the N terminal and RBD regions of the SARS-CoV-2 spike protein, including N501Y, Y144del, and E484K.

[0081] FIG. 8A-8E is a series of illustrations of exemplary miSHERLOCK devices: a CRISPR-enabled POC diagnostic that integrates mechanical, electronic, biochemical, and optical components, related to the exemplary integrated testing device and related systems of FIGS. 3 to 6. (A) Exploded schematic of an integrated duplexed miSHERLOCK device with the two modules shown. (B) Photograph of miSHERLOCK device after reaction with positive and negative saliva samples. (C) Oblique view of miSHERLOCK device before use. (D) Adjunctive mobile phone application supports automated quantitation and result interpretation. (E) Workflow timing and representative examples of results.

[0082] FIG. 9A-9F shows sample processing with miSHERLOCK improves the detection of SARS-CoV-2 and variants. (A) Table summarizing performance near the limit of detection of four SARS-CoV-2 assays in the miSHERLOCK device. (B) Table showing experimental results of Universal SARS-CoV-2 assay using 100,000 cp/mL spiked in saliva compared to healthy saliva negative control (NC). (C) SARS-CoV-2 spike genomic map indicating the target sequences and selected gRNA sequences that are used in this study. (D- F) Sequences of the wildtype (WT) and N501Y, Y144del, and E484K mutant SARS-CoV-2 genomic regions and gRNAs. Mutation-specific gRNAs show high SHERLOCK activity when tested against full-length viral RNA containing each of the indicated mutations (left), but only minimal SHERLOCK activation when challenged with wildtype full-length SARS- CoV-2 RNA (right). For (D-F), WT control reactions were tested at 2,000,000 cp/mL input RNA. Error bars represent the standard deviation of triplicate experiments. [0083] FIG. 10A-10B is a series of graphs of experimental results indicating miSHERLOCK accurately detects SARS-CoV-2 in clinical saliva samples. (A) Receiver operating characteristic (ROC) curve analysis of the patient sample data collected for the universal SARS-CoV-2 assay using results from 27 RT-qPCR confirmed positive and 21 negative human saliva samples. (B) Clinical COVID-19 saliva sample RT-qPCR cycle threshold (CT) plotted against fluorescent readout on miSHERLOCK demonstrates dose- dependent semi-quantitative results. RT-qPCR positive saliva samples (CT range 14-38) are plotted in orange (shown on left side of graph), and RT-qPCR negative samples (CT > 40) are sorted by fluorescence and plotted in gray (shown on right side of graph).

[0084] FIG. 11 is a bar graph of experimental results showing testing of the universal SARS-CoV-2 N gene assay using full length synthetic RNA spiked in water. The limit of detection was 20,000 cp/mL.

[0085] FIG. 12 is a bar graph of experimental results showing universal SARS-CoV-2 N gene assay showed no significant cross-reactivity with common endemic Human coronavirus OC34 and 299E. Template is RNA spiked into water. NC indicates no template negative control.

[0086] Fig. 13A-13C are Heatmaps of RPA primer screens to detect SARS-CoV-2 variants. For each mutation, up to 110 different primer sets (forward denoted by “F”, reverse denoted by “R”) were screened in pairs to identify those that yielded the highest fluorescence signal in SHERLOCK assays. (A-C) Heatmaps of primer pairs for variant mutations N501 Y, Y144del, and E484K.

[0087] Fig. 14A-14F are experimental results showing testing of N501Y, Y144del, and E484K mutation-specific SARS-CoV-2 SHERLOCK assays in water. Mutation-specific gRNAs for N501Y (A-B), Y144del (C-D), and E484K (E-F) show high SHERLOCK activity when tested against full-length variant RNA matching mutant target RNA. Error bars represent the standard deviation of triplicate experiments.

[0088] Fig. 15A-15D is a series of bar graphs of experimental results from optimization of multiple reaction conditions of SHERLOCK assays in solution. Different reaction conditions were optimized in one-pot SHERLOCK reactions that combined recombinase polymerase amplification (RPA) with Casl2a amplicon detection in reaction mixtures containing either Ocp/ml or 1 x 10⁵ cp/ml full-length synthetic SARS-CoV-2 RNA. (A) Buffer with HEPES and PEG had a higher signal-to-noise ratio as compared to standard RPA buffer supplied by commercial vendor TwistDx. (B) RT enzymes from different manufacturers were tested in one-pot SHERLOCK reactions. Protoscript from NEB was used in miSHERLOCK as it led to higher signal-to-noise ratios. (C) Quenched fluorescent reporter concentrations (e.g., also referred to herein as sensors) for SHERLOCK reactions were optimized. (D) RNase H (0.05U/pl) improved the signal-to-noise ratio in SHERLOCK assays. Error bars represent standard deviations of triplicate technical replicates.

[0089] Fig. 16 is a bar graph of experimental results showing unprocessed human saliva non-specifically activates SHERLOCK assays. SARS-CoV-2 RNA spiked in unprocessed human saliva (orange) and in water (blue) demonstrate that saliva sample pre treatment is required to avoid false positive signals in SHERLOCK assays.

[0090] Fig. 17 is a bar graph showing experimental results of chemical and heat pretreatment inactivates salivary nucleases. Healthy human saliva alone and saliva spiked with lfM full-length synthetic SARS-CoV-2 RNA were pre-treated with a range of buffers and 95°C heating for 5 min. Buffers that contained EGTA and DTT showed the highest signal-to-noise ratios in subsequent SHERLOCK reactions. Error bars represent standard deviations of triplicate technical replicates.

[0091] Fig. 18 is a bar graph of experimental results showing the flow rate through PES membranes affects RNA capture efficiency. The capture efficiency of 5 aM synthetic, full- length SARS-CoV-2 RNA in water filtered through a PES membrane at different flow rates was measured. PES membranes that contained concentrated RNA were then added to one-pot SHERLOCK reactions. Flow rates slower than 1 min/mL were ideal to concentrate SAR.S- CoV-2 RNA. Error bars represent the standard deviation of triplicate technical replicates. [0092] Fig. 19 is a bar graph of experimental results that show human saliva flow rate is faster with larger aperture diameters of the PES membrane. The flow rate in miSHERLOCK’s sample preparation chamber was optimized by flowing 2.5 mL of human saliva through different aperture diameters (mm) of impermeable tape covering the PES membrane at the bottom of the flow column. Apertures between 2mm- 10mm were tested and found to yield acceptable results. Smaller apertures led to slower flow rates. Preferably apertures that result in flow rates approximately .5 to 5 min/ml would be used in the device (e.g., for convenience and/or to minimize evaporation in the membrane). Error bars represent the standard deviation of triplicate technical replicates.

[0093] Fig. 20A-20D is a series of photograph of miSHERLOCK triplex and quadruplex 3D printed devices. (A) An assembled 3D printed triplexed miSHERLOCK device with a representative reaction of SARS-CoV-2 negative saliva showing one positive test (RNaseP positive control) and two negative tests (SARS-CoV-2 NP and N501 Y). (B) The components of the triplexed miSHERLOCK reader (L-R): plunger, saliva collector, sample preparation column, reaction chamber with heater, LEDs, and orange acrylic transilluminator filter. (C) An assembled 3D printed quadruplexed mi SHERLOCK device with a representative reaction showing three positive samples and one negative sample. (D) The components of the quadruplexed mi SHERLOCK reader (L-R): plunger, saliva collector, sample preparation column, reaction chamber with heater, LEDs, and orange acrylic transilluminator filter.

[0094] Fig. 21A-21C is a photograph and two bar graphs of experimental results showing fluorescence readouts in the miSHERLOCK app are comparable to those measured in standard laboratory plate readers. (A) Representative photo of visual fluorescence signal of a single pair of negative and positive reactions in the miSHERLOCK device. A dilution series of reactions was performed, and fluorescence values were quantified utilizing a BioTEK NEO HTS plate reader and used as a comparison to (B) quantitation using our custom-built phone app and (C) ImageJ quantitation of the fluorescent area of the photo.

It was observed that both methods can be used to interpret the results from miSHERLOCK devices semi-quantitatively. Error bars represent the standard deviation of triplicate measurements.

[0095] Fig. 22A-22H shows sensitivity of miSHERLOCK diagnostic for universal SARS-CoV-2 [(nucleoprotein or NP assay), (A-B)], N501K (C-D), Y144del (E-F), and E484K (G-H) mutation detection by comparison of probit regression curves and fit characteristics.

[0096] Fig. 23 is a bar graph of experimental results of clinical saliva samples tested with miSHERLOCK Human RNaseP assay. The RNaseP assay performed well when tested with clinical saliva samples. NC indicates negative control (water only, as there were no non-human saliva samples available).

[0097] Fig. 24 is a graphical representation of experimental data indicating miSHERLOCK heater temperature can be controlled and maintained over long periods of time. A DS18B20 digital temperature sensor attached to an Arduino Uno was used to confirm that the reaction chamber maintained the desired temperature of 37°C for at least 2 hours (typical reaction time 1 hour). Device temperature can be maintained far beyond the time required for typical reactions without the need for additional heating or cooling elements.

[0098] Fig. 25A-25C are circuit diagrams for temperature and LED control. (A) The reaction chamber temperature circuit consists of a MOSFET transistor that is attached to the polyimide heater and the trip-point temperature sensor. The temperature sensor is programmed to 37°C by placing a 1201<W resistor between pins 3 and 5. The heater and trip- point sensor are both attached to a 12 V battery source. (B) The lysis chamber temperature circuit consists of a polyimide heater attached to a 24 V battery source. There is no additional temperature control needed, because the polyimide heater was shown to maintain the high temperature necessary to lyse viral particles and denature potential nucleases with an appropriate voltage source alone. (C) The LED circuit consists of two royal blue LEDs in series attached to a 12 V voltage source by a 270 W resistor to keep the current within the optimal range of 20 mA.

[0099] Fig. 26A-26C are photographs of miSHERLOCK electronics integrated into a 3D printed device. (A) An assembled 3D printed reusable temperature control housing containing two heaters for the two distinct temperature zones needed. (B) The optics housing contains two LEDs to excite the fluorophores released in the SHERLOCK reaction. (C) The assembled temperature controller circuit beneath the electronics box provides temperature regulation for the reaction chamber of the miSHERLOCK platform.

PET ATT /ED DESCRIPTION

[0100] Described herein is the development of a low-cost, self-contained, point of care (POC) diagnostic, referred to herein as miSHERLOCK (Minimally Instrumented SHERLOCK), that is capable of concurrent universal detection of a pathogen (e.g., SARS- CoV-2) as well as specific detection of the pathogen variants (e.g., SARS-CoV-2 variants B.1.1.7, B.1.351, or P.l). The miSHERLOCK platform integrates an optimized one-pot SHERLOCK reaction with an RNA capture method (e.g., paper/membrane capture) compatible with in situ nucleic acid amplification and Cas detection. Aspects of the invention combine instrument-free, built-in sample preparation from saliva, room- temperature stable reagents, battery-powered incubation, and simple visual and mobile phone-enabled output interpretation shown to have a limit of detection that matches US Centers for Disease Control and Prevention (CDC) RT-qPCR assays for SARS-CoV-2 of 1,000 copies/mL (cp/mL) (Fig. 7A).

[0101] Aspects of the invention relate to the integrated diagnostic testing device, components thereof, and methods of use for detecting a pathogen from a saliva sample. In some embodiments, the device and methods and components are specifically adapted for detection of SARS-CoV-2, although the skilled artisan will recognize that detection of other pathogens, especially pathogens containing RNA, is also possible. Although saliva is not a commonly used clinical sample for SARS-CoV-2, several studies demonstrate comparable performance between saliva and nasopharyngeal samples for the detection of SARS-CoV-2 (29). Additionally, in paired collection samples in hospitalized patients, salivary SARS-CoV-2 viral load has been shown to be marginally higher than nasopharyngeal swabs and positive for a greater number of days (30). There are also FDA-approved home-based saliva collection kits for mail-in SARS-CoV-2 diagnosis (37). Saliva offers the significant advantage of easy, instrument-free, non-invasive self-collection, which avoids dependence on limiting equipment such as swabs and transport media, and decreases infectious risk to medical personnel and use of personal protective equipment during collection (32). However, saliva samples typically require several processing steps prior to use. Described herein is a novel combined filtration and concentration step from untreated saliva that is directly processed on the platform without separate processing steps, that significantly enhances assay sensitivity. [0102] In the assay, detection of the pathogen only requires two simple steps which can be performed by the user. The assay is readily adjustable for additional variants or pathogen targets, and does not require transfer of amplicons, which significantly reduces the risk of cross-contamination by lay users. The device and methods of the invention can be used for general pathogen (e.g., SARS-CoV-2) detection as well as the specific detection of pathogen mutations (e.g., SARS-CoV-2 N501Y and E484K mutations) with the goal of locally tracking variant strains and assessing the need for variant-specific booster vaccines (33, 34) such as those targeting SARS-CoV-2 E484K due to its effects on the efficacy of current vaccines.

The invention is highly flexible, demonstrating high performance detection of the SARS- CoV-2 Y144del mutation. The assay may utilize a simple, low cost device, examples of which are described herein. The process is streamlined and straightforward enough that it is possible for the subject to perform the method themselves (e.g., with the use of the integrated diagnostic device described herein) after depositing their saliva sample into the container. Alternatively, the subject may deposit the saliva sample into the container, with the skilled practitioner performing the remaining steps of the method.

[0103] Use of the device in the methods described herein results in highly sensitive and accurate detection of the target pathogen. The limit of detection (LOD) is comparable to high-performance SARS-CoV-2 RT-qPCR assays (40). Accuracy with respect to false positives and cross reactivity is miminal. For example, the SARS-CoV-2 detection showed no significant cross-reactivity against Human coronavirus OC43 or Human coronavirus 229E genomic RNA, when tested. Sensitivity of detection of 1, 100 cp/mL may be achieved through utilization of the appropriate gRNA sequences and RPA primers (forward and reverse) for the target nucleic acid within the target pathogen. [0104] Diagnostic Testing Device

[0105] Aspects of the invention relate to an integrated diagnostic testing device for the detection of a pathogen from saliva of a subject. A desirable aspect of an integrated diagnostic device is that a single contained system is used for sample preparation and the near-immediate detection of a pathogen in the prepared sample (e.g., saliva sample) obtained from the subject, without the delays typically associated with sending a sample to a laboratory including having to wait for the test result.

[0106] Referring to FIG. 1A, a cross-sectional view of an exemplary integrated diagnostic testing device 100 is depicted. Integrated diagnostic testing devices are discussed in more detail throughout this disclosure. In certain implementations, integrated diagnostic testing device 100 can include one or more features similar to those described for FIGS. 8 A to 8E and FIGS. 20A to 20D that are in addition to, or in lieu of, the features described for FIG. 1. For example, the integrated diagnostic testing device 100 can include dual zone mi SHERLOCK systems that incorporate the sample preparation methodologies with SHERLOCK reactions and provide direct visual readouts for determining testing outcomes for the detection of pathogens. For miSHERLOCK systems, the process includes on-device sample preparation along with RNA concentration onto a capture matrix (e.g., a PES membrane) followed by on-device physical transfer of the RNA-containing capture membrane into one-pot SHERLOCK reactions (e.g., via a reactant pellet).

[0107] The integrated diagnostic testing device 100 includes a base structure 110 and one or more heating mechanisms 113, 116. The base structure 110 can provide a flat base to support the components of the testing device 100, and in some implementations, an integrated wall structure 131, as depicted in FIG. 1, or a secured wall structure 132 extends upwardly from the flat base. A power source 118 is connected via wiring (complete electrical connection not shown) to various electrical components of the testing device 100. For example, one or more battery packs (e.g., two 12V batteries, one 24V battery) of the power source 118 may be connected to, among other components, the one or more heating mechanisms 113, 116, a light source 120 (e.g., one or more light-emitting diodes; the one or more light emitting diodes including at least two royal blue LEDs), and in some implementations, one or more temperature sensors 114, 117 associated with at least one of the heating mechanisms 113,

116. In some implementations, the power source 118 may be external to the integrated testing device 100, internal to the integrated testing device 100, or some hybrid of internal and external. In addition, the power source can include batteries or can be a plug-in device, such as a transformer. [0108] It is contemplated that the base structure 110 can take multiple shape configurations beyond the L-shaped cross-section depicted in FIG. 1. For example, a base structure for an integrated diagnostic device can include different combinations of a bottom structure, along with partial or full side walls extending upwardly from a bottom structure that can be generally rectangular, round, elliptical, or trapezoidally shaped. In certain implementations, the base structure 110 supports the one or more heating mechanisms 113, 116, a high-heat lysis chamber 130, and a low-heat reaction chamber 140, and/or their related components. Furthermore, a base structure may also provide the support for any electrical connections between a power supply and the electrical components of the integrated diagnostic testing device, such as the one or more heating mechanisms 113, 116 or a light source 120. The wall structures 131, 132 may or may not be formed as one piece with the base structure 110.

[0109] A high-heat lysis chamber 130 is formed by one or more wall structures, such as wall structures 131, 132, that are positioned adjacent to and extending upwardly from the flat base of the base structure 110. The high-heat lysis chamber 130 provides an area for the preparation of a sample, such as a saliva sample 172, 173 received by the integrated diagnostic testing device 100. The high-heat lysis chamber 130 is in thermal connection with one or more heating mechanisms, such as the heating mechanism 113.

[0110] The integrated diagnostic testing device 100 further includes a low-heat reaction chamber 140 adjacent (for example, see shared wall structure 132) to the high-heat lysis chamber 130. The low-heat reaction chamber 140 is in thermal connection with at least one of the one or more heating mechanisms, such as the heating mechanism 116. The low-heat reaction chamber 140 includes one or more individual reaction sub-chambers 150, 155 positioned within an interior space 142. The individual reaction sub-chambers 150, 155 provide an area for analyzing an individual sample, such as saliva samples 172, 173. The low-heat reaction chamber 140 further includes a transilluminator filter 145 that may also serve as another wall structure of the integrated diagnostic testing device 100.

[0111] In some implementations, the low-heat reaction chamber 140 may also include one or more sealed water reservoirs 352, 357 (see, for example, FIGS. 3 and 8A) for reaction mixture hydrating. In some aspects, reaction mixture hydrating may instead include, or be, a manual operation where water is added into the top (e.g., see top 255 in FIG. 2) of the one or more individual reaction sub-chambers 150, 155 using, for example, a pipette or dropper. [0112] The integrated diagnostic testing device 100 further includes a saliva collection interface 160 connected to one or more removable sample preparation columns 170, 175 that are disposed within the high-heat lysis chamber 130 during sample preparation. In some implementations, the one or more removable sample preparation columns 170, 175 include a capture matrix 171, 176 at abase 177 of the columns 170, 175. The capture matrix 171, 176 includes materials for capturing nucleic acid from a sample, such as saliva samples 172, 173, received in the one or more removable sample preparation columns 170, 175 during heating (e.g., by heating mechanism 113).

[0113] An absorbent filter 179 is positioned in the high-heat lysis chamber 130 below the capture matrix 171, 176 and the one or more removable sample preparation columns 170,

175. The absorbent filter 179 causes a received sample, such as saliva samples 172, 173, to move or flow during heating through the capture matrix 178 via capillary action. In some implementation, the absorbent filter 179 causes the sample to move at a flow rate of at least about 1 min/mL. The absorbent filter 179 may be disposed immediately below the capture matrix 171, 176 and in some aspects is a cellulose filter material. In some implementations, a saliva sample moves during heating through the capture matrix at a flow rate between about 1.3 min/mL to about 1.7 min/mL. In some implementation, the saliva sample moves during heating through the capture matrix at a flow rate of about 1.5 min/mL.

[0114] In some implementations, a saliva sample can be between about 0.2 mL and about 5 mL in volume. In some implementations, the saliva sample is about 0.5 mL, 0.6 mL, 0.7 mL, 0.8 mL, 0.9 mL, 1.0 mL, 1.1 mL, 1.2 mL, 1.3 mL, 1.4 mL, 1.5 mL, 1.6 mL, 1.7 mL, 1.8 mL,

1.9 mL, 2.0 mL, 2.1 mL, 2.2 mL, 2.3 mL, 2.4 mL, 2.5 mL, 2.6 mL, 2.7 mL, 2.8 mL, 2.9 mL,

3.0 mL, 3.1 mL, 3.2 mL, 3.3 mL, 3.4 mL, 3.5 mL, 3.6 mL, 3.7 mL, 3.8 mL, 3.9 mL, 4.0 mL,

4.1 mL, 4.2 mL, 4.3 mL, 4.4 mL, 4.5 mL, 4.6 mL, 4.7 mL, 4.8 mL, 4.9 mL, or about 5.0 mL in volume.

[0115] In some implementations, the capture matrix 171, 176 is a paper capture membrane (e.g., a PES membrane, optionally functionalized with a hydropilic surface treatment). In some aspects, the capture matrix is a porous membrane that can bind to nucleic acids and is compatible with in situ amplification.

[0116] The integrated diagnostic testing device 100 may include a capture matrix extraction mechanism 180 that is provides for transferring an extracted individual capture matrix, such as individual capture matrix 182 or 184, that are respectively extracted from the corresponding capture matrix 171 and 176 that are prepared during the sample preparation phase in the high-heat lysis chamber 130. As one example, the extracted individual capture matrix 182 is transferred via the capture matrix extraction mechanism 180 to one of the individual reaction sub-chambers 150, 155 within the low-heat chamber 140. In some implementations, the capture matrix extraction mechanism 180 provides for the extraction and transfer of one, two, three, four, five, six, seven, or more individuals capture matrices. In the exemplary aspect depicted in FIG. 1, two individual capture matrices 182, 184 are extracted and transferred to the to the individual reaction sub-chambers 150, 155. In some implementations, the capture matrix extraction mechanism 180 includes an extraction mechanism cover 181 and an extraction mechanism plunger 185, that may include multiple elongated hollow cylinders for extracting and transferring the individual captures matrices from the high-heat lysis chamber 130 to the low-heat reaction chamber 140. The plunger is inserted into the sample preparation column to dislodge the capture matrix from the column and allow an individual capture matrix, such as individual capture matrix 182 or 184, to be extracted and deposited into the individual reaction sub-chamber(s), along with the addition of reaction water.

[0117] The reaction of an individual capture matrix in the reaction sub-chambers, such as reaction sub-chambers 150, 155, occurs following the hydrating of the individual capture matrices when placed in contact with the reaction water, such as reaction water 188, 189, in the reaction sub-chambers. As discussed elsewhere in this disclosure, the reaction water 188, 189 may be added manually into each of the reaction sub-chambers, e.g., 150, 155, or following the puncturing of sealed reaction water reservoirs (e.g., see elements 352, 357 in FIG. 3) as the capture matrix extraction mechanism 180 is transferred into the low-heat reaction chamber 140.

[0118] As depicted in the exemplary aspect of FIG. 1, the light source 120 is positioned to illuminate the interior space 142 of the low-heat reaction chamber 140 to allow a visual florescence determination of analyzed samples captured in the respective individual capture matrix 182, 184 by viewing visual florescence associated with the analyzed samples that passes through the transilluminator filter 145 in response to the illumination from the light source 120. The visual florescence determination can be made by the human eye and/or through the aid of a handheld smart device implementing an application configured to interpret the visual florescence.

[0119] In some implementations, an application operating on a smart device 190, such as a smartphone, can support the automated quantification and result interpretation of the visual florescence from the analyzed sample of the capture matrix that is projected through 145 transilluminator filter of the integrated diagnostic device 100 in response to the illumination of the interior space 142. FIG. 8D also depicts an exemplary smartphone device, similar to smart device 190, and further includes a display of the results of the implementation of a color segmentation process for detecting and quantifying florescence of received illumination projected though a transilluminator filter (e.g., an orange colored acrylic filter) of an integrated diagnostic device. The illumination is provided by the light source 120 that transmits illumination through the reaction sub-chambers 150, 155 causing visual florescence from the analyzed sample of the capture matrix to project through the transilluminator filter 145 for either visual observation 195 (e.g., see humane eye) or receipt by a camera 191 of the smart device 190. The smart device may be wirelessly connected to other processing and/or storage devices (not shown) for storage and/or further processing of data representing the illumination received in the camera of the smart device 190.

[0120] In some implementations, an integrated diagnostic device, such as integrated diagnostic device 100 includes a smart device 190, such as a smartphone having an at least partially embedded camera 191 for receiving florescence projected through the transilluminator filter 145 in response to illumination of the interior space 142. One or more processors 192 may be embedded within the smart device 190 that are configured to implement a color segmentation algorithm stored in memory 193 on the smart device 190. The color segmentation algorithm provides for the detection and quantification, via the embedded camera 191 and processor(s) 192 of the smart device 190, of florescence of received illumination from the transilluminator filter 145. Quantifying the visual florescence includes quantifying a number of pixels corresponding to a predetermined florescence color to determine a result for the analyzed nucleic acid samples. The transilluminated output can be read or analyzed visually or via the application on the smart device 190.

[0121] In some implementations, the one or more heating mechanisms of an integrated diagnostic testing device are operational to heat the high-heat lysis chamber from about 70° C to about 99° C, to about 95° C, or to a temperature that extracts RNA molecules and inactivates nucleases. In some implementations, the one or more heating mechanisms are operational to heat the low-heat reaction chamber from about 34° C to about 40⁰ C, to about 37° C, from about 34° C to about 65⁰ C, or to a temperature that regulates amplification and detection reactions. In some implementations, the one or more heating mechanisms cyclically heat the low-heat reaction chamber between at least two different temperatures during diagnostic testing, such as temperatures typically used for polymerase chain reaction (e.g, about 95-100°C, then about 45-60 °C, then about 72-75 °C, cycling several times).

[0122] In some implementations, one or more of a high heat lysis chamber, a low-heat reaction chamber, a sample preparation column, and an extraction mechanism are modular and disposable. Furthermore, one or more heating mechanisms, and optionally a light source can be housed in a modular, reusable portion of an integrated diagnostic testing device. In some implementations, the modular, reusable portion of the integrated diagnostic testing device is a base structure. In some implementations, the one or more of the heating mechanisms include a temperature sensitive circuit linked to a polyimide heater and a temperature sensor. In some implementations, the low-heat reaction chamber further comprises a temperature circuit.

[0123] Turning now to FIG. 2, a cross-sectional view of an exemplary individual reaction sub-chamber 250 is depicted, similar to the individual reaction sub-chambers 150, 155 from FIG. 1, that may be a component in an integrated diagnostic testing device. The individual reaction sub-chamber 250 can include an individual capture matrix 280 extracted from a capture matrix after sample preparation and transferred to the individual reaction sub chamber 250 using a mechanism, such as the capture matrix extraction mechanism 180 described for FIG. 1. A capture matrix, such as the capture matrix 178 described for FIG. 1, from which an individual capture matrix 280 is extracted, can comprise, among other things, a porous membrane that binds nucleic acids and is also compatible with in situ amplification, or have other features described elsewhere herein. In some implementations, an individual capture matrix 280 may be a PES membrane that in some aspects contains 0.22 um pores and is optionally functionalized with a hydrophilic surface treatment. Membranes with a pore sizes 5 pm or smaller, optionally no smaller than 50 nm, can be used. In some embodiments, a membrane with pore sizes of from 0.1 to 0.5 pm can be used. In some embodiments, pore size can be from 0.2 to 0.45 pm.

[0124] The thicker a membrane, the longer a sample will take to flow through the capture matrix, presuming the pore size remain constant. In some implementations, the thickness of a membrane, such as a PES membrane, can range from about 50 to 1,000 micrometers, from about 100 to 500 micrometers, from about 100 to 300 micrometers, from about 150 to 250 micrometers, from about 150 to 200 micrometers, or from about 160 to 185 micrometers. [0125] In some implementations, the individual reaction sub-chamber 250 can include or be positioned below a sealed (e.g., foil seal) water reservoir, such as water reservoir 352 or 357 in FIG. 3, to provide for reaction mixture hydrating after an individual capture matrix 280 is transferred into the individual reaction sub-chamber 250. Reaction water 288 from the water reservoir, along with the individual reaction matrix 282 with concentrated RNA from a saliva sample and reaction components 290 (e.g., freeze-dried one-pot SHERLOCK pellet), initiate a diagnostic reaction. In some implementations, the reaction components are already present in the individual reaction sub-chamber 250 into which the individual capture matrix 282 is deposited (e.g., in dry or lyophilized form with the addition of a small amount of aqueous solution, such as 50 ul of water, to re-hydrate as appropriate). Alternatively, in some implementations, the reaction components may be added (e.g., as a dry pellet, fresh components, or a combination of dry and fresh components) shortly after the addition of the individual capture matrix 282 to the reaction sub-chamber 250.

[0126] Referring now to FIG. 3, an exploded perspective view and an oblique view of an exemplary integrated diagnostic testing device 300 is depicted. Similar to the exemplary integrated diagnostic testing device 100 from FIG. 1 but with modified configurations, the integrated diagnostic testing device 300 includes a base structure 310, heating mechanisms 313, 316, and a capture matrix (not shown) seated immediately above an absorbent filter 379 that is supported by the base structure 310. The base structure can support one or more wall structures, such as vertical wall structure 331, extending upwardly from a top surface of the base structure 310 that form at least a portion of one or more chambers. The integrated diagnostic testing device 300 further includes a high-heat lysis chamber 330, a low-heat reaction chamber 340, a saliva collection interface 360, sample preparation columns 370, 375, a capture matrix extraction mechanism 385, individual reaction sub-chambers 350, 355, light source(s) 320, 322, and a transilluminator filter 345, such as an orange acrylic filter that can also serve as a wall structure for one of the sides of the low-hear reaction chamber 340. [0127] In some implementations, the low-heat reaction chamber 340 includes one or more sealed water reservoirs, such as water reservoirs 352, 357, for reaction mixture hydrating. The sealed water reservoirs may be disposed above corresponding reaction sub-chambers, such as sub-chambers 350 or 355, such that as the extraction mechanism 385 enters the low- heat reaction chamber 340 it punctures the sealed water reservoirs 352, 357 and allow the reaction water to flow downward into the corresponding reaction sub-chambers 350, 355. In some implementations, the capture matrix extraction mechanism 385 is a plunger for insertion into the sample preparation column and to release the water from the sealed reservoir. In FIG. 3, the reaction water 384, 388 is shown already released from the sealed water reservoirs 352, 357. In some implementations, the sample preparation column 370,

375 is removable from the high-heat lysis chamber 330 into the low-heat reaction chamber 340 for transfer of the individual capture matrix 382, 384 (shown already transferred to reaction sub-chambers) to the individual reaction sub-chambers 350, 355.

[0128] The integrated diagnostic testing device further can include a sample (e.g., saliva) collection interface 360 connected to the sample preparation columns 370, 375 that have a capture matrix disposed therein (see FIG. 1 and related descriptions). An electronic box 318 is depicted adjacent to one of the wall structures define a portion of the high-heat lysis chamber 330 and the low-heat reaction chamber 340. FIG. 4 depicted the integrated diagnostic testing device 300 prior to use and immediately before a sample is deposited into the sample collection interface 360 (e.g., a subject depositing a saliva sample).

[0129] Referring now to FIGS. 5A and 5B, the exemplary integrated diagnostic testing device 300 is depicted during the sample preparation (FIG. 5A) and reaction (FIG. 5B) stages. In FIG. 5A, the integrated diagnostic testing device is ready to receive a saliva sample in the sample collection interface 360. The saliva sample then flows down the sample preparation columns 370, 375, but can include more or fewer sample columns depending on the number of desired reactions for the individual sample. The sample preparation columns, and thus, the sample are heated within the high-heat lysis chamber 330. The sample preparation columns can extend down to the absorbent filter 379, which assists with drawing the heated saliva sample through the capture matrix (not shown). Once the sample preparation is completed, the sample preparation column 370, 375 with the capture matrix disposed therein can then transferred from the high-heat lysis chamber 330 to the low-heat reaction chamber 340 for activation and incubation of the sample, as depicted in FIG. 5B. A plunger 385 is used as a capture matrix extraction mechanism to dislodged individual capture matrices, such as matrix 382 and 384, from the sample preparation column, push the dislodged individual sample matrices through corresponding sealed water reservoirs 352,

357, and into individual reaction sub-chambers 350, 355. Matrix 382 and matrix 384 are depicted in FIG. 5B after being dislodged and deposited in the corresponding reaction sub chambers 350, 355.

[0130] Referring now to FIG. 6, the exemplary integrated diagnostic testing device 300 from FIGS. 5A and 5B is depicted during the illumination and related reaction reading stages where florescence of received illumination 325 is projected though a transilluminator filter 345 of the integrated diagnostic device 300 for quantification as discussed elsewhere herein including for FIG. 1 and the related smart device 190. The illumination 325 is generated by light sources 320, 322, which in some aspects, as blue light-emitting diodes. The illumination 325 causes visual florescence (see FIG. 8E) from the individual capture matrix, such as matrix 382 and matrix 384, and the reaction mixture in the reaction sub-chambers, such as sub-chambers 350, 355, that is projected toward and through the transilluminator filter 345. In some aspects, as depicted in FIG. 8E, the resulting visual florescence or lack thereof can lead to a determination of presence of a target nucleic acid such as RNA. In some embodiments the target nucleic acid (e.g., RNA) is pathogen specific and as such detection is of the pathogen. In such embodiments, the resulting visual fluorescence or lack thereof can lead to a determination of (i) no detection of a pathogen (e.g., SARS-CoV-2 not detected) in any of the reaction sub-chamber mixtures, (ii) a pathogen being detected (e.g., SARS-CoV-2 detected), or (iii) a variant of the pathogen being detected (e.g., SARS-CoV-2 specific variant detected).

[0131] In some implementations of the integrated diagnostic testing devices, such as devices 100, 300, the duration of the sample preparation is dependent on the diameter and/or pore size of the capture matrix. For example, it is desirable for the capture matrix to capture enough RNA from a sample, such as a saliva sample, but to do so quickly enough to optimize the test time.

[0132] In some implementations, the number of sample preparation columns and reaction sub-chambers can vary, including providing the ability to simultaneously run one, two, four, six, or more reaction tests. In some implementations, the reaction testing may include a control sample.

[0133] In some implementations, multiplexing to test for multiple pathogens is contemplated. For example, each assay is a single-plex test, but an integrated diagnostic testing device can be configured to simultaneously allow two, three, four, or more different assays.

[0134] In some implementations, an integrated diagnostic testing device includes two chambers operable at two different temperatures, one operating at high heat and the other at low heat. The testing device including a saliva collection interface and channeling structure above and in fluid communication with the one or more sample preparation column disposed within the high-heat lysis chamber. The sample preparation column includes a capture matrix and absorbent material for facilitating flow of the saliva sample through the capture matrix. The high-heat lysis chamber is heated, thereby heating the sample preparation column contained therein, via a battery powered heater or other heating mechanism to at least 70 degrees Celsius or higher including up to approximately 95 degrees Celsius. The heating causes lysis allowing RNA molecules to be extracted from the saliva sample, and further causes the inactivation of nucleases present. The nucleic acid (e.g., RNA) within the saliva sample is collected on the capture matrix as the saliva sample passes through, an extraction mechanism/device is then used to remove (e.g., dislodge) the capture matrix from the sample preparation chamber and to thereby transfer the capture matrix to a low-heat reaction chamber operating at about 37 degrees Celsius. The low-heat reaction chamber acts as an incubator for regulating amplification and detection reactions. The extraction device includes a plunger for pushing through a column to drop the RNA-carrying filters (and optionally water from a sealed reservoir, if not then water is added manually such as with a dropper) into a reaction subchamber disposed within the low-heat reaction chamber, that in some implementations can be referred to as the Sherlock reaction chamber. A light source provides illumination into the reaction chambers that results in visual florescence projected through a transilluminator filter to provide the results of the reaction through either visual observation or through pixel analysis on a smart device. In the reaction sub-chamber, the RNA-carrying capture matrixcombines with reaction water and freeze-dried SHERLOCK pellets to initiate a diagnostic reaction. In some implementations, the reaction takes about an hour and results are determined based on an increase in fluorescence

[0135] Method for Detecting Pathogen

[0136] Aspect of the invention relate to a method for detecting a pathogen in a subject by detecting the pathogen in a saliva sample of the subject. The skilled practitioner will also recognize the method may also be used to detect a target nucleic acid (e.g., target RNA) of the subject. The method can be conveniently described in two parts, the first of which is rapid single step isolation of nucleic acids from an unprocessed saliva sample from the subject. The sample is deposited into a container (e.g., the sample preparation column of the diagnostic testing device described herein), and mixed with a reducing agent (e.g., DTT to a final concentration of about 10 mM to about 100 mM) and a metal chelating agent (e.g., EGTA to a final concentration of about 5mM). For convenience, the reducing agent and metal chealting agent may already be present in the container into which the saliva is deposited, or may be added after the sample. The sample is then heated to a temperature of about 70°C to about 99°C (herein referred to as “high heat”) for a short period of time sufficient to lyse pathogen (or cells) present and inactivate nucleases (e.g., 3-6 minutes at 95°C). This may be accomplished, for example, in the high-heat lysis chamber of the diagnostic testing device, described herein. The sample is further filtered through a capture matrix such as a membrane (e.g., polyethersulfone membrane functionalized with a hydrophilic surface treatment) designed for capture and concentration of nucleic acid (e.g., RNA) from the sample as well as elimination of other saliva components (e.g., by flow through). Optimal design of the container and other components results in flow rates that allow filtering and heating to take place simultaneously (e.g., at least 1 min/mL, such as 1.5 min/mL), thereby minimizing the time frame of the nucleic acid isolation (e.g., from 3-6 minutes total). This first part of the method is described in further detail below under “Nucleic Acid Sample Prep”.

[0137] The resulting nucleic acid (e.g., RNA) isolated is of sufficient quantity, quality and purity to be analyzed for content by isothermal amplification and cas mediated detection such as by one-pot SHERLOCK (specific high-sensitivity enzymatic reporter unlocking) analysis, to yield highly sensitive and accurate detection of a pathogen (or other target RNA) present in the subject. In the second part of the method, the capture matrix containing the nucleic acid is transferred to another container (e.g., the low-heat reaction chamber of the diagnostic device described herein) combined with additional components of the amplification and detection reaction (e.g., one-pot SHERLOCK). For convenience, the reaction components may already be present in the container into which the capture matrix is deposited (e.g., in dry/lyophilized form with the addition of a small amount of aqueous solution, such as 50 ul of water, to re hydrate as necessary). Alternatively, they may be added (e.g., as a dry pellet, fresh components, or a combination of dry and fresh components) shortly after the addition of the capture matrix. It has been found that the simple transfer of the capture matrix and addition of a small amount of water to the sample, with one-pot SHERLOCK components in dry form, combined with heating at appropriate temperature for the SHERLOCK enzymatic reactions (herein referred to as “low-heat”, e.g. about 37°C), is sufficient to promote the analysis reaction and yield highly sensitive and accurate detection of the pathogen (or other target RNA).

[0138] Determination of assay results and identification of the presence of the pathogen (or other target RNA) is ultimately accomplished through detection of a signal generated from a reporter molecule (also referred to herein as “sensors”) within the reaction components. In some embodiments, the reporter molecule emits a fluorescent signal indicating pathogen presence. The signal can be observed or otherwise detected and quantitated to indicate results of the assay. The signal may be enhanced by lighting, such as with a LED/filter that works for excitation/emission of a fluorescent reporter used in the assay (e.g., blue LEDs, and by filtering, such as with an orange acrylic filter, as shown in one embodiment of the diagnostic device described herein). The signal (e.g., fluorescence) can be detected and quantitated throughout the incubation period, or alternatively at the end of the incubation period, such as with an automated reader (e.g., as a camera). In some embodiments, the signal is detected visually, such as by the skilled artisan. In some embodiments, a negative control (reaction mixture with a sample lacking the target/pathogen) and a positive control (reaction mixture with a sample containing the target RNA or target pathogen) are run simultaneously to facilitate clear determination of the results.

[0139] In some embodiments, universal detection of the pathogen or target RNA (e.g., SAR.S- CoV-2 virus) can be achieved at a limit of detection of about 1,200 cp/mL. In some embodiments, the detection is l,200cp/mL with a 95% confidence interval (Cl: 730-10,000). Such detection can be achieved, for example, through the use of RPA primers/guide RNAs specific for a highly conserved region of a gene (e.g., the N gene, such as with RPA primers/guide RNAs specific for the region of the N gene that codes for amino acids 170-230). In some embodiments, detecting specific variants or strains of a pathogen (specific detection) can be achieved at a limit of detection of from about 1,100 cp/mL to about 49,000 cp/mL (e.g., about 1,100 cp/mL, 1,200 cp/mL, 49,000 cp/mL) for example with 95% confidence interval ranging from 590-19,000 (e.g., 49,000 cp/mL (95% Cl: 21,000-81,000 (or 21, GOO- 89, 000)), 1,100 cp/mL (95% Cl: 590 - 15,000), and 1,200 cp/mL (95% Cl: 660 - 19,000). Such detection can be achieved, for example, through the use of RPA primers/guide RNAs specific for single nucleotide polymorphisms unique to specific variants/strains of the pathogen (e.g., in the N-terminal domain and/or the receptor binding domain regions of the spike gene of the SARS-CoV-2 virus). In some embodiments, detection of a plurality of SNPs for specific detection of a target pathogen variant is accomplished by performing two or more separate reactions on isolated nucleic acid from a saliva sample of a subject.

[0140] Components of the One-Pot SHERLOCK Reactions

[0141] In some embodiments, the capture matrix containing the nucleic acid (e.g. RNA) is added to a reaction mixture containing all components needed for detection of the target nucleic acid, such as by one-pot SHERLOCK analysis ((Gootenberg JS, Abudayyeh OO, Lee JW, Essletzbichler P, Dy AJ, Joung J, Verdine V, Donghia N, Daringer NM, Freije CA, Myhrvold C, Bhattacharyya RP, Livny J, Regev A, Koonin EV, Hung DT, Sabeti PC, Collins JJ and Zhang F. Nucleic acid detection with CRISPR-Casl3a/C2c2

Science 356: 438-442 (2017)).. For one-pot SHERLOCK, such components include, without limitation Casl2a, gRNA and RPA primers specific for the target pathogen, reverse transcriptase, single stranded DNA fluorescent quenched reporter, and salts and buffer components.

[0142] In some embodiments, the Casl2a is present at from about 50 nM to about 300 nM.

In some embodiments, the Casl2a is present at from about 100 nM to about 250 nM, at from about 150 nM to about 250 nM, at from about 175 nM to about 250 nM, at from about 175 nM to about 225 nM. In some embodiments, the Casl2 is present at about 200 nM. In some embodiments, the Casl2a is from Lachnospiraceae bacterium. In some embodiments, the Casl2a is Lba Casl2a (e.g., EnGen Lba Casl2a, New England Biolabs). In some embodiments, the Casl2a has a guide RNA length of from -41-44 nt. In some embodiments, the Casl2a has a protospacer adjacent motif (PAM ) of TTTN. In some embodiments, the Cast 2a has a cleavage recognition site of- 18 bases 3^' of the PAM. In some embodiments, the Cast 2a generates a 5’ overhang in the cleaved product. In some embodiments, the Casl2a is Class II Type V. In some embodiments, the Casl2a has a RuvC nuclease domain. In some embodiments, the Cast 2a has only a RuvC nuclease domain. In some embodiments, the Ca t 2a is AsCasl2a.

[0143] In some embodiments, the amount of gRNA used in the one-pot SHERLOCK reaction is from about lOOmM to about 800 mM gRNA, from about 150 mM to about 750 mM gRNA, from about 200 mM to about 700 mM gRNA, from about 250 mM to about 650 mM gRNA, from about 300 mM to about 600 mM gRNA, or from about 350 mM to about 550 mM gRNA (e.g., about 350, 375, 400, 425, 450, 475, 500, 525, or 550 mM). In some embodiments, about 400 nM gRNA is used.

[0144] In some embodiments, the amount of RPA primer used in the one-pot SHERLOCK reaction is from about 100 mM to about 800 mM one or both primers, from about 150 mM to about 750 mM, from about 200 mM to about 700 mM, from about 250 mM to about 650 mM, from about 300 mM to about 600 mM, or from about 350 mM to about 550 mM (e.g., about 350, 375, 400, 425, 450, 475, 500, 525, or about 550 mM). In some embodiments, about 400 nM, 410 nM, 415 nM, 420 nM, 425 nM, 430 nM, 435 nM, 440 nM, 445 nM, or 450 nM of one or both RPA primer is used. In some embodiments, about 430 nM each of the RPA primers is used.

[0145] The one-pot SHERLOCK reaction further contains a single stranded DNA fluorescent- quenched reporter (e.g., 56-FAM/TTATT/3IABkEQ SEQ ID NO: 1). In some embodiments, the reaction contains from about 0.1 to 10 uM of the reporter (e.g., about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0,7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0 uM, etc).

In some embodiments, about 1 mM of the reporter is present. Various lengths and fluorescent dyes for labeleing of the reporter are contemplated (e.g, such as those disclosed in U.S. Patent Application Publication 20210317527). In some embodiments, the reporter used generates a result that is readily distinguished as positive or negative by the naked eye.

[0146] In some embodiments, the one-pot SHERLOCK reaction mixture contains RNAse H (e.g., about 0.01 U/pL, 0.02 U/pL, 0.03 U/pL 0.04 U/pL, 0.05 U/pL, 0.06 U/pL, 0.07 U/pL, 0.08 U/pL, 0.09 U/pL, 0.1 U/pL or more). In some embodiments, the reaction mixture does not contain RNAse H.

[0147] In some embodiments, the one-pot SHERLOCK reaction mixture contains reverse transcriptase at concentration of from about 2.5 U/pL to about 7.5 U/pL. In some embodiments, the reaction mixture contains about 5 U/pL reverse transcriptase. In some embodiments, the reverse transcriptase is recombinant and has been developed for enhanced properties such as reduced RNAse H activity and/or increased thermostability (e.g., Protoscript® from New England Biolabs). In some embodiments, the reverse transcriptase is recombinant M-MuLV reverse transcriptase with reduced RNase H activity and increased thermostability (e.g., Protoscript II® from New England Biolabs).

[0148] In some embodiments, the one-pot SHERLOCK reaction mixture contains recombinase polymerase amplification enzymes (recombinase, recombinase loading factor, single stranded binding protein, DNA polymerase, and buffer components required for the RPA reaction (Piepenburg et al., PLOS Biology, 2006; vol 4, issue 7, p 1115-1121)). In some embodiments, the recombinase is T4 uvsX (e.g., from 60-960 ng/mΐ, such as 120ng/pl) and T4 gp32. In some embodiments, the recombinase loading factor is uvsY, from 10-80 ng/mΐ, such as 30ng/pl). In some embodiments the single stranded binding protein is gp32 (e.g., from 150-1000 ng/mΐ, such as 900ng/pl). In some embodiments, the DNA polymerase is large fragment of Bacillus subtilis Pol I (e.g., from 15-60, such as 30ng/pl). In some embodiments, the reaction is performed in about 50 mM Tris (pH 7.9), about 100 mM potassium acetate, about 14 mM magnesium acetate, about 2 mM DTT, about 5%Carbowax 20M, about 2001M dNTPs, about 3 mM ATP, about 50 mM phosphocreatine, about 100 ng/11 creatine kinase, and about 30 ng/11 Bsu. In some embodiments, about 300 nM to about 500 nM each primer are used.

[0149] In some embodiments, commercially provided salt and buffer components are utilized (e.g., TwistDx TwistAmp Basic kit or RPA pellet, which contains RPA and polyvinyl alcohol, catalog number TABAS03KIT). In some embodiments, salt and buffer components include, without limitation, one or more of NaCl, HEPES, PEG, magnesium acetate (e.g., in the below described amounts). In some embodiments, salt and buffer components include NaCl, HEPES, PEG, magnesium acetate (e.g., in the below described amounts). In some embodiments, salt and buffer components include, NaCl, HEPES, PEG, magnesium acetate (e.g., in the below described amounts) and nothing else.

[0150] In some embodiments, NaCl is present at about 60 mM. In some embodiments, NaCl is present between 40mM and 80mM.

[0151] In some embodiments, HEPES is present at about 20mM. In some embodiments, HEPES is present between 10 mM and 30 mM. In some embodiments, the HEPES is pH between 6.5 and 7.0 (e.g, pH 6.5, 6.6, 6.7, 6.8, 6.9, 7.0). In some embodiments, the HEPES is pH 6.8.

[0152] In some embodiments, the one-pot SHERLOCK reaction mixture contains a molecule for molecular crowding such as polyethylene glycol (PEG), dextrans or Ficoll, to make the reaction more efficient. In some embodiments, the reaction mixture contains about 1% to about 10% PEG. In some embodiments, the reaction mixture contains about 2.0% to about 5% PEG (e.g., about 2%, about 2.5%, about 3%, about 3.5%, about 4%, about 4.5%, about 5%). In some embodiments, the reaction mixture contains about 5% to about 10% PEG (e.g., about 5%, about 5.5%, about 6%, about 6.5%, about 7%, about 7.5%, about 8%, about 8.5%, about 9%, about 9.5%, or about 10% PEG).

[0153] In some embodiments, the one-pot SHERLOCK reaction mixture contains from about 7 mM to about 28 mM magnesium acetate (e.g., about 7 mM, about 8 mM, about 9 mM, about 10 mM, about 11 mM, about 12 mM, about 13 mM, about 14 mM, about 15 mM, about 16 mM, about 17 mM, about 18 mM, about 19 mM, about 20 mM, about 21 mM, about 22 mM, about 23 mM, about 24, about 25 mM, about 26 mM, about 27 mM, or about 28 mM).

In some embodiments, the reaction mixture contains about 14 mM magnesium acetate.

In some embodiments, the one-pot SHERLOCK reaction comprises 200 nM Casl2a, 400 nM gRNA, lOmM MgCl² (e.g., from the presence of lx NEB buffer 2.1 (50 mM NaCl, 10 mM Tris-HCl, 10 mM MgCk ,100 pg/ml BSA, pH 7.9@25°C)), 430 nM each RPA primer, 5 U/pL recombinant reverse transcriptase, 0.05 U/pL RNase H, 20 mM HEPES pH 6.8, 60 mM NaCl, 5% PEG, 1 pM fluorophore-quenched ssDNA fluorescent reporter (56- FAM/TTATT/3IABkEQ), 14 mM magnesium acetate (TwistDx), and 1 TwistAmp Basic RPA pellet (contains RPA and polyvinyl alcohol).

[0154] Reaction time and temperature

[0155] Upon transfer of the capture matrix and addition of a small amount of water to the sample, with one-pot SHERLOCK components in dry form, the reaction is heated at appropriate temperature for the SHERLOCK enzymatic reactions (herein referred to as “low- heat”). For example, heating at low-heat may be about 37°C, although slightly lower (e.g., about 36 °C, 35 °C, 34 °C, 33°C, 32°C, or about 31°C) and slightly higher temperatures are also envisioned (e.g., about 38 °C, 39 °C, 40 °C, 41°C, 42°C, 43°C, 44°C, or about 45°C). The reaction is allowed to take place for a period of time sufficient to yield accurate, reproducible results (e.g, about 50 minutes). In some embodments, the reaction is about 20- 120 minutes, 20-70 minutes, about 25-65 minutes, or about 30-55 minutes. In some embodiments, the reaction is about 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or about 30 minutes or longer. In some embodiments, the reaction is about 31, 32, 33, 34, 35, 36, 37,38, 39, or about 40 minutes or longer. In some embodiments, the reaction is about 41, 42, 43, 44, 45, 46, 47, 48, 49 or about 50 minutes, or longer. In some embodiments, the reaction is about 51, 52, 53, 54, 55, 56, 57, 58, 59, or about 60 minutes or longer.

[0156] Sequences and Lengths of gRNA and RPA primers [0157] The gRNA used in the one-pot SHERLOCK reaction, or in any amplification/detection reaction used, may be specific for a highly conserved target RNA (such as a pathogen nucleic acid ) (for universal detection) or specific for a SNP unique to one or more alleles or variant/strain/serotype of a pathogen (for specific detection). In embodiments where universal detection of SARS-CoV-2 is desired, the target nucleic acid may be within the N-gene, specifically a highly conserved region of the N-gene (e.g, the region of the N gene that codes for amino acids 170-230). One such example of such a gRNA sequence is the nucleoprotein gRNA shown in Table 3. Other such gRNA sequences include, without limitation, UAAUUUCUACUAAGUGUAGAUcccaauaauacugcgucuug (SEQ ID NO: 2), UAAUUUCUACUAAGUGUAGAUaucgcgccccacugcguucu (SEQ ID NO: 3), UAAUUUCUACUAAGUGUAGAUuugaacuguugcgacuacgu (SEQ ID NO: 4), and UAAUUUCUACUAAGUGUAGAUcugcugcuugacagauugaa (SEQ ID NO: 5). In embodiments where specific detection of a SARS-CoV-2 variant is desired, the target nucleic acid may be within the spike gene (e.g., within the N-terminal domain and/or receptor binding domain), specifically at a distinct SNP within the spike gene. Examples of such gRNA sequences are N501Y, Y144del, E484K, Y144-gRNA4, Y144-gRNA5, N501YgRNAlm, N501YgRNAlm2, N501YgRNAlw, Y144-gRNA2, Y144-gRNA3, as shown in Table 3. It may be useful to detect a human-specific RNA as a positive control for the sample/assay. For example, Human RNaseP, specific gRNA sequences for which are provided in Table 3. The Casl2a protein recognizes and binds the invariant handle region of the gRNA, while the specificity to the target nucleic acid is determined by the sequence of the spacer region of the gRNA, which is located downstream (3’) of the handle region. The sequence of the spacer region of exemplified gRNAs is shown in Table 3, in conjunction with the invariant Casl2a handle region (UAAUUUCUACUAAGUGUAGAUUGGGU SEQ ID NO: 6). The skilled practitioner will recognize that the spacer regions described herein are specific for the target nucleic acid, and may also be used in conjunction with a different handle region as determined by the Cas protein used in the reaction.

[0158] In some embodiments, the gRNA for the selected target RNA (e.g, pathogen nucleic acid such as the N-gene) has exact target matches in at least about 80%, 85%, or 90% (e.g., about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, or higher) of all target RNA (e.g, pathogen such as SARS-CoV-2) sequences, and has minimal target matches in non-target. In some embodiments, such as for specific pathogen detection, the gRNA for the selected target pathogen nucleic acid (e.g, the spike-gene) has exact target matches in at least about 80%, 85%, or 90% (e.g., about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, or higher) of one or more target pathogen (e.g., SARS-CoV-2 variants) sequences, and has minimal target matches in non-target pathogen. When it is desired to capture more than one variant/serotype/ strain of the pathogen (e.g, for universal detection or identification of shared SNPs) the gRNA may match one variant/serotype/ strain to a higher percentage than others in the targeted subset. In some embodiments, the gRNA for the selected target pathogen nucleic acid (e.g., the spike-gene) has exact target matches in at least about 95%, 96%, 97%, 98%, 99% or higher (e.g., about 99.1%, 99.2%, 99.3%, 99.4%,

99.5%, 99.6%, 99.7%, 99.8%, 99.9%, or 100%) of one or more target pathogen (e.g., SARS- CoV-2 variants) sequences, and has minimal target matches in non-target pathogen.

[0159] The size of the gRNA may be from about 15 nt to 25 nt in length (e.g. 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 nt), or from about 19-20 nt in length, for Casl2a. Longer and shorter sizes are also envisioned, such as those described herein with resepct to CRISPER Cas mediated detection. Mutation specific gRNAs may contain the target mutation (e.g. substitution, insertion or deletion) at any location within the spacer region of the gRNA. In some embodiments, the mutation is located central to the entire gRNA spacer region. In some embodiments, the mutation is located at or near the 5’ or 3’ end of the gRNA spacer region.

[0160] RPA primers (forward and reverse) specific for the target nucleic acid are included in the (e.g., one-pot SHERLOCK) reaction mixture. In embodiments where universal detection of SARS-CoV-2 is desired, the target nucleic acid may be within the N-gene, specifically a highly conserved region of the N-gene (e.g, the region of the N gene that codes for amino acids 170-230). Examples of such RPA primers are SARS-CoV-2 Nucleoprotein Forward Primer and SARS-CoV-2 Nucleoprotein Reverse Primer, as shown in Table 3. In embodiments where specific detection of a SARS-CoV-2 variant is desired, the target nucleic acid may be within the spike gene, specifically at a distinct SNP within the spike gene (e.g., the N-terminal domain and/or receptor binding domain). Examples of such RPA primers are N501Y Forward Primer, N501Y Reverse Primer, Y144 Forward Primer, Y144 Reverse Primer, E484K Forward Primer, E484K Reverse Primer, Y144-ForlRPA, Y144-For3RPA, Y144-For4RPA, Y144-For5RPA, Y144-RevlRPA, Y144-Rev2RPA, Y144-Rev3RPA, Y144-Rev5RPA, N501Y-F1, N501Y-F2, N501Y-F3, N501Y-F4, N501Y-F5, N501Y-R2, N501Y-R3, N501Y-R4, N5501Y-R5, N501Y-F6, N501Y-F7, N501Y-F9, N501Y-F10, N501Y-R6, N501Y-R7, N501Y-R8, N501Y-R9, N501Y-R10, N501Y-R11, E484-RPA-F1, E484-RPA-F3, E484-RPA-F4, E484-RPA-F5, E484-RPA-F6, E484-RPA-R2, E484-RPA- R3, E484-RPA-R4, E484-RPA-R5, and E484-RPA-R6, as shown in Table 3. It may be useful to detect a human-specific RNA as a positive control for the sample/assay. For example, Human RNaseP, specific primer sequences for which are shown in Table 3.

[0161] One or both primers can be from 15 - 75 nt, 30-60 nt, 25-40 nt in length. In some embodiments, primer lengths are between 25-40 nt. Longer and shorter lengths are also envisioned, such as discussed further in relation to CRISPR Cas detection. Total amplicon size may be from 50 bp to 500 bp, 30 bp to 350 bp, or from 100-200 bp total size.

[0162] In some embodiments, one or more of the RPA primers (forward and/or reverse) for the selected target nucleic acid (e.g,. pathogen nucleic acids such as with the N gene or spike gene) have exact target matches in at least about 80%, 85%, 90%, 95%, (e.g., about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or higher) of all target pathogen (e.g., SARS-CoV-2) sequences. In some embodiments, one or more of the RPA primers have exact target matches for at least 96%, 97%, 98%, 99% or higher exact target matches. In some embodiments, one or more of the RPA primers have exact target matches for at least 97.4% (forward primer) and 97.0% (reverse primer) of NCBI SARS-CoV-2 genomes.

Other Amplification/Detection Reactions

[0163] The use of amplification and detection reactions other rthan one-pot SHERLOCK in the methods is also envisioned. For example, other amplification reactions, discussed herein (e.g,. isothermal) may be used. Such amplification products may further rbe analyzed by a variaety of methods to identify the product, examples of which are provided herein.

Nucleic Acid Sample Prep

[0164] Disclosed herein are methods, compositions and devices for the preparation of nucleic acids (e.g., RNA) from unprocessed saliva using reagents that are compatible with downstream nucleic acid amplification reactions such as SHERLOCK or one-pot SHERLOCK. The nucleic acids prepared using the methods, compositions and devices described herein do not require further isolation or purification prior to amplification; that is, the prepped nucleic acid sample can be subjected to an isothermal or other amplification reaction without need for additional processing or isolation steps, or can be added directly to e.g., an isothermal amplification reaction to generate accurate and sensitive results with low levels of background noise. In some embodiments the nucleic acids prepared are from a pathogen present in the saliva, such as a DNA or RNA containing pathogen. In some embodiments, the pathogen is a virus such as SARS-CoV-2.

[0165] One aspect of the invention relates to a composition for preparing nucleic acids (e.g., RNA) from the unprocessed saliva as described herein. The composition comprises one or more reducing agents and one or more metal chelating agents in aqueous suspension.

Together these agents function as lysis reagents. In some embodiments, the composition does not contain any added nuclease inhibitors. In some embodiments, the reducing agent is dithiothreitol (DTT) and/or the metal chelating agent is ethylene glycol tetraacetic acid (EGTA). In some embodiments, the composition further comprises the unprocessed saliva and/or a capture matrix as described herein (e.g., a porous membrane for nucleic acid binding compatible with in situ amplification). The composition is for use in the method of preparing nucleic acids from unprocessed saliva, described herein. In some embodiments, the composition is added to a sample preparation column described herein, either before or after the addition of unprocessed saliva.

[0166] Other reducing agents contemplated for use in the composition for preparing nucleic acids (e.g., RNA) as described herein include, without limitation, dimethyl sulfoxide (DMSO), tertiary butyl alcohol, beta-mercaptoethanol, tris(2-carboxyethyl)phosphine, among others. In some embodiments, the reducing agent is not tris(2-carboxyethyl)phosphine. In some embodiments, the final concentration of DTT or other reducing agent used in the sample preparation is in the range of 5-10mM, 5-100mM, 5-150mM, 10-150mM, lO-lOOmM, 10-75 mM, 10-50mM, 25-100mM, 50-100mM, 25-75mM, 25-70mM, 25-65mM, 25-60mM, 25-55mM, 25- 50mM, 40-60nM, 40-50nM, 50-60nM, 40-65mM, 40-70mM, 40-75mM, 40- lOOmM, or l-500mM, 10-500mM, 10-400 mM, 10-300mM, 10-200mM, 20-500mM, 20-400 mM, 20-300mM, 20-200mM, 25-100mM, 50-100mM, inclusive. In some embodiments, the concentration is about 5mM, about lOmM, about 15 mM, about 20mM, about 25mM, about 30mM, about 35mM, about 40mM, about 45mM. In some embodiments, the concentration is about 50mM, about 55 mM, about 60mM, about 65mM, about 70mM, about 75mM, about 80mM, about 85mM about 90mM, or about lOOmM. In some embodiments, the concentration is about 105mM, llOmM, about 115mM, about 120mM, about 125mM, about 130mM, about 135mM, about 140mM, about 145mM, about 150mM, 155mM, 160mM, about 165mM, about 170mM, about 175mM, about 180mM, about 185mM, about 190mM, about 195mM, about 200mM, 205mM, 210mM, about 215mM, about 220mM, about 225mM, about 230mM, about 235mM, about 240mM, about 245mM, about 250mM, 255mM, 260mM, about 265mM, about 270mM, about 275mM, about 280mM, about 285mM, about 290mM, about 295mM, about 300mM, 305mM, 310mM, about 315mM, about 320mM, about 325mM, about 330mM, about 335mM, about 340mM, about 345mM, about 350mM, 355mM, 360mM, about 365mM, about 370mM, about 375mM, about 380mM, about 385mM, about 390mM, about 395mM, about 400mM, 405mM, 410mM, about 415mM, about 420mM, about 425mM, about 430mM, about 435mM, about 440mM, about 445mM, about 450mM, 455mM, 460mM, about 465mM, about 470mM, about 475mM, about 480mM, about 485mM, about 490mM, about 495mM, or about 500mM, inclusive.

[0167] Metal chelating agents contemplated for use as described herein include, without limitation, ethylene glycol tetraacetic acid (EGTA), ethylenediaminetetraacetic Acid (EDTA), 8-hydroxyquinoline, hexadecylpyridinium bromide, sodium tartrate, citrate salts, and sodium gluconate. In some embodiments, the chelating agent is not EDTA. In some embodiments, the final concentration of the EGTA or other chelating agent in the sample preparation is in the range of 1 mM to 50 mM, or 1 mM to 10 mM. In some embodiments, the final concentration is about 1 mM, 5mM, lOmM, 15 mM, 20 mM, 25mM, 30mM, 35 mM, 40 mM, 45mM or about 50 mM. In some embodiments, the final concentration is about 1 mM, 2mM, 3mM, 4 mM, 5 mM, 6mM, 7mM, 8 mM, 9mM, or about lOmM. In some embodiments the final concentration is about 5 mM.

[0168] In some embodients, the lysis reagent does not contain a combination of tris(2- carboxyethyl)phosphine and EDTA.

[0169] The final concentration of the reducing agent and chelating agents can vary depending on the specific agents, but should not be in such large concentrations that would interfere with planned downstream enzymatic reactions.

[0170] In some embodiments, the unprocessed saliva to be added to the composition (e.g., in the context of a sample preparation column) is from about 0.5mL to about 5 mL in volume, and the appropriate amount of the reducing agent and metal chelating agent is added to achieve the desired concentration. In some embodiments, the unprocessed saliva is about 0.5 mL, 0.6 mL, 0.7 mL, 0.8 mL, 0.9 mL, 1.0 mL, 1.1 mL, 1.2 mL, 1.3 mL, 1.4 mL, 1.5 mL, 1.6 mL, 1.7 mL, 1.8 mL, 1.9 mL, 2.0 mL, 2.1 mL, 2.2 mL, 2.3 mL, 2.4 mL, 2.5 mL, 2.6 mL, 2.7 mL, 2.8 mL, 2.9 mL, 3.0 mL, 3.1 mL, 3.2 mL, 3.3 mL, 3.4 mL, 3.5 mL, 3.6 mL, 3.7 mL, 3.8 mL, 3.9 mL, 4.0 mL, 4.1 mL, 4.2 mL, 4.3 mL, 4.4 mL, 4.5 mL, 4.6 mL, 4.7 mL, 4.8 mL, 4.9 mL, or about 5.0 mL in volume.

[0171] The addition of the necessary reducing agent and metal chelating agent to the unprocessed saliva prefereably dilutes the saliva only minimally. Dilution of no more than 25% is contemplated. In some embodiments, the saliva is diluted less than about 25%, (e.g., about 24%, 23%, 22%, 21%, 20%, 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%, about 11% or less). In some embodiments, the saliva is diluted no more than about 11%. In some embodiments, the saliva is diluted less than about 11% (e.g., about 10%, 9%, 8%, 7%, about 6% or less). In some embodiments, the saliva is diluted no more than about 6%. In some embodiments, the saliva is diluted less than about 6% (e.g., about 5%, 4%, 3%, about 2% or less). In some embodiments, the saliva is diluted no more than about 2%. In some embodiments, the saliva is diluted less than about 2% (e.g., about 1.5%, 1%, about 0.5%, or less).

[0172] Other aspects of the invention relate to a rapid method for preparing nucleic acid (e.g., RNA) from an unprocessed saliva sample, wherein the isolated nucleic acid is concentrated onto a capture matrix. This is particularly useful in preparing nucleic acid from a pathogen present in the saliva sample. The nucleic acid on the capture matrix can then be directly used in an amplification/detection reaction such as one pot SHERLOCK, described herein (e.g., to identify and further characterize the pathogen). The method comprises adding the lysis reagents: one or more reducing agents (e.g., DTT) and one or more metal chelating agents (e.g., EGTA), as described herein (e.g., DTT to final concentration of from about 10 mM to about lOOmM and EGTA to a final concentration of from about 5 mM to about 50 mM), to unprocessed saliva. The resulting saliva sample is then heated to a temperature ranging from about 70°C to about 99°C for a time period sufficient to lyse cells and/or pathogen (e.g., virus such as SARS-CoV-2) present in the saliva, release the nucleic acid, and inactivate nucleases present in the sample. In some embodiments, the heating is a single step process. The released nucleic acid (e.g., pathogen RNA) is concentrated on a capture matrix. This may be accomplished by heating the saliva sample in the presence of the capture matrix. The heated saliva sample may further flow through the capture matrix (e.g., by capillary action) to thereby deposit the nucleic acid onto the capture matrix. Flowing of the sample through the capture matrix may take place during the heating process, as long as the flow rate is slow enough to allow for the required lysis, nuclease inactivation and nucleic acid deposition onto the capture matrix. In some embodiments, the saliva sample flows through the capture matrix and the unbound materials are thereby removed from the capture matrix. This has the added advantage of removing other components of the saliva sample rather than requiring further manipulation to physically isolate the capture matrix from the sample. The cell lysis, nuclease inactivation and deposition of the nucleic acids onto the capture matrix, can be accomplished, for example, by using the sample preparation column described herein (e.g., in the integrated diagnostic testing device described herein). The capture matrix containing the deposited nucleic acid may then be added to an amplification/detection reaction for characterization (e.g, isothermal amplification and/or one pot SHERLOCK analysis). This can be accomplished, for example, by using the integrated diagnostic testing device described herein.

[0173] Heating of the saliva sample may be to a temperature ranging from about 70°C to about 99°C. In some embodiments, the sample is heated to about 70°C, 71°C, 72°C, 73°C, 74°C, 75°C, 76°C, 77°C, 78°C, 79°C, 80°C, 81°C, 82°C, 83°C, 84°C, 85°C, 86°C, 87°C, 88°C, 89°C, 90°C, 91°C, 92°C, 93°C, 94°C, 95°C, 96°C, 97°C, 99°C, or about 99°C. In some embodiments, the saliva sample is heated to about 95 °C. When heated at the lower end of the temperature range, a longer period of time may be required to accomplish optimal lysing and nuclease inactivation, than when heating at the higher end of the temperature range. For example, incubation at 80°C performed for 20 min may be as effective as or used in place of incubation at 95° for 6 min. It is within the skill set of one of ordinary skill in the art to optimize the temperature and reaction time to achieve suitable nucleic acid preparation as described herein.

[0174] In some embodiments, the saliva sample is heated to a temperature ranging from 75°C to about 99°C. In some embodiments, the saliva sample is heated to a temperature ranging from 75°C to about 95°C. In some embodiments, the saliva sample is heated to a temperature ranging from 80°C to about 95°C. In some embodiments, the saliva sample is heated to a temperature ranging from 80°C to about 99°C. In some embodiments, the saliva sample is heated to a temperature ranging from 85°C to about 95°C. In some embodiments, the saliva sample is heated to a temperature ranging from 85°C to about 99°C.

[0175] The optimal time period for heating will depend somewhat on the temperature of the heating. In some embodiments, the heating is for a period ranging from about 1 minute to about 20 minutes. In some embodiments, the heating is for a period ranging from about 1 minutes to about 5 minutes. In some embodiments, the heating is for a period ranging from about 5 minutes to about 10 minutes. In some embodiments, the heating is for a period ranging from about 5 minutes to about 20 minutes. In some embodiments, the heating is for a period ranging from about 10 minutes to about 20 minutes. In some embodiments, heating is for about 1 minute, about 1.5 minutes, about 2 minutes, about 2.5 minutes, about 3 minutes, about 3.5 minutes, about 4 minutes, about 4.5 minutes, about 5 minutes, about 5.5 minutes, about 6 minutes. In some embodiments, heating is for a period of greater than 6 minutes (e.g., 7, 8, 9, 10, etc). In some embodiments, the heating for the indicated time period takes place concurrently with flow through the capture matrix. In some embodiments, the heating and flow of the saliva sample through the capture matrix is for about 3-6 minutes (e.g., with 2 mL saliva and a capture matrix of 4 mm in diameter).

[0176] Flow rate will be affected by various factors, including the thickness, pore size and size (e.g., diameter) of the capture matrix, the size of the aperture of the device such as a column the sample is in, the amount of sample, the size and shape of the sample container (e.g., column) and method of the flow. In some embodiments, the flow is achieved by capillary action and/or gravity. In some embodiments, an absorbent material (e.g., cellulose) such as an absorbent filter (e.g., a cellulose filter) is located adjacent to the capture matrix on the opposite side of the deposited sample to facilitate flow through the matrix by capillary action. Other methods of achieving appropriate flow are envisioned including the application of suction or pressure at either end of the capture matrix. In some embodiments, the flow rate is slower than 1 min/mL. In some embodiments, the flow rate is faster than 1 min/mL. In some embodiments, the flow rate is about 1.5 min/mL. Other flow rates are envisioned, such as 0.5 min/mL, 0.6 min/mL, 0.7 min/mL, 0.8 min/mL, 0.9 min/mL, 1 min/mL, 1.1 min/mL, 1.2 min/mL, 1.3 min/mL, 1.4 min/mL, 1.5 min/mL, 1.6 min/mL, 1.7 min/mL, 1.8 min/mL,

1.9 min/mL, 2 min/mL, 2.1 min/mL, 2.2 min/mL, 2.3 min/mL, 2.4 min/mL, 2.5 min/mL, 2.6 min/mL, 2.7 min/mL, 2.8 min/mL, 2.9 min/mL, 3 min/mL, 3.1 min/mL, 3.2 min/mL, 3.3 min/mL, 3.4 min/mL, 3.5 min/mL or slower. In one embodiment, the capture matrix is 4 mm in diameter, contains 0.22 um pores (e.g., PES functinalized with a hydrophilic surface treatment), has a cellulose filter located adjacent the capture matrix to facilitate capillary action and gravity, and a flow rate about 1 min/mL or slower (e.g., about 1.5 min/mL) is achieved.

[0177] Sample Collection and Preparation System

[0178] Some implementations of the present disclosure relate to a specialized system used for collection and preparation of the nucleic acid (e.g., RNA, such as pathogen RNA, such as SARS-CoV-2 RNA), herein referred to as a sample collection and preparation system, or sample preparation system. The sample preparation system contains a receptacle (e.g. a cylindrically shaped chamber, having two openings at opposite ends, for receiving a liquid sample such as unprocessed saliva sample), referred to herein as a sample preparation column. The sample preparation column is described herein in connection with the integrated diagnostic testing device, and can be used with the integrated diagnostic testing device or used independently to collect and prepare sample for future analysis (e.g., after transport). [0179] Referring to FIG. IB, a cross-sectional view of an exemplary sample collection and preparation system 100’ is depicted that may be a separate standalone device for receiving liquid samples. In some implementations, the sample collection and preparation system may be used in conjunction with diagnostic features, such as those described for FIG. 1 A and elsewhere, including a reaction chamber and systems for detecting a target, such as a target nucleic acid.

[0180] The sample collection and preparation system 100’ can include a sample preparation column, such as sample preparation columns 170’, 175’ (e.g. a cylindrically shaped chamber, having two openings at opposite ends, for receiving a liquid sample such as unprocessed saliva sample). The sample preparation column can further include a capture matrix, such as capture matrices 17G or 176’ positioned at a respective base 177’ of the sample preparation columns 170’, 175’. As described elsewhere herein, the capture matrix captures nucleic acid during heating of a saliva sample, such as saliva samples 172’, 173’ received in exemplary sample preparation columns 170’, 175’. For example, select materials may be placed in the capture matrix for capturing nucleic acid during heating of a liquid sample.

[0181] An absorbent filter is disposed below the capture matrix of the sample preparation column, similar to absorbent filter 179’ being disposed below one or more of capture matrices 17G, 176’ of sample preparation columns 170’, 175’. The absorbent filter causes a received sample, such as saliva samples 172’, 173’, to move, or flow, during heating through the capture matrix via capillary action. In some implementation, the absorbent filter causes the sample to move at a flow rate of at least about 1 min/mL. In some implementations, the absorbent filter may be disposed immediately below the capture matrix.

[0182] The sample preparation and collection system 100’ can further include a high-heat lysis chamber 130’ in thermal connection with one or more heating mechanisms, such as heating mechanism 113’. The sample preparation column, such as sample preparation columns 170’, 175’ can be disposed within the high-heat lysis chamber 130. In addition, in some implementations, the sample preparation column can include a saliva collection interface, such as saliva collection interface 160’ that is connected to an end opposite the base 177’ of a sample preparation column, such as sample preparation column 170’ or 175’. In some implementations, a saliva sample moves during heating through the capture matrix, such as sample matrix 17G or 176’, at a flow rate between about 1.3 min/mL to about 1.7 min/mL. In some implementation, the saliva sample moves during heating through the capture matrix at a flow rate of about 1.5 min/mL. [0183] It is contemplated that in some implementations, the sample preparation and collection system 100’ can include miSHERLOCK systems that incorporate the sample preparation methodologies described herein for on-device sample preparation along with RNA concentration onto a capture matrix (e.g., a PES membrane).

[0184] In some implementations, the high-heat lysis chamber 130’ of the sample collection and preparation system 100’ is defined by a base structure 110 and one or more integrated wall structures, such as wall structures 13 G, 132’ that extended upwardly from a flat base structure, such as base structure 110’ In some implementations, a power source 118’ is connected via wiring (complete electrical connection not shown) to various electrical components of the sample collection and preparation system 100’. For example, one or more battery packs (e.g., two 12V batteries, one 24V battery) of the power source 118’ may be connected to, among other components, the one or more heating mechanisms, such as heating mechanism 113’. In some implementations, a heating mechanism may be incorporated into or integral with the sample preparation column. In some implementations, a temperature sensor 114’ may be associated with at least one of the heating mechanisms, such as heating mechanism 113’. In some implementations, the power source 118 may be external to the sample collection and preparation system 100’, internal, or some hybrid of internal and external. In addition, the power source can include batteries or can be a plug-in device, such as a transformer. It is contemplated that the base structure 110’, such as different combinations of a bottom structure, along with partial or full side walls extending upwardly from a bottom structure that can be generally rectangular, round, elliptical, or trapezoidally shaped. In certain implementations, the base structure 110’ supports the one or more heating mechanisms (e.g., heating mechanism 113’), a high-heat lysis chamber 130’, and/or their related components. Furthermore, a base structure may also provide the support for any electrical connections between a power supply and the electrical components of the sample collection and preparation system 110’. The wall structures 13 G, 132’ may or may not be formed as one piece with the base structure 110’.

[0185] In some implementations, the capture matrix of the sample collection and preparation system 100’, such as capture matrix 17G or 176’, is a porous membrane that can bind to nucleic acids and is compatible with in situ amplification. In some implementations, the capture matrix is a polyethersulfone (PES) membrane that contains 0.22 um pores and is optionally functionalized with a hydrophilic surface treatment. In some implementations, the capture matrix is a membrane containing pores ranging from between about 0.1 um to about 0.5 um. In some implementations, the saliva sample is between about 0.2 mL and 5 mL in volume.

[0186] In some implementations, the sample preparation column, such as sample preparation columns 170’ or 175’, are reversibly disposed within the high-heat lysis chamber and/or the absorbent filter is reversibly disposed below the capture matrix.

[0187] In some implementations, the sample collection and preparation system 100’ includes a cap (not shown) that securely attaches to the base of the sample preparation column containing the capture matrix, such as at the base 177’ of sample preparation columns 170’, 175’, upon removal of the absorbent filter 179’, to cover and protect the capture matrix, such as capture matrix 17 or 176’.

[0188] In some implementations, it is contemplated that a sample preparation column, such as at least one of sample preparation column 170’ or 175’, has a capture matrix, such as capture matrix 17 , 176’, located at one end (e.g., the base 177’ of the column) for capturing the nucleic acid during heating. The sample preparation column has a second end (e.g., just below the saliva collection interface 160’) opposite the base 177’ that can be configured for receiving the sample. The capture matrix (e.g., capture matrix 17 , 176’) is a solid or semi-solid material (e.g., a membrane) that permits flow of the sample through it while generally retaining its shape and structure. In one embodiment, the capture matrix is a thin matrix that spans most of or the entire base of the column (e.g., sample preparation column 170’, 175’). An absorbent filter 179’ may be disposed (e.g., removably) immediately adjacent the side of the capture matrix (e.g., capture matrix 17 , 176’) that faces away from the sample preparation column so as to cause the sample (e.g., saliva) to move during heating in the column through the capture matrix via capillary action at an appropriate flow rate (e.g, at least about 1 min/mL, such as about 1.5 min/mL). The sample preparation column (e.g., sample preparation coilumn 170’, 175’) is or can be disposed within a chamber (e.g., high- heat lysis chamber 130’) for heating. The high-heat lysis chamber 130’ is in thermal connection with one or more heating mechanisms (e.g., heating mechanism 113’) to result in appropriate heating of the sample. The heating chamber may be separate from the integrated diagnostic testing device (e.g., see FIG. 1 A) described herein, or may be a part of the integrated diagnostic testing device (the high-heat lysis chamber). If separate, the heating chamber has similar properties and can heat the sample similarly to the high-heat lysis chamber described herein.

[0189] In some embodiments, the end of the receptacle configured for receiving the sample is connected (reversibly or irreversibly) to a saliva collection interface 160’ where unprocessed saliva is to be deposited (e.g, by a subject spitting into the interface). The saliva collection interface 160’ may be of a shape and/or material that facilitates collection and transfer of the saliva into the column. In one embodiment, the saliva collection interface 160’ is conical, with the wide aperture being the collection end, and the smaller aperture being the deposition end connected to the column. In some embodiments, more than one columns (e.g., sample preparation columns 170’, 175’) are connected to a single saliva collection interface, to allow for the deposition of saliva from one subject into two or more columns at once. The column may be made of a material that is opaque or material that is transparent to allow for visualization of the deposited sample. The column may have markings to indicate how much sample has been deposited, and/or to indicate a preferred amount of sample to be deposited. [0190] In some embodiments, the sample preparation column (e.g., sample preparation columns 170’, 175’) is preloaded with lysis reagents described herein, including, without limitation, a reducing agent and a metal chelating agent. In some embodiments, the reducing agent is DTT present at a concentration to result in a final concentration of from about 10 mM to about 100 mM, and the metal chelating agent is EGTA present at a concentration to result in a final concentration of about 5mM, in an added saliva sample. In some embodiments, the reducing agent is DTT present at a concentration to result in a final concentration of 10 mM DDT, and the metal chelating agent is EGTA present at a concentration to result in a final concentration from about 1 mM to about 50 mM EGTA in an added saliva sample.

[0191] In some embodiments, the heating chamber and/or the absorbent filter can be removed (e.g, for transport of the column). In some embodiments, the column may further include one or more caps that securely attach to one or more ends of the column. For example, a cap may attach to the end of the column after removal of the absorbent filter and/or heating chamber, to cover and protect the capture matrix containing bound nucleic acid sample.

[0192] The absorbent filter may be made of any material that will facilitate capillary flow of the saliva sample through the capture matrix. Preferably the material of the absorbent filter will not interfere with the function of the capture matrix or result in deposition of any materials onto the filter that may inhibit future analysis of deposited nucleic acid. In some embodiments, the filter is immediately adjacent the capture matrix, and of sufficient size to contact all or most of the capture matrix. Other sizes and configurations of the absorbent filter can be envisioned that will result in the appropriate transfer of the saliva sample through the capture matrix. In some embodiments, the absorbent filter absorbs all of the saliva sample. In some embodiments, the absorbent filter is made of an absorbent polymer (e.g,. cellulose). In some embodiments the absorbent filter is made of one or more of cellulose, carboxymethylcellulose (CMC), silica gel, hydrogel, Polyvinyl alcohol/cellulose nanocrystals/poly(2 -Hydroxy ethyl methacrylate) (PVA/CNC/polyHEMA) and PVA/CNC/poly(N'-methylenebisacrylamide) (PVA/CNC/polyMBA) hydrogels.

[0193] In some embodiments, the sample collection and preparation system is designed to be compatible with the integrated diagnostic testing device described herein. In some embodiments, the sample preparation column is compatible with the high-heat reaction chamber of the integrated diagnostic testing device, and is further compatible with the low- low heat reaction chamber of the diagnostic testing device, fitting into the device and conducting heat appropriately for use of the diagnostic device.

[0194] Isothermal Nucleic Acid Amplification Methods

[0195] The RNA prepared using the methods and compositions described herein can be used with essentially any isothermal nucleic acid amplification and detection method. Exemplary isothermal nucleic acid amplification methods include, but are not limited to, Specific High Sensitivity Enzymatic Reporter UnLOCKing (SHERLOCK) (e g., one-pot SHERLOCK), recombinase polymerase amplification (RPA), Loop-mediated isothermal amplification (LAMP), nucleic acid sequence-based amplification (NASBA), reverse transcription recombinase polymerase amplification (RT-RPA), reverse transcription Loop-mediated isothermal amplification (RT-LAMP), reverse transcription nucleic acid sequence-based amplification (RT-NASBA), transcription mediated amplification (TMA), helicase dependent amplification (HD A), multiple displacement amplification (MDA), strand displacement amplification (SDA), rolling circle amplification (RCA), single primer isothermal amplification (SPIA), restriction aided rolling circle amplification, and nicking enzyme amplification reaction (NEAR).

[0196] Nucleic acids prepared using the methods and compositions described herein can be used in isothermal amplification reactions with or without modifying the nucleic acid. Optional modifications can include, for example, denaturation, digestion, nicking, unwinding, incorporation and/or ligation of heterogeneous sequences, addition of epigenetic modifications, addition of labels (e.g., radiolabels such as ³²P, ³³P, ¹²⁵I, or ³⁵S; enzyme labels such as alkaline phosphatase; fluorescent labels such as fluorescein isothiocyanate (FITC); or other labels such as biotin, avidin, digoxigenin, antigens, haptens, fluorochromes), and the like. [0197] Components of an isothermal amplification reaction can include, for example, one or more primers (e.g., individual primers, primer pairs, primer sets, oligonucleotides, multiple primer sets for multiplex amplification, and the like), nucleic acid target(s) or templates (e.g., target nucleic acid from a sample), one or more polymerases, nucleotides (e.g., dNTPs and the like), and a suitable buffer (e.g., a buffer comprising a detergent, a reducing agent, monovalent ions, and divalent ions as appropriate). An amplification reaction can further include a reverse transcriptase, in some embodiments. An amplification reaction can further include one or more detection agents, including but not limited to a probe that generates a signal when cleaved by an enzyme activated in a target-dependent manner.

[0198] Additional components can be used in a typical isothermal amplification reaction including, but not limited to components and/or common additives such as salts, buffers, detergents, ions, oils, proteins, polymers and the like. In some embodiments, components of an amplification reaction can include non-enzymatic components and enzymatic components. Non-enzymatic components can include, for example, primers, nucleotides, buffers, salts, reducing agents, detergents, and ions; and generally do not include proteins (e.g., nucleic acid binding proteins), enzymes, or proteins having enzymatic activity such as, for example, polymerases, reverse transcriptases, helicases, topoisomerases, ligases, exonucleases, endonucleases, restriction enzymes, nicking enzymes, recombinases and the like. In some embodiments, an enzymatic component can comprise a polymerase, either in the presence or absence of a reverse transcriptase. Accordingly, polymerase enzymatic components are distinguished from other proteins (e.g., nucleic acid binding proteins and/or proteins having other enzymatic activities) such as, for example, helicases, topoisomerases, ligases, exonucleases, endonucleases, restriction enzymes, nicking enzymes, recombinases, and the like. Typically, the methods and compositions described herein for the preparation of nucleic acids will inactivate endogenous enzymes prior to initiation of an isothermal amplification reaction.

[0199] Essential co-factors of isothermal amplification reactions are known to those of skill in the art and are dependent on the enzyme(s) used. They can be organic or inorganic chemical compounds. Inorganic chemical compounds, for example, can be selected from the group comprising metal ions, e.g., Mg, Mn, Ca, Fe, Cu and Ni. Organic co-factors can include vitamins, proteins, biotin, nicotinamide adenine dinucleotide, and nucleotides, e.g. ATP.

[0200] Isothermal amplification reactions can be conducted at a range of temperatures, depending upon the exact reaction chosen and the enzyme(s) or factors used in the amplification. Some isothermal amplification reactions can proceed at room temperature. More often, an elevated temperature, e.g., around 37 degrees Celsius or higher, e.g., 37 degrees Celsius to about 75 degrees Celsius, e.g., about 38 degrees Celsius, about 39 degrees Celsius, about 40 degrees Celsius, about 41 degrees Celsius, about 42 degrees Celsius, about 43 degrees Celsius, about 44 degrees Celsius, about 45 degrees Celsius, about 46 degrees Celsius, about 47 degrees Celsius, about 48 degrees Celsius, about 49 degrees Celsius, about 50 degrees Celsius, about 51 degrees Celsius, about 52 degrees Celsius, about 53 degrees Celsius, about 54 degrees Celsius, about 55 degrees Celsius, about 56 degrees Celsius, about 57 degrees Celsius, about 58 degrees Celsius, about 59 degrees Celsius, about 60 degrees Celsius, about 61 degrees Celsius, about 62 degrees Celsius, about 63 degrees Celsius, about 64 degrees Celsius, about 65 degrees Celsius, about 66 degrees Celsius, about 67 degrees Celsius, about 68 degrees Celsius, about 69 degrees Celsius, about 70 degrees Celsius, about 71 degrees Celsius, about 72 degrees Celsius, about 73 degrees Celsius, about 74 degrees Celsius, or about 75 degrees Celsius. This is referred to herein as “low heat”.

[0201] The isothermal amplification methods used herein can be conducted over a certain length of time and will typically be conducted until a detectable nucleic acid amplification product is generated. A nucleic acid amplification product can be detected by any suitable detection process and/or a detection process compatible with isothermal amplification methods (e.g. Cas mediated detection). In some embodiments, an amplification process is conducted over a length of time within about 2 hours or less, 2.5 hours or less, 60 minutes or less, for example 50 minutes or less, 40 minutes or less, 30 minutes or less, 20 minutes or less, 10 minutes or less or 5 minutes or less. In some embodiments, the amplification process is conducted for about 1 minute, about 2 minutes, about 3 minutes, about 4 minutes, about 5 minutes, about 6 minutes, about 7 minutes, about 8 minutes, about 9 minutes, about 10 minutes, about 11 minutes, about 12 minutes, about 13 minutes, about 14 minutes, about 15 minutes, about 16 minutes, about 17 minutes, about 18 minutes, about 19 minutes, or about 20 minutes. In some embodiments, an amplification process is conducted over a length of time within about 10 minutes or less.

[0202] In some embodiments, the nucleic acid targets are amplified without exposure to agents or conditions that denature or destabilize nucleic acids in the preparation, including, but not limited to thermal conditions (e.g., high temperatures), pH conditions (e.g., high or low pH), chemical agents (e.g., formamide, urea, dimethyl sulfoxide (DMSO), betaine sodium hydroxide, hydrochloric acid), proteins (e.g., enzymatic agents, such as helicases), and the like.

[0203] In some embodiments, it is desirable to design an isothermal amplification reaction to generate a short amplification product, for example, for rapid detection of a target sequence. In such embodiments, the nucleic acid amplification product can be up to 50 bases in length (e.g., about 15 to about 40 bases long or 15 bases long, 16 bases long, 17 bases long, 18 bases long, 19 bases long, 20 bases long, 21 bases long, 22 bases long, 23 bases long, 24 bases long, 25 bases long, 26 bases long, 27 bases long, 28 bases long, 29 bases long, 30 bases long, 31 bases long, 32 bases long, 33 bases long, 34 bases long, 35 bases long, 36 bases long, 37 bases long, 38 bases long, 39 bases long, or 40 bases long. In some embodiments, an amplification product is about 20 to about 40 bases long. In some embodiments, an amplification product is about 20 to about 30 bases long.

[0204] The nucleic acids generated using the methods and compositions described herein are contemplated for use in a multiplex amplification format (i.e., amplification or more than one target sequence).

[0205] Although the nucleic acids prepared as described herein are not considered ideal for conventional nucleic acid amplification methods using cycling temperatures (e.g., PCR), it is thought that this is due to a sensitivity of the PCR thermocycling enzymes to divalent metal ion concentration. Where the compositions and methods described herein chelate divalent metal ions, e.g., to limit target-independent nuclease cleavage of detection probes, it can be exacting to achieve, for example, a magnesium ion concentration optimal for PCR while also limiting target-independent nuclease cleavage. Nonetheless, it is also specifically contemplated that the nucleic acid preparation methods and compositions described herein can be used in thermocycling nucleic acid amplification methods when a thermostable enzyme that maintains activity or specificity at reduced divalent metal cation concentrations is used. Under such circumstances, the low-heat reaction chamber would cycle between low and higher heat such as requeried for PCR thermocycling.

[0206] Primers for Amplification

[0207] A primer is generally characterized as an oligonucleotide that includes a nucleotide sequence capable of hybridizing or annealing to a target nucleic acid, at or near (e.g., adjacent to) a specific region of interest (i.e., target sequence). Primers can allow for specific determination of a target nucleic acid nucleotide sequence or detection of the target nucleic acid (e.g., presence or absence of a sequence), or feature thereof, for example. A primer can be naturally occurring or synthetic. The term “specific,” or “specificity”, generally refers to the binding or hybridization of one molecule to another molecule, such as a primer for a target polynucleotide. That is, specific or specificity refers to the recognition, contact, and formation of a stable complex between two molecules, as compared to substantially less recognition, contact, or complex formation of either of those two molecules with other molecules. The term “anneal” or “hybridize” generally refers to the formation of a stable base-paired nucleic acid complex, e.g., via hydrogen bonding, between two nucleic acid molecules or, where relevant, between complementary portions of a single nucleic acid molecule. The terms primer, oligo, or oligonucleotide can be used interchangeably herein, when referring to primers.

[0208] A primer can be designed and synthesized using suitable processes, and can be of any length suitable for hybridizing to a target sequence and permitting extension for an amplification process described herein. Primers are generally designed according to a sequence in a target nucleic acid. A primer in some embodiments can be about 5 bases in length to about 30 bases in length. For example, a primer can be 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 or 30 bases in length. In some embodiments, a primer is less than 28 bases in length. In some embodiments, a primer is about 8 to about 16 bases in length. In some embodiments, a primer is about 10 to about 12 bases in length. A primer can be composed of naturally occurring and/or non-naturally occurring nucleotides (e.g., labeled nucleotides), or a mixture thereof. Primers suitable for use with methods described herein can be synthesized and labeled using any suitable technique. For example, primers can be chemically synthesized according to the solid phase phosphoramidite triester method first described by Beaucage and Caruthers, Tetrahedron Letts., 22:1859-1862, 1981, using an automated synthesizer, as described inNeedham- VanDevanter et al., Nucleic Acids Res. 12:6159-6168, 1984. Purification of primers can be effected, for example, by native acrylamide gel electrophoresis or by anion-exchange high- performance liquid chromatography (HPLC), for example, as described in Pearson and Regnier, J. Chrom., 255:137-149, 1983.

[0209] All or a portion of a primer sequence can be complementary or substantially complementary to a target nucleic acid, in some embodiments. Substantially complementary with respect to sequences generally refers to nucleotide sequences that will hybridize with each other. The stringency of the hybridization conditions can be altered to tolerate varying amounts of sequence mismatch. In some embodiments, target and primer sequences are at least 75% complementary to each other. For example, target and primer sequences can be 75% or more, 76% or more, 77% or more, 78% or more, 79% or more, 80% or more, 81% or more, 82% or more, 83% or more, 84% or more, 85% or more, 86% or more, 87% or more, 88% or more, 89% or more, 90% or more, 91% or more, 92% or more, 93% or more, 94% or more, 95% or more, 96% or more, 97% or more, 98% or more or 99% or more complementary to each other.

[0210] In some embodiments, primers comprise a pair of primers. A pair of primers can include a forward primer and a reverse primer (e.g., primers that bind to the sense and antisense strands of a target nucleic acid). In some embodiments, primers consist of a pair of primers, however, in certain instances, an amplification reaction can include additional primer pairs for amplifying different target sequences, such as in a multiplex amplification. In some embodiments, primers consist of a pair of primers, however, in certain instances, an amplification reaction can include additional primers, oligonucleotides or probes for a detection process that are not considered part of amplification.

[0211] A primer, in certain embodiments, can contain a modification such as one or more inosines, abasic sites, locked nucleic acids, minor groove binders, duplex stabilizers (e.g., acridine, spermidine), Tm modifiers or any modifier that changes the binding properties of the primer. A primer, in certain embodiments, can contain a detectable molecule or entity (e.g., a fluorophore, radioisotope, colorimetric agent, particle, enzyme and the like).

[0212] Polymerases

[0213] Polymerases are proteins capable of catalyzing the specific incorporation of nucleotides to extend a 3' hydroxyl terminus of a primer molecule, such as, for example, an amplification primer described herein, against a nucleic acid target sequence (e.g., to which a primer is annealed). While not necessarily a required property, polymerases useful in the compositions and methods described herein can include, for example, thermophilic or hyperthermophilic polymerases that can have activity at an elevated reaction temperature (e.g., above 55 degrees Celsius, above 60 degrees Celsius, above 65 degrees Celsius, above 70 degrees Celsius, above 75 degrees Celsius, above 80 degrees Celsius, above 85 degrees Celsius, or higher). In some embodiments, a polymerase can incorporate about 1 to about 50 nucleotides in a single synthesis. For example, a polymerase can incorporate about 5, 10, 15, 20, 25, 30, 35, 40, 45 or 50 nucleotides in a single synthesis. In other embodiments, a polymerase is more processive, and can incorporate 50 or more nucleotides in a single synthesis. In some embodiments, amplification reaction components comprise one or more DNA polymerases.

[0214] Exemplary DNA polymerases can be obtained commercially and include, but are not limited to, a 9° N DNA polymerase; 9°Nm™ DNA polymerase; Therminator™ DNA Polymerase; Therminator™ II DNA Polymerase; Therminator™ III DNA Polymerase; Therminator™ g DNA Polymerase; Bst DNA polymerase; Bst DNA polymerase (large fragment); Phi29 DNA polymerase, DNA polymerase I ( E . coli ), DNA polymerase I, large (Klenow) fragment; Klenow fragment (3 '-5' exo-); T4 DNA polymerase; T7 DNA polymerase; Deep VentR™ (exo-) DNA Polymerase; Deep VentR™ DNA Polymerase; DyNAzyme™ EXT DNA; DyNAzyme™ II Hot Start DNA Polymerase; Phusion™ High- Fidelity DNA Polymerase; VentR® DNA Polymerase; VentR® (exo-) DNA Polymerase; RepliPHI™ Phi29 DNA Polymerase; rBst DNA Polymerase, large fragment (IsoTherm™ DNA Polymerase); Master Amp™ AmpliTherm™ DNA Polymerase; Tag DNA polymerase; Tth DNA polymerase; Tfl DNA polymerase; Tgo DNA polymerase; SP6 DNA polymerase; Tbr DNA polymerase; DNA polymerase Beta; and ThermoPhi DNA polymerase.

[0215] In some embodiments, a polymerase can possess reverse transcription capabilities. In such instances, an amplification reaction can amplify RNA targets, for example, in a single step without the use of a separate reverse transcriptase. Non-limiting examples of polymerases that possess reverse transcriptase capabilities include Bst (large fragment), 9° N DNA polymerase, 9°Nm™ DNA polymerase, Therminator™, Therminator™ II, Protoscript™ Reverse Transcriptase (New England Biolabs), and the like. In some embodiments, amplification reaction components comprise one or more separate reverse transcriptases. In some embodiments, more than one polymerase can be included in an amplification reaction. For example, an amplification reaction can comprise a polymerase having reverse transcriptase activity and a second polymerase having no reverse transcriptase activity.

[0216] Detection and Quantification

[0217] Nucleic acids prepared using the methods, compositions and devices described herein can be subjected to reactions that detect one or more target nucleic acids. In one embodiment, the detection can be performed without a prior amplification. In other embodiments, the detection is performed on amplified nucleic acid products. Thus, an amplification method as described herein, including but not limited to an isothermal amplification method, can further comprise detecting and/or quantifying a nucleic acid amplification product using any detection method or quantification method known to those of skill in the art. Non-limiting examples of detection and/or quantification methods include RNA-guided nuclease (e.g., Cas) mediated cleavage and activation of a fluorophore, molecular beacon (e.g., real-time, endpoint), lateral flow, fluorescence resonance energy transfer (FRET), fluorescence polarization (FP), surface capture, 5' to 3' exonuclease hydrolysis probes (e.g., TAQMAN), intercalating/binding dyes, absorbance methods (e.g., colorimetric, turbidity), electrophoresis (e.g., gel electrophoresis, capillary electrophoresis), mass spectrometry, nucleic acid sequencing, digital amplification, a primer extension method (e.g., iPLEX™), Molecular Inversion Probe (MIP) technology from Affymetrix, restriction fragment length polymorphism (RFLP) analysis, allele specific oligonucleotide (ASO) analysis, methylation-specific PCR (MSPCR), pyrosequencing analysis, acycloprime analysis, Reverse dot blot, GeneChip microarrays, Dynamic allele-specific hybridization (DASH), Peptide nucleic acid (PNA) and locked nucleic acids (LNA) probes, AlphaScreen, SNPstream, genetic bit analysis (GBA), Multiplex mini sequencing, SNaPshot, GOOD assay, Microarray miniseq, arrayed primer extension (APEX), Microarray primer extension, Tag arrays, Coded microspheres, Template-directed incorporation (TDI), colorimetric oligonucleotide ligation assay (OLA), sequence-coded OLA, microarray ligation, ligase chain reaction, padlock probes, invader assay, hybridization using at least one probe, hybridization using at least one fluorescently labeled probe, cloning and sequencing, the use of hybridization probes and quantitative real time polymerase chain reaction (QRT-PCR), nanopore sequencing, chips and combinations thereof. In some embodiments, detecting a nucleic acid amplification product comprises use of a real-time detection method (i.e., product is detected and/or continuously monitored during an amplification process). In some embodiments, detecting a nucleic acid amplification product comprises use of an endpoint detection method (i.e., product is detected after completing or stopping an amplification process). Nucleic acid detection methods can also employ the use of labeled nucleotides incorporated directly into a target sequence or into probes containing complementary sequences to a target. Such labels can be radioactive and/or fluorescent in nature and can be resolved in any of the manners discussed herein. In some embodiments, quantification of a nucleic acid amplification product can be achieved using certain detection methods described below. In certain instances, a detection method can be used in conjunction with a measurement of signal intensity, and/or generation of (or reference to) a standard curve and/or look-up table for quantification of a nucleic acid amplification product.

[0218] In some embodiments, detecting a nucleic acid amplification product comprises use of molecular beacon technology. The term molecular beacon generally refers to a detectable molecule, where the detectable property of the molecule is detectable under certain conditions, thereby enabling the molecule to function as a specific and informative signal. Non-limiting examples of detectable properties include, optical properties (e.g., fluorescence), electrical properties, magnetic properties, chemical properties and time or speed through an opening of known size. Molecular beacons for detecting nucleic acid molecules can be, for example, hair-pin shaped oligonucleotides containing a fluorophore on one end and a quenching dye on the opposite end. The loop of the hair-pin can contain a probe sequence that is complementary to a target sequence and the stem is formed by annealing of complementary arm sequences located on either side of the probe sequence. A fluorophore and a quenching molecule can be covalently linked at opposite ends of each arm. Under conditions that prevent the oligonucleotides from hybridizing to its complementary target or when the molecular beacon is free in solution, the fluorescent and quenching molecules are proximal to one another preventing fluorescence resonance energy transfer (FRET). When the molecular beacon encounters a target molecule (e.g., a nucleic acid amplification product), hybridization can occur, and the loop structure is converted to a stable more rigid conformation causing separation of the fluorophore and quencher molecules leading to fluorescence (Tyagi et al. Nature Biotechnology 14: March 1996, 303-308). Due to the specificity of the probe, the generation of fluorescence generally is exclusively due to the synthesis of the intended amplified product. In some instances, a molecular beacon probe sequence hybridizes to a sequence in an amplification product that is identical to or complementary to a sequence in a target nucleic acid. In some instances, a molecular beacon probe sequence hybridizes to a sequence in an amplification product that is not identical to or complementary to a sequence in a target nucleic acid (e.g., hybridizes to a sequence added to an amplification product by way of a tailed amplification primer or ligation).

[0219] Molecular beacons are highly specific and can discern a single nucleotide polymorphism. Molecular beacons also can be synthesized with different colored fluorophores and different target sequences, enabling simultaneous detection of several products in the same reaction (e.g., in a multiplex reaction). For quantitative amplification processes, molecular beacons can specifically bind to the amplified target following each cycle of amplification, and because non-hybridized molecular beacons are dark, it is not necessary to isolate the probe-target hybrids to quantitatively determine the amount of amplified product. The resulting signal is proportional to the amount of amplified product. Detection using molecular beacons can be done in real time or as an end-point detection method. In some instances, certain reaction conditions can be optimized for each primer/probe set to ensure accuracy and precision.

[0220] In some embodiments, detecting a nucleic acid amplification product comprises use of fluorescence resonance energy transfer (FRET). FRET is an energy transfer mechanism between two chromophores: a donor and an acceptor molecule. Briefly, a donor fluorophore molecule is excited at a specific excitation wavelength. The subsequent emission from the donor molecule as it returns to its ground state can transfer excitation energy to the acceptor molecule through a long range dipole-dipole interaction. The emission intensity of the acceptor molecule can be monitored and is a function of the distance between the donor and the acceptor, the overlap of the donor emission spectrum and the acceptor absorption spectrum and the orientation of the donor emission dipole moment and the acceptor absorption dipole moment. FRET can be useful for quantifying molecular dynamics, for example, in DNA-DNA interactions as described for molecular beacons. For monitoring the production of a specific product, a probe can be labeled with a donor molecule on one end and an acceptor molecule on the other. Probe-target hybridization brings a change in the distance or orientation of the donor and acceptor and FRET change is observed.

[0221] Nucleic acid amplification methods (e.g., isothermal nucleic acid amplification) can be conducted in the presence of native nucleotides, such as, for example, dideoxyribonucleoside triphosphates (dNTPs), and/or derivatized nucleotides. A native nucleotide generally refers to adenylic acid, guanylic acid, cytidylic acid, thymidylic acid, or uridylic acid. A derivatized nucleotide generally is a nucleotide other than a native nucleotide. Nucleotides typically are designated as follows. A ribonucleoside triphosphate is referred to as NTP or rNTP, where N can be A, G, C, U. A deoxynucleoside triphosphate substrate is referred to as dNTP, where N can be A, G, C, T, or U. Monomeric nucleotide subunits can be denoted as A, G, C, T, or El herein with no particular reference to DNA or RNA. In some embodiments, non-naturally occurring nucleotides or nucleotide analogs, such as analogs containing a detectable label (e.g., fluorescent or colorimetric label), can be used. For example, nucleic acid amplification can be carried out in the presence of labeled dNTPs, such as, for example, radiolabels such as ³²P, ³³P, ¹²⁵I, or ³⁵S; enzyme labels such as alkaline phosphatase; fluorescent labels such as fluorescein isothiocyanate (FITC); or other labels such as biotin, avidin, digoxigenin, antigens, haptens, or fluorochromes. In some embodiments, nucleic acid amplification can be carried out in the presence of modified dNTPs, such as, for example, heat activated dNTPs (e.g., CleanAmp™ dNTPs from TriLink). [0222] CRISPR Cas- mediated detection of a target sequence

[0223] In some embodiments, the isothermal amplification methods use a CRISPR-Cas method for detecting the presence of a target sequence in the pool of amplified nucleic acids. The CRISPR-Cas enzyme can be from an organism from a genus comprising, for example, Streptococcus, Campylobacter, Nitratifr actor, Staphylococcus, Parvibaculum, Roseburia, Neisseria, Gluconacetobacter, Azospirillum, Sphaerochaeta, Lactobacillus, Eubacterium, Corymbacter, Carnobacterium, Rhodobacter, Listeria, Paludibacter, Clostridium, Lachnospiraceae, Clostridiaridium, Leptotrichia, Francisella, Legionella, Alicyclobacillus, Methanomethyophilus, Porphyromonas, Prevotella, Bacteroidetes, Helcococcus, Letospira, Desulfovibrio, Desulfonatronum, Opitutaceae, Tuberibacillus, Bacillus, Brevibacilus, Methyl obacterium or Acidaminococcus.

[0224] In the context of formation of a CRISPR complex, the term “target sequence” or “target nucleic acid” refers to a sequence to which a guide sequence is designed to have complementarity, where hybridization between a target sequence and a guide sequence promotes the formation of a CRISPR complex. The section of the guide sequence through which complementarity to the target sequence is important for cleavage activity is referred to herein as the seed sequence. A target sequence can be DNA or RNA. Generally, the term ‘target nucleic acid’ refers to a polynucleotide that has or contains the target sequence. In other words, the target nucleic acid can be a polynucleotide or a part of a polynucleotide to which a part of the gRNA, i.e. the guide sequence, is designed to have complementarity and to which the effector function mediated by the complex comprising CRISPR effector protein and a gRNA is to be directed. In some embodiments, a target sequence is located in a pathogen such as a parasite, bacterial or viral genome.

[0225] It is noted that the enzyme system can be a DNA targeting CRISPR-Cas protein or an RNA targeting CRISPR-Cas protein. Exemplary CRISPR-Cas proteins include, but are not limited to, Cas 13, Cas 12a, Casl, CaslB, Cas2, Cas3, Cas4, Cas5, Cas6, Cas7, Cas8, Cas9 (also known as Csnl and Csxl2), CaslO, Csyl, Csy2, Csy3, Csel, Cse2, Cscl, Csc2, Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6, Cmrl, Cmr3, Cmr4, Cmr5, Cmr6, Csbl, Csb2, Csb3, Csxl7, Csxl4, CsxlO, Csxl6, CsaX, Csx3, Csxl, Csxl5, Csfl, Csf2, Csf3, Csf4, homologues thereof, or modified versions thereof. In some embodiments, the effector protein Cas 9, Casl2a, Casl3a, or Casl4. In some embodiments, the effector protein is Casl3.

[0226] As used herein, the terms “guide nucleic acid,” “guide sequence,” “crRNA,” “guide RNA,” or “single guide RNA,” or “gRNA” refers to a polynucleotide comprising any polynucleotide sequence having sufficient complementarity with a target nucleic acid sequence to hybridize with the target nucleic acid sequence and to direct sequence-specific binding of a CRISPR complex comprising the guide sequence and a CRISPR effector protein to the target nucleic acid sequence. In some example embodiments, the degree of complementarity, when optimally aligned using a suitable alignment algorithm, is about or more than about 50%, 60%, 75%, 80%, 85%, 90%, 95%, 97.5%, 99%), or more. Optimal alignment can be determined with the use of any suitable algorithm for aligning sequences. Exemplary algorithms for determining optimal alignment include, but are not limited to, the Smith-Waterman algorithm, the Needleman-Wunsch algorithm, algorithms based on the Burrows- Wheeler Transform (e.g., the Burrows Wheeler Aligner), ClustalW, Clustal X, BLAT, Novoalign (Novocraft Technologies; available atwww.novocraft.com), ELAND (Illumina, San Diego, CA), SOAP (available at soap.genomics.org.cn), and Maq (available at maq.sourceforge.net).

[0227] The guide nucleic acid strand can be any length. For example, the guide nucleic acid strand can be about or more than about 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 75, or more nucleotides in length. In some embodiments, a nucleic acid strand is less than about 75, 50, 45, 40, 35, 30, 25, 20, 15, 12, or fewer nucleotides in length. Preferably the guide nucleic acid sequence is 10-30 nucleotides long.

[0228] Typically, the presence of a target nucleic acid sequence to which the guide RNA hybridizes, will activate the Cas enzyme to non-specifically cleave a reporter molecule, for example, a ssDNA reporter, releasing or activating a fluorophore that indicates the presence of the target nucleic acid. Thus, when the targeted DNA (double or single stranded) is present in the sample (e.g., in some cases above a threshold amount), the result is cleavage of the reporter molecule, which can be detected using a labeled single stranded detector DNA of the present disclosure.

[0229] Reporter Molecules for Cas Detection

[0230] A reporter molecule, for example, a ssDNA reporter, will typically comprise a label such as a fluorophore. Releasing or activating the label by cleavage of the reporter molecule indicates the presence of the target nucleic acid. Other detectable labels for the reporter molecule are also envisioned.

[0231] In some embodiments, the reporter molecule comprises a single-stranded DNA (ssDNA) of from about 5 nucleotides in length to about 15 nucleotides in length, where a fluorophore is attached to the 5' end of the ssDNA, and a quencher is attached to the 3' end of the ssDNA. The signal partners of such a quencher/fluor pair will thus produce a detectable signal when the partners are separated (e.g., after cleavage of the detector ssDNA by a Type V CRISPR/Cas effector protein (e.g., a Casl2 protein such as Casl2a, Casl2b, Casl2c,

Cas 12d, Casl2e)), but the signal will be quenched when the partners are in close proximity (e.g., prior to cleavage of the detector ssDNA by a Type V CRISPR/Cas effector protein (e.g., a Cas 12 protein such as Cas 12a, Cas 12b, Cas 12c, Cas 12d, Cas 12e)). Suitable fluorophores and quenchers are known in the art, and any known fluorophore/quencher pair can be used. In some cases, the signal moiety is a fluorescent label. In some such cases, the quencher moiety quenches the signal (the light signal) from the fluorescent label (e.g., by absorbing energy in the emission spectra of the label). Thus, when the quencher moiety is not in proximity with the signal moiety, the emission (the signal) from the fluorescent label is detectable because the signal is not absorbed by the quencher moiety. Any convenient donor acceptor pair (signal moiety/quencher moiety pair) can be used and many suitable pairs are known in the art. Examples of fluorescent labels include, without limitation, an Alexa Fluor.RTM. dye, an ATTO dye (e.g, ATTO 390, ATTO 425, ATTO 465, ATTO 488, ATTO 495, ATTO 514, ATTO 520, ATTO 532, ATTO Rho6G, ATTO 542, ATTO 550, ATTO 565, ATTO Rho3B, ATTO Rholl, ATTO Rhol2, ATTO Thiol2, ATTO RholOl, ATTO 590, ATTO 594, ATTO Rhol3, ATTO 610, ATTO 620, ATTO Rhol4, ATTO 633, ATTO 647, ATTO 647N, ATTO 655, ATTO Oxal2, ATTO 665, ATTO 680, ATTO 700, ATTO 725, ATTO 740), aDyLight dye, a cyanine dye (e.g., Cy2, Cy3, Cy3.5, Cy3b, Cy5, Cy5.5, Cy7, Cy7.5), a FluoProbes dye, a Sulfo Cy dye, a Seta dye, an IRIS Dye, a SeTau dye, an SRfluor dye, a Square dye, fluorescein (FITC), tetramethylrhodamine (TRITC), Texas Red, Oregon Green, Pacific Blue, Pacific Green, and Pacific Orange. Examples of quencher moieties include, without limitation, a dark quencher, a Black Hole Quencher.RTM. (BHQ.RTM.) (e.g., BHQ-0, BHQ-1, BHQ-2, BHQ-3), a Qxl quencher, an ATTO quencher (e.g., ATTO 540Q, ATTO 580Q, and ATTO 612Q), dimethylaminoazobenzenesulfonic acid (Dabsyl), Iowa Black RQ, Iowa Black FQ, IRDye QC-1, a QSY dye (e.g., QSY 7, QSY 9, QSY 21), AbsoluteQuencher, Eclipse, and metal clusters such as gold nanoparticles, and the like. For examples of some fluorescent dyes and/or quencher moieties, see, e.g., Bao et al., Annu Rev Biomed Eng. 2009; 11:25-47; as well as U.S. Pat. Nos. 8,822,673 and 8,586,718; U.S. patent publications 20140378330, 20140349295, 20140194611, 20130323851, 20130224871, 20110223677, 20110190486, 20110172420, 20060179585 and 20030003486; and international patent applications: W0200142505 and W0200186001, all of which are hereby incorporated by reference in their entirety.

[0232] In some embodiments, the reporter molecule comprises a ssDNA of from about 5 nucleotides in length to about 15 nucleotides in length; e.g., the ssDNA has a length of 5 nucleotides (nt), 6 nt, 7 nt, 8 nt, 9 nt, 10 nt, 11 nt, 12 nt, 13 nt, 14 nt, or 15 nt. In some cases, the ssDNA has a length of 5 nucleotides. In some cases, the ssDNA has a length of 6 nucleotides. In some cases, the ssDNA has a length of 7 nucleotides. In some cases, the ssDNA has a length of 8 nucleotides. In some cases, the ssDNA has a length of 9 nucleotides. In some cases, the ssDNA has a length of 10 nucleotides. In some cases, the ssDNA has a length of 11 nucleotides. In some cases, the ssDNA has a length of 12 nucleotides. In some cases, the ssDNA has a length of 13 nucleotides. In some cases, the ssDNA has a length of 14 nucleotides. In some cases, the ssDNA has a length of 15 nucleotides.

[0233] SHERLOCK Detection

[0234] SHERLOCK, also known as “Specific high-sensitivity enzymatic reporter unlocking,” is a nucleic acid detection method that is used to detect RNA or DNA target sequences depending upon the particular enzymes used. SHERLOCK utilizes isothermap amplificaitn and CRISPR Cas mediated detection described herein. In each instance, SHERLOCK detection is based on the target sequence-dependent activation of an RNA-guided nuclease, which, once activated, cleaves not only the target sequence, but other nucleic acids. When the other nucleic acid is a labeled probe (otherwise referred to herein as as “reporter molecule”) that generates a signal upon cleavage, e.g., via separation of a fluorophore and a quencher, a sensitive target-sequence detection assay is provided. These are the hallmarks of a SHERLOCK detection assay as described herein - that is, as used herein, a SHERLOCK detection assay includes the use of an RNA-guided nuclease, a guide RNA including complementarity to a desired target nucleic acid, and a labeled probe that generates a signal upon cleavage by the promiscuous activity of the target-sequence-activated RNA-guided nuclease. When that target- sequence detection assay is coupled with a target-specific isothermal nucleic acid amplification reaction, a single-pot amplification and detection assay is provided that has extremely high sensitivity. This combined isothermal amplification/RNA-guided nuclease detection approach is the assay initially published as SHERLOCK - see Gootenberg et ah, Science 356: 438-442 (2017), incorporated herein by reference. The isothermal amplification approach is coupled with reverse transcription to detect RNA targets in a highly sensitive manner by first generating amplified cDNA, and then detecting with RNA-guided nuclease that targets DNA. When the RNA-guided nuclease is one that cleaves RNA, e.g., a Casl3a enzyme, a single-stranded RNA probe, other wise referred to herein as reporter molecule, can be used (Gootenberg et ah, Science 356: 438-442 (2017)). When the RNA-guided nuclease is one that cleaves DNA, e.g., a Casl2a enzyme, a DNA probe, otherwise referred to herein as reporter molecule, can be used; see, e.g., Gootenberg et ah, Science 360: 439-444 (2018), and Li et ah, Cell Discovery 4, 20 (2018) see https:// at doi.org/10.1038/s41421-018-0028-z, each of which is incorporated herein by reference. The RNA sample preparation compositions and methods described herein are well-suited for preparing biological samples for use in isothermal nucleic acid amplification reactions, as well as for SHERLOCK detection (e.g., one-pot SHERLOCK) of target nucleic acid sequences, and generating low background in such reactions.

[0235] SARS-CoV-2 and Other Pathogens

[0236] The devices, methods and compositions described herein used for nucleic acid preparation and detection permit detection of a pathogen in a biological sample (e.g., a saliva sample). A pathogen can be, for example, a virus, a bacterium, a fungus, or an intracellular parasite. In some embodiments the pathogen is a virus (e.g, an RNA containing virus). In some embodiments, the pathogen is Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). In some embodiments, the SARS-CoV-2 is broadly detected (universal detection) by detection of highly conserved regions in the genome (e.g., specific regions of the N-Gene). In some embodiments, a specific variant or a subset of variants that share the same mutations (e.g., in the spike protein) are detected by specific detection of single nucleotide polymorphisms unique to the specific variant(s). The skilled practitioner will recognize that it may be useful to detect single nucleotide polymorphisms in a combination of genes to identify some variants.

[0237] A single nucleotide polylmorphism, also referred to herein as a mutation, refers to a single change in an organism’s genome (genetic code). Mutations happen very frequently, but only sometimes change the characteristics of the virus. Specific mutations can be used to identify different variants, strains, etc. Mutations in SARS-CoV-2 that occur in the coding sequence for the spike protein of the virus are particularly useful in identifying specific variants and lineages. The methods and devices described herein can be used to identify a variant/lineage or a subset of variants/lineages by specifically detecting mutations unique to the variant (e.g., in the spike protein).

[0238] SARS-CoV-2 has many identified and evolving variants and lineages, some of which are described herein (Zhang et al., Communications Biology volume 4, Article number: 1196 (2021)). In February 2020 the first whole genome of the novel coronavirus, now known as SARS CoV-2, was published. Three complete genome sequences were submitted to GISAID (BetaCoV/W uhan/IVDC-HB-01/2019, accession ID: EPI ISL 402119;

BetaCoV/W uhan/IVDC-HB-04/2020, accession ID: EPI ISL 402120;

BetaCoV/W uhan/IVDC-HB-05/2019, accession ID: EPI ISL 402121). Since then, a number of specific viral variants have been identified and continue to be identified as they evolve and emerge in the population.

[0239] The Center for Disease Control monitors the prevelance of variants circulating in the United States. Several variants of SARS-CoV-2 presently being monitored and some of the mutations present (in the spike protein) are referred to herein and listed below in Table 1. The skilled practitioner realizes that variants with mutations in the spike protein, referred to herein, may also contain mutations in coding sequences other than the spike protein which are not specified herein. Such other mutations may also be useful in identifying variants by the methdods and devices described herein (e.g., alone or in combination with other mutations). Mutations in the spike protein and/or other mutations specific for variants are disclosed (e.g., at https://www.rndsystems.com/products/proteins-coronavirus- research#spikevariant.)

[0240] Table 1: SARS-CoV-2 Variants and Spike Protein Mutations

[0241] Other pathogenic viruses can also be detected by the methods and devices described herein, with the appropriate target nucleic acids, gRNAs and primers. These include, without limitation, the Dengue virus, Zika virus, Severe Acute Respiratory Syndrome Coronavirus 1 (SARS-CoVl), Middle Eastern Respiratory Syndrome Coronavirus (MERS-CoV) virus, Hepatitis A, Hepatitis B, Hepatitis C, Hepatitis D, Heptatis E, Herpes virus, Varicella virus, Cytomegalovirus, Epstein-Barr virus, Human herpesvirus 6, Human herpesvirus8, adenovirus, influenza, parainfluenza, respiratory syncytial virus, or Chikungunya virus. Other exemplary viruses that can be detected as described herein include genera of viruses: Adenoviridae, Alfamovirus, Allexivirus, Allolevivirus, Alphacryptovirus, Alphaherpesvirinae, Alphanodavirus, Alpharetrovirus, Alphavirus, Aphthovirus, Apscaviroid, Aquabirnavirus, Aquareovirus, Arenaviridae, Arenavirus, Arteriviridae, Arterivirus, Ascoviridae, Ascovirus, Asfarviridae, Asfivirus, Astroviridae, Astrovirus, Aureusvirus, Avenavirus, Aviadenovirus, Avibirnavirus, Avihepadnavirus, Avipoxvirus, Avsunviroid, Avsunviroidae, Baculoviridae, Badnavirus, Barnaviridae, Barnavirus, Bdellomicrovirus, Begomovirus, Benyvirus, Betacryptovirus, Betaherpesvirinae, Betanodavirus, Betaretrovirus, Betatetravirus, Birnaviridae, Bornaviridae, Bornavirus, Bracovirus, Brevidensovirus, Bromoviridae, Bromovirus, Bunyaviridae, Bunyavirus, Bymovirus, "c2-like viruses, " Caliciviridae, Capillovirus, Capripoxvirus, Cardiovirus, Carlavirus, Carmovirus, "Cassava vein mosaic like viruses, " Caulimoviridae, Caulimovirus, Chlamydiamicrovirus, Chloriridovirus, Chlorovirus, Chordopoxyirinae, Chrysovirus, Circoviridae, Circovirus, Closteroviridae, Closterovirus, Cocadviroid, Coleviroid, Coltivirus, Comoviridae, Comovirus, Coronaviridae, Coronavirus, Corticoviridae, Corticovirus, "Cricket paralysis-like viruses, " Crinivirus, Cucumovirus, Curtovirus, Cypovirus, Cystoviridae, Cystovirus, Cytomegalovirus, Cytorhabdovirus, Deltarelrovirus, Deltavirus, Densovirinae, Densovirus, Dependovirus, Dianthovirus, "Ebola-like viruses, " Enamovirus, Enterovirus, Entomobirnavirus, Entomopoxyirinae, Entomopoxvirus A, Entomopoxvirus B, Entomopoxvirus C, Ephemerovirus, Epsilonretrovirus, Errantivirus, Erythrovirus, Fabavirus, Fijivirus, Filoviridae, Flaviviridae, Flavivirus, Foveavirus, Furovirus, Fuselloviridae, Fusellovirus, Gammaherpesvirinae, Gammaretrovirus, Geminiviridae, Giardiavirus, Granulovirus, Hantavirus, Hemivirus, Hepacivirus, Hepadnaviridae, "Hepatitis E-like viruses, " Hepatovirus, Herpesviridae, Hordeivirus, Hostuviroid, Hypoviridae, Hypovirus, Ichnovirus, "Ictalurid herpes-like viruses, " Idaeovirus, Ilarvirus, "Infectious laryngotracheitis-like viruses, " Influenzavirus A, Influenzavirus B, Influenzavirus C, Inoviridae, Inovirus, Ipomovirus, Iridoviridae, Iridovirus, Iteravirus, "L5-like viruses, " Lagovirus, "-like viruses, " Leishmaniavirus, Lentivirus, Leporipoxvirus, Leviviridae, Levivirus, Lipothrixviridae, Lipothrixvirus, Luteoviridae, Luteovirus, Lymphocryptovirus, Lymphocystivirus, Lyssavirus, Machlomovirus, Macluravirus, Marafivirus, "Marburg-like viruses, " "Marek's disease-like viruses, " Mastadenovirus, Mastrevirus, Metapneumovirus, Metaviridae, Metavirus, Microviridae, Microvirus, Mitovirus, Molluscipoxvirus, Morbillivirus, "Mu-like viruses, " Muromegalovirus, Myoviridae, Nairovirus, Nanovirus, Narnaviridae, Narnavirus, Necrovirus, Nepovirus, Nodaviridae, "Norwalk-like viruses, " Novirhabdovirus, Nucleopolyhedrovirus, Nucleorhabdovirus, Oleavirus, Omegatetravirus, Ophiovirus, Orbivirus, Orthohepadnavirus, Orthomyxoviridae, Orthopoxvirus, Orthoreovirus, Oryzavirus, Ourmiavirus, "P 1-like viruses, " "P2-like viruses, " "P22-like viruses, " Panicovirus, Papillomaviridae, Papillomavirus, Paramyxoviridae, Paramyxovirinae, Parapoxvirus, Parechovirus, Partitiviridae, Partitivirus, Parvoviridae, Parvovirinae, Parvovirus, Pecluvirus, Pelamoviroid, Pestivirus, "Petunia vein clearing-like viruses, " Phaeovirus, "-29-like viruses, " "-H-like viruses, " Phlebovirus, Phycodnaviridae, Phytoreovirus, Picornaviridae, Plasmaviridae, Plasmavirus, Plectrovirus, Pneumovirinae, Pneumovirus, Podoviridae, Polerovirus, Polydnaviridae, Polyomaviridae, Polyomavirus, Pomovirus, Pospiviroid, Pospiviroidae, Potexvirus, Potyviridae, Potyvirus, Poxyiridae, Prasinovirus, Prions, Prymnesiovirus, Pseudoviridae, Pseudovirus, "Ml -like viruses", Ranavirus, Reoviridae, Respirovirus, Retroviridae, Rhabdoviridae, Rhadinovirus,

Rhinovirus, Rhizidiovirus, "Rice tungro bacilliform-like viruses, " Roseolovirus, Rotavirus, Rubivirus, Rubulavirus, Rudiviridae, Rudivirus, Rymovirus, "Sapporo-like viruses, " Satellites, Sequiviridae, Sequivirus, Simplexvirus, Siphoviridae, Sobermovirus, "Soybean chlorotic mottle-like viruses, " Spiromicrovirus, "SPO 1-like viruses, " Spumavirus,

Suipoxvirus, "Sulfolobus SNDV-like viruses, " "T l -like viruses, " "T4-like viruses, " "T5-like viruses, " "T7-like viruses, " Tectiviridae, Tectivirus, Tenuivirus, Tetraviridae, Thogotovirus, Tobamovirus, Tobravirus, Togaviridae, Tombusviridae, Tombusvirus, Torovirus, Tospovirus, Totiviridae, Totivirus, Trichovirus, Tritimovirus, Tymovirus, Umbravirus, Varicellovirus, Varicosavirus, Vesiculovirus, Vesivirus, Viroids, Vitivirus, Wakavirus, and Yatapoxvirus. [0242] A bacterium that can be detected using the methods and compositions described herein can be a gram negative bacterium, a gram positive bacterium, an anaerobic bacterium, an aerobic bacterium, a facultative anaerobic bacterium, or an intracellular bacterium. Examples of gram-negative bacteria include cocci, nonenteric rods, and enteric rods. The genera of Gram-negative bacteria include, for example, Neisseria, Spirillum, Pasteurella, Brucella, Yersinia, Francisella, Haemophilus, Bordetella, Escherichia, Salmonella, Shigella, Klebsiella, Proteus, Vibrio, Pseudomonas, Bacteroides, Acetobacter, Aerobacter, Agrobacterium, Azotobacter, Spirilla, Serratia, Vibrio, Rhizobium, Chlamydia, Rickettsia, Treponema , and Fusobacterium. Exemplary gram-positive bacteria include, but are not limited to, cocci, nonsporulating rods, and sporulating rods. The genera of Gram-positive bacteria include, for example, Actinomyces, Bacillus, Clostridium, Corynebacterium, Erysipelothrix, Lactobacillus, Listeria, Mycobacterium, Myxococcus, Nocardia, Staphylococcus, Streptococcus , and Streptomyces.

[0243] Additional bacteria that can be detected as described herein include bacteria from one or more of the following genera: genera of the domain of Bacteria (or Eubacteria): Abiotrophia, Acetitomaculum, Acetivibrio, Acetoanaerobium, Acetobacter, Acetobacterium, Acetofilamentum, Acetogenium, Acetohalobium, Acetomicrobium, Acetonema, Acetothermus, Acholeplasma, Achromatium, Achromobacter, Acidaminobacter, Acidaminococcus, Acidimicrobium, Acidiphilium, Acidisphaera, Acidithiobacillus, Acidobacterium, Acidocella, Acidomonas, Acidothermus, Acidovorax, Acinetobacter, Acrocarpospora, Actinoalloteichus, Actinobacillus, Actinobaculum, Actinobispora, Actinocorallia, Actinokineospora, Actinomadura, Actinomyces, Actinoplanes, Actinopolymorpha, Actinopolyspora, Actinopycnidium, Actinosporangium, Actinosynnema, Aegyptianella, Aequorivita, Aerococcus, Aeromicrobium, Aeromonas, Afipia, Agitococcus, Agreia, Agrobacterium, Agrococcus, Agromonas, Agromyces, Ahrensia, Albibacter, Albidovulum, Alcaligenes, Alcalilimnicola, Alcanivorax, Algoriphagus, Alicycliphilus, Alicyclobacillus, Alishewanella, Alistipes, Alkalibacterium, Alkalilimnicola, Alkaliphilus, Alkalispirillum, Alkanindiges, Allisonella, Allochromatium, Allofustis, Alloiococcus, Allomonas, Allorhizobium, Alterococcus, Alteromonas, Alysiella, Amaricoccus, Aminobacter, Aminobacterium, Aminomonas, Ammonifex, Ammoniphilus, Amoebobacter, Amorphosphorangium, Amphibacillus, Ampullariella, Amycolata, Amycolatopsis, Anaeroarcus, Anaerobacter, Anaerobaculum, Anaerobiospirillum, Anaerobranca, Anaerococcus, Anaerofilum, Anaeroglobus, Anaerolinea, Anaeromusa, Anaeromyxobacter, Anaerophaga, Anaeroplasma, Anaerorhabdus, Anaerosinus, Anaerostipes, Anaerovibrio, Anaerovorax, Anaplasma, Ancalochloris, Ancalomicrobium, Ancylobacter, Aneurinibacillus, Angiococcus, Angulomicrobium, Anoxybacillus, Anoxynatronum, Antarctobacter, Aquabacter, Aquabacterium, Aquamicrobium, Aquaspirillum, Aquifex, Arachnia, Arcanobacterium, Archangium, Arcobacter, Arenibacter, Arhodomonas, Arsenophonus, Arthrobacter, Asaia, Asanoa, Aster oleplasma, Asticcacaulis, Atopobacter, Atopobium, Aurantimonas, Aureobacterium, Azoarcus, Azomonas, Azomonotrichon, Azonexus, Azorhizobium, Azorhizophilus, Azospira, Azospirillum, Azotobacter, Azovibrio, Bacillus, Bacterionema, Bacteriovorax, Bacteroides, Bactoderma, Balnearium, Balneatrix, Bartonella, Bdellovibrio, Beggiatoa, Beijerinckia, Beneckea, Bergeyella, Beutenbergia, Bifidobacterium, Bilophila, Blastobacter, Blastochloris, Blastococcus, Blastomonas, Blattabacterium, Bogoriella, Bordetella, Borrelia, Bosea, Brachybacterium, Brachymonas, Brachyspira, Brackiella, Bradyrhizobium, Branhamella, Brenneria, Brevibacillus, Brevibacterium, Brevinema, Brevundimonas, Brochothrix, Brucella, Brumimicrobium, Buchnera, Budvicia, Bulleidia, Burkholderia, Buttiauxella, Butyrivibrio, Caedibacter, Caenibacterium, Calderobacterium, Caldicellulosiruptor, Caldilinea, Caldimonas, Caldithrix, Caloramator, Calor anaerobacter, Calymmatobacterium, Caminibacter, Caminicella, Campylobacter, Capnocytophaga, Capsularis, Carbophilus, Carboxydibrachium, Carboxydobrachium, Carboxydocella, Carboxydothermus, Cardiobacterium, Carnimonas, Carnobacterium, Caryophanon, Caseobacter, Catellatospora, Catenibacterium, Catenococcus, Catenuloplanes, Catonella, Caulobacter, Cedecea, Cellulomonas, Cellulophaga, Cellulosimicrobium, Cellvibrio, Centipeda, Cetobacterium, Chainia, Chelatobacter, Chelatococcus, Chitinophaga, Chlamydia, Chlamydophila, Chlorobaculum, Chlorobium, Chloroflexus, Chloroherpeton, Chloronema, Chondromyces, Chromatium, Chromobacterium, Chromohalobacter, Chryseobacterium, Chryseomonas, Chrysiogenes, Citricoccus, Citrobacter, Clavibacter, Clevelandina, Clostridium, Cobetia, Coenonia, Collinsella, Colwellia, Comamonas, Conexibacter, Conglomeromonas, Coprobacillus, Coprococcus, Coprothermobacter, Coriobacterium, Corynebacterium, Couchioplanes, Cowdria, Coxiella, Craurococcus, Crenothrix, Crinalium (not validly published), Cristispira, Croceibacter, Crocinitomix, Crossiella, Cryobacterium, Cryomorpha, Cryptobacterium, Cryptosporangium, Cupriavidus, Curtobacterium, Cyclobacterium, Cycloclasticus, Cystobacter, Cytophaga, Dactylosporangium, Dechloromonas, Dechlorosoma, Deferribacter, Defluvibacter, Dehalobacter, Dehalospirillum, Deinobacter, Deinococcus, Deleya, Delftia, Demetria, Dendrosporobacter, Denitrobacterium, Denitrovibrio, Dermabacter, Dermacoccus, Dermatophilus, Derxia, Desemzia, Desulfacinum, Desulfitobacterium, Desulfobacca, Desulfobacter, Desulfobacterium, Desulfobacula, Desulfobulbus, Desulfocapsa,

Desulfocella, Desulfococcus, Desulfofaba, Desulfofrigus, Desulfofustis, Desulfohalobium, Desulfomicrobium, Desulfomonas, Desulfomonile, Desulfomusa, Desulfonatronovibrio, Desulfonatronum, Desulfonauticus, Desulfonema, Desulfonispora, Desulforegula, Desulforhabdus, Desulforhopalus, Desulfosarcina, Desulfospira, Desulfosporosinus, Desulfotalea, Desulfotignum, Desulfotomaculum, Desulfovibrio, Desulfovirga, Desulfurella, Desulfurobacterium, Desulfuromonas, Desulfuromusa, Dethiosulfovibrio, Devosia, Dialister, Diaphorobacter, Dichelobacter, Dichotomicrobium, Dictyoglomus, Dietzia, Diplocalyx, Dolosicoccus, Dolosigranulum, Dorea, Duganella, Dyadobacter, Dysgonomonas, Ectothiorhodospira, Edwardsiella, Eggerthella, Ehrlichia, Eikenella, Elytrosporangium, Empedobacter, Enhydrobacter, Enhygromyxa, Ensifer, Enterobacter, Enterococcus, Enterovibrio, Entomoplasma, Eperythrozoon, Eremococcus, Erwinia, Erysipelothrix, Erythrobacter, Erythromicrobium, Erythromonas, Escherichia, Eubacterium, Ewingella, Excellospora, Exiguobacterium, Facklamia, Faecalibacterium, Faenia, Falcivibrio, Ferribacterium, Ferrimonas, Fervidobacterium, Fibrobacter, Filibacter, Filifactor, Filobacillus, Filomicrobium, Finegoldia, Flammeovirga, Flavimonas, Flavobacterium, Flectobacillus, Flexibacter, Flexistipes, Flexithrix, Fluoribacter, Formivibrio, Francisella, Frankia, Frateuria, Friedmanniella, Frigoribacterium, Fulvimarina, Fulvimonas, Fundibacter, Fusibacter, Fusobacterium, Gallibacterium, Gallicola, Gallionella, Garciella, Gardmrella, Gelidibacter, Gelria, Gemella, Gemmata, Gemmatimonas, Gemmiger, Gemmobacter, Geobacillus, Geobacter, Geodermatophilus, Georgenia, Geothrix, Geotoga, Geovibrio, Glaciecola, Globicatella, Gluconacetobacter, Gluconoacetobacter, Gluconobacter, Glycomyces, Gordonia, Gordonia, Gracilibacillus, Grahamella, Granulicatella, Grimontia, Haemobartonella, Haemophilus, Hafiiia, Hahella, Halanaerobacter, Halanaerobium, Haliangium, Haliscomenobacter, Hallella, Haloanaerobacter, Haloanaerobium, Halobacillus, Halobacteroides, Halocella, Halochromatium, Haloincola, Halomicrobium, Halomonas, Halonatronum, Halorhodospira, Halospirulina, Halothermothrix, Halothiobacillus, Halovibrio, Helcococcus, Heliobacillus, Helicobacter, Heliobacterium, Heliophilum, Heliorestis, Heliothrix, Herbaspirillum, Herbidospora, Herpetosiphon, Hippea, Hirschia, Histophilus, Holdemania, Hollandina, Holophaga, Holospora, Hongia, Hydrogenobacter, Hydrogenobaculum, Hydrogenophaga, Hydrogenophilus, Hydrogenothermus, Hydrogenovibrio, Hymenobacter, Hyphomicrobium, Hyphomonas, Ideonella, Idiomarina, Ignavigranum, Ilyobacter, Inquilinus, Intrasporangium, Iodobacter, Isobaculum, Isochromatium, Isosphaera, Janibacter, Jannaschia, Janthinobacterium, Jeotgalibacillus, Jeotgalicoccus, Johnsonella, Jonesia, Kerstersia, Ketogulonicigenium, Ketogulonigenium, Kibdelosporangium, Kineococcus, Kineosphaera, Kineosporia, Kingella, Kitasatoa, Kitasatospora, Kitasatosporia, Klebsiella, Kluyvera, Knoellia, Kocuria, Koserella, Kozakia, Kribbella, Kurthia, Kutzneria, Kytococcus, Labrys, Lachnobacterium, Lachnospira, Lactobacillus, Lactococcus, Lactosphaera, Lamprobacter, Lamprocystis, Lampropedia, Laribacter, Lautropia, Lawsonia, Lechevalieria, Leclercia, Legionella, Leifsonia, Leisingera, Leminorella, Lentibacillus, Lentzea, Leptonema, Leptospira, Leptospirillum, Leptothrix, Leptotrichia, Leucobacter, Leuconostoc, Leucothrix, Levinea, Lewinella, Limnobacter, Limnothrix, Listeria, Listonella, Lonepinella, Longispora, Lucibacterium, Luteimonas, Luteococcus, Lysobacter, Lyticum, Macrococcus, Macromonas, Magnetospirillum, Malonomonas, Mannheimia, Maricaulis, Marichromatium, Marinibacillus, Marinilabilia, Marinilactibacillus, Marinithermus, Marinitoga, Marinobacter, Marinobacterium, Marinococcus, Marinomonas, Marinospirillum, Marmoricola, Massilia, Megamonas, Megasphaera, Meiothermus, Melissococcus, Melittangium, Meniscus, Mesonia, Mesophilobacter, Mesoplasma, Mesorhizobium, Methylarcula, Methylobacillus, Methylobacter, Methylobacterium, Methylocaldum, Methylocapsa, Methylocella, Methylococcus, Methylocystis, Methylomicrobium, Methylomonas, Methylophaga, Methylophilus, Methylopila, Methylorhabdus, Methylosarcina, Methylosinus, Methylosphaera, Methylovorus, Micavibrio, Microbacterium, Microbispora, Microbulbifer, Micrococcus, Microcyclus, Microcystis, Microellobosporia, Microlunatus, Micromonas, Micromonospora, Micropolyspora, Micropruina, Microscilla, Microsphaera, Microtetraspora, Microvirga, Microvirgula, Mitsuokella, Mobiluncus,

Mode stobac ter, Moellerella, Mogibacterium, Moorella, Moraxella, Morganella, Moritella, Morococcus, Muricauda, Muricoccus, Mycetocola, Mycobacterium, Mycoplana, Mycoplasma, Myroides, Myxococcus, Nannocystis, Natroniella, Natronincola, Natronoincola, Nautilia, Neisseria, Neochlamydia, Neorickettsia, Neptunomonas, Nesterenkonia, Nevskia, Nitrobacter, Nitrococcus, Nitrosococcus, Nitrosolobus, Nitrosomonas, Nitrosospira, Nitrospina, Nitrospira, Nocardia, Nocardioides, Nocardiopsis, Nonomuraea, Nonomuria, Novosphingobium, Obesumbacterium, Oceanicaulis, Oceanimonas, Oceanisphaera, Oceanithermus, Oceanobacillus, Oceanobacter, Oceanomonas, Oceanospirillum, Ochrobactrum, Octadecabacter, Oenococcus, Oerskovia, Okibacterium, Oleiphilus, Oleispira, Oligella, Oligotropha, Olsenella, Opitutus, Orenia, Oribaculum, Orientia, Ornithinicoccus, Ornithinimicrobium, Ornithobacterium, Oscillochloris, Oscillospira, Oxalicibacterium, Oxalobacter, Oxalophagus, Oxobacter, Paenibacillus, Pandoraea, Pannonibacter, Pantoea, Papillibacter, Parachlamydia, Paracoccus, Paracraurococcus, Paralactobacillus, Paraliobacillus, Parascardovia, Parvularcula, Pasteurella, Pasteuria, Paucimonas, Pectinatus, Pectobacterium,

Pediococcus, Pedobacter, Pedomicrobium, Pelczaria, Pelistega, Pelobacter, Pelodictyon, Pelospora, Pelotomaculum, Peptococcus, Peptoniphilus, Peptostreptococcus, Persephonella, Persicobacter, Petrotoga, Pfennigia, Phaeospirillum, Phascolarctobacterium, Phenylobacterium, Phocoenobacter, Photobacterium, Photorhabdus, Phyllobacterium, Pigmentiphaga, Pilimelia, Pillotina, Pimelobacter, Pirella, Pirellula, Piscirickettsia, Planctomyces, Planktothricoides, Planktothrix, Planobispora, Planococcus,

Planomicrobium, Planomonospora, Planopolyspora, Planotetraspora, Plantibacter, Pleisomonas, Plesiocystis, Plesiomonas, Polaribacter, Polaromonas, Polyangium, Polynucleobacter, Porphyrobacter, Porphyromonas, Pragia, Prauserella, Prevotella, Prochlorococcus, Prochloron, Prochlorothrix, Prolinoborus, Promicromonospora, Propionibacter, Propionibacterium, Propionicimonas, Propioniferax, Propionigenium, Propionimicrobium, Propionispira, Propionispora, Propionivibrio, Prosthecobacter, Prosthecochloris, Prosthecomicrobium, Proteus, Protomonas, Providencia, Pseudaminobacter, Pseudoalteromonas, Pseudoamycolata, Pseudobutyrivibrio, Pseudocaedibacter, Pseudomonas, Pseudonocardia, Pseudoramibacter, Pseudorhodobacter, Pseudospirillum, Pseudoxanthomonas, Psychrobacter, Psychroflexus, Psychromonas, Psychroserpens, Quadricoccus, Quinella, Rahnella, Ralstonia, Ramlibacter, Raoultella, Rarobacter, Rathayibacter, Reichenbachia, Renibacterium, Rhabdochromatium, Rheinheimera, Rhizobacter, Rhizobium, Rhizomonas, Rhodanobacter, Rhodobaca, Rhodobacter, Rhodobium, Rhodoblastus, Rhodocista, Rhodococcus, Rhodocyclus, Rhodoferax, Rhodoglobus, Rhodomicrobium, Rhodopila, Rhodoplanes, Rhodopseudomonas, Rhodospira, Rhodospirillum, Rhodothalassium, Rhodothermus, Rhodovibrio, Rhodovulum, Rickettsia, Rickettsiella, Riemerella, Rikenella, Rochalimaea, Roseateles, Roseburia, Roseibium, Roseiflexus, Roseinatronobacter, Roseivivax, Roseobacter, Roseococcus, Roseomonas, Roseospira, Roseospirillum, Roseovarius, Rothia, Rubrimonas, Rubritepida, Rubrivivax, Rubrobacter, Ruegeria, Rugamonas, Ruminobacter, Ruminococcus, Runella, Saccharobacter, Saccharococcus, Saccharomonospora, Saccharopolyspora, Saccharospirillum, Saccharothrix, Sagittula, Salana, Salegentibacter, Salibacillus, Salinibacter, Salinibacterium, Salinicoccus, Salinisphaera, Salinivibrio, Salmonella, Samsonia, Sandaracinobacter, Sanguibacter, Saprospira, Sarcina, Sarcobium, Scardovia, Schineria, Schlegelella, Schwartzia, Sebaldella, Sedimentibacter, Selenihalanaerobacter, Selenomonas, Seliberia, Serpens, Serpula, Serpulina, Serratia, Shewanella, Shigella, Shuttleworthia, Silicibacter, Simkania, Simonsiella, Sinorhizobium, Skermanella, Skermania, Slackia, Smithella, Sneathia, Sodalis, Soehngenia, Solirubrobacter, Solobacterium, Sphaerobacter, Sphaerotilus, Sphingobacterium, Sphingobium, Sphingomonas, Sphingopyxis, Spirilliplanes, Spirillospora, Spirillum, Spirochaeta, Spiroplasma, Spirosoma, Sporanaerobacter, Sporichthya, Sporobacter, Sporobacterium, Sporocytophaga, Sporohalobacter, Sporolactobacillus, Sporomusa, Sporosarcina, Sporotomaculum, Staleya, Staphylococcus, Stappia, Starkeya, Stella, Stenotrophomonas, Sterolibacterium, Stibiobacter, Stigmatella, Stomatococcus, Streptacidiphilus, Streptimonospora, Streptoalloteichus, Streptobacillus, Streptococcus, Streptomonospora, Streptomyces: S. abikoensis, S. erumpens, S. erythraeus, S. michiganensis, S. microflavus, S. zaomyceticus, Streptosporangium, Streptoverticillium, Subtercola, Succiniclasticum, Succinimonas, Succinispira, Succinivibrio, Sulfitobacter, Sulfobacillus, Sulfurihydrogenibium, Sulfurimonas, Sulfurospirillum,

Sutterella, Suttonella, Symbiobacterium, Symbiotes, Synergistes, Syntrophobacter, Syntrophobotulus, Syntrophococcus, Syntrophomonas, Syntrophosphora, Syntrophothermus, Syntrophus, Tannerella, Tatlockia, Tatumella, Taylorella, Tectibacter, Teichococcus,

Telluria, Tenacibaculum, Tepidibacter, Tepidimonas, Tepidiphilus, Terasakiella, Teredinibacter, Terrabacter, Terracoccus, Tessaracoccus, Tetragenococcus, Tetrasphaera, Thalassomonas, Thalassospira, Thauera, Thermacetogenium, Thermaerobacter, Thermanaeromonas, Thermanaerovibrio, Thermicanus, Thermithiobacillus, Thermoactinomyces, Thermoanaerobacter, Thermoanaerobacterium, Thermoanaerobium, Thermobacillus, Thermobacteroides, Thermobifida, Thermobispora, Thermobrachium, Thermochromatium, Thermocrinis, Thermocrispum, Thermodesulfobacterium, Thermodesulforhabdus, Thermodesulfovibrio, Thermohalobacter, Thermohydrogenium, Thermoleophilum, Thermomicrobium, Thermomonas, Thermomonospora, Thermonema, Thermosipho, Thermosyntropha, Thermoterrabacterium, Thermothrix, Thermotoga, Thermovenabulum, Thermovibrio, Thermus, Thialkalicoccus, Thialkalimicrobium, Thialkalivibrio, Thioalkalicoccus, Thioalkalimicrobium, Thioalkalispira, Thioalkalivibrio, Thiobaca, Thiobacillus, Thiobacterium, Thiocapsa, Thiococcus, Thiocystis, Thiodictyon, Thioflavicoccus, Thiohalocapsa, Thiolamprovum, Thiomargarita, Thiomicrospira, Thiomonas, Thiopedia, Thioploca, Thiorhodococcus, Thiorhodospira, Thiorhodovibrio, Thiosphaera, Thiospira, Thiospirillum, Thiothrix, Thiovulum, Tindallia, Tissierella, Tistrella, Tolumonas, Toxothrix, Trabulsiella, Treponema, Trichlorobacter, Trichococcus,

Tropheryma, Tsukamurella, Turicella, Turicibacter, Tychonema, Ureaplasma, Ureibacillus, Vagococcus, Vampirovibrio, Varibaculum, Variovorax, Veillonella, Verrucomicrobium, Verrucosispora, Vibrio, Victivallis, Virgibacillus, Virgisporangium, Virgosporangium, Vitellibacter, Vitreoscilla, Vogesella, Volcaniella, Vulcanithermus, Waddlia, Weeksella, Weissella, Wiggle sw or thia, Williamsia, Wolbachia, Wolinella, Xanthobacter, Xanthomonas, Xenophilus, Xenorhabdus, Xylanimonas, Xylella, Xylophilus, Yersinia, Yokenella, Zavarzinia, Zobellia, Zoogloea, Zooshikella, Zymobacter, Zymomonas, and Zymophilus.

[0244] Exemplary intracellular parasites that can be detected using the methods and compositions described herein include, but are not limited to Plasmodium falciparum, Plasmodium vivax, Plasmodium ovale, Plasmodium malariae, Babesia sp. Leishmaniasis spp. Toxoplasmosis spp. and filarial nematodes.

[0245] Nucleic Acids

[0246] Nucleic acids that can be prepared and analyzed using the methods and compositions described herein can include RNA and DNA. RNA includes, without limitation, viral RNA, mRNA (messenger RNA), mtRNA (mitochondrial RNA), rRNA (ribosomal RNA), tRNA (transfer RNA), nRNA (nuclear RNA), snRNA (small nuclear RNA), snoRNA (small nucleolar RNA), scaRNA (Small Cajal Body specific RNA), microRNA, ribozyme and riboswitch RNAs. DNA includes without limitation, chromosomal DNA, nDNA (nuclear DNA), snDNA (small nuclear DNA), dsDNA (double-stranded DNA), ssDNA (single- stranded DNA), as well as cDNA (complementary DNA), , LNA (locked nucleic acid), siRNA (short interfering RNA), plasmid DNA, cosmid DNA, or the like. A nucleic acid can be a nucleic acid of a pathogen, such as from a virus (e.g., RNA, DNA), a parasite (including intracellular parasites), or a bacterium. Nucleic acids of pathogens are typically pathogen DNA, RNA, cDNA or mRNA. Unless specifically limited, the term “nucleic acid” encompasses nucleic acids containing known analogs of natural nucleotides that have similar binding properties as the reference nucleic acid and are metabolized in a manner similar to naturally occurring nucleotides.

[0247] In some embodiments, the nucleic acids prepared using the methods and compositions described herein are used as templates or targets for nucleic acid amplification, particularly those using isothermal nucleic acid amplification methods. Target nucleic acids can also be referred to as target sequences, trigger nucleic acids, target polynucleotides, and/or target polynucleotide sequences, and can include double-stranded and single-stranded nucleic acid molecules. Where the target nucleic acid is double stranded, the target nucleic acid generally includes a first strand and a second strand. A first strand and a second strand may be referred to as a forward strand and a reverse strand and generally are complementary to each other. Where the target nucleic acid is single stranded, a complementary strand may be generated, for example by polymerization and/or reverse transcription, rendering the target nucleic acid double stranded and having a first/forward strand and a second/reverse strand.

[0248] A target nucleic acid sequence can refer to either the sense or antisense strand of a nucleic acid sequence, and can also refer to sequences as they exist on target nucleic acids, amplified copies, or amplification products, of the original target sequence. A target sequence can be a subsequence within a larger polynucleotide. For example, a target sequence can be a short sequence (e.g., 20 to 50 bases) within a nucleic acid fragment, a viral genome, a bacterial genome or a genome of a parasite, that is targeted for amplification. In some embodiments, a target sequence can refer to a sequence in a target nucleic acid that is complementary to an oligonucleotide (e.g., primer) used for amplifying a nucleic acid. Thus, a target sequence can refer to the entire sequence targeted for amplification or can refer to a subsequence in the target nucleic acid where an oligonucleotide binds.

[0249] Subjects [0250] Saliva or other biological samples can be obtained from any suitable biological specimen or sample. The samples may be obtained directly from a subject, such as with point of care diagnostics. A subject can be any living or non-living organism, including but not limited to a human, a non-human animal. Any human or non-human animal can be selected, including but not limited to a mammal, reptile, avian, amphibian, fish, ungulate, ruminant, bovine (e.g., cattle), equine (e.g., horse), caprine and ovine (e.g., sheep, goat), swine (e.g., pig), camelid (e.g., camel, llama, alpaca), monkey, ape (e.g., gorilla, chimpanzee), ursid (e.g., bear), poultry, dog, cat, mouse, rat, fish, dolphin, whale and shark. A subject can be a male or female, and a subject can be any age (e.g., an embryo, a fetus, infant, child, adult).

[0251] Samples

[0252] Samples from which the nucleic acids are prepared using the methods, devices and compositions described herein are typically biological samples such as unprocessed saliva. It is envisioned that the devices, methods and compositions may be adapted for use with other biological samples. The biological sample (e.g., saliva sample) can be obtained by removing a sample from a subject, but can also be accomplished by using a previously isolated sample (e.g. isolated at a prior timepoint and isolated by the same or another person). To collect saliva, the user spits into a receptacle. Alternatively, a saliva collection device can be used such as those commercially available (e.g., Sarstedt Salivette Cotton Swab for Saliva

swab-sal i va-eoli ecu on/50809199; Super· SAL™ Universal Saliva Collection Kit, Oasis Diagnostics® www.4saliva.com/products/super-sal/). In some embodiments of any of the aspects, the test sample can be a frozen test sample, e.g., a saliva sample. The frozen sample can be thawed before employing methods, assays and systems described herein.

[0253] A biological sample can be any specimen that is isolated or obtained from a subject or part thereof. Non-limiting examples of specimens include fluid or tissue from a subject, including, without limitation, saliva, blood or a blood product (e.g., serum, plasma, or the like), a nasopharyngeal swab sample, an oropharyngeal swab sample, nasal mucus, sputum, urine, umbilical cord blood, bone marrow, chorionic villi, amniotic fluid, cerebrospinal fluid, spinal fluid, lavage fluid (e.g., bronchoalveolar, gastric, peritoneal, ductal, ear, arthroscopic), biopsy sample, cells (e.g., blood cells) or parts thereof (e.g., mitochondrial, nucleus, extracts, or the like), washings of female reproductive tract, feces, prostate fluid, semen, lymphatic fluid, bile, tears, sweat, breast milk, breast fluid, hard tissues (e.g., liver, spleen, kidney, lung, or ovary), the like or combinations thereof. The term “blood” encompasses whole blood, blood product or any fraction of blood, such as serum, plasma, buffy coat, or the like as conventionally defined. Blood plasma refers to the fraction of whole blood resulting from centrifugation of blood treated with anticoagulants. Blood serum refers to the watery portion of fluid remaining after a blood sample has coagulated. Fluid or tissue samples often are collected in accordance with standard protocols hospitals or clinics generally follow. For blood, an appropriate amount of peripheral blood (e.g., between 3-40 milliliters) often is collected and can be stored according to standard procedures prior to or after preparation. [0254] A biological sample can include samples containing parasites, viruses, bacteria, spores, cells, nucleic acid from prokaryotes or eukaryotes, or any free nucleic acid. A sample can be isolated from any material suspected of containing a target sequence, such as from a subject described above. In certain instances, a target sequence can be present in air, plant, soil, or other materials suspected of containing biological organisms of interest.

[0255] It is envisioned that the devices, methods and compositions may be adapted for use with other samples containing nucleic acids, such as samples collected from another device (e.g, with a capture matrix withing the other device). Such samples could be rehydrated or otherwise dispersed as needed into the sample collection column for further preparation of the nucleic acids contained therein and collection onto the capture matrix of the sample collection column. For example, a membrane such as a PES that has a collected sample obtained from another device such as a facemask which has collected the sample bound to it via aerosol within the face mask. Such a membrane could be deposited into the sample collection column, and the bound sample dispersed into the column, processed as described herein, to collect resulting nucleic acids onto the capture matrix of the sample preparation column. The capture matrix of the sample preparation column can then be transported or further processed as described herein for further analysis (e.g., on the integrated diagnostic testing device).

[0256] Kits

[0257] Also provided herein are kits for nucleic acid preparation, which at a minimum include a reducing agent (described herein) and a metal ion chelating agent (described herein) in aqueous suspension, or for preparation of an aqueous suspension. In some embodiments, the reducing agent is dithiothreitol (DTT) and the metal chelating agent is EGTA. The reducing agent and chelating agent can be provided in an admixture or can be provided separately with instructions to generate an admixture, for example, comprising 10-30% w/v of the final composition including the biological sample (e.g, unprocessed saliva). The reducing agent and metal chelating agent can be provided in concentrated stock solutions or in pre-measured aliquots. The kit may further contain one or more sample preparation columns, and may further contain saliva collection interfaces or sample collection and preparation systems containing the sample preparation columns, as described herein. The sample preparation column’s contained within the kits may also be preloaded with the appropriate amount of reducing agent and metal chelating agent for an expected amount of sample (e.g. unprocessed saliva). In some embodiments, the kit does not contain any nuclease inhibitors.

[0258] In addition, a kit can comprise one or more reagents for performing an isothermal amplification and/or detection method, such as one-pot SHERLOCK, for example, one or more polymerases, Cas enzyme (e.g., Casl2a), reporter molecule (e.g., ssDNA fluorescent quenched), buffer components, dNTPs, etc, and optionally one or more reverse transcriptases. Such kits would be for use in detecting a target RNA (e.g., pathogen) in a subject from the saliva of the subject. In some embodiments, a gRNA and corresponding pair of primers (forward and reverse) can be included in the kit for a desired target sequence, such as for detection of SARS-CoV-2. Where multiple target sequences are to be amplified and detected, a plurality of gRNAs and corresponding primer pairs can be included in the kit. A kit can include one or more control polynucleotides and one or more of the components described below. One or more of these reagents may be provided in dried (e.g., lyophyilized) form. The components can, for example, be lyophilized, freeze dried, or in a stable buffer, either all in the same container or in separate respective contains. Aliquots of an aqueous solution or water may further be provided (e.g, for hydration of the dried reagents). In some embodiments, the kit does not contain any nuclease inhibitors.

[0259] Kits can also comprise one or more of the components in any number of separate vessels, chambers, containers, packets, tubes, vials, microtiter plates and the like, or the components can be combined in various combinations in such containers. Components of the kit can, for example, be present in one or more containers. In some embodiments, all of the components are provided in one container. In some embodiments, the enzymes (e.g., polymerase(s) and/or reverse transcriptase(s)) can be provided in a separate container from the primers. The components can, for example, be lyophilized, freeze dried, or in a stable buffer, either all in the same container or in separate respective contains. In one example, polymerase(s) and/or reverse transcriptase(s) are in lyophilized form in a single container, and the primers are either lyophilized, freeze dried, or in buffer, in a different container. In some embodiments, polymerase(s) and/or reverse transcriptase(s), and the primers are, in lyophilized form, in a single container. In some embodiments, the kit comprises the integrated diagnostic device described herein. In some embodiments, the kit contains one or more modular (e.g. reusable or disposable) portions of the integrated diagnostic device described herein (e.g., the sample preparation column, extraction mechanism, sealed water reservoirs, reaction subchambers for sample analysis, and/or absorbent filter). In some embodiments, the kit contains the reusable portion of the integrated diagnostic device described herein (e.g, the base containing the heating mechanisms, the high heat and low heat chambers, the exterior transilluminiator wall, and the light source).

[0260] Kits can further comprise, for example, dNTPs used in the reaction (e.g., in aqueous solution or in lyophilized form), or modified nucleotides, vessels, cuvettes or other containers used for the reaction, or a vial of water or buffer for re-hydrating lyophilized components.

The buffer used can, for example, be appropriate for both polymerase and primer annealing activity.

[0261] Kits can also comprise instructions for performing one or more methods described herein and/or a description of one or more components described herein. Instructions and/or descriptions can be in printed form and can be included in a kit insert. A kit also can include a written description of an internet location that provides such instructions or descriptions.

[0262] Kits can further comprise reagents used for detection methods, such as, for example, reagents used for FRET, lateral flow devices, dipsticks, fluorescent dye, colloidal gold particles, latex particles, a molecular beacon, or polystyrene beads.

[0263] In some embodiments, kits comprise all reagents necessary for one-pot SHERLOCK detection of a pathogen (e.g, SARS-CoV-2), by universal and/or specific detection.

[0264] In one embodiment, a kit for detecting SARS-CoV-2 comprising the components described in the Examples section is specifically contemplated. In some embodiments all reaction comonents for the amplification and detection are within a container (e.g, the reaction subchamber of the integrated diagnostic device, such as in lyophilized form).

[0265] Unless otherwise defined herein, scientific and technical terms used in connection with the present application shall have the meanings that are commonly understood by those of ordinary skill in the art. Further, unless otherwise required by context, singular terms shall include pluralities and plural terms shall include the singular.

[0266] It should be understood that this invention is not limited to the particular methodology, protocols, and reagents, etc., described herein and as such may vary. The terminology used herein is for the purpose of describing particular embodiments only, and is not intended to limit the scope of the present invention, which is defined solely by the claims. [0267] Other than in the operating examples, or where otherwise indicated, all numbers expressing quantities of ingredients or reaction conditions used herein should be understood as modified in all instances by the term “about.” The term “about” when used to described the present invention, in connection with percentages means ±1%, or ±5% .

[0268] In one respect, the present invention relates to the herein described compositions, methods, and respective component s) thereof, as essential to the invention, yet open to the inclusion of unspecified elements, essential or not (“comprising). In some embodiments, other elements to be included in the description of the composition, method or respective component thereof are limited to those that do not materially affect the basic and novel characteristic(s) of the invention (“consisting essentially of’). This applies equally to steps within a described method as well as compositions and components therein. In other embodiments, the inventions, compositions, methods, and respective components thereof, described herein are intended to be exclusive of any element not deemed an essential element to the component, composition or method (“consisting of’).

[0269] All patents, patent applications, and publications identified are expressly incorporated herein by reference for the purpose of describing and disclosing, for example, the methodologies described in such publications that might be used in connection with the present invention. These publications are provided solely for their disclosure prior to the filing date of the present application. Nothing in this regard should be construed as an admission that the inventors are not entitled to antedate such disclosure by virtue of prior invention or for any other reason. All statements as to the date or representation as to the contents of these documents is based on the information available to the applicants and does not constitute any admission as to the correctness of the dates or contents of these documents. [0270] The invention may be as described in any one of the following numbered paragraphs: 1. A sample collection and preparation system, comprising: a) a sample preparation column having a capture matrix at a base of the column, the capture matrix being configured to capture nucleic acid during heating from a saliva sample in the column; b) an absorbent filter disposed below the capture matrix of the sample preparation column to cause a received saliva sample to move during heating through an individual capture matrix via capillary action at a flow rate of at least about 1 min/mL; c) a high-heat lysis chamber in thermal connection with one or more heating mechanisms, wherein the sample preparation column is disposed within the high-heat lysis chamber.

2. The sample collection and preparation system of paragraph 1 further comprising a saliva collection interface connected at a second end opposite the base of the sample preparation column.

3. The sample collection and preparation system of any of paragraphs 1 - 2, wherein the sample preparation column is preloaded with lysis reagents comprising a reducing agent and a metal chelating agent.

4. The sample collection and preparation system of paragraph 3, wherein the reducing agent is DTT present at a concentration to result in a final concentration of from about 10 mM to about 100 mM, and the metal chelating agent is EGTA present at a concentration to result in a final concentration of about 5mM, in an added saliva sample.

5. The sample collection and preparation system of any of paragraphs 3-4, wherein the reducing agent is DTT present at a concentration to result in a final concentration of 10 mM DDT, and the metal chelating agent is EGTA present at a concentration to result in a final concentration from about 1 mM to about 50 mM EGTA in an added saliva sample.

6. The sample collection and preparation system of any of paragraphs 1-5, wherein the capture matrix is a porous membrane that can bind to nucleic acids and is compatible with in situ amplification.

7. The sample collection and preparation system of paragraph 6, wherein the capture matrix is a polyethersulfone (PES) membrane that contains 0.22 um pores and is optionally functionalized with a hydrophilic surface treatment.

8. The sample collection and preparation system of paragraph 6, wherein the capture matrix is a membrane containing pores ranging from between about 0.1 um to about 0.5 um.

9. The sample collection and preparation system of any of paragraphs 1-8, wherein the saliva sample is between about 0.2 mL and 5 mL in volume.

10. The sample collection and preparation system of paragraph 9, wherein the saliva sample is about 0.5 mL, 0.6 mL, 0.7 mL, 0.8 mL, 0.9 mL, 1.0 mL, 1.1 mL, 1.2 mL, 1.3 mL,

1.4 mL, 1.5 mL, 1.6 mL, 1.7 mL, 1.8 mL, 1.9 mL, 2.0 mL, 2.1 mL, 2.2 mL, 2.3 mL, 2.4 mL,

2.5 mL, 2.6 mL, 2.7 mL, 2.8 mL, 2.9 mL, 3.0 mL, 3.1 mL, 3.2 mL, 3.3 mL, 3.4 mL, 3.5 mL,

3.6 mL, 3.7 mL, 3.8 mL, 3.9 mL, 4.0 mL, 4.1 mL, 4.2 mL, 4.3 mL, 4.4 mL, 4.5 mL, 4.6 mL,

4.7 mL, 4.8 mL, 4.9 mL, or about 5.0 mL in volume. 11. The sample collection and preparation system of any of paragraphs 1 - 10, wherein the sample preparation column is reversibly disposed within the high-heat lysis chamber and/or the absorbent filter is reversibly disposed below the capture matrix.

12. The sample collection and preparation system of any of paragraphs 1 - 11, further comprising a cap that securely attaches to the base of the sample preparation column containing the capture matrix, upon removal of the absorbent filter, to cover and protect the capture matrix.

13. The sample collection and preparation system of any of paragraphs 1-12, that is for use within an integrated diagnostic testing device.

14. An integrated diagnostic testing device comprising: a) one or more heating mechanisms; b) a high-heat lysis chamber in thermal connection with the one or more heating mechanisms; c) a low-heat reaction chamber adjoining the lysis chamber and in thermal connection with the one or more heating mechanisms, the low-heat reaction chamber including one or more individual reaction sub-chambers for sample analysis, the low-heat reaction chamber including an exterior transilluminator filter; d) a saliva collection interface connected to one or more sample preparation columns disposed within the high-heat lysis chamber, the one or more sample preparation columns having a capture matrix at a base of the columns configured to capture nucleic acid during heating from a saliva sample in the one or more sample preparation columns; e) an absorbent filter disposed in the high-heat lysis chamber below the capture matrix of the one or more sample preparation columns to cause a received saliva sample to move during heating through an individual capture matrix via capillary action at a flow rate at least about 1 min/mL; f) an extraction mechanism for transferring the individual capture matrix to the individual reaction sub-chamber within the low-heat chamber; and g) a light source positioned to illuminate an interior of the low-heat reaction chamber to allow a visual florescence determination of the saliva sample in the individual capture matrix through the transilluminator filter. 15. The system of any one of paragraphs 1-13 or the device of paragraph 14, wherein the one or more heating mechanisms are configured to heat the high-heat lysis chamber to about 70° to about 99° C.

16. The system of any one of paragraphs 1-13 or the device of paragraph 14, wherein the one or more heating mechanisms are configured to heat the high-heat lysis chamber to about 95 ° C.

17. The device of paragraph 15, wherein the one or more heating mechanisms are configured to heat the high-heat lysis chamber to a temperature that extract RNA molecules and inactivates nucleases.

18. The device of any one of paragraphs 14 to 17, wherein the one or more heating mechanisms are configured to heat the low-heat reaction chamber to about 34⁰ to about 40⁰ C.

19. The device of any one of paragraphs 14 to 17, wherein the one or more heating mechanisms are configured to heat the low-heat reaction chamber to about 37° C.

20. The device of any one of paragraphs 14 to 17, wherein the one or more heating mechanisms are configured to heat the low-heat reaction chamber to about 34⁰ to about 65⁰ C.

21. The device of any one of paragraphs 14 to 20, wherein the one or more heating mechanisms are configured to heat the low-heat reaction chamber to a temperature that regulates amplification and detection reactions.

22. The system of any one of paragraphs 1-13 or the device of any one of paragraphs 14 to 21, wherein the absorbent filter is disposed immediately below the capture matrix.

23. The system of paragraph 1-13 or the device of any one of paragraphs 14 to 22, wherein the saliva sample moves during heating through the capture matrix at a flow rate of about 1.3 min/mL to about 1.7 min/mL.

24. The system of any one of paragraphs 1-13 or the device of any one of paragraphs 14 to 22, wherein the saliva sample moves during heating through the capture matrix at a flow rate of about 1.5 min/mL.

25. The device of any one of paragraphs 14 to 24, wherein low-heat reaction chamber further includes one or more sealed water reservoirs for reaction mixture hydrating.

26. The device of paragraph 25, wherein the extraction mechanism is a plunger for insertion into the sample preparation column to release the water from the sealed reservoir. 27. The device of any one of paragraphs 14 to 24, wherein the low-heat reaction chamber is configured to allow manual reaction mixture hydrating within the low-heat reaction chamber.

28. The device of any one of paragraphs 14 to 27, wherein the one or more heating mechanisms are configured to cyclically heat the low-heat reaction chamber cycle between at least two different temperatures during diagnostic testing.

29. The device of paragraph 28, wherein the low-heat reaction chamber cycles from about 95-100°C, to about 45-60 °C, to about 72-75 °C, for several cycles.

30. The device of any one of paragraphs 13 to 23, wherein the sample preparation column is removable from the high heat lysis chamber into the low-heat reaction chamber for transfer of the individual capture matrix to the individual reaction sub-chambers.

31. The system of any one of paragraphs 1-13 or the device of any one of paragraphs 14 to 30, wherein the sample preparation column is preloaded with lysis reagents to thereby result in a final concentration of 10 mM DTT and 5 mM EGTA in the saliva sample.

32. The system of any one of paragraphs 1-13 or the device of any one of paragraphs 14-

31, wherein saliva sample is between about 0.2 mL and 5 mL in volume.

33. The system of any one of paragraphs 1-13 or the device of any one of paragraphs 14-

32, wherein the saliva sample is about 0.2 mL, 0.3 mL, 0.4 mL, 0.5 mL, 0.6 mL, 0.7 mL, 0.8 mL, 0.9 mL, 1.0 mL, 1.1 mL, 1.2 mL, 1.3 mL, 1.4 mL, 1.5 mL, 1.6 mL, 1.7 mL, 1.8 mL, 1.9 mL, 2.0 mL, 2.1 mL, 2.2 mL, 2.3 mL, 2.4 mL, 2.5 mL, 2.6 mL, 2.7 mL, 2.8 mL, 2.9 mL, 3.0 mL, 3.1 mL, 3.2 mL, 3.3 mL, 3.4 mL, 3.5 mL, 3.6 mL, 3.7 mL, 3.8 mL, 3.9 mL, 4.0 mL, 4.1 mL, 4.2 mL, 4.3 mL, 4.4 mL, 4.5 mL, 4.6 mL, 4.7 mL, 4.8 mL, 4.9 mL, or about 5.0 mL in volume.

34. The system of any one of paragraphs 1-13 or the device of any one of paragraphs 14-

33, wherein the capture matrix is a porous membrane that can bind to nucleic acids and is compatible with in situ amplification.

35. The system or device of paragraph 34, wherein the capture matrix is a paper capture membrane.

36. The system or device of paragraph 34, wherein the capture matrix is a polyethersulfone (PES) membrane that contains 0.22 um pores and is functionalized with a hydrophilic surface treatment.

37. The device of paragraph 30 or 31, wherein the extraction mechanism is a plunger for insertion into the sample preparation column to dislodge the capture matrix from the column and deposit the capture matrix and the water into the reaction sub-chamber. 38. The device of any one of paragraphs 14-37, wherein one or more of the high heat lysis chamber, the low-heat reaction chamber, the sample preparation column, and the extraction mechanism are modular, optionally disposable, and wherein the heating mechanisms, and optionally the light source are housed in a modular, reusable portion of the device.

39. The device of any of paragraphs 14-38, wherein the reaction sub-chamber comprises one or more components of a reaction mixture necessary for one-pot SHERLOCK detection of target nucleic acid.

40. The device of paragraph 39, wherein the one or more components are in a lyophilized state.

41. The device of paragraph 39, wherein the one or more components comprise Casl2a, gRNA, RPA primers, reverse transcriptase, and/or single stranded DNA fluorescent quenched reporter.

42. The device of paragraph 41, wherein the one or more components further comprise RNAse H and/or appropriate buffers and salts.

43. The device of paragraph 39 - 42, wherein the reaction mixture comprises: a) 200 nM Casl2a, 400 nM gRNA, lx NEB buffer 2.1, 430 nM each RPA primer, 5 U/pL recombinant reverse transcriptase, 0.05 U/pL RNase H, 20 mM HEPES pH 6.8, 60 mM NaCl, 5% PEG, 1 pM fluorophore-quenched ssDNA fluorescent reporter (e.g., 56-FAM/TTATT/3IABkEQ), 14 mM magnesium acetate, and 1 TwistAmp Basic RPA pellet.

44. The device of any one of paragraphs 39-42, wherein the one or more components comprises RPA primers and/or guide RNA specific for universal detection of SARS-CoV-2 nucleic acid.

45. The device of paragraph 44, wherein the RPA primers and guide RNAs detect regions of SARS-CoV-2 nucleic acid conserved across most variants (e.g., the N gene).

46. The device of paragraph 45, wherein the RPA primers are CGGCAGTCAAGCCTCTTCTCGTTCCTCATC (SEQ ID NO: 7) and CAGACATTTTGCTCTCAAGCTGGTTCAATC (SEQ ID NO: 8), and the guide RNA is UAAUUUCUACUAAGUGUAGAUUUGAACUGUUGCGACUACGU (SEQ ID NO: 9).

47. The device of any one of paragraphs 39-42, wherein the one or more components comprises RPA primers and guide RNA for detection of human RNaseP for use as a control.

48. The device of any one of paragraphs 14-46, wherein use of the device in a method for detecting a pathogen results in sensitivity of detection of the pathogen at least 1,200 cp/mL with 95% confidence interval (Cl) 730-10,000. 49. The device of any one of paragraphs 44-48, wherein the RPA primers and guide RNAs are for specific detection of single nucleotide polymorphisms unique to specific SARS-CoV-2 variants.

50. The device of paragraph 49, wherein the single nucleotide polymorphisms are in the spike protein gene.

51. The device of any one of paragraphs 43-49, wherein the RPA primers and guide RNAs are selected from the group consisting of: a) forward primer: GGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATC (SEQ ID NO: 10) reverse primer: TTT AGGTCC AC AAAC AGTT GCTGGTGC ATGT AGAAGTT (SEQ ID NO: 11) gRNA: UAAUUUCUACUAAGUGUAGAUCAACCCACUUAUGGUGUUGG (SEQ ID NO: 12) (N501Y); b) forward primer: AAGACCCAGTCCCTACTTATTGTTAATAACGC (SEQ ID NO: 13) reverse primer: AAAGTGCAATTATTCGCACTAGAATAAACTCTGAACTC (SEQ ID NO: 14) gRNA: UAAUUUCUACUAAGUGUAGAUUGUUUUUGUGGU AAAC ACC (SEQ ID NO: 15) (Y144del); and c) forward primer: CCTTTTGAGAGAGATATTTCAACTGAAATCTAT (SEQ ID NO: 16) reverse primer: AC CAT AT GATT GT A A AGGA A AGT A AC A ATT A A A AC (SEQ ID NO: 17 ) gRNA: UAAUUUCUACUAAGUGUAGAUACACCAUUACAAGGUGUGCU (SEQ ID NO: 18) (E484K).

52. The device of any one of paragraphs 14-51, wherein use of the device in a method for detecting a pathogen results in sensitivity of detection of the pathogen from about 1,100 cp/mL to about 49,000 cp/mL (e.g., about 1,100 cp/mL, 1,200 cp/mL, 49,000 cp/mL).

53. The device of any one of paragraphs 14-52, wherein use of the device in a method for detecting a pathogen results in greater than or equal to about 96% sensitivity and greater than or equal to about 95% specificity for the detection of a pathogen in saliva samples across a range of viral loads (e.g., SARS-CoV-2 in clinical saliva samples).

54. The device of any of paragraphs 48-53, wherein the pathogen is a RNA containing pathogen 55. The device of any of paragraphs 48-54, wherein the pathogen is SARS-CoV-2.

56. The integrated diagnostic device of any one of paragraphs 14 - 55, further including a smartphone device comprising: a) an embedded camera for receiving illumination projected through the transilluminator filter; and b) one or more processors configured to implement a color segmentation algorithm stored in memory for detecting and quantifying florescence of the received illumination, wherein quantifying florescence includes quantifying the number of pixels corresponding to a predetermined florescence color to determine a result for the rehydrated nucleic acid samples.

57. The system of any one of paragraphs 1-13 or the device of any one of paragraphs 14- 56, wherein one or more of the heating mechanisms includes a temperature sensitive circuit linked to a polyimide heater and a temperature sensor.

58. The system of any one of paragraphs 1-13 or the device of paragraph 14-57, wherein the heating mechanism is connected to a power source.

59. The device of any of paragraphs 14-58, wherein the low-heat reaction chamber further comprises a temperature circuit.

60. The device of any of paragraphs 14-59, wherein the light source includes one or more LEDs.

61. The device of paragraph 60, wherein the one or more LEDs include two royal blue LEDs.

62. A high-heat lysis chamber, a low-heat reaction chamber, an extraction mechanism, and/or a base structure housing one or more heating mechanisms for use within the device of any one of paragraphs 14- 61.

63. A method for detecting a pathogen in a subject comprising: a) providing a device of any of paragraphs 14 - 61, wherein the device comprises a reaction mixture comprising dried components necessary for SHERLOCK detection of pathogen specific nucleic acid in the individual reaction sub-chamber using a fluorescent label readout; b) depositing unprocessed saliva of the subject into the saliva collection interface and activating the heating mechanism to heat the high-heat lysis chamber for a period sufficient to lyse pathogen, inactivate nucleases and allow for deposition of pathogen nucleic acids onto the capture matrix; c) transferring the individual capture matrix and water from the sealed water reservoir to the individual reaction sub-chamber using the extraction mechanism, and activating the heating mechanism to heat the low-heat reaction chamber for a period sufficient to promote sample analysis; and d) detecting visual florescence through the transilluminator filter to thereby determine presence or absence of the pathogen.

64. The method of paragraph 63, wherein the method results in sensitivity of detection of the pathogen at least 1,200 cp/mL with 95% confidence interval (Cl): 730 - 10,000.

65. The method of paragraph 63, wherein the method results in sensitivity of detection of the pathogen from 1,100 cp/mL to 49,000 cp/mL with 95% confidence interval: 590-19,000.

66. The method of any one of paragraphs 63-65, wherein the method results in greater than or equal to about 96% sensitivity and greater than or equal to about 95% specificity for the detection of a pathogen in saliva samples across a range of viral loads.

67. The method of any one of paragraphs 63-66, wherein the pathogen is a RNA containing pathogen.

68. The method of any one of paragraphs 63-67, wherein the pathogen is SARS-CoV-2.

69. The method of any one of paragraphs 63-68, the saliva sample is between about 0.5 mL and 5 mL in volume.

70. The method of any one of paragraphs 63-69, wherein the saliva sample is about 0.5 mL, 0.6 mL, 0.7 mL, 0.8 mL, 0.9 mL, 1.0 mL, 1.1 mL, 1.2 mL, 1.3 mL, 1.4 mL, 1.5 mL, 1.6 mL, 1.7 mL, 1.8 mL, 1.9 mL, 2.0 mL, 2.1 mL, 2.2 mL, 2.3 mL, 2.4 mL, 2.5 mL, 2.6 mL, 2.7 mL, 2.8 mL, 2.9 mL, 3.0 mL, 3.1 mL, 3.2 mL, 3.3 mL, 3.4 mL, 3.5 mL, 3.6 mL, 3.7 mL, 3.8 mL, 3.9 mL, 4.0 mL, 4.1 mL, 4.2 mL, 4.3 mL, 4.4 mL, 4.5 mL, 4.6 mL, 4.7 mL, 4.8 mL, 4.9 mL, or about 5.0 mL in volume.

71. A composition for RNA preparation from an unprocessed saliva sample, the composition comprising a reducing agent and a metal chelating agent in aqueous suspension.

72. The composition of paragraph 71, wherein the reducing agent is DTT present at a concentration to result in a final concentration of from about 10 mM to about 100 mM, and the reducing agent is EGTA present at a concentration to result in a final concentration of about 5mM, in an added saliva sample.

73. The composition of any one of paragraphs 71-72, which does not contain any added nuclease inhibitors. 74. The composition of any one of paragraphs 71-73, in admixture with a saliva sample comprising unprocessed saliva which is diluted no more than 11%, no more than 6%, or no more than 2%.

75. The composition of any one of paragraphs 71-74, further comprising a porous membrane containing 0.22 um pores and functionalized with a hydrophilic surface treatment.

76. A method for preparing RNA, comprising: a) depositing an unprocessed saliva sample into a composition comprising: i) DTT present at a concentration from about 10 mM to about 500 mM; and ii) EGTA present at a concentration from about 5 mM to about 50mM; b) heating the composition with saliva sample to about 70⁰ to 99° C for a period sufficient to lyse a pathogen present within the saliva and inactivate nucleases; and c) concentrating RNA present in the heated composition on a capture matrix by flowing the heated composition through the capture matrix to thereby deposit the RNA onto the capture matrix.

77. The method of paragraph 76, wherein heating step b) is to about 95⁰ C.

78. The method of paragraph 76 or 77, wherein the RNA on the capture matrix is further analyzed for content by isothermal amplification and specific high-sensitivity enzymatic reporter unlocking (SHERLOCK) detection of one or more target nucleic acids.

79. The method of paragraph 78, wherein the SHERLOCK is one-pot SHERLOCK.

80. The method of any one of paragraphs 76 - 79, wherein heating is at least about 3 minutes, wherein the capture matrix is a porous membrane compatible with in situ amplification, and concentration is by filtering the composition through the porous membrane, wherein heating and concentration occurs within about 6 minutes or less.

81. The method of paragraph 80, wherein the porous membrane contains 0.22 um pores and is functionalized with a hydrophilic surface treatment.

82. The method of any one of paragraphs 76 - 81, wherein heating is about 1 minute, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 5.5, about 6 minutes, or greater than 6 minutes.

83. A method for preparing RNA, comprising: a) depositing an unprocessed saliva sample into a sample preparation column comprising: i) 10 mM DTT and 5 mM EGTA final concentration; ii) a capture matrix at a base of the columns for capturing nucleic acid during heating; iii) an absorbent filter disposed immediately below the capture matrix of the one or more sample preparation columns to cause the saliva sample to move during heating through the capture matrix at a flow rate of at least about 1 minute/mL; b) heating the column containing the saliva sample to about 70⁰ to 99° C for a period sufficient to lyse a pathogen present within the saliva and inactivate nucleases and allow for deposition RNA onto the capture matrix; and c) flowing the sample through the capture matrix to thereby deposit the RNA onto the capture matrix.

84. The method of paragraph 83, wherein the RNA on the capture matrix is further analyzed for content by specific high-sensitivity enzymatic reporter unlocking (SHERLOCK).

85. The method of paragraph 84, wherein the SHERLOCK is one-pot SHERLOCK.

86. The method of paragraph 83, wherein, heating and flowing takes place within about 3-6 minutes.

87. The method of paragraph 83, wherein the capture matrix is a polyethersulfone (PES) membrane that contains 0.22 um pores and is functionalized with a hydrophilic surface treatment.

88. A kit for RNA preparation from a saliva sample, comprising: a) the composition of any one of paragraphs 71-75, or the sample collection and preparation system of any one of paragraphs 1-13; and b) instructions for use.

89. The kit of paragraph 82, that comprises a sample collection and preparation system of any one of paragraphs 1-13, and further comprises water and/or a composition comprising a reducing agent and a metal chelating agent in aqueous suspension.

90. The kit of paragraph 89, wherein the reducing agent is DTT present at a concentration to result in a final concentration of from about 10 mm to about 100 mM, and the reducing agent is EGTA present at a concentration to result in a final concentration of about 5mM, in an added saliva sample.

91. The kit of any one of paragraphs 88-90, which does not contain any nuclease inhibitors.

92. A kit for detecting a pathogen in a subject, comprising: a) the device of any one of paragraphs 14-61; and b) instructions for use. 93. The kit of paragraph 92, that further comprises water and/or a composition comprising a reducing agent and a metal chelating agent in aqueous suspension.

94. The kit of paragraph 93, wherein the reducing agent is DTT present at a concentration to result in a final concentration of from about 10 mm to about 100 mM, and the reducing agent is EGTA present at a concentration to result in a final concentration of about 5mM, in an added saliva sample.

95. The kit of any one of paragraphs 90 - 94, wherein the saliva sample is about 0.5 mL,

0.6 mL, 0.7 mL, 0.8 mL, 0.9 mL, 1.0 mL, 1.1 mL, 1.2 mL, 1.3 mL, 1.4 mL, 1.5 mL, 1.6 mL,

1.7 mL, 1.8 mL, 1.9 mL, 2.0 mL, 2.1 mL, 2.2 mL, 2.3 mL, 2.4 mL, 2.5 mL, 2.6 mL, 2.7 mL,

2.8 mL, 2.9 mL, 3.0 mL, 3.1 mL, 3.2 mL, 3.3 mL, 3.4 mL, 3.5 mL, 3.6 mL, 3.7 mL, 3.8 mL,

3.9 mL, 4.0 mL, 4.1 mL, 4.2 mL, 4.3 mL, 4.4 mL, 4.5 mL, 4.6 mL, 4.7 mL, 4.8 mL, 4.9 mL, or about 5.0 mL in volume.

96. The kit of any one of paragraphs 92-95, which does not contain any nuclease inhibitors.

97. The kit of any one of paragraphs 92-96, further comprising one or more of: a) a reaction mixture comprising one or more components necessary for SHERLOCK detection of target nucleic acid; b) RPA primers and/or guide RNA specific for universal detection of SAR.S-CoV-2 nucleic acid; and/or c) RPA primers and/or guide RNAs for specific detection of single nucleotide polymorphisms unique to specific SAR.S-CoV-2 variants.

98. The kit of paragraph 97, wherein the single nucleotide polymorphisms are in the spike protein gene.

99. The kit of paragraph 97 - 98, wherein the RPA primers are CGGCAGTCAAGCCTCTTCTCGTTCCTCATC (SEQ ID NO: 19) and CAGACATTTTGCTCTCAAGCTGGTTCAATC (SEQ ID NO: 20), and/or the guide RNA is UAAUUUCUACUAAGUGUAGAUUUGAACUGUUGCGACUACGU (SEQ ID NO:

21).

100. The kit of paragraph 97-98, wherein the RPA primers and/or guide RNAs are selected from the group consisting of: a) forward primer: GGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATC (SEQ ID NO: 22) reverse primer: TTT AGGTCC AC AAAC AGTT GCTGGTGC ATGT AGAAGTT (SEQ ID NO: 23 ) gRNA: UAAUUUCUACUAAGUGUAGAUCAACCCACUUAUGGUGUUGG (SEQ ID NO: 24) (N501Y); b) forward primer: AAGACCCAGTCCCTACTTATTGTTAATAACGC (SEQ ID NO: 25) reverse primer: AAAGTGCAATTATTCGCACTAGAATAAACTCTGAACTC (SEQ ID NO: 26) gRNA: UAAUUUCUACUAAGUGUAGAUUGUUUUUGUGGUAAACACC (SEQ ID NO: 27) (Y144del); and c) forward primer: CCTTTTGAGAGAGATATTTCAACTGAAATCTAT (SEQ ID NO: 28) reverse primer: AC CAT AT GATT GT A A AGGA A AGT A AC A ATT A A A AC (SEQ ID NO: 29) gRNA: UAAUUUCUACUAAGUGUAGAUACACCAUUACAAGGUGUGCU (SEQ ID NO: 30) (E484K).

[0271] The invention is further illustrated by the following examples, which should not be construed as further limiting.

[0272] EXAMPLES [0273] Introduction

[0274] Described herein is the development of a low-cost, self-contained, POC diagnostic called miSHERLOCK (Minimally Instrumented SHERLOCK) that is capable of concurrent universal detection of SARS-CoV-2 as well as specific detection of the B.l.1.7, B.1.351, or P.l variants. The miSHERLOCK platform integrates an optimized one-pot SHERLOCK reaction with an RNA paper-capture method compatible with in situ nucleic acid amplification and Cas detection. miSHERLOCK combines instrument-free, built-in sample preparation from saliva, room-temperature stable reagents, battery-powered incubation, and simple visual and mobile phone-enabled output interpretation with a limit of detection that matches US Centers for Disease Control and Prevention (CDC) RT-qPCR assays for SARS- CoV-2 of 1,000 copies/mL (cp/mL) (Fig. 7A).

[0275] Although saliva is not a commonly used clinical sample, several studies demonstrate comparable performance between saliva and nasopharyngeal samples for the detection of SARS-CoV-2 (29). Additionally, in paired collection samples in hospitalized patients, salivary SARS-CoV-2 viral load has been shown to be marginally higher than nasopharyngeal swabs and positive for a greater number of days (30). There are also FDA- approved home-based saliva collection kits for mail-in SARS-CoV-2 diagnosis (31). Saliva offers the significant advantage of easy, instrument-free, non-invasive self-collection, which avoids dependence on limiting equipment such as swabs and transport media, and decreases infectious risk to medical personnel and use of personal protective equipment during collection (32). However, saliva samples typically require several processing steps prior to use. We describe a novel combined filtration and concentration step from untreated saliva that is directly processed on our platform without separate processing steps and significantly enhances our assay sensitivity.

[0276] This novel platform only requires two simple user steps, is readily adjustable for additional variants or pathogen targets, and does not require transfer of amplicons, which significantly reduces the risk of cross-contamination by lay users. The usage of miSHERLOCK is expected for general SARS-CoV-2 detection as well as the specific detection of N501Y and E484K mutations with the goal of locally tracking variant strains and assessing the need for variant-specific booster vaccines (33, 34) such as those targeting E484K due to its effects on the efficacy of current vaccines. To showcase the flexibility of miSHERLOCK, high performance detection of the Y144del mutation is also demonstrated. [0277] Results

[0278] Bioinformatic analysis and selection of SARS-CoV-2 target regions. A key aspect of coronavirus replication is nested transcription, which produces high levels of sub-genomic RNA from the 3’ end of the SARS-CoV-2 viral genome during active infections (35) including the nucleoprotein (N) gene (Fig. 7B) (36). To identify potential targets for the assays, bioinformatic analysis of conserved regions with minimal secondary structure near the 3’ end of the SARS-CoV-2 genome was performed. A region of the N gene that was highly conserved among SARS-CoV-2 sequences and that did not show significant homology to other coronaviruses (Fig. 7B) was identified. SHERLOCK assays were designed for this target.

[0279] SHERLOCK consists of two components: isothermal nucleic acid amplification and Cas-mediated detection. Recombinase polymerase amplification (RPA) primer sets and gRNAs were systematically evaluated to determine the most sensitive combinations using commercially obtained full-length synthetic SARS-CoV-2 genomic RNA standards (Twist Biosciences MT106054.1). The best performing N gene gRNA from a set of 30 tested showed exact target matches in 90.7% of all full-length SARS-CoV-2 sequences deposited at the US National Center for Biotechnology Information (NCBI) (~43k genomes) (Table 2). Mismatches were mostly due to a 3’ C>T single nucleotide polymorphism (SNP) in 7.4% of sequences, which is not expected to affect Casl2a targeting since Casl2a gRNA function has been shown to be mediated primarily through 5’ interactions (37). The best performing N gene RPA primers from a set of 100 pairs tested showed exact target matches in 97.4% (forward primer) and 97.0% (reverse primer) of NCBI SARS-CoV-2 genomes.

[0280] To ensure the universality of the N gene gRNA and RPA primers for SARS-CoV-2 variants, full-length high-quality sequences (>29,000 nucleotides (nt), <1% Ns, and <0.05% unique amino-acid mutations not seen in other genomes) were obtained from GISAID (38) for the B.l.1.7 (50,001 genomes), B.1.351 (577 genomes), and P.l (78 genomes) variants and aligned as separate groups. The N gene gRNA exactly matched 99.7%, 100%, and 100% of B.l.1.7, B.1.351, and P.l genomes, respectively. TheN gene forward RPA primer matched 99.8%, 99.5% and 100% of B.l.1.7, B.1.351, and P.l genomes, respectively. The N gene reverse RPA primer exactly matched only 0.06% of B.l.1.7 genomes due to a OT SNP at the +3 position from the 5’ end in 99.94% of B.l.1.7 genomes. This primer SNP is not expected to have any significant effect on RPA amplification efficiency based on the length of RPA primers and prior studies on RPA primer design, which demonstrate a tolerance of 1- 3 nucleotide mismatches (39). The N gene reverse RPA primer exactly matched 100% of B.1.351 and P.l genomes.

[0281] The N gene SHERLOCK assay limit of detection (LOD) using a dilution series of heat-inactivated SARS-CoV-2 RNA [American Type Culture Collection (ATCC) VR- 1986HK] spiked into water was 20,000 copies/mL with a SHERLOCK reaction time of 55 min (Fig. 11). This LOD is comparable to high-performance SARS-CoV-2 RT-qPCR assays (40), with a faster time to result. Additionally, the assay did not show any significant cross reactivity against Human coronavirus OC43 or Human coronavirus 229E genomic RNA spiked in water (Fig. 12).

[0282] SHERLOCK assays that specifically identify SARS-CoV-2 variants. To identify the B.l.1.7, B.1.351, and P.l SARS-CoV-2 variants, SHERLOCK assays were designed that targeted a panel of key spike protein mutations that are currently representative of these variants: N501Y, Y144del, and E484K (Fig. 7B). For each mutation, several gRNA sequences were designed and tested with up to 110 primer pairs in order to obtain the lowest LOD (Fig. 13).

[0283] N501 Y is a mutation in the spike RBD resulting from an A23063U SNP that is shared by the B.l.1.7, B.1.351, and P.l SARS-CoV-2 variants. The N501Y gRNA exactly matched 99.8% of B.l.1.7 genomes, 98.8% of B.1.351 genomes, and 100% of P.l genomes (Table 2). TheN501YRPA reverse primer exactly matched 99.6%, 95.3% and 100% of B.l.1.7, B.1.351, and P.l genomes, respectively. The N501Y RPA forward primer exactly matched 98.7%, 0.17%, and 0% of the B.l.1.7, B.1.351, and P.l genomes, respectively. The lack of exact matches to the B.1.351 and P.1 genomes is due to a G>A SNP at the genomic position corresponding to the +7 position from the 5’ end of the forward RPA primer in 99.3% of B.1.351 and 100% of P.l genomes. This primer SNP is not expected to have any significant effect on RPA amplification efficiency (39). Our assay targeting N501 Y effectively discriminated mutant versus wildtype virus with an LOD of 100,000 copies/mL using full- length synthetic B.l.1.7 variant SARS-CoV-2 RNA spiked into water (Fig. 14A-B).

[0284] The Y144del spike mutation is a 3 nt deletion characteristic of B.1.1.7 SARS-CoV-2 variants that is not present in B.1.351 and P.1 variants. Its presence together with N501 Y strongly suggests a B.l.1.7 variant. The Y144del gRNA showed exact matches to 98.0% of B.l.1.7 genomes and 0% of B.1.351 and P.l genomes. The forward and reverse RPA primers exactly matched 99.7% and 99.8% of B.l.1.7 genomes, respectively (Table 2). The assay clearly distinguished between wildtype and Y144del target RNA to an LOD of 10,000 copies/mL using full-length synthetic B.l.1.7 variant RNA diluted in water (Fig. 14C-D). [0285] The E484K mutation is a critical spike RBD mutation present in the B.1.351, B.1.525, and P.l SAR.S-CoV-2 variants, which has drawn significant attention. This mutation has been identified as a potential major contributor to reduced efficacy of current vaccinations and immunity resulting from natural non-variant SARS-CoV-2 infections with demonstrably lower viral neutralizing potency from convalescent and post-vaccinated patient sera and significantly reduced susceptibility to several therapeutic monoclonal antibodies against SARS-CoV-2 (22, 24, 25). The G23012A SNP that causes E484K also creates a new TTTN protospacer adjacent motif (PAM) site in the antisense strand that is needed for maximal Casl2a function. This is expected to allow differentiation between E484K mutant RNA and wildtype viral RNA. The E484K gRNA and forward and reverse RPA primers all exactly matched 100% of B.1.351 and P.l genomes (Table 2). The E484K gRNA and RPA primers also exactly matched to nearly 100% of B.l.1.7 genomes, but because B.l.1.7 lacks the G23012A SNP that causes E484K and therefore the TTTN PAM site, our E484K assay will have significantly reduced activation by B.l.1.7 genomes. We confirmed clear differentiation between E484K mutant and wildtype viral full-length RNA spiked into water at an LOD of 10,000 copies/mL after a reaction time of 55 minutes (Fig. 14E-F).

[0286] SHERLOCK assay optimization and instrument-free viral RNA capture and concentration. For POC testing targeted toward non-specialist users, it is critical to minimize the number of user steps in order to reduce the likelihood of user error and contamination. Several engineering solutions were applied to simplify and enhance sample preparation, one- pot SHERLOCK reactions, signal readout, and result interpretation.

[0287] SHERLOCK reaction conditions were extensively optimized by varying buffers ( 6 , 8 , 14 ), reverse transcriptases, and reporter concentrations to obtain the lowest LOD (Fig. 15A- C). In agreement with a prior report (75), the addition of RNase H to the SHERLOCK reaction was found to improve reaction kinetics and increased overall fluorescent output (Fig. 15D), likely due to enhanced reverse transcriptase efficiency via degradation of inhibitory RNA:DNA hybrid intermediates.

[0288] SHERLOCK assays were next adapted for use with saliva, which has been identified as an alternative to nasopharyngeal and nasal swabs for SARS-CoV-2 diagnosis. Saliva has several advantages, including being readily available, easy to self-collect, and not requiring swabs or other collection equipment aside from a simple container, which enables mass collection (29, 41). Unprocessed saliva cannot be used directly in a SHERLOCK assay without pre-treatment due to salivary nucleases that hydrolyze quenched fluorescent reporters and lead to high false positive signals (Fig. 16). Unprocessed saliva is also viscous and typically requires several sample preparation steps including centrifugation and a series of manual manipulations in order to release genomic material from viral particles and purify them from inhibitors of nucleic acid amplification and detection reactions (41). POC nucleic acid tests generally require prior sample preparation via commercial kits (11, 29, 40, 41), which are not suitable for applications in resource-limited settings or for at-home use by non specialist users.

[0289] To avoid nucleic acid purification kits that are costly, labor-intensive, and require specialized equipment and user training, a novel technique was developed to inactivate nucleases in unprocessed saliva, lyse viral particles, and concentrate resultant nucleic acids onto a porous membrane that can be directly added to SHERLOCK detection reactions. A variety of buffers and heating conditions were tried (Fig. 17) to inactivate nucleases and release nucleic acids from viral particles. The addition of 10 mM dithiothreitol (DTT) and 5 mM ethylene glycol-bis(2-aminoethylether)-N,N,N',N'-tetraacetic acid (EGTA) followed by heating to 95°C for 3 minutes was found to effectively eliminate the false positive signal associated with salivary nucleases without inhibiting the performance of downstream SHERLOCK-based target nucleic acid detection.

[0290] Nucleic acid capture and concentration onto porous membranes compatible with in situ amplification has been described previously as a sample preparation method for nucleic acid tests (42-44). The skilled artisn will recognize that to be compatible with in situ amplification, such membranes must not contain any chemicals or contaminants that would disrupt or otherwise negatively impact the results of an in situ amplification reaction. Preferably buffer ranges for pH 6-8, maintaining appropriate ionic concentrations will preserve the required reactions. Preferably, strong chaotropic agents and high concentations of proteinase K, or high amounts of still active sample nucleases are to be avoided. A column was engineered that collects 2 mL of user saliva (Fig. 7A) and flows the saliva to a 4 mm polyethersulfone (PES) membrane (Millipore) through gravity and capillary action from an absorbent cellulose filter applied under the membrane. The overall efficiency of nucleic acid capture is determined by the transfer rate of RNA from bulk solution to the capture matrix and the subsequent and separate binding rate of RNA to the capture matrix. The highest capture efficiency was found to be achieved by transport rates of at least 1 min/mL (Fig. 18). The RNA flow rate can be finely tuned by changing the diameter of the PES membrane (Fig. 19). Slowing the flow rate to 1.5 min/mL did not significantly increase RNA recovery, but given the sharp drop-off in RNA recovery at flow rates faster than 1 min/mL, we aimed for a total flow time of 3-6 minutes to maximize RNA capture from our 2 mL sample volume, which was achieved by flowing through a 4 mm-diameter PES membrane (Fig. 18, 19). The PES membrane contains 0.22 pm pores and is functionalized with a hydrophilic surface treatment that serves as a porous matrix to capture and concentrate nucleic acids including SARS-CoV-2 RNA. The simplicity of this design allows instrument- free, intuitive liquid-handling while simultaneously achieving significant specimen concentration to enable 2-20 fold improvement in overall signal (discussed further below). [0291] As described earlier for FIG. 19, the human saliva flow rate is faster with larger aperture diameters of a PES membrane. For example, the flow rate in miSHERLOCK’s sample preparation chamber was optimized by flowing 2.5 mL of human saliva through different aperture diameters (mm) of impermeable tape covering the PES membrane at the bottom of the flow column. Smaller apertures led to slower flow rates. In some implementations, aperture diameters in a diagnostic test can range from about 2 mm to about 10 mm. The flow rate for a diagnostic test will vary based on the sample liquid and the aperture diameter. In some impelementations, flow rates are less than about 0.5 minutes/ml. In some implementations, the flow rates range between about 0.5 to 5 minutes/ml. Flow rates slower than about 5 minutes/ml can lead to extended assay times for certain implementations where there may be sensitivity to evaporation capture matrix resulting from heating to inactivate, for example, a virus of interest. [0292] As described earlier for FIG. 19, the human saliva flow rate is faster with larger aperture diameters of a PES membrane. For example, the flow rate in miSHERLOCK’s sample preparation chamber was optimized by flowing 2.5 mL of human saliva through different aperture diameters (mm) of impermeable tape covering the PES membrane at the bottom of the flow column. Smaller apertures led to slower flow rates. In some implementations, aperture diameters in a diagnostic test can range from about 2 mm to about 10 mm. The flow rate for a diagnostic test will vary based on the sample liquid and the aperture diameter. In some impelementations, flow rates are less than about 0.5 minutes/ml. In some implementations, the flow rates range between about 0.5 to 5 minutes/ml. Flow rates slower than about 5 minutes/ml can lead to extended assay times for certain implementations where there may be sensitivity to evaporation capture matrix resulting from heating to inactivate, for example, a virus of interest. [0293] Construction of the miSHERLOCK integrated POC diagnostic device. The instrument-free method of heat- and chemical -based inactivation of salivary nucleases and viral lysis was combined with the instrument-free method of nucleic acid recovery and concentration from saliva into a low-cost, easy-to-use, integrated diagnostic device. To this end, miSHERLOCK was created, which incorporates the sample preparation methodology with SHERLOCK reactions and enables direct visual readout. In miSHERLOCK, on-device sample preparation and RNA concentration onto a PES membrane are followed by on-device physical transfer of the RNA-containing capture membrane into one-pot SHERLOCK reactions. The device was designed with two zones: a high-heat 95°C lysis area that contains an absorbent cellulose filter that wicks saliva for filtration, and a low-heat 37°C reaction area that regulates SHERLOCK reaction temperature. The low-heat area contains LEDs and an orange acrylic optical filter for transillumination and fluorescent readout (Fig. 8A- C). A duplexed device (for two SHERLOCK reactions) is demonstrated and validated here (Fig. 8), but the platform was designed to be scalable and modular, and triplex (three reactions) and quadruplex (four reactions) miSHERLOCK versions were also constructed (Fig. 20). The heater and temperature regulator units are detachable and reusable. The various components of one specific embodiment of the diagnostic device are shown in Table 4, and is estimated to cost $15, but reuse of electronics/heaters lowers costs to $6 per duplexed assay, which is mostly comprised of the cost of commercially obtained enzymatic components of the amplification and detection reactions (Tables 4-5).

[0294] In the miSHERLOCK diagnostic workflow, the user introduces 2 mL of saliva into the collector, which contains preloaded lysis reagents. The user activates the heater on the device, and after 3-6 minutes, viral particles have been lysed, salivary nucleases have been inactivated, and the saliva has been wicked into the filter, leaving concentrated purified RNA on the PES membrane. The user then removes the collector and transfers the sample preparation column to the reaction chamber. The user pushes a plunger into the column, which punctures a water reservoir to rehydrate and activate the SHERLOCK reaction as well as deposits the PES membrane inside the reaction chamber. The user returns in 55 minutes to observe the visual fluorescence readout through the transilluminator filter (Fig. 20, 21, Fig. 8E).

[0295] While SHERLOCK results are easily visually assessed by most users, a companion mobile phone application (app) was also created to help provide automated quantitation and simplified interpretation of SHERLOCK results. The app uses the embedded camera in a smartphone in combination with a color segmentation algorithm to detect and quantify observed fluorescence at the end of the incubation period as compared to a fluorescence standard placed on the same reader (Fig. 21). The app quantifies the number of pixels corresponding to the selected fluorescence color to provide a simple qualitative metric of “positive” or “negative” result (Fig. 8D). Test results can also be sent to an online database for real-time distributed disease reporting and strain tracking as required.

[0296] Evaluation of miSHERLOCK performance and validation with clinical samples. To assess the analytical sensitivity of our assays, LOD studies were performed to determine the lowest concentration at which greater than or equal to 95% of all (true positive) replicates test positive. For initial tests of miSHERLOCK performance, we used heat-inactivated SARS-CoV-2 (ATCC VR-1986HK) spiked into commercially obtained healthy human saliva to measure the LOD of our N gene universal SARS-CoV-2 assay in the integrated device.

The miSHERLOCK device functioned well across a range of concentrations and showed a LOD of 1,240 copies/milliliter (cp/mL) [95% confidence interval (Cl): 730 - 10,000] on the device (Fig. 9A-B, Fig. 22).

[0297] To ensure that saliva samples contain enough genetic material for testing, a SHERLOCK assay was designed that targets the human RNaseP gene and validated its performance using clinical samples (Fig. 23). This assay serves as a positive control for RNA extraction and reagent stability in the miSHERLOCK platform. Full-length synthetic RNA representative of the SARS-CoV-2 variants B.l.1.7 (Twist B.1.1.7_601443), P.l (Twist EPI ISL 792683), and B.1.351 (Twist EPI ISL 678597) containing N501 Y, Y144del, and E484K mutations, were tested by spiking them into commercially obtained healthy human saliva. The miSHERLOCK platform worked well across a range of concentrations and also lowered the LOD 2-20 fold, as compared to one-pot SHERLOCK assays performed with equivalent concentrations of synthetic full-length SARS-CoV-2 variant RNA spiked in water (Fig. 14). Cising the miSHERLOCK device, the LODs were determined with observed positive rates > 95% for the N501Y, Y144del, and E484K assays were 49,000 cp/mL (95% Cl: 21,000-81,000), 1,100 cp/mL (95% Cl: 590 - 15,000), and 1,200 cp/mL (95% Cl: 660 - 19,000) (Fig. 9A, 9D-F, Fig. 22). Given the successful integration of sample handling, salivary nuclease inactivation, viral RNA extraction, purification, and concentration, and one- pot SHERLOCK in the mi SHERLOCK device with improved overall signal output, clinical saliva samples were obtained from 27 RT-qPCR positive COVID-19 patients (Boca Biolistics) to test the performance of miSHERLOCK with clinical samples. 21 healthy human saliva control samples (BioIVT) were also tested. The miSHERLOCK device demonstrated 96% sensitivity and 95% specificity (Fig. 10A) for the detection of SARS- CoV-2 in clinical saliva samples across a range of viral loads as confirmed by concurrent RT- qPCR (cycle threshold (CT) range 14-38) (Fig. 10B).

[0298] Discussion

[0299] Described herein is the design of miSHERLOCK as a low-cost, portable, self- contained, and integrated diagnostic capable of highly sensitive universal detection of SARS- CoV-2 that equals CDC RT-qPCR performance guidelines, as well as being the only POC diagnostic capable of specific detection of SARS-CoV-2 variants. Several innovative features of the design address critical limitations of current diagnostics in the areas of assay sensitivity, ability to detect viral genomic mutations, simplicity of use, and prevention of laboratory amplicon contamination. One key feature of the design is the incorporation of a unique instrument-free method of RNA isolation from saliva that does not require laboratory equipment, yet achieves specimen filtration and concentration of sample RNA and increases assay sensitivity 2-20 fold. This was accomplished with a simple low-cost membrane by engineering the flow-rate mediated by gravity and capillary action. Other CRISPR-based diagnostics for SARS-CoV-2 have been described, but used commercial RNA extraction kits for sample preparation (13, 45) or use simplified lysis that still require several pipetting steps in order to perform the detection reactions (11, 46).

[0300] Another innovative feature is the ability of the miSHERLOCK device to accept modular target assay components that can be easily exchanged and scaled for multiplexing as needed. Consistency of signal output interpretation is enhanced via an automated mobile phone app, which also allows distributed tracking and reporting. Highly sensitive universal detection of SARS-CoV-2 as well as three high-performance variant diagnostic modules was demonstrated. Notably, these can be easily and rapidly adapted for future variants or pathogens and deployed in accordance with local conditions and diagnostic goals. The reusable heater and temperature regulator electronics minimize the cost, waste, and environmental footprint of mi SHERLOCK. The device can be printed using off-the-shelf 3D printers with commonly available biodegradable polylactic acid to further reduce plastic waste. Cost analysis indicates the miSHERLOCK device has a total cost of $15, but reusing the electronics and heaters would reduce the cost to $11 per duplexed assay, mostly due to commercially obtained enzyme reagent costs that may be significantly reduced with large scale purchasing and manufacturing (Table 5). Lastly, amplicon contamination in nucleic acid testing is a pervasive problem that has affected several COVID-19 clinical and research laboratories (47). By eliminating the need to handle and transfer post-amplification reactions, we significantly reduce the risk of cross contamination, which is especially important for non-specialist users.

[0301] Limitations of the study include the small set of clinical COVID-19 saliva samples tested due to the fact that saliva is not routinely collected in most biorepositories and was difficult to obtain within the context of a proof-of-concept exploratory study. Similarly, clinical samples of SARS-CoV-2 variants were not tested due to lack of availability.

However, miSHERLOCK showed highly sensitive and specific detection with commercially sourced full-length variant RNA spiked into control human saliva and showed near-perfect concordance with RT-qPCR when detecting SARS-CoV-2 from clinical samples of unprocessed saliva. The E484K variant testing relied on the difference in signal obtained in the presence of a mutated Casl2a PAM site. AsCasl2a and LbaCasl2a have both been shown to exhibit reduced but still present cis nucleic acid cleavage despite a TTTV to TTCV mutation, with reductions of -80% and -60% in cleavage efficiency in human cells, respectively (48). However, the effect of PAM mutations on collateral cleavage is unclear. Collateral cleavage in the absence of a TTTG PAM site has been reported for LbaCasl2a (45), but a significant difference was observed in collateral cleavage signal between a mutated PAM site and a canonical PAM site. It is conceivable that a PAM site mutated at a single SNP (i.e., TTTA to TTCA) has a larger inhibitory effect than the complete absence of a PAM site. It is possible that eventually the genetic linkage between different mutations amongst variants would disappear as genetic drift continues. It is also possible that background mutations surrounding clinically important mutation sites may eventually make non-sequencing-based nucleic acid diagnosis of these mutations challenging. However, the number of genomes that show even a few background SNPs adjacent to the clinically relevant mutations mentioned above is extraordinarily small, and CRISPR-based SARS-CoV-2 mutation characterization will continue to have meaningful utility. [0302] Given the rapid time to result of one hour, mi SHERLOCK POC testing for SARS- CoV-2 variant strains will be highly useful for the control and management of the COVID-19 pandemic. For example, one duplex configuration could include modules for universal SARS-CoV-2 identification as well as identification of the N501 Y mutation, which would detect the B.1.1.7, B.1.351, and P.1 variants. This may trigger decisions about increased social distancing or lockdowns in response to the increased infectivity associated with N501 Y variants. Another possibility is to detect the E484K mutation in order to guide the distribution of potential vaccine boosters (32, 33) targeted to this variant due to the observed reduction in vaccine efficacy associated with the B.1.351 and P.l strains (20, 22). As ongoing clinical studies progress, mutation-specific diagnostics may also guide specific protocols in treatment and hospital infection control. For example, the diagnostic may be most useful at the point of care in low-resource settings. While commercially prepared therapeutic cocktails of monoclonal antibodies are unlikely to be widely available in such environments due to cost, convalescent sera is expected to be more readily available and has been shown to be effective in reducing the progression to severe COVID-19 (49). However, current studies indicate that B.l.1.7 variants remain generally susceptible to convalescent sera while E484K-containing variants are highly resistant to neutralization by convalescent sera (22). The use of the variant-focused diagnostic may therefore optimize the usage of this treatment or guide infection control policies. Although targeted to specific known mutations, miSHERLOCK may also be used as a method to triage clinical samples for further analysis with full genome sequencing for detailed epidemiological monitoring.

[0303] As new SARS-CoV-2 variants continue to evolve, the ability to identify variants and rapidly adapt diagnostics to track them will be critical to the successful treatment and containment of the ongoing COVID-19 pandemic. The streamlined workflow and flexible modular design of miSHERLOCK represent important, timely advances in the translation of CRISPR-based assays to field-applicable POC tests, particularly for low-resource settings. [0304] Materials and Methods

[0305] Bioinformatic analysis of SARS-CoV-2 genomes and gRNA and RPA primer design. For universal SARS-CoV-2 detection, 43,305 full-length sequences were downloaded from NCBI and aligned using MAFFT (50). For B.l.1.7 SARS-CoV-2 variants, 50,001 full- length high-quality sequences (>29,000 nt, <1% Ns, <0.05% unique amino acid mutations) genomes were downloaded from GISAID (38) and aligned using MAFFT. For B.1.351 SARS-CoV-2 variants, 577 full-length, high-quality sequences were downloaded from GISAID and aligned using MAFFT. For P.l SARS-CoV-2 variants, 78 full-length, high- quality sequences were downloaded from GISAID and aligned using MAFFT.

[0306] Casl2a gRNAs consist of two parts: the handle region

(UAAUUUCUACUAAGUGUAGAU (SEQ ID NO: 31)) that the Cas protein recognizes and binds, and a user-defined spacer region added to the 3’ end of the handle that determines the specificity to the target. Spacer regions were selected following established guidelines (57). For RPA amplification 10 to 21 forward and reverse RPA primers were designed for each variant target. RPA primers for the universal SARS-CoV-2 assay (52) were selected after testing a range of RPA primers, including some obtained from the literature. Primers were 25-40 nt and total amplicon size was 100-200 bp.

[0307] Sequences were analyzed using Biopython (53) and JalView (54). Exact binding percentages of gRNAs and RPA primers for each assay to SARS-CoV-2 and variant genomes are shown in Table 2. All gRNA and RPA primer sequences are listed in Table 3.

[0308] Clinical samples and ethics statement. De-identified clinical samples from the Dominican Republic were obtained from Boca Biolistics under their ethical approvals. RT- qPCR was performed by Boca Biolistics using the Perkin Elmer New Coronavirus Nucleic Acid Detection kit. The Institutional Review Board at the Wyss Institute and Harvard University as well as the Harvard Committee on Microbiological Safety approved the use of the clinical samples in this study.

[0309] Simulated clinical samples. Simulated SARS-CoV-2 (wildtype) samples were prepared by diluting commercially purchased heat-inactivated SARS-CoV-2 (ATCC VR- 1986HK) quantified by qPCR into water or commercially purchased human saliva (BioIVT). Specificity targets of purified genomic RNA for Human Coronavirus OC43 and Human Coronavirus-229E were purchased from the American Type Culture Collection (ATCC) and diluted in water. Simulated variant SARS-CoV-2 samples were prepared by spiking full- length commercially purchased variant strains for B.1.1.7 (Twist Biosciences B.l.1.7 601443), P.l (Twist Biosciences EPI ISL 792683), and B.1.351 (Twist Biosciences EPI ISL 678597) in water or human saliva (BioIVT) followed by serial dilutions. Synthetic RNA of mutant target regions were also generated for initial assay characterization. To produce mutant RNA target sequences, synthetic DNA with an upstream T7 promoter sequence (5' GAAATTAATACGACTCACTATAGGG (SEQ ID NO: 98) 3') was purchased from Integrated DNA Technologies (IDT) and in vitro transcribed to generate 150-500 base- pair RNA targets for different mutant regions using the Hi Scribe T7 High Yield RNA Synthesis kit from New England Biolabs (NEB). Reactions were incubated for 16 hours at 37°C, treated with DNase I (NEB), and purified using the RNA Clean & Concentrator-25 kit (ZymoResearch). RNA was quantified (ng/pL) on a Nanodrop 2000 (Thermo Fisher Scientific). The concentration of target RNA was calculated by RT-qPCR, using a standard curve with quantified gene block DNA. Table 3 lists the synthetic targets and qPCR primers. [0001] SHERLOCK RPA primer and gRNA screening. RPA primers were ordered from IDT and the design strategy for the nucleoprotein and variant spike gene regions is described in the Results. To synthesize gRNA, DNA sequences with an upstream T7 promoter sequence (IDT) were transcribed with the HiScribe T7 High Yield RNA Synthesis kit (NEB). Reactions were incubated for 16 hours at 37°C, treated with DNase I (NEB), and purified using the RNA Clean & Concentrator-25 kit (ZymoResearch). We performed gRNA screens in 10 pL volumes using 100 nM Casl2a (NEB), 200 nM gRNA, lx NEB 2.1 buffer (NEB), 1 pM ssDNA fluorescent quenched reporter (56-FAM/TTATT/3IABkFQ (SEQ ID NO: 99), IDT) and 100 pM spiked target DNA standard diluted in water. Reactions were incubated at 37°C for 30 minutes and fluorescence kinetics were measured using a BioTek NEO HTS plate reader (BioTek Instruments) with readings every 2 minutes (excitation: 485 nm; emission 528 nm). For the SARS-CoV-2 wildtype assay, gRNAs with the highest fluorescent signal to be tested against RPA primer combinations were selected. For variant assays, we additionally tested gRNAs against 100 pM concentrations of a wildtype dsDNA gene block template of the target region to ensure that Casl2a could effectively discriminate between the two targets. Best performing gRNAs with the highest fluorescent signal and discriminating ability were screened against multiple RPA primer sets (Fig. 13). RPA screens were performed as per manufacturer’s instructions using 7.5 pL reaction volumes from the RPA Liquid Basic kit (TwistDx) with addition of 10 U/pL of Protoscript reverse transcriptase (NEB). 10 pL of RPA primer screen reaction was added to a 1.25 pL Cas reaction with the same reaction conditions as described for the gRNA screen. Selected RPA primers and gRNAs are shown in Table 3.

[0002] Sample preparation and concentration. To demonstrate paper-based RNA capture and concentration, an Aladdin single-syringe infusion pump (World Precision Instruments) was used to test different rates of low-concentration RNA flow through PES membranes (Millipore, cat# GPWP04700). An Integra surgical biopsy punch (Fisher Scientific) was used to create a 3 mm PES membrane disc that was compressed into the tip of a 21 -gauge hypodermic needle (Becton Dickinson) and secured onto the tip of a 5 mL syringe (Becton Dickinson). The syringe was loaded onto an Aladdin infusion pump and 2 mL volumes of SARS-CoV-2 RNA (Twist Biosciences MT106054.1) at a concentration of 500 copies/mL in water were flowed at rates of 0.25 min/mL, 0.5 min/mL, 1 min/mL, and 1.5 min/mL through the syringe.

[0003] To optimize the flow column parameters, a 1 cm x 1 cm square of PCR sealing tape (ThermoScientific) was cut and fitted to the bottom of the column. Different flow- through apertures were punched into the squares using Integra surgical biopsy punches at 1 mm, 3.5 mm, 5 mm, and 7 mm diameters, and the flow columns were loaded with PES membranes at 2 mm, 4 mm, 6 mm, and 8 mm diameters, respectively. One mL, 2 mL, and 2.5 mL of SARS-CoV-2 RNA (Twist Biosciences) at a 1000 copies/mL concentration in saliva were then flowed through the column. To test the sample pre-treatment reagents to lyse virions and to inactivate the nucleases, multiple detergents were tried with and without the addition of 5mM EGTA including 0.5% Tween-20 (Sigma Aldrich), 1% Tween, 0.5%

Sodium dodecyl sulfate (SDS) (Sigma Aldrich), 1% SDS. We tested a lysis buffer comprised of 4 M guanidinium thiocyanate (GITC, Sigma Aldrich), 55 mM Tris-HCl (Sigma Aldrich), 25 mM EDTA (Ethylenediaminetetraacetic acid, Sigma Aldrich), and 3% (v/v) Triton X-100 (Sigma Aldrich). The reducing agent, dithiothreitol (DTT, Thermo Fischer Scientific), was tested at 10 mM, 50 mM, and 100 mM.

[0004] One-pot lyophilized SHERLOCK assay. CRISPR-based sensor reactions were prepared using 200 nM EnGen Lba Casl2a (New England Biolabs), 400 nM gRNA, lx NEB buffer 2.1 (50 mM NaCl , 10 mM Tris-HCl, 10 mM MgCk, 100 pg/ml BSA, pH 7.9@25°C), 430 nM each of the RPA primers (IDT), 5 U/pL Protoscript reverse transcriptase (NEB), 0.05 U/pL RNase H (Ambion), 20 mM HEPES pH 6.8 (Thomas Scientific), 60 mM NaCl (Sigma Aldrich), 5% PEG (Sigma Aldrich), 1 pM fluorophore-quenched ssDNA fluorescent reporter (56-FAM/TT ATT/3 IABkFQ (SEQ ID NO: 100)) (IDT), 14 mM magnesium acetate (TwistDx), and 1 TwistAmp Basic RPA pellet (TwistDx) (contains RPA and polyvinyl alcohol). Prepared sensor reactions excluding the magnesium acetate were deposited into 0.2 mL PCR tubes that were snap-frozen. Magnesium acetate was then added to the pellet and the PCR tube was snap-frozen again prior to lyophilization (Labconco) for 4- 6 hours. In-device activation of sensors (detection reaction mixtures) was achieved by rehydration with 50 pL water and deposition of the PES membrane with captured RNA into the reaction. SHERLOCK reactions were activated by RNA triggers diluted in water alone. Reactions proceeded for 60-120 minutes at 37°C and fluorescent readout was measured either continuously in a Biotek NEO HTS plate reader (BioTek Instruments) or at the beginning and end of a ran when reactions were performed in the mi SHERLOCK device. Measurements from the mi SHERLOCK device were performed via extraction of 3 pL aliquots from the reaction tube and quantitation in the plate reader, although naked eye visual fluorescent readout was also observable in the device.

[0005] Construction of point-of-care diagnostic device. The mi SHERLOCK platform was designed using Autodesk’s Fusion 360 3D CAD software. The housing and components were printed using a Formlabs Form 3 printer (FormLabs). Black resin was chosen to print the housing to minimize reflectance when reading the fluorescence assays. A 2 mm orange acrylic sheet (McMaster-Carr) was laser cut (Universal Laser Systems VLS2.30) to 2.75 cm x 2.25 cm, 2.75 cm x 3.2 cm, or 2.75 cm x 4.0 cm for the duplex, triplex, or quadruplex transilluminator filter, respectively. Double-sided tape (Scotch) was used to tightly line the water reservoir with aluminum foil (Reynolds) and 50 pL of nuclease- free water was loaded for each run. Twenty sheets of Whatman gel blotting paper GB003 (Sigma Aldrich) were loaded into the sample preparation zone for absorption of filtered saliva. Electronic components for the polyimide heaters (Alibaba), temperature controller (DigiKey), and LED lights (Adafruit) were soldered, with heat shrink applied to all wires. Product numbers are listed in Table 4. The set point for the temperature controller circuit was programmed to 37°C by selecting a 120 1<W resistor (DigiKey) and confirmed using a Dallas DS18B20 digital temperature sensor (Fig. 24). The LEDs were soldered in series with a 220 W for the duplex, a 100 W resistor for the triplex, with no resistor needed for the quadruplex (DigiKey) to allow for a current of 25 mA when attached to the 12 V battery source. The temperature sensor circuit and LEDs were mounted to the housing and connected to the battery pack. Fig. 25 illustrates the miSHERLOCK circuit diagrams, Fig. 26 shows the electronics placement in the device, and Fig. 20 shows triplexed and quadruplexed versions of the miSHERLOCK platform.

[0006] In this study, a mobile app was built using Xcode, C++, Objective-c, OpenCV

3.1 and Swift for iOS (Fig. 8D). The mobile application architecture consists of a camera interface that assists in continuous capturing of fluorescence images as produced by the testing device, which are segmented based on the image colors selected by the user when the user clicks over the screen showing the fluorescent regions in a standard sample. The OpenCV libraries were primarily used for image processing, which included pixel-level color detection, filtering, binarization, and masking. From a usability perspective, the software is presented as an iOS native app icon. Upon loading the app, the user can select the desired color for detection from the standard assay, to then proceed towards measuring fluorescence on user-collected test tubes. The analysis events can be screenshot and saved on the smartphone to report assay results for epidemiological purposes.

[0007] On-device miSHERLOCK reactions. Experiments on the mi SHERLOCK platform were performed to validate the sample preparation and one-pot lyophilized SHERLOCK reaction with patient samples. First, the 95°C heater was attached to a 24V battery source (two 12V batteries) and the 37°C heater, temperature regulator, and LEDs were attached to a 12V battery source. The LEDs were inserted into their slots above the reaction chamber (Fig. 26B) and the temperature regulator was inserted into the electronics box (Fig. 26C). The water reservoir was covered with a piece of foil held in place with double-sided tape and filled with 50pL of water for reaction rehydration, the lyophilized reactions were placed within the reaction chamber, the transilluminator filter was slotted into place, the cellulose absorbent filter was placed at the bottom of the lysis chamber, and the PES filters were attached to the bottom of the sample preparation column (Fig. 8A). The sample preparation column was placed within the lysis chamber and topped with the saliva collector. For a duplexed (two-target) reaction 4 mL of saliva, 40 pL of a 1 M DTT and 500mM EGTA solution was added (final concentration lOmM DTT and 5mM EGTA) and then deposited into the saliva collector whereupon saliva was separated by gravity into separate sample preparation and lysis chambers. Within the lysis chamber, the saliva was inactivated by the 95°C heater and the RNA was captured on the filter at the bottom of the column (Fig. 8E, step 1). Following the concentration, the saliva collector was removed and the sample preparation column was moved above the water reservoir. The plunger was used to deposit the filter and the water within the reservoir into the lyophilized reactions in the reaction chamber. The plunger additionally acted as a cover for the reactions and prevented evaporation during incubation (Fig. 8E, step 2). The SHERLOCK reactions incubated for 55 to 120 minutes and were periodically monitored visually by observing the fluorescence through the transilluminator filter (Fig. 8E, step 3). Results were typically visible within 55 minutes of incubation and were further confirmed through the mobile application.

[0008] Data analysis. Fluorescence values are reported as absolute for all experiments used for LOD calculation. Background-subtracted fluorescence, in which the fluorescence value at the initial time point (0 minutes) is subtracted from the end time point (usually 60 minutes) is reported for initial screening experiments. Due to different baseline initial fluorescence units between runs, it was more effective to compare background- subtracted fluorescence than raw fluorescence. The relationship between the proportion of replicates testing positive and the corresponding sensitivity was examined using Probit regression to estimate 95% LOD and 95% Cl of each target. Image analysis of the fluorescence intensities by ImageJ (Fig. 21): images of the tubes inside a miSHERLOCK device were captured with a mobile phone camera. We measured grayscale signal intensities of the areas inside the tubes and subtracted the values from background noise to obtain normalized grayscale intensities. All data were plotted and statistical tests were performed using GraphPad Prism 8. Figures were created using Biorender or Adobe Illustrator 2020.

[0009] Tables

[0010] Table 2: Genomic analysis of gRNAs and RPA primers used to detect key

SARS-CoV-2 variants. The table shows percentages of exact matches between binding regions of our engineered guide RNAs and RPA primers and the SARS-CoV-2 genomes of mixed strains or the variant strains that contain mutations Y144del, E484K and N501Y. SARS-Cov-2 mixed genomes were downloaded from NCBI and variant SARS-CoV-2 genomes were downloaded from GISAID. All genome groups were aligned using MAFFT. See Results for explanations of low percentages of exact matches for some gRNAs and RPA primers to certain genome groups.

[0011] Table 3: Oligonucleotide sequences used

Table 4: miSHERLOCK duplexed diagnostic device and assay.

[0259] Table 5: miSHERLOCK duplexed diagnostic device components when produced at 10,000+ scale for a surface mount design.

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Claims

1. A sample collection and preparation system, comprising: a) a sample preparation column having a capture matrix at a base of the column, the capture matrix being configured to capture nucleic acid during heating from a sample comprising saliva and/or breath condensate in the column; b) an absorbent filter disposed below the capture matrix of the sample preparation column to cause a received sample comprising saliva and/or breath condensate to move during heating through an individual capture matrix via capillary action at a flow rate of at least about 1 min/mL; and c) a high-heat lysis chamber in thermal connection with one or more heating mechanisms, wherein the sample preparation column is disposed within the high-heat lysis chamber.

2. The sample collection and preparation system of claim 1 further comprising a saliva collection interface connected at a second end opposite the base of the sample preparation column.

3. The sample collection and preparation system of any of claims 1 - 2, wherein the sample preparation column is preloaded with lysis reagents comprising a reducing agent and a metal chelating agent.

4. The sample collection and preparation system of claim 3, wherein the reducing agent is DTT present at a concentration to result in a final concentration of from about 10 mM to about 100 mM, and the metal chelating agent is EGTA present at a concentration to result in a final concentration of about 5mM, in an added saliva sample.

5. The sample collection and preparation system of any of claims 3-4, wherein the reducing agent is DTT present at a concentration to result in a final concentration of 10 mM DDT, and the metal chelating agent is EGTA present at a concentration to result in a final concentration from about 1 mM to about 50 mM EGTA in an added saliva sample.

6. The sample collection and preparation system of any of claims 1-5, wherein the capture matrix is a porous membrane that can bind to nucleic acids and is compatible with in situ amplification.

7. The sample collection and preparation system of claim 6, wherein the capture matrix is a polyethersulfone (PES) membrane that contains 0.22 um pores and is optionally functionalized with a hydrophilic surface treatment.

8. The sample collection and preparation system of claim 6, wherein the capture matrix is a membrane containing pores ranging from between about 0.1 um to about 0.5 um.

9. The sample collection and preparation system of any of claims 1-8, wherein the saliva sample is between about 0.2 mL and 5 mL in volume.

10. The sample collection and preparation system of claim 9, wherein the saliva sample is about 0.5 mL, 0.6 mL, 0.7 mL, 0.8 mL, 0.9 mL, 1.0 mL, 1.1 mL, 1.2 mL, 1.3 mL, 1.4 mL,

1.5 mL, 1.6 mL, 1.7 mL, 1.8 mL, 1.9 mL, 2.0 mL, 2.1 mL, 2.2 mL, 2.3 mL, 2.4 mL, 2.5 mL,

2.6 mL, 2.7 mL, 2.8 mL, 2.9 mL, 3.0 mL, 3.1 mL, 3.2 mL, 3.3 mL, 3.4 mL, 3.5 mL, 3.6 mL,

3.7 mL, 3.8 mL, 3.9 mL, 4.0 mL, 4.1 mL, 4.2 mL, 4.3 mL, 4.4 mL, 4.5 mL, 4.6 mL, 4.7 mL,

4.8 mL, 4.9 mL, or about 5.0 mL in volume.

11. The sample collection and preparation system of any of claims 1 - 10, wherein the sample preparation column is reversibly disposed within the high-heat lysis chamber and/or the absorbent filter is reversibly disposed below the capture matrix.

12. The sample collection and preparation system of any of claims 1 - 11, further comprising a cap that securely attaches to the base of the sample preparation column containing the capture matrix, upon removal of the absorbent filter, to cover and protect the capture matrix.

13. The sample collection and preparation system of any of claims 1-12, that is for use within an integrated diagnostic testing device.

14. An integrated diagnostic testing device comprising: a) one or more heating mechanisms; b) a high-heat lysis chamber in thermal connection with the one or more heating mechanisms; c) a low-heat reaction chamber adjoining the lysis chamber and in thermal connection with the one or more heating mechanisms, the low-heat reaction chamber including one or more individual reaction sub-chambers for sample analysis, the low-heat reaction chamber including an exterior transilluminator filter; d) a saliva collection interface connected to one or more sample preparation columns disposed within the high-heat lysis chamber, the one or more sample preparation columns having a capture matrix at a base of the columns configured to capture nucleic acid during heating from a saliva sample in the one or more sample preparation columns; e) an absorbent filter disposed in the high-heat lysis chamber below the capture matrix of the one or more sample preparation columns to cause a received saliva sample to move during heating through an individual capture matrix via capillary action at a flow rate at least about 1 min/mL; f) an extraction mechanism for transferring the individual capture matrix to the individual reaction sub-chamber within the low-heat chamber; and g) a light source positioned to illuminate an interior of the low-heat reaction chamber to allow a visual florescence determination of the saliva sample in the individual capture matrix through the transilluminator filter.

15. The device of any of claims 1-13, wherein the one or more heating mechanisms are configured to heat the high-heat lysis chamber to a temperature that extract RNA molecules and inactivates nucleases.

16. The device of any one of claims 14 to 15, wherein the one or more heating mechanisms are configured to heat the low-heat reaction chamber to a temperature that regulates amplification and detection reactions.

17. The system of any one of claims 1-13 or the device of any one of claims 14 to 16, wherein the absorbent filter is disposed immediately below the capture matrix.

18. The system of any one of claims 1-13 or the device of any one of claims 14 to 17, wherein the saliva sample moves during heating through the capture matrix at a flow rate of about 1.5 min/mL.

19. The device of any one of claims 14 to 18, wherein low-heat reaction chamber further includes one or more sealed water reservoirs for reaction mixture hydrating.

20. The device of claim 19, wherein the extraction mechanism is a plunger for insertion into the sample preparation column to release the water from the sealed reservoir.

21. The device of any one of claims 14 to 20, wherein the sample preparation column is removable from the high heat lysis chamber into the low-heat reaction chamber for transfer of the individual capture matrix to the individual reaction sub-chambers.

22. The system of any one of claims 1-13 or the device of any one of claims 14 to 21, wherein the sample preparation column is preloaded with lysis reagents to thereby result in a final concentration of 10 mM DTT and 5 mM EGTA in the saliva sample.

23. The system of any one of claims 1-13 or the device of any one of claims 14-22, wherein the capture matrix is a porous membrane that can bind to nucleic acids and is compatible with in situ amplification.

24. The device of claim 21 or 22, wherein the extraction mechanism is a plunger for insertion into the sample preparation column to dislodge the capture matrix from the column and deposit the capture matrix and the water into the reaction sub-chamber.

25. The device of any one of claims 14-24, wherein one or more of the high heat lysis chamber, the low-heat reaction chamber, the sample preparation column, and the extraction mechanism are modular, optionally disposable, and wherein the heating mechanisms, and optionally the light source are housed in a modular, reusable portion of the device.

26. The device of any of claims 14-25, wherein the reaction sub-chamber comprises one or more components of a reaction mixture necessary for one-pot SHERLOCK detection of target nucleic acid.

27. The device of claim 26, wherein the one or more components comprises RPA primers and/or guide RNA specific for universal detection of SARS-CoV-2 nucleic acid.

28. The device of claim 27, wherein the RPA primers and guide RNAs detect regions of SARS-CoV-2 nucleic acid conserved across most variants (e.g., the N gene).

29. The device of claim 26, wherein the one or more components comprises RPA primers and guide RNA for detection of human RNaseP for use as a control.

30. The device of any one of claims 27-29, wherein the RPA primers and guide RNAs are for specific detection of single nucleotide polymorphisms unique to specific SARS-CoV-2 variants.

31. The device of claim 30, wherein the single nucleotide polymorphisms are in the spike protein gene.

32. The device of any one of claims 14-31, wherein use of the device in a method for detecting a pathogen results in greater than or equal to about 96% sensitivity and greater than or equal to about 95% specificity for the detection of a pathogen in saliva samples across a range of viral loads.

33. The device of claim 32, wherein the pathogen is a RNA containing pathogen.

34. The device of any of claims 32-33, wherein the pathogen is SARS-CoV-2.

35. The integrated diagnostic device of any one of claims 14 - 34, further including a smartphone device comprising: a) an embedded camera for receiving illumination projected through the transilluminator filter; and b) one or more processors configured to implement a color segmentation algorithm stored in memory for detecting and quantifying florescence of the received illumination, wherein quantifying florescence includes quantifying the number of pixels corresponding to a predetermined florescence color to determine a result for the rehydrated nucleic acid samples.

36. The system of any one of claims 1-13 or the device of any one of claims 14-35, wherein one or more of the heating mechanisms includes a temperature sensitive circuit linked to a polyimide heater and a temperature sensor.

37. The device of any of claims 14-36, wherein the light source includes one or more LEDs.

38. A high-heat lysis chamber, a low-heat reaction chamber, an extraction mechanism, and/or a base structure housing one or more heating mechanisms for use within the device of any one of claims 14- 37.

39. A method for detecting a pathogen in a subject comprising: a) providing a device of any of claims 14 - 37, wherein the device comprises a reaction mixture comprising dried components necessary for SHERLOCK detection of pathogen specific nucleic acid in the individual reaction sub-chamber using a fluorescent label readout; b) depositing unprocessed saliva of the subject into the saliva collection interface and activating the heating mechanism to heat the high-heat lysis chamber for a period sufficient to lyse pathogen, inactivate nucleases and allow for deposition of pathogen nucleic acids onto the capture matrix; c) transferring the individual capture matrix and water from the sealed water reservoir to the individual reaction sub-chamber using the extraction mechanism, and activating the heating mechanism to heat the low-heat reaction chamber for a period sufficient to promote sample analysis; and d) detecting visual florescence through the transilluminator filter to thereby determine presence or absence of the pathogen.

40. A method for preparing RNA, comprising: a) depositing an unprocessed saliva sample into a composition comprising: i) DTT present at a concentration from about 10 mM to about 500 mM; and ii) EGTA present at a concentration from about 5 mM to about 50mM; b) heating the composition with saliva sample to about 70⁰ to 99° C for a period sufficient to lyse a pathogen present within the saliva and inactivate nucleases; and c) concentrating RNA present in the heated composition on a capture matrix by flowing the heated composition through the capture matrix to thereby deposit the RNA onto the capture matrix.

41. The method of claim 40, wherein heating step b) is to about 95⁰ C.

42. A method for preparing RNA, comprising: a) depositing an unprocessed saliva sample into a sample preparation column comprising: i) 10 mM DTT and 5 mM EGTA final concentration; ii) a capture matrix at a base of the columns for capturing nucleic acid during heating; iii) an absorbent filter disposed immediately below the capture matrix of the one or more sample preparation columns to cause the saliva sample to move during heating through the capture matrix at a flow rate of at least about 1 minute/mL; b) heating the column containing the saliva sample to about 70⁰ to 99° C for a period sufficient to lyse a pathogen present within the saliva and inactivate nucleases and allow for deposition RNA onto the capture matrix; and c) flowing the sample through the capture matrix to thereby deposit the RNA onto the capture matrix.

43. A kit for RNA preparation from a saliva sample, comprising: a) the sample collection and preparation system of any one of claims 1-13; and b) instructions for use.

44. A kit for detecting a pathogen in a subject, comprising: a) the device of any one of claims 14-37; and b) instructions for use.

45. The kit of claim 43 or 44, that further comprises water and/or a composition comprising a reducing agent and a metal chelating agent in aqueous suspension.

46. The kit of claim 45, wherein the reducing agent is DTT present at a concentration to result in a final concentration of from about 10 mm to about 100 mM, and the reducing agent is EGTA present at a concentration to result in a final concentration of about 5mM, in an added saliva sample.

47. The kit of any one of claims 43-46, which does not contain any nuclease inhibitors.

48. The kit of any one of claims 43-47, further comprising one or more of: a) a reaction mixture comprising one or more components necessary for SHERLOCK detection of target nucleic acid; b) RPA primers and/or guide RNA specific for universal detection of SARS-CoV-2 nucleic acid; and/or c) RPA primers and/or guide RNAs for specific detection of single nucleotide polymorphisms unique to specific SARS-CoV-2 variants.

49. The kit of claim 48, wherein the single nucleotide polymorphisms are in the spike protein gene.

50. The kit of any one of claims 43-49, or the method of claim 63, wherein the pathogen is SARS-CoV-2.

51. The kit of claim 50, wherein the RPA primers are CGGCAGTCAAGCCTCTTCTCGTTCCTCATC (SEQ ID NO: 98) and CAGACATTTTGCTCTCAAGCTGGTTCAATC (SEQ ID NO: 99), and the guide RNA is UAAUUUCUACUAAGUGUAGAUUUGAACUGUUGCGACUACGU (SEQ ID NO:

101).

52. The kit of claim 50, wherein the RPA primers and guide RNAs are selected from the group consisting of: a) forward primer: GGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATC (SEQ ID NO: 102) reverse primer: TTT AGGTCC AC AAAC AGTT GCTGGTGC ATGT AGAAGTT (SEQ ID NO: 103) gRNA: UAAUUUCUACUAAGUGUAGAUCAACCCACUUAUGGUGUUGG (SEQ ID NO: 104) (N501Y); b) forward primer: AAGACCCAGTCCCTACTTATTGTTAATAACGC (SEQ ID NO: 105) reverse primer: AAAGTGCAATTATTCGCACTAGAATAAACTCTGAACTC (SEQ ID NO: 106) gRNA: UAAUUUCUACUAAGUGUAGAUUGUUUUUGUGGU AAAC ACC (SEQ ID NO: 107) (Y144del); and c) forward primer: CCTTTTGAGAGAGATATTTCAACTGAAATCTAT (SEQ ID NO: 108) reverse primer: AC CAT AT GATT GT A A AGGA A AGT A AC A ATT A A A AC (SEQ ID NO: 109) gRNA: UAAUUUCUACUAAGUGUAGAUACACCAUUACAAGGUGUGCU (SEQ ID NO: 110) (E484K).