Methods and systems for processing a biological sample

Abstract

The present disclosure provides methods, compositions, systems and kits for processing a biological sample.

Description

METHODS AND SYSTEMS FOR PROCESSING A BIOLOGICAL SAMPLECROSS-REFERENCE

[0001] This application claims the benefit of U.S. Provisional Patent Application No. 63 / 670,623 filed on July 12, 2024, which is incorporated by reference in its entirety.BACKGROUND

[0002] Rapid and accurate molecular diagnosis is critical for timely detection and treatment of infectious human or agricultural pathogens. Molecular Diagnostic (Dx) technologies typically involve nucleic acid amplification and detection by expensive, sophisticated equipment such as quantitative PCR (qPCR), which cannot be deployed in field or true point-of-care (PoC) scenarios, leading to delays in diagnosis and treatment. Recent pandemics have highlighted the necessity of instrument-free, cost-effective molecular Dx technologies that can be used by anyone, deployed anywhere and easily configured for any disease target. The gold standard amplification technology, PCR, requires specialized thermocycling equipment, trained (skilled) technical operators, and stringent experiment design, among other constraints. Unlike PCR, existing isothermal amplification technologies, such as LAMP, HAD, or RPA do not require a thermocycler, but still require an incubator for maintaining a constant elevated temperature. Additionally, these methods have specific design constraints, are prone to non-specific amplification which can inhibit specificity and sensitivity of detection, and cannot easily differentiate single nucleotide mismatches in target sequences. Therefore, these methods require an additional enzymatic technology for specific and sensitive detection at PoC, such as CRISPR / Cas-based SHERLOCK and DETECTR technologies. Consequently, these methods increase total detection time, manufacturing costs, and assay design complexity. There is also a current lack of effective near PON diagnostic tests utilizing real-time detection designed for very high-throughput, with little training required or medium training involved, which can be operated at a low-medium cost with medium-high sensitivity and very high specificity in small clinical labs. Recognized herein is a need for technical solutions to address these hurdles in the field.

[0003] Furthermore, nucleic acid testing (NAT) biosensing technologies, such as those employing the use of fluorophores or redox sensors, or other physicochemical detectors, are currently used in numerous applications for the detection of nucleic acids (NA) of a particular pathogen or mutated genes in an organism. NATs use the specificity and sensitivity afforded by nucleic acid base pairing to detect different NA sequences, sometimes differing by asingle nucleotide. However, for a NAT to work effectively, the detectable target sequence for the probe sequence needs to be single-stranded DNA and / or RNA. This allows for a probe having a physicochemical detector (e.g., a genosensor probe) to hybridize to its complementary sequence, which is usually a single-stranded DNA and / or RNA target.

[0004] The most used nucleic acid amplification test (NAAT) is PCR which remains the gold standard of current diagnostics. However, PCR is difficult to conduct in a point-of-need setting because of the requirement of specific cycling temperatures: for example, (i) a very high temperature (usually 95°C) required for thermal melting of dsDNA / dsRNA (either the starting sequence or the amplicons after the first amplification cycle), (ii) annealing temperature (usually between 50-70°C) for the primers to bind to, and (iii) the extension temperature for the corresponding amplification by the common polymerases (e.g., Taq (72°C)). Additionally, PCR and real-time PCR are limited to the time required for each cycle, thereby increasing the total time of the reactions. Other isothermal NAATs, such as LAMP (loop-mediated isothermal amplification), HDA (helicase-dependent isothermal DNA amplification), SDA (strand displacement amplification), NASBA (nucleic acid sequencebased amplification), RCA (rolling circle amplification), can amplify DNA or RNA in a simpler setting by avoiding the need for a cycling method. However, all the aforementioned methods still require either thermal melting of the dsDNA or dsRNA, incubation at a temperature higher than 50°C, or require the addition of finicky nucleases adding to the complexity of the process.

[0005] Additionally, most NAATs can amplify if there is contamination or are prone to primer artefact generation, and therefore nested amplification strategies or primer modifications are utilized to make the amplicon results more specific. Furthermore, most NAATs utilize a dual-strand amplification strategy to increase the number of copies exponentially. However, this results in dsDNA amplicons, which may need to be denatured before being detected by a hybridization probe sequence. While asymmetric amplification strategies can be used to amplify mostly single-stranded DNA, it heavily limits the amplification rate to a linear rate instead of the exponential rate of the dual-strand approach. While there are additional probe design strategies which rely on specific modifications in the probe or the addition of another enzyme to facilitate a change in probe structure or sequence, most of these methods can complicate the amplification design strategy or result in probe artefact generation. Recognized herein is a need for technical solutions that address these technical problems in the field.SUMMARY

[0006] Recognized herein is a need for effective extraction, amplification, and / or detection systems and methods to address the aforementioned technical problems. Recognized herein is a need for such systems and methods that can be used in the field. Recognized herein is a need for systems and methods to process samples more efficiently than preexisting technologies. It is an objective of the present invention to provide systems, compositions, and methods that allow for amplifying target double-stranded and singlestranded amplicons bound to in reaction probe while also inhibiting non-specific binding. Embodiments of the present invention can be freely combined with each other if they are not mutually exclusive.

[0007] Any feature or combination of features described herein are included within the scope of the present invention provided that the features included in any such combination are not mutually inconsistent as will be apparent from the context, this specification, and the knowledge of one of ordinary skill in the art. Additional advantages and aspects of the present invention are apparent in the following detailed description and claims. Still other objects and advantages of the present disclosure will become readily apparent by those skilled in the art from the following detailed description, wherein it is shown and described only the preferred embodiments, simply by way of illustration of the best mode. As will be realized, the disclosure is capable of other and different embodiments, and its several details are capable of modifications in various obvious respects, without departing from the disclosure. Accordingly, the description is to be regarded as illustrative in nature and not as restrictive.

[0008] The present disclosure provides a system for processing a biological sample. In some embodiments, the system comprises a first channel comprising a first opening. In some embodiments, the first channel is configured to couple thereto a biological sample. In some embodiments, the system comprises a second channel comprising a cellulose substrate coupled thereto. In some embodiments, the second channel comprises a second opening, wherein the second opening comprises an incline having a slope of about 1° to about 50°. In some embodiments, upon a coupling of the second opening to the first opening, the biological sample is transferred from the first channel to the second channel. In some embodiments, the system comprises a third channel comprising an elution solution. In some embodiments, the third channel comprises a third opening, wherein upon a coupling of the second opening to the third opening, the elution solution is transferred from the third channel to the second channel. In some embodiments, the second opening comprises an incline having a slope ofabout 3°. In some embodiments, the second opening comprises an incline having a slope of about 45°. In some embodiments, the binding membrane is disposed along an inside perimeter of the second channel. In some embodiments, the cellulose substrate has a surface area of about 0.1 to about 1.7 square inches (in2). In some embodiments, the cellulose substrate has a surface area of about 0.6 to about 0.7 in2. In some embodiments, the cellulose substrate has a surface area of about 0.4 to about 0.5 in2. In some embodiments, the first channel further comprises a filtration device. In some embodiments, the filtration device is configured to filter the biological sample prior to the transfer of the biological sample from the first channel to the second channel. In some embodiments, the first channel further comprises a lysis solution. In some embodiments, the processing comprises an extraction of an analyte from the biological sample. In some embodiments, the processing comprises a nucleic acid extraction. In some embodiments, the nucleic acid comprises a DNA or an RNA or both. In some embodiments, the processing comprises binding a plurality of nucleic acids to the cellulose substrate. In some embodiments, the processing further comprises eluting at least a portion of the bound plurality of nucleic acids into the elution solution. In some embodiments, a detection of amplified extracted nucleic acids determines the presence or absence of a target sequence. In some embodiments, the target sequence is a nucleic acid sequence of a virus or a bacterium. In some embodiments, the target sequence is a DNA sequence or RNA sequence or both. In some embodiments, the DNA sequence is related to a genetic trait. In some embodiments, the DNA sequence or RNA sequence is animal genomic DNA or genomic RNA. In some embodiments, amplification is performed via a quantitative polymerase chain reaction (qPCR), PCR, or isothermal amplification. In some embodiments, the isothermal amplification is RPA or ANINA. In some embodiments, a connector is configured to couple the third channel to the second channel. In some embodiments, the connector is configured to couple the first channel to the second channel. In some embodiments, the system further comprises a dropper cap. In some embodiments, the first channel is configured to transfer the biological sample to the second channel through the dropper cap. In some embodiments, the dropper cap is configured to couple to the first channel. In some embodiments, the first channel is a vial, or a flexible tube. In some embodiments, the second channel is a vial. In some embodiments, the third channel is a vial. In some embodiments, the cellulose substrate is affixed to the second channel. In some embodiments, the second channel comprises a single chamber. In some embodiments, the first channel or the second channel comprise a particulate filter having a pore size of greater than about 10 pm. In some embodiments, the particulate filter is configured to retain particleswhen the biological sample is transferred from the first channel to the second channel. In some embodiments, either the first channel or second channel comprises an adapter. In some embodiments, the adapter, when in use, couples the first channel to the second channel. In some embodiments, the adapter comprises internal threads. In some embodiments, either the first channel or the second channel comprises internal treads. In some embodiments, the internal treads, when in use, couple the first channel to the second channel. In some embodiments, either the first channel or the second channel comprises a flexible tubing. In some embodiments, the flexible tubing, when in use, couples the first channel to the second channel. In some embodiments, a first channel comprising the biological sample is configured to transfer the biological sample to a port of the second channel. In some embodiments, the first channel comprises a lysis solution. In some embodiments, the system further comprises a dropper cap. In some embodiments, the first channel, when in use, transfers the biological sample through the dropper cap to the port. In some embodiments, a connector is configured to couple the third channel to the port. In some embodiments, the third channel comprises an elution solution. In some embodiments, the coupling of the third channel to the port transfers the elution solution to and from the second channel. In some embodiments, transferring the elution solution to and from the second channel occurs in less than about 30 seconds.

[0009] The present disclosure provides a system for preparation of a nucleic acid from a biological sample, the system comprising a housing comprising: a cellulose substrate coupled to the housing; and a port configured to (i) receive the biological sample and (ii) provide the biological sample to the cellulose substrate, wherein the port comprises an incline having a slope of about 1° to about 50°. In some embodiments, the port comprises an incline having a slope of about 3°. In some embodiments, the port comprises an incline having a slope of about 45°. In some embodiments, the cellulose substrate is disposed along an inside perimeter of the housing. In some embodiments, the cellulose substrate has a surface area of about 0.1 to about 1.7 square inches (in2). In some embodiments, the cellulose substrate has a surface area of about 0.6 to about 0.7 in2. In some embodiments, the cellulose substrate has a surface area of about 0.4 to about 0.5 in2. In some embodiments, the nucleic acid comprises a DNA, an RNA, or both. In some embodiments, the cellulose substrate is configured to bind a plurality of nucleic acids. In some embodiments, the housing is a bottle. In some embodiments, the housing is a vial. In some embodiments, the cellulose substrate remains affixed to the housing. In some embodiments, the housing comprises a single chamber. In some embodiments, the system does not further comprise an actuator. In some embodiments,the system does not further comprise a centrifuge. In some embodiments, the system does not further comprise or a vacuum. In some embodiments, the biological sample is a biological fluid. In some embodiments, the biological sample is a swab sample. In some embodiments, the biological sample is a nasal swab, oral swab, tongue swab, throat swab, wound swab, or a vaginal swab. In some embodiments, the biological sample is a tissue sample, such as skeletal, muscle, spleen, embedded (FFPE), or liver tissue. In some embodiments, the tissue sample is a skeletal tissue, a muscle tissue, a spleen tissue, an embedded tissue or a liver tissue. In some embodiments, the tissue sample has a mass of about 5 to about 200 milligrams (mg). In some embodiments, the tissue sample has a mass of at least about 25 mg. In some embodiments, the biological sample is an animal sample. In some embodiments, the biological sample is a bacteria sample. In some embodiments, the biological sample comprises water, such as water derived from a natural source, tap water, aquarium(s), or wastewater. In some embodiments, the water comprises wastewater, water derived from a pond, or water derived from aquarium. In some embodiments, the biological sample is a plant sample.

[0010] The present disclosure provides a method for processing a biological sample. In some embodiments, the method comprises coupling a biological sample to a first channel comprising a first opening. In some embodiments, the method further comprises coupling the first opening of the first channel to a second opening of a second channel, thereby transferring the biological sample from the first channel to the second channel. In some embodiments, the second channel has a cellulose substrate coupled thereto. In some embodiments, the second opening comprises an incline having a slope of about 1° to about 50°. In some embodiments, the method further comprises coupling the second opening of the second channel to a third opening of a third channel. In some embodiments, the third channel comprises an elution solution. In some embodiments, the coupling of the second opening to the third opening transfers the elution solution to the second channel. In some embodiments, the method further comprises removing the elution solution from the second channel. In some embodiments, the second opening comprises an incline having a slope of about 3°. In some embodiments, the second opening comprises an incline having a slope of about 45°. In some embodiments, the binding membrane is disposed along an inside perimeter of the second channel. In some embodiments, the cellulose substrate has a surface area of about 0.1 to about 1.7 square inches (in2) In some embodiments, the cellulose substrate has a surface area of about 0.6 to about 0.7 in2. In some embodiments, the cellulose substrate has a surface area of about 0.4 to about 0.5 in2. In some embodiments, subsequent to the removing the elutionfrom the second channel, the elution solution is transferred from the second channel back into the third channel. In some embodiments, the first channel further comprises a filtration device. In some embodiments, the filtration device filters the biological sample prior to the transfer of the biological sample from the first channel to the second channel. In some embodiments, the first channel further comprises a lysis solution. In some embodiments, the processing comprises an extraction of an analyte from the biological sample. In some embodiments, the processing comprises a nucleic acid extraction. In some embodiments, the nucleic acid comprises a DNA or an RNA or both. In some embodiments, the processing comprises binding a plurality of nucleic acids to the cellulose substrate. In some embodiments, the processing further comprises eluting at least a portion of the bound plurality of nucleic acids into the elution solution. In some embodiments, a detection of amplified extracted nucleic acids determines the presence or absence of a target sequence. In some embodiments, the target sequence is a nucleic acid sequence of a virus or a bacteria. In some embodiments, the target sequence is a DNA sequence or RNA sequence or both. In some embodiments, the DNA sequence is related to a genetic trait. In some embodiments, the DNA sequence or RNA sequence is animal genomic DNA or genomic RNA. In some embodiments, the amplification is performed via a quantitative polymerase chain reaction (qPCR), PCR, or isothermal amplification. In some embodiments, the isothermal amplification is RPA or ANINA. In some embodiments, a connector couples the third channel to the second channel. In some embodiments, the connector couples the first channel to the second channel. In some embodiments, the first channel further comprises a dropper cap. In some embodiments, the first channel transfers the biological sample to the second channel through the dropper cap. In some embodiments, the dropper cap couples to the first channel. In some embodiments, the first channel is a vial. In some embodiments, the first channel is a flexible tube. In some embodiments, the second channel is a vial. In some embodiments, the third channel is a vial. In some embodiments, the cellulose substrate is affixed to the second channel. In some embodiments, the second channel comprises a single chamber. In some embodiments, the first channel or the second channel comprises a particulate filter having a pore size of greater than about 10 um. In some embodiments, the particulate filter retains particles when the biological sample is transferred from the first channel to the second channel during the coupling the first opinion of the first channel to the second opening of the second channel. In some embodiments, either the first channel or second channel comprises an adapter. In some embodiments, the adapter, when in use, couples the first channel to the second channel. In some embodiments, the adapter comprisesinternal threads. In some embodiments, either the first channel or the second channel comprises internal treads. In some embodiments, the internal treads, when in use, couple the first channel to the second channel. In some embodiments, either the first channel or the second channel comprises a flexible tubing. In some embodiments, the flexible tubing, when in use, couples the first channel to the second channel. In some embodiments, a first channel comprising the biological sample transfers the biological sample to a port of the second channel. In some embodiments, the first channel comprises a lysis solution. In some embodiments, the method further comprises using a dropper cap. In some embodiments, the first channel comprises the dropper cap. In some embodiments, when in use, the first channel transfers the biological sample through the dropper cap to the port. In some embodiments, a connector couples the third channel to the port. In some embodiments, the third channel comprises an elution solution. In some embodiments, the coupling of the third channel to the port transfers the elution solution to and from the second channel. In some embodiments, transferring the elution solution to and from the second channel occurs in less than about 30 seconds.

[0011] The present disclosure provides a composition for processing a biological sample, the composition comprising: sodium hydroxide (NaOH) at a concentration of about 0.2 to about 2 molar (M) of the composition; and triton-X 100 at a concentration of about 0.25% v / v to about 2% v / v of the composition. In some embodiments, the composition further comprises antifoam at a concentration of about 0.01% v / v to about 2% v / v of the composition. In some embodiments, the sodium hydroxide (NaOH) is at a concentration of about 1 molar of the composition. In some embodiments, the triton-X 100 is at a concentration of about 1.5% v / v of the composition. In some embodiments, the antifoam is at a concentration of about 0.05 % v / v to about 2% v / v of the composition.

[0012] The present disclosure provides a composition for processing a biological sample, the composition comprising: (a) lysozyme at a concentration of about 10 mg / mL to about 150mg / mL; and (b) detergent, wherein the detergent comprises: (i) tween80 at a concentration of about 0.025% v / v to about 1.5% v / v of the composition; (ii) triton-X 100 at a concentration of about 0.025% v / v to about 1.5% v / v of the composition; or (iii) any combination of (i) and (ii). In some embodiments, the lysozyme is at a concentration of about 50 mg / mL of the composition. In some embodiments, the tween80 is at a concentration of about 0.05% v / v of the composition. In some embodiments, the triton-X 100 at a concentration of about 0.05% v / v of the composition.

[0013] The present disclosure provides a composition for processing a biological sample,the composition comprising: sodium hydroxide (NaOH) at a concentration of about 0.2 molar to about 2 molar (M) of the composition; triton-X 100 at a concentration of about 0.025% v / v to about 2% v / v of the composition; lysozyme at a concentration of about lOmg / mL to about 150mg / mL of the composition; and tween80 at a concentration of about 0.025% v / v to about 0.5% v / v of the composition. In some embodiments, the lysozyme is at a concentration of about 50 mg / mL. In some embodiments, the tween80 is at a concentration of about 0.05% v / v of the composition. In some embodiments, sodium hydroxide (NaOH) is at a concentration of about 0.5 molar of the composition; and triton-X 100 at a concentration of about 1.5% of the composition. In some embodiments, the composition further comprises antifoam at a concentration of about 0.01% v / v to about 2% v / v of the composition. In some embodiments, antifoam is at a concentration of about 1 % v / v of the composition. In some embodiments, the composition further comprises EDTA at a concentration from about 0.01 mM to about 1.0 mM. In some embodiments, the composition further comprises Tris at a concentration from about 1 mM to about 100 mM.

[0014] The present disclosure provides a composition for processing a biological sample, the composition comprising: Tris HC1 at a concentration of about 10 millimolar (mM) to about 100 mM of the composition; NaCl at a concentration of about 25 mM to about 500 mM of the composition; triton x-100 at a concentration of about 0.1% to about 5% of the composition; and TCEP at a concentration of about 1 mM to about 100 mM of the composition. In some embodiments, the composition further comprises PBS buffer at a concentration of about 5 mM to about 100 mM of the composition. In some embodiments, the Tris HC1 is at a concentration of about 25 mM of the composition. In some embodiments, NaCl is at a concentration of about 300 mM of the composition. In some embodiments, triton x-100 is at a concentration of about 0.5% to about 1% of the composition, and TCEP is at a concentration of about 10 mM to about 20 mM of the composition.

[0015] The present disclosure provides a system for processing a biological sample, the system comprising a first channel comprising a first opening, wherein the first channel is configured to couple thereto a biological sample. In some embodiments, the system further comprises a second channel comprising a substrate coupled thereto. In some embodiments, the second channel further comprises a second opening. In some embodiments, the second opening is configured to couple to the first opening. In some embodiments, upon the coupling of the second opening to the first opening, the biological sample is transferred from the first channel to the second channel. In some embodiments, the system further comprises a third channel comprising an elution solution. In some embodiments, the third channel furthercomprises a third opening. In some embodiments, the third opening is configured to couple to the second opening. In some embodiments, upon the coupling of the second opening to the third opening, the elution solution is transferred from the third channel to the second channel. In some embodiments, when the sample comprises a pathogenic bacterium, said first channel further comprises a lysis solution comprising sodium hydroxide (NAOH) at a concentration of at least about 200 mM. In some embodiments, the lysis solution comprises one or more of the following: triton-X 100 at a concentration of about 0.1% v / v to about 2% v / v of the composition; lysozyme at a concentration of about 10 mg / mL to about 150mg / mL of the composition; tween80 at a concentration of about 0.025 to about 1.5% of the composition; EDTA at a concentration from about 0.01 mM to about 1.0 mM of the composition; Tris HC1 at a concentration from about 1 mM to about 100 mM of the composition; or Antifoam at a concentration of about 0.01% to about 2% of the composition. In some embodiments, the second opening comprises an incline having a slope of about 45°. In some embodiments, the second opening comprises an incline having a slope of about 3°. In some embodiments, one or more nucleic acid analytes from lysed pathogenic bacterium present in the biological sample bind to the substrate. In some embodiments, the one or more nucleic acid analytes bound to the substrate are separated from the lysis solution. In some embodiments, the one or more nucleic acid analytes bound to the substrate are eluted into the third channel comprising the elution solution. In some embodiments, the processing comprises an extraction of an analyte from the biological sample. In some embodiments, the processing comprises a nucleic acid extraction. In some embodiments, the nucleic acid comprises a DNA. In some embodiments, the nucleic acid comprises an RNA. In some embodiments, the processing comprises binding a plurality of nucleic acids to the substrate. In some embodiments, the processing further comprises eluting at least a portion of the bound plurality of nucleic acids into the elution solution. In some embodiments, the biological sample comprises a target sequence. In some embodiments, the target sequence is a nucleic acid sequence of a pathogenic bacterium. In some embodiments, the target sequence is a nucleic acid sequence of an acid-fast bacteria. In some embodiments, the target sequence is a nucleic acid sequence of Mycobacterium tuberculosis. In some embodiments, the target sequence comprises a conserved sequence within the Mycobacterium tuberculosis genome. In some embodiments, the target sequence comprises a mutated sequence within the Mycobacterium tuberculosis genome, that leads to antibiotic resistance. In some embodiments, the substrate is affixed to the second channel. In some embodiments, a detection of amplified target sequence determines the presence of a pathogenic bacterium in the biological sample. In someembodiments, a lack of detection of amplified target sequence determines the absence of a pathogenic bacterium in the biological sample. In some embodiments, detection of amplified target sequence determines the presence of Mycobacterium tuberculosis in the biological sample. In some embodiments, a lack of detection of amplified target sequence determines the absence of Mycobacterium tuberculosis in the biological sample.

[0016] The present disclosure provides a system for preparation of a nucleic acid from a biological sample, the system comprising a housing. In some embodiments, the housing comprises a substrate affixed to the housing. In some embodiments, the housing further comprises a port configured to receive the biological sample, wherein the port is configured to provide the biological sample to the substrate. In some embodiments, the port is further configured to receive a lysis solution. In some embodiments, when the biological sample is a pathogenic bacterium, the lysis solution or the enzymatic lysis solution comprises sodium hydroxide (NaOH) at a concentration of at least about 200 mM, and one or more of the following: triton-X 100 at a concentration of about 0.1% v / v to about 2% v / v of the composition; lysozyme at a concentration of about 10 mg / mL to about 150mg / mL of the composition; tween80 at a concentration of about 0.025 to about 1.5% of the composition; EDTA at a concentration from about 0.01 mM to about 1.0 mM of the composition; Tris HC1 at a concentration from about 1 mM to about 100 mM of the composition; or Antifoam at a concentration of about 0.01% to about 2% of the composition. In some embodiments, the biological sample comprises nucleic acid. In some embodiments, the nucleic acid comprises a DNA or an RNA. In some embodiments, the substrate is configured to bind a plurality of nucleic acids. In some embodiments, substrate comprises cellulose. In some embodiments, the lysis solution is a chemical lysis solution. In some embodiments, the chemical lysis solution comprises an alkaline lysis buffer solution. In some embodiments, the alkaline lysis buffer solution comprises sodium hydroxide or sodium acetate at a concentration of between about 0.2 M to about 2 M. In some embodiments, the alkaline lysis buffer solution comprises sodium hydroxide at a concentration of between about 0.5 M to about 1.2 M. In some embodiments, the alkaline lysis buffer solution comprises sodium hydroxide at a concentration of about 1.0 M. In some embodiments, the alkaline lysis buffer solution comprises a detergent. In some embodiments, the detergent comprises Triton-X 100 at a concentration of between about 0.5% to about 2.0% of the alkaline lysis buffer solution. In some embodiments, the detergent comprises Triton-X 100 at a concentration of about 1.5% of the alkaline lysis buffer solution. In some embodiments, the alkaline lysis buffer solution comprises an antifoam reagent at a concentration between about 0.01% to about 2.0% of thealkaline lysis buffer solution. In some embodiments, the chemical lysis solution further comprises a chelating agent, such as EDTA at a concentration of about 0.01 mM to about 1.0 mM. In some embodiments, the chemical lysis solution further comprises an enzymatic lysis solution. In some embodiments, the lysis solution is a chemical lysis solution. In some embodiments, the enzymatic lysis solution comprises lysozyme at a concentration of between about 10 mg / mL to about 150 mg / mL of the enzymatic lysis buffer solution. In some embodiments, the enzymatic lysis solution comprises a detergent, such as Tween80 at a concentration of between about 0.05% to about 0.5% of the enzymatic lysis buffer solution.In some embodiments, the lysis solution effectively lyses pathogenic bacterium present in the biological sample. In some embodiments, the effective lysis of the pathogenic bacterium does not require use of a mechanical lysis method. In some embodiments, the pathogenic bacterium present in the biological sample comprises one or more of Mycobacterium tuberculosis complex, Mycobacterium avium, Mycobacterium abscessus, Mycobacterium smegmatis, Streptococcus pyrogenes, Streptococcus pneumoniae, Francisella philomiragia, and Bacillus thuringiensis. In some embodiments, the pathogenic bacterium present in the biological sample comprises one or more species from Mycobacterium tuberculosis complex (MT BC), including but not limited to Mycobacterium tuberculosis, Mycobacterium africanum, Mycobacterium bovis, Mycobacterium orygis, and Mycobacterium canetti. In some embodiments, the pathogenic bacterium present in the biological sample comprises Mycobacterium tuberculosis. In some embodiments, the biological sample does not comprise a detectable amount of Mycobacterium tuberculosis . In some embodiments, effective lysis of pathogenic bacterium present in the biological sample occurs in less than about 30 minutes. In some embodiments, the biological sample is processed in about 30 minutes or less. In some embodiments, the system does not further comprise an actuator. In some embodiments, the system does not further comprise a centrifuge. In some embodiments, the system does not further comprise a vacuum. In some embodiments, the biological sample is a swab sample, such as oral swab, tongue swab, buccal swab, throat swab, nasal swab, wound swab, skin swab, vaginal swab, urethral swab, anal swab. In some embodiments, the biological sample is an oral swab sample. In some embodiments, the biological sample is a biological fluid. In some embodiments, the biological fluid is whole blood, serum, saliva, sputum, tears, lung lavage, cell lysates, menstrual blood, urine, processed swab samples, processed tissue samples, amniotic fluid, cerebrospinal fluid, tears, or semen. In some embodiments, the biological sample is a tissue sample. In some embodiments, the tissue sample is a skeletal tissue, a muscle tissue, a spleen tissue, an embedded tissue, or a liver tissue. In someembodiments, the biological sample is a bacteria culture.

[0017] The present disclosure provides a kit comprising any system as disclosed herein and instructions for use. In some embodiments, the instructions designate a protocol for use as a field kit. In some embodiments, the instructions designate a detection of a bacterial infection. In some embodiments, the bacterial infection is a pathogenic bacterium infection. In some embodiments, the bacterial infection is an acid-fast bacterial infection. In some embodiments, the bacterial infection is a tuberculosis-causing infection. In some embodiments, the bacterial infection is a Mycobacterium tuberculosis infection. In some embodiments, the instructions for use are written on an instruction card for isothermal, nucleic acid target sequence amplification. In some embodiments, the instructions for use are written on an instruction card for isothermal, real time nucleic acid target sequence amplification.

[0018] The present disclosure provides a method for processing a biological sample, the method comprising: coupling a biological sample to a first channel comprising a first opening; coupling the first opening of the first channel to a second opening of a second channel, thereby transferring the biological sample from the first channel to the second channel, wherein the second channel has a substrate coupled thereto; coupling the second opening of the second channel to a third opening of a third channel, wherein the third channel comprises an elution solution, and wherein the coupling of the second opening to the third opening transfers the elution solution to the second channel; and removing the elution solution from the second channel. In some embodiments, the first channel further comprises a lysis solution, wherein when said biological sample is a pathogenic bacterium said lysis solution comprises sodium hydroxide (NaOH) at a concentration of at least about 200 mM, and one or more of the following: triton-X 100 at a concentration of about 0.1% v / v to about 2% v / v of the composition; lysozyme at a concentration of about 10 mg / mL to about 150mg / mL of the composition; tween80 at a concentration of about 0.25% v / v to about 1.5% v / v of the composition; EDTA at a concentration from about 0.01 mM to about 1.0 mM of the composition; Tris HC1 at a concentration from about 1 mM to about 100 mM of the composition; or Antifoam at a concentration of about 0.01% v / v to about 2% v / v of the composition. In some embodiments, the second opening comprises an incline having a slope of about 45°. In some embodiments, the second opening comprises an incline having a slope of about 3°. In some embodiments, one or more nucleic acid analytes from lysed pathogenic bacterium present in the biological sample bind to the substrate. In some embodiments, the one or more nucleic acid analytes bound to the substrate are separated from the lysis solution.In some embodiments, the one or more nucleic acid analytes bound to the substrate are eluted into the third channel comprising the elution solution. In some embodiments, the processing comprises an extraction of an analyte from the biological sample. In some embodiments, the processing comprises a nucleic acid extraction. In some embodiments, the nucleic acid comprises a DNA. In some embodiments, the nucleic acid comprises an RNA. In some embodiments, the processing comprises binding a plurality of nucleic acids to the substrate. In some embodiments, the processing further comprises eluting at least a portion of the bound plurality of nucleic acids into the elution solution. In some embodiments, a detection of amplified extracted nucleic acids determines the presence or absence of a target sequence. In some embodiments, the target sequence is a nucleic acid sequence of a pathogenic bacterium. In some embodiments, the target sequence is a nucleic acid sequence of an acid-fast bacteria. In some embodiments, the target sequence is a nucleic acid sequence of Mycobacterium tuberculosis. In some embodiments, the target sequence comprises a conserved sequence within the Mycobacterium tuberculosis genome. In some embodiments, the target sequence comprises a mutated sequence within the Mycobacterium tuberculosis genome, that leads to antibiotic resistance. In some embodiments, the substrate is affixed to the second channel. In some embodiments, the method further comprises amplification of the extracted nucleic acids. In some embodiments, the amplification is performed via a quantitative polymerase chain reaction (qPCR), PCR, or isothermal amplification. In some embodiments, the isothermal amplification is RPA or ANINA. In some embodiments, the isothermal amplification is real time ANINA. In some embodiments, the amplification produces detectable amplified target sequence in less than about 30, 25, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, or 8 minutes following the start of the amplification reaction. In some embodiments, detection of amplified target sequence determines the presence of a pathogenic bacterium in the biological sample. In some embodiments, a lack of detection of amplified target sequence determines the absence of a pathogenic bacterium in the biological sample. In some embodiments, detection of amplified target sequence determines the presence of Mycobacterium tuberculosis in the biological sample. In some embodiments, a lack of detection of amplified target sequence determines the absence of Mycobacterium tuberculosis in the biological sample.

[0019] The present disclosure provides a method of processing a biological sample, the method comprising bringing the sample in contact with a lysis solution under conditions sufficient to lyse the biological sample in 30 minutes or less, wherein when said biological sample is a pathogenic bacterium, said lysis solution comprises sodium hydroxide (NaOH) ata concentration of at least about 200 mM, and one or more of the following: triton-X 100 at a concentration of about 0.1% v / v to about 2% v / v of the composition; lysozyme at a concentration of about 10 mg / mL to about 150mg / mL of the composition; tween80 at a concentration of about 0.025% v / v to about 1.5% v / v of the composition; EDTA at a concentration from about 0.01 mM to about 1.0 mM of the composition; Tris HC1 at a concentration from about 1 mM to about 100 mM of the composition; or Antifoam at a concentration of about 0.01% v / v to about 2% v / v of the composition. In some embodiments, the biological sample comprises nucleic acid. In some embodiments, the nucleic acid comprises a DNA or an RNA. In some embodiments, the substrate binds a plurality of nucleic acids. In some embodiments, substrate comprises cellulose. In some embodiments, the lysis solution is a chemical lysis solution. In some embodiments, the chemical lysis solution comprises an alkaline lysis buffer solution. In some embodiments, the alkaline lysis buffer solution comprises sodium hydroxide at a concentration of between about 0.2 M to about 2 M of the alkaline lysis buffer solution. In some embodiments, the alkaline lysis buffer solution comprises sodium hydroxide at a concentration of between about 0.5 M to about 1.2 M of the alkaline lysis buffer solution. In some embodiments, the alkaline lysis buffer solution comprises sodium hydroxide at a concentration of about 1 M of the alkaline lysis buffer solution. In some embodiments, the alkaline lysis buffer solution comprises a detergent. In some embodiments, the detergent comprises Triton-X 100 at a concentration of between about 0.5% to about 2.0% of the alkaline lysis buffer solution. In some embodiments, the detergent comprises Triton-X 100 at a concentration of about 1.5% of the alkaline lysis buffer solution. In some embodiments, the alkaline lysis buffer solution comprises an antifoam reagent at a concentration between about 0.01% to about 2.0% of the alkaline lysis buffer solution. In some embodiments, the lysis solution is an enzymatic lysis solution. In some embodiments, the enzymatic lysis solution comprises lysozyme at a concentration of between about 10 mg / mL to about 150 mg / mL of the enzymatic lysis buffer solution. In some embodiments, the enzymatic lysis solution comprises lysozyme at a concentration of about 50 mg / mL of the enzymatic lysis buffer solution. In some embodiments, the enzymatic lysis solution comprises a detergent. In some embodiments, the detergent comprises Tween80 at a concentration of between about 0.05% to about 0.5% of the enzymatic lysis buffer solution. In some embodiments, the detergent comprises Tween80 at a concentration of about 0.05% of the enzymatic lysis buffer solution. In some embodiments, the detergent further comprises Triton-X 100 at a concentration of about 0.05% of the enzymatic lysis buffer solution. In some embodiments, the lysis solutioncomprises Tris HC1 at a concentration of about 10 millimolar (mM) to about 100 mM of the composition. In some embodiments, the lysis solution comprises NaCl at a concentration of about 25 mM to about 500 mM of the composition. In some embodiments, the lysis solution comprises triton x-100 at a concentration of about 0.1% to about 5% of the composition. In some embodiments, the lysis solution comprises TCEP at a concentration of about 1 mM to about 100 mM of the composition. In some embodiments, Tris HC1 is at a concentration of about 25 mM of the composition. In some embodiments, NaCl is at a concentration of about 300 mM of the composition. In some embodiments, triton x-100 is at a concentration of about 1% of the composition. In some embodiments, TCEP is at a concentration of about 20 mM of the composition. In some embodiments, the lysis solution effectively lyses pathogenic bacterium present in the biological sample. In some embodiments, the effective lysis of the pathogenic bacterium does not require use of a mechanical lysis method. In some embodiments, the pathogenic bacterium present in the biological sample comprises one or more of Mycobacterium tuberculosis, Mycobacterium avium, Mycobacterium abscessus, Mycobacterium smegmatis, Francisella philomiragia, Yersinia enterocolitica, Bacillus thuringiensis, Pseudomonas aeruginosa, Moraxella catarrhalis, o Klebsiella pneumoniae. In some embodiments, the pathogenic bacterium present in the biological sample comprises Mycobacterium tuberculosis. In some embodiments, the biological sample does not comprise a detectable amount of Mycobacterium tuberculosis . In some embodiments, effective lysis of pathogenic bacterium present in the biological sample occurs in less than about 30 minutes. In some embodiments, the biological sample is processed in about 30 minutes or less. In some embodiments, the method does not further comprise an actuator, a centrifuge, or a vacuum. In some embodiments, the biological sample is a biological fluid. In some embodiments, the biological fluid is whole blood, serum, saliva, tears, lung lavage, cell lysates, menstrual blood, urine, processed tissue samples, amniotic fluid, cerebrospinal fluid, tears, saliva, or semen. In some embodiments, the biological sample is a tissue sample. In some embodiments, the tissue sample is a skeletal tissue, a muscle tissue, a spleen tissue, an embedded tissue, or a liver tissue. In some embodiments, the biological sample is a bacteria culture.

[0020] A system for processing a biological sample, the system comprising: a first channel comprising a first opening, wherein the first channel is configured to couple thereto a biological sample; a second channel comprising (i) a cellulose substrate coupled thereto and (ii) a second opening, wherein the second opening is configured to couple to the first opening, and wherein upon the coupling of the second opening to the first opening, thebiological sample is transferred from the first channel to the second channel; and a third channel comprising (i) an elution solution and (ii) a third opening, wherein the third opening is configured to couple to the second opening, and wherein upon the coupling of the second opening to the third opening, the elution solution is transferred from the third channel to the second channel. In some embodiments, the biological sample is processed in about 5 minutes or less. In some embodiments, the biological sample is processed in about 4 minutes or less. In some embodiments, the biological sample is processed in about 3 minutes or less. In some embodiments, the biological sample is processed in about 2 minutes or less. In some embodiments, the biological sample is processed in about 1 minute or less. In some embodiments, the system does not further comprise an actuator, a centrifuge, or a vacuum. In some embodiments, following a period of time, the elution solution is transferred from the second channel back into the third channel. In some embodiments, the biological sample is a biological fluid. In some embodiments, the biological fluid has a volume of less than about 50 mL. In some embodiments, the biological fluid has a volume of about 5 mL. In some embodiments, the biological fluid is whole blood, serum, saliva, tears, lung lavage, cell lysates, menstrual blood, urine, processed tissue samples, amniotic fluid, cerebrospinal fluid, tears, saliva, semen. In some embodiments, the biological sample is a tissue sample. In some embodiments, the tissue sample is a skeletal tissue, a muscle tissue, a spleen tissue, an embedded tissue, or a liver tissue. In some embodiments, the tissue sample is a shrimp hepatopancreas, a shrimp tail, and a shrimp pleopods. In some embodiments, the tissue sample has a mass of about 5 to about 200 milligrams (mg). In some embodiments, the tissue sample has a mass of at least about 50 mg. In some embodiments, the tissue sample has a mass of at least about 25 mg. In some embodiments, the biological sample is a mammalian sample. In some embodiments, the biological sample is a bacteria culture. In some embodiments, the biological sample comprises water. In some embodiments, the biological sample is a plant sample. In some embodiments, the first channel further comprises a lysis solution. In some embodiments, the lysis solution has a neutral pH. In some embodiments, the lysis solution has an acidic pH. In some embodiments, the lysis solution comprises guanidine hydrochloride, proteinase K, or both. In some embodiments, the lysis solution has a basic pH. In some embodiments, the lysis solution comprises sodium acetate, sodium chloride, sodium hydroxide, Tris HC1, SDS, sodium dodecyl, glucose, or any combination thereof. In some embodiments, the processing comprises an extraction of an analyte from the biological sample. In some embodiments, the processing comprises a nucleic acid extraction. In some embodiments, the nucleic acid comprises a DNA. In some embodiments, the nucleicacid comprises an RNA. In some embodiments, the processing comprises binding a plurality of nucleic acids to the cellulose substrate. In some embodiments, the processing further comprises eluting at least a portion of the bound plurality of nucleic acids into the elution solution. In some embodiments, the extracted nucleic acids are capable of being amplified. In some embodiments, the amplified extracted nucleic acids determine the presence or absence of a target sequence. In some embodiments, the target sequence is a nucleic acid sequence of a virus or a bacteria. In some embodiments, the virus is an African Swine Fever Virus, White Spot Syndrome Virus (WSSV), RSV, Influenza, or EBV. In some embodiments, the bacteria comprises a sexually transmitted infection-causing bacteria. In some embodiments, the sexually transmitted infection-causing bacteria is gonorrhea, chlamydia, or syphilis. In some embodiments, the target sequence is a DNA sequence. In some embodiments, the DNA sequence is related to a genetic trait. In some embodiments, the genetic trait is photic sneeze or alcohol flush. In some embodiments, the DNA sequence is mammalian gDNA. In some embodiments, the amplification is performed via a quantitative polymerase chain reaction (qPCR), PCR, or isothermal amplification. In some embodiments, the isothermal amplification is RPA or ANINA. In some embodiments, the amplified extracted nucleic acids have a QC value that is less than or almost equal to a CQ value of amplified nucleic acids extracted via centrifugation. In some embodiments, the extracted nucleic acids have an average yield of at least 150 ng / mg. In some embodiments, the extracted nucleic acids have a yield of about 350 ng / mg of tissue to about 1400 ng / mg of tissue. In some embodiments, the extracted nucleic acids have a 260 / 280 ratio of more than 1.4. In some embodiments, a connector is configured to couple the third channel to the second channel. In some embodiments, the system further comprises a dropper cap, wherein the first channel transfers the biological sample to the second channel through the dropper cap. In some embodiments, the dropper cap couples to the first channel. In some embodiments, the first channel is a vial. In some embodiments, the third channel is a vial. In some embodiments, the second channel is a bottle. In some embodiments, the cellulose substrate is affixed to the second channel. In some embodiments, the second channel comprises a single chamber. In some embodiments, the first channel or the second channel comprise a particulate filter having a pore size of greater than about 10 pm, and wherein the particulate filter is configured to retain particles when the biological sample is transferred from the first channel to the second channel. In some embodiments, either the first channel or second channel comprises an adapter, wherein the adapter, when in use, couples the first channel to the second channel. In some embodiments, the adapter comprises external treads. In some embodiments, either the firstchannel or the second channel comprises internal treads, wherein the internal treads, when in use, couple the first channel to the second channel. In some embodiments, either the first channel or the second channel comprises a flexible tubing, wherein the flexible tubing, when in use, couples the first channel to the second channel. In some embodiments, the water comprises wastewater, water derived from a pond, or water derived from aquarium. In some embodiments, the waste water is urine. In some embodiments, the first channel further comprises a filtration device. In some embodiments, the filtration device filters the biological sample prior to the transfer of the biological sample from the first channel to the second channel.

[0021] A system for preparation of a nucleic acid from a biological sample, the system comprising: a housing comprising: a cellulose substrate affixed to the housing; and a port, wherein the port is configured to receive the biological sample, and wherein the port is configured to provide the biological sample to the cellulose substrate. In some embodiments, the nucleic acid is prepared in about 5 minutes or less. In some embodiments, the nucleic acid is prepared in about 4 minutes or less. In some embodiments, the nucleic acid is prepared in about 3 minutes or less. In some embodiments, the nucleic acid is prepared in about 2 minutes or less. In some embodiments, the nucleic acid is prepared in about 1 minute or less. In some embodiments, the system does not further comprise an actuator, a centrifuge or a vacuum. In some embodiments, the biological sample is a biological fluid. In some embodiments, the biological fluid has a volume of less than about 50 mL. In some embodiments, the biological fluid is whole blood, serum, saliva, tears, lung lavage, cell lysates, menstrual blood, urine, processed tissue samples, amniotic fluid, cerebrospinal fluid, tears, saliva, semen. In some embodiments, the biological fluid has a volume of about 5 mL. In some embodiments, the biological sample is a tissue sample. In some embodiments, the tissue sample is a skeletal tissue, a muscle tissue, a spleen tissue, an embedded tissue, or a liver tissue. In some embodiments, the tissue sample is a shrimp hepatopancreas, a shrimp tail, and a shrimp pleopods. In some embodiments, the biological sample is a bacteria culture. In some embodiments, the biological sample comprises water. In some embodiments, the biological sample is a plant sample. In some embodiments, the tissue sample has a mass of about 5 to about 200 milligrams (mg). In some embodiments, the tissue sample has a mass of at least about 50 mg. In some embodiments, the tissue sample has a mass of at least about 25 mg. In some embodiments, the biological sample is a mammalian sample. In some embodiments, the port is further configured to receive a lysis solution. In some embodiments, the lysis solution has a neutral pH. In some embodiments, the lysis solution has an acidic pH.In some embodiments, the lysis solution comprises guanidine hydrochloride, proteinase K, or both. In some embodiments, the lysis solution has a basic pH. In some embodiments, the lysis solution comprises sodium acetate, sodium chloride, Tris HC1, SDS, sodium dodecyl, sodium hydroxide, glucose, or any combination thereof. In some embodiments, the preparation of the nucleic acid comprises an extraction of the nucleic acid from the biological sample. In some embodiments, the nucleic acid comprises a DNA. In some embodiments, the nucleic acid comprises an RNA. In some embodiments, the nucleic acid is capable of being amplified. In some embodiments, the amplification is a quantitative polymerase chain reaction (qPCR), PCR, or isothermal amplification. In some embodiments, the isothermal amplification is RPA or ANINA In some embodiments, the nucleic acid has a CQ value that is less than or almost equal to a CQ value of a nucleic acid extracted via centrifugation. In some embodiments, the nucleic acid has an average yield of at least 150 ng / mg. In some embodiments, the extracted nucleic acids have a yield of about 350 ng / mg of tissue to about 1400 ng / mg of tissue. In some embodiments, the extracted nucleic acids have a 260 / 280 ratio of more than 1.4 In some embodiments, a first channel comprising the biological sample is configured to transfer the biological sample to the port of the housing. In some embodiments, the first channel comprises a lysis solution. In some embodiments, the system further comprises a dropper cap, wherein, when in use, the first channel transfers the biological sample through the dropper cap to the port. In some embodiments, a connector is configured to couple a second channel to the port, wherein the second channel comprises an elution solution, wherein the coupling of the second channel to the port transfers the elution solution to and from the housing. In some embodiments, the first channel is a vial. In some embodiments, the second channel is a vial. In some embodiments, transferring the elution solution to and from the housing occurs in less than about 30 seconds. In some embodiments, the housing is a bottle. In some embodiments, the cellulose substrate remains affixed to the housing. In some embodiments, the housing comprises a single chamber. In some embodiments, the water comprises wastewater, water derived from a pond, or water derived from aquarium. In some embodiments, the waste water is urine. In some embodiments, the first channel further comprises a filtration device. In some embodiments, the filtration device filters the biological sample prior to the transfer of the biological sample from the first channel to the second channel.

[0022] A method for processing a biological sample, the method comprising: coupling a biological sample to a first channel comprising a first opening; coupling the first opening of the first channel to a second opening of a second channel, thereby transferring the biologicalsample from the first channel to the second channel, wherein the second channel has a cellulose substrate coupled thereto; and coupling the second opening of the second channel to a third opening of a third channel, wherein the third channel comprises an elution solution, and wherein the coupling of the second opening to the third opening transfers the elution solution to the second channel; and removing the elution solution from the second channel. In some embodiments, the biological sample is processed in about 5 minutes or less. In some embodiments, the biological sample is processed in about 4 minutes or less. In some embodiments, the biological sample is processed in about 3 minutes or less. In some embodiments, the biological sample is processed in about 2 minutes or less. In some embodiments, the biological sample is processed in about 1 minute or less. In some embodiments, the elution solution is transferred to and removed from the second channel in about 30 seconds or less. In some embodiments, the biological sample is transferred from the first channel to the second channel in about 30 seconds or less. In some embodiments, the method does not further comprise centrifuging the biological sample, vacuuming the biological sample, or subjecting the biological sample to an actuator. In some embodiments, the biological sample is a biological fluid. In some embodiments, the biological fluid is whole blood, serum, saliva, tears, lung lavage, cell lysates, menstrual blood, urine, processed tissue samples, amniotic fluid, cerebrospinal fluid, tears, saliva, or semen. In some embodiments, the biological fluid has a volume of less than about 50 mL. In some embodiments, the biological fluid has a volume of about 5 mL. In some embodiments, the biological sample is a tissue sample. In some embodiments, the tissue sample comprises a skeletal tissue, a muscle tissue, a spleen tissue, an embedded tissue, or a liver tissue. In some embodiments, the tissue sample is a shrimp hepatopancreas, a shrimp tail, and a shrimp pleopods. In some embodiments, the tissue sample has a mass of about 5 to about 200 milligrams (mg). In some embodiments, the tissue sample has a mass of about 50 mg. In some embodiments, the tissue sample has a mass of at least 25 mg. In some embodiments, the biological sample is a bacteria culture. In some embodiments, the biological sample comprises water. In some embodiments, the biological sample is a plant sample. In some embodiments, the biological sample is a mammalian sample. In some embodiments, the biological sample comprises a first portion, wherein the first portion comprises a nucleic acid, and wherein the first portion binds to the cellulose substrate. In some embodiments, the method further comprises removing a second portion of the biological sample from the second channel. In some embodiments, the method comprises eluting the nucleic acid from the first portion of the biological sample via the elution solution. In some embodiments, the elution solution has abasic pH. In some embodiments, the elution solution comprises salts. In some embodiments, the elution solution has a neutral pH. In some embodiments, the method further comprises removing the eluted nucleic acid analytes from second channel. In some embodiments, the method further comprises processing the eluted plurality of analytes. In some embodiments, the processing of the biological sample comprises extracting a nucleic acid from the biological sample. In some embodiments, the method further comprises amplifying the extracted nucleic acid. In some embodiments, the amplification comprises quantitative polymerase chain reaction (qPCR), PCR, or isothermal amplification. In some embodiments, the isothermal amplification is RPA or ANINA. In some embodiments, the amplified nucleic acid has a CQ value that is less than or almost equal to a CQ value of amplified nucleic acids extracted via centrifugation. In some embodiments, the method further comprises using the amplified nucleic acid to detect a presence or an absence of a target sequence. In some embodiments, the target sequence comprises a target sequence from a virus or a bacteria. In some embodiments, the bacteria comprises a sexually transmitted infection-causing bacteria. In some embodiments, the sexually transmitted infection-causing bacteria is gonorrhea, chlamydia, or syphilis. In some embodiments, the target sequence is a DNA sequence. In some embodiments, the DNA sequence is related to a genetic trait. In some embodiments, the genetic trait is photic sneeze or alcohol flush. In some embodiments, the DNA sequence is mammalian gDNA. In some embodiments, the target sequence is African Swine Fever Virus, White Spot Syndrome Virus (WSSV), RSV, Influenza, or EBV. In some embodiments, the extracted nucleic acids have an average yield of at least 150 ng / mg. In some embodiments, the extracted nucleic acids have a yield of about 350 ng / mg of tissue to about 1400 ng / mg of tissue. In some embodiments, the extracted nucleic acids have a 260 / 280 ratio of more than 1.4. In some embodiments, the cellulose substrate remains coupled to the second chamber. In some embodiments, the first channel further comprises a lysis solution. In some embodiments, the lysis solution has a neutral pH. In some embodiments, the lysis solution has an acidic pH. In some embodiments, the lysis solution comprises guanidine hydrochloride, proteinase K, or both. In some embodiments, the lysis solution has a basic pH. In some embodiments, the lysis solution comprises sodium acetate, Tris HC1, SDS, sodium dodecyl, sodium chloride, sodium hydroxide, glucose, or any combination thereof. In some embodiments, a gravitational force (i) transfers the biological sample from the first channel to the second channel and (ii) transfers the elution solution to the second channel. In some embodiments, the method further comprises transferring the biological sample from the first opening through a dropper cap to the second opening. In some embodiments, the methodfurther comprises homogenizing the biological sample in the first channel. In some embodiments, the biological sample is homogenized in less than about 30 seconds. In some embodiments, the method further comprises using a connector to couple the third opening and the second opening. In some embodiments, the first channel is a vial. In some embodiments, the third channel is a vial. In some embodiments, the second channel is a bottle. In some embodiments, the cellulose substrate is affixed to the second channel.

[0023] Another aspect of the present disclosure provides a non-transitory computer readable medium comprising machine executable code that, upon execution by one or more computer processors, implements any of the methods above or elsewhere herein.

[0024] Another aspect of the present disclosure provides a system comprising one or more computer processors and computer memory coupled thereto. The computer memory comprises machine executable code that, upon execution by the one or more computer processors, implements any of the methods above or elsewhere herein.BRIEF DESCRIPTIONS OF THE DRAWINGS

[0025] The novel features described herein are set forth with particularity in the appended claims. A better understanding of the features and advantages of the features described herein will be obtained by reference to the following detailed description that sets forth illustrative examples, in which the principles of the features described herein are utilized, and the accompanying drawings of which.

[0026] FIG. 1A depicts the average gDNA yield (ng / mg) for mouse skeletal muscle tissue from a study on three frozen mouse skeletal muscle tissue samples after processing.

[0027] FIG. IB shows the average gDNA quality (260 / 280) for mouse skeletal muscle tissue from a study on three frozen mouse skeletal muscle tissue samples after processing.

[0028] FIG. 1C shows the average Cqfor a target sequence in mouse GAPDH gene amplified with qPCR in the processed mouse skeletal muscle tissue samples.

[0029] FIG. 2A shows the average gDNA yield (ng / mg) for processed mouse skin tissue.

[0030] FIG. 2B shows the average gDNA quality (260 / 280) for mouse skin tissue.

[0031] FIG. 2C shows the average Cqfor a target sequence in mouse GAPDH gene amplified with qPCR in mouse skin tissue samples.

[0032] FIG. 3A shows the average gDNA concentration (ng / pL) for processed mouse spleen tissue.

[0033] FIG. 3B shows the average gDNA quality (260 / 280) for processed mouse spleen tissue.

[0034] FIG. 3C shows the average Cqfor a target sequence in mouse GAPDH gene amplified by qPCR in the processed mouse spleen tissue samples.

[0035] FIG. 4A shows the average gDNA yield (ng / mg) for processed mouse liver tissue.

[0036] FIG. 4B shows the average gDNA quality (260 / 280) for processed mouse liver tissue.

[0037] FIG. 4C shows the average Cqfor a target sequence in mouse GAPDH gene amplified in mouse liver tissue samples.

[0038] FIG. 5A shows the average gDNA concentration (ng / pL) for processed human skeletal tissue.

[0039] FIG. 5B shows the average gDNA quality (260 / 280) for processed human skeletal tissue.

[0040] FIG. 5C shows the average Cqfor a target sequence in human GAPDH gene amplified with qPCR in the processed human skeletal tissue samples.

[0041] FIG. 6A shows the average gDNA concentration (ng / pL) for processed embedded human tissue.

[0042] FIG. 6B shows the average gDNA quality (260 / 280) for processed embedded human tissue.

[0043] FIG. 6C shows the average gDNA yield (ng / mg) for processed embedded human tissue.

[0044] FIG. 6D shows the average Cqfor a target sequence in human GAPDH gene amplified with qPCR in the processed embedded human tissue samples.

[0045] FIG. 6E shows an agarose gel run for amplified nucleic acids in the processed embedded human tissue samples.

[0046] FIG. 7A shows elute concentrations (ng / pL) of processed samples of human saliva spiked with RSV infected cells.

[0047] FIG. 7B shows the average lysate and elute qualities (260 / 280) of processed samples of human saliva spiked with RSV infected cells.

[0048] FIG. 7C shows the average Cqfor a target sequence of the RSV genome that was amplified from processed samples of 1 mL of human saliva spiked with RSV infected cells.

[0049] FIG. 8A shows elute concentrations (ng / pL) of processed samples of human saliva spiked with RSV infected cells.

[0050] FIG. 8B shows the average lysate and elute qualities (260 / 280) of processed samples of human saliva spiked with RSV infected cells.

[0051] FIG. 8C shows the average Cqfor a target sequence of the RSV genome that wasamplified from processed samples of 1 mL of human saliva spiked with RSV infected cells.

[0052] FIG. 9A shows amplified nucleic acids run on a 2% agarose gel of a target sequence in RSV RNA from processed RSV-spiked human saliva sample.

[0053] FIG. 9B shows amplified nucleic acids run on a 2% agarose gel of a target sequence in RSV RNA from processed RSV-spiked human saliva sample.

[0054] FIG. 10A shows elute concentrations (ng / pL) of processed samples of human saliva spiked with RSV infected cells that were lysed with a lysis buffer containing SDS.

[0055] FIG. 10B shows the average lysate and elute qualities (260 / 280) of processed samples of human saliva spiked with RSV infected cells that were lysed with a lysis buffer containing SDS.

[0056] FIG. 10C shows the average Cqfor a target sequence of the RSV genome that was amplified from processed samples of 1 mL of human saliva spiked with RSV infected cells that were lysed with a lysis buffer containing SDS.

[0057] FIG. 11A shows elute concentrations (ng / pL) of processed samples of human saliva spiked with RSV infected cells that were lysed with a lysis buffer that was free of SDS.

[0058] FIG. 11B shows the average lysate and elute qualities (260 / 280) of processed samples of human saliva spiked with RSV infected cells that were lysed with a lysis buffer that was free of SDS.

[0059] FIG. 11C shows the average Cqfor a target sequence of the RSV genome that was amplified from processed samples of 1 mL of human saliva spiked with RSV infected cells that were lysed with a lysis buffer free of SDS.

[0060] FIG. 12A shows elute concentrations (ng / pL) of processed samples of human saliva spiked with RSV infected cells that were lysed with an alkaline lysis buffer.

[0061] FIG. 12B shows the average lysate and elute qualities (260 / 280) of processed samples of human saliva spiked with RSV infected cells that were lysed with an alkaline lysis buffer.

[0062] FIG. 12C shows the average Cqfor a target sequence of the RSV genome that was amplified from processed samples of 1 mL of human saliva spiked with RSV infected cells that were lysed with an alkaline lysis buffer.

[0063] FIG. 13A shows elute concentrations (ng / pL) of processed samples of human saliva spiked with RSV infected cells that were lysed with a lysis buffer that had its components doubled.

[0064] FIG. 13B shows the average lysate and elute qualities (260 / 280) of processed samples of human saliva spiked with RSV infected cells that were lysed with a lysis bufferthat had its components doubled.

[0065] FIG. 13C shows the average Cqfor a target sequence of the RS V genome that was amplified from processed samples of 1 mL of human saliva spiked with RSV infected cells that were lysed with a lysis buffer that had its components doubled.

[0066] FIG. 13D shows the sample from the previous figure run on a 2% agarose gel.

[0067] FIG. 14A shows elute RNA concentrations (ng / pL) of processed samples of human saliva spiked with RSV infected cells.

[0068] FIG. 14B shows the average RNA quality (260 / 280) of processed samples of human saliva spiked with RSV infected cells.

[0069] FIG. 14C shows the average Cqfor a target RNA sequence of the RSV genome that was amplified from processed samples of 1 mL of human saliva spiked with RSV infected cells.

[0070] FIG. 14D shows the samples from the previous figure run on a 2% agarose gel.

[0071] FIG. 15A shows elute RNA concentrations (ng / pL) of processed samples of human saliva spiked with RSV infected cells lysed with buffers comprising various concentrations of guanidine HC1.

[0072] FIG. 15B shows the average RNA quality (260 / 280) of processed samples of human saliva spiked with RSV infected cells lysed with buffers comprising various concentrations of guanidine HC1.

[0073] FIG. 15C shows the average Cqfor a target RNA sequence of the RSV genome that was amplified from processed samples of 1 mL of human saliva spiked with RSV infected cells lysed with buffers comprising various concentrations of guanidine HC1.

[0074] FIG. 15D shows the samples from the previous figure as run on a 2% agarose gel.

[0075] FIG. 16A shows elute RNA concentrations (ng / pL) of processed samples of human saliva spiked with RSV infected cells lysed with buffers comprising various concentrations of Tween 20.

[0076] FIG. 16B shows the average RNA quality (260 / 280) of processed samples of human saliva spiked with RSV infected cells lysed with buffers comprising various concentrations of Tween 20.

[0077] FIG. 16C shows the average Cqfor a target RNA sequence of the RSV genome that was amplified from processed samples of 1 mL of human saliva spiked with RSV infected cells lysed with buffers comprising various concentrations of Tween 20.

[0078] FIG. 16D shows the samples from the previous figure as run on a 2% agarose gel.

[0079] FIG. 17A shows elute RNA concentrations (ng / pL) of processed samples ofhuman saliva spiked with RSV infected cells lysed with buffers comprising various concentrations of Triton X.

[0080] FIG. 17B shows the average RNA quality (260 / 280) of processed samples of human saliva spiked with RSV infected cells lysed with buffers comprising various concentrations of Triton X.

[0081] FIG. 17C shows the average Cqfor a target RNA sequence of the RSV genome that was amplified from processed samples of 1 mL of human saliva spiked with RSV infected cells lysed with buffers comprising various concentrations of Triton X.

[0082] FIG. 17D shows the samples from the previous figure as run on a 2% agarose gel.

[0083] FIG. 18A shows elute RNA concentrations (ng / pL) of processed samples of human saliva spiked with RSV infected cells lysed with buffers comprising various concentrations of NaCl.

[0084] FIG. 18B shows the average RNA quality (260 / 280) of processed samples of human saliva spiked with RSV infected cells lysed with buffers comprising various concentrations of NaCl .

[0085] FIG. 18C shows the average Cqfor a target RNA sequence of the RSV genome that was amplified from processed samples of 1 mL of human saliva spiked with RSV infected cells lysed with buffers comprising various concentrations of NaCl.

[0086] FIG. 18D shows the samples from the previous figure as run on a 2% agarose gel.

[0087] FIG. 19A shows elute RNA concentrations (ng / pL) of processed samples of human saliva spiked with RSV infected cells lysed with buffers comprising various concentrations of guanidine thiocyanate.

[0088] FIG. 19B shows the average RNA quality (260 / 280) of processed samples of human saliva spiked with RSV infected cells lysed with buffers comprising various concentrations of guanidine thiocyanate.

[0089] FIG. 19C shows the average Cqfor a target RNA sequence of the RSV genome that was amplified from processed samples of 1 mL of human saliva spiked with RSV infected cells lysed with buffers comprising various concentrations of guanidine thiocyanate.

[0090] FIG. 20A shows elute RNA concentrations (ng / pL) of processed samples of human saliva spiked with RSV infected cells lysed with buffers comprising various concentrations of guanidine thiocyanate.

[0091] FIG. 20B shows the average RNA quality (260 / 280) of processed samples of human saliva spiked with RSV infected cells lysed with buffers comprising various concentrations of guanidine thiocyanate.

[0092] FIG. 20C shows the average Cqfor a target RNA sequence of the RS V genome that was amplified from processed samples of 1 mL of human saliva spiked with RSV infected cells lysed with buffers comprising various concentrations of guanidine thiocyanate.

[0093] FIG. 21A shows elute RNA concentrations (ng / pL) of processed samples of human saliva spiked with RSV infected cells lysed with buffers comprising various concentrations of DTT.

[0094] FIG. 21B shows the average RNA quality (260 / 280) of processed samples of human saliva spiked with RSV infected cells lysed with buffers comprising various concentrations of DTT.

[0095] FIG. 21C shows the average CQ for a target RNA sequence of the RSV genome that was amplified from processed samples of 1 mL of human saliva spiked with RSV infected cells lysed with buffers comprising various concentrations of DTT.

[0096] FIG. 22A shows elute RNA concentrations (ng / pL) of processed samples of human saliva spiked with RSV infected cells lysed with various buffers.

[0097] FIG. 22B shows the average RNA quality (260 / 280) of 1 mL samples of human saliva spiked with RSV infected cells lysed with various buffers.

[0098] FIG. 22C shows the average CQ for a target RNA sequence of the RSV genome that was amplified from processed samples of 1 mL of human saliva spiked with RSV infected cells lysed with various buffers.

[0099] FIG. 23 shows a kit for the processing and sequencing of a biological sample.

[0100] FIG. 24 shows a kit for the processing of a biological sample.

[0101] FIG. 25A shows a first channel receiving a lysis solution.

[0102] FIG. 25B shows a first channel receiving a biological sample.

[0103] FIG. 25C shows a first channel transferring a biological sample to a second channel.

[0104] FIG. 26A shows a first channel receiving and transferring a biological sample.

[0105] FIG. 26B shows a housing receiving an elution solution from a third channel and transferring an elute to the third channel.

[0106] FIG. 26C shows analytes being extracted from a biological sample.

[0107] FIG. 27 shows a first channel transferring dual-labelled WSSV target DNA amplicons into a second channel.

[0108] FIG. 28A shows a Lateral Flow Analysis (LFA) detecting an DNA amplicon.

[0109] FIG. 28B depicts a Lateral Flow Analysis being conducted on a processed sample.

[0110] FIG. 29 shows the results of a Lateral Flow Analysis conducted on a processed sample.

[0111] FIG. 30 shows a mean density analysis of the lateral flow analysis test line.

[0112] FIG. 31 shows the results of a molecular lateral flow analysis for human saliva samples spiked with EBV.

[0113] FIG. 32A shows the concentration (ng / pL) of nucleic acids extracted from various processed human biological samples.

[0114] FIG. 32B shows the quality (260 / 280) of nucleic acids extracted from various processed human biological samples.

[0115] FIG. 32C shows the average CQ for a target that was amplified from various processed human biological samples.

[0116] FIG. 33A shows a comparison of the quality (260 / 280) of DNA extracted from whole blood processed by a buffer containing sodium hydroxide and from whole blood processed by a buffer containing sodium acetate.

[0117] FIG. 33B shows a comparison of the CQ values for a target sequence of DNA extracted from whole blood processed by a buffer containing sodium hydroxide and from whole blood processed by a buffer containing sodium acetate.

[0118] FIG. 34A shows the gDNA yield (ng / mg) of WSSV extracted from shrimp muscle tissue and shrimp pleopod tissue.

[0119] FIG. 34B shows the gDNA quality (260 / 280) of WSSV extracted from shrimp muscle tissue and shrimp pleopod tissue.

[0120] FIG. 34C shows the normalized qPCR results (WSSV copies / pL) for shrimp muscle tissue at various time points post-infection.

[0121] FIG. 34D shows the normalized qPCR results (WSSV copies / pL) for shrimp pleopod tissue at various time points post-infection.

[0122] FIG. 35A shows the time required to process a shrimp muscle tissue sample, including grinding time.

[0123] FIG. 35B shows the average yield of gDNA (ng / mg) of shrimp muscle tissue samples processed by different methods.

[0124] FIG. 35C shows a comparison between the elute quality (260 / 280) ratio of gDNA extracted from processed shrimp muscle tissue samples.

[0125] FIG. 35D shows the qPCR detection accuracy of the presence of WSSV in a shrimp muscle tissue sample.

[0126] FIG. 36A shows the average qPCR analysis of shrimp 24 hours post-infection.

[0127] FIG. 36B shows a molecular lateral flow analysis strip results for infected shrimp samples 24-hours post infection.

[0128] FIG. 36C shows a mean density analysis of a lateral flow analysis test line.

[0129] FIG. 37A shows an average DNA concentration (ng / pL) obtained from samples of whole blood spiked with a various % volume of bacterial suspension.

[0130] FIG. 37B shows an average quality (260 / 280) of DNA obtained from samples of whole blood spiked with a various % volume of bacterial suspension.

[0131] FIG. 37C shows a lateral flow analysis of DNA from samples of whole human blood spiked with a various % volume of a bacterial suspension after the DNA was amplified by recombinase polymerase amplification.

[0132] FIG. 38A shows the average concentration (ng / pL) of extracted DNA from a simulated bodily fluid spiked with Neisseria gonorrhea.

[0133] FIG. 38B shows the average quality (260 / 280) of extracted DNA from a simulated bodily fluid spiked with Neisseria gonorrhea.

[0134] FIG. 38C shows the average CQ for a target sequence that was amplified from processed samples of simulated bodily fluid spiked with Neisseria gonorrhea.

[0135] FIG. 39A shows an absorbance plot for plasmid samples grown in E. Coli that were processed by an extraction kit disclosed herein (e.g., Seek Extraction kit).

[0136] FIG. 39B shows DNA purity results for pCRTOPO-4 DNA plasmids grown in E.Coli post DNA extraction using an extraction method disclosed herein (e.g., Seek Extraction) and Promega Wizard Extraction Kits.

[0137] FIG. 39C shows Full plasmid Nanopore sequencing from extracted materials without further cleanup after extraction (e.g., after Seek Extraction). FIG. 39D shows Full plasmid Nanopore sequencing from extracted materials without further cleanup after extraction from a control.

[0138] FIG. 40 shows Internal analysis for WSSV-infected shrimp showing (A) locations of shrimp samples collected, (B) time of extraction, (C) infection levels via qPCR, (D) UV- Vis 260 / 280 absorbance ratio, and (E) average yield.

[0139] FIG. 41 shows Animal Aquatic Health Lab (AAHL) analysis for WSSV-infected shrimp showing (A) total sample processing time (B) DNA yield normalized per mg of tissue, (C) UV-Vis 260 / 280 absorbance ratio, and (D) percentage accuracy for specificity and sensitivity derived from qPCR results.

[0140] FIG. 42 shows (A) Total extracted nucleic acid concentration and (B) Cq values from qPCR GAPDH detection for mouse skeletal muscle, spleen, skin, and liver tissuesamples.

[0141] FIG. 43 shows (A) Total extracted nucleic acid concentration and (B) Cq values for the qPCR detection of GAPDH for human whole blood, skeletal tissue, and FFPE tissue samples.

[0142] FIG. 44 shows (A) qRT-PCR detection of Respiratory Syncytial Virus (RSV) RNA extracted from 1 mL saliva samples spiked with 0, 5 or 10 uL of cultured cells containing active RSV infection. (B) qPCR detection of Neisseria gonorrhoeae (N.g) extracted from Simulated Cervical Mucus Fluid (SCMF) or Simulated Vaginal Fluid (SVF) spiked with serial dilutions of N.g bacterial culture.

[0143] FIG. 45 shows Native PAGE showing increasing amplification with increased elute concentration of gDNA template extracted from WSSV-infected shrimp.

[0144] FIG. 46A shows an extraction disclosed herein (e.g., Seek Extraction) with shrimp tissue.

[0145] FIG. 46B shows an extraction disclosed herein (e.g., Seek Extraction) with mouse tissue.

[0146] FIG. 46C shows an extraction disclosed herein (e.g., Seek Extraction) with human tissue.

[0147] FIG. 47 shows Full plasmid Nanopore sequencing from extracted materials without further cleanup after extraction (e.g., by Seek Extraction).

[0148] FIG. 48 depicts a workflow procedure for processing a biological sample using an extraction device as disclosed herein (e.g., Seeklt extraction device).

[0149] FIG. 49 depicts a workflow procedure for processing a biological sample using an extraction device as disclosed herein (e.g., Seeklt extraction device).

[0150] FIG. 50A depicts a housing comprising a port and a substrate and is an embodiment of an extraction device as disclosed herein (e.g., Seek It extraction device).

[0151] FIG. 50B depicts a workflow procedure for processing a biological sample.

[0152] FIG. 51 A shows a diagram of laboratory kit contents and equipment used for Mycobacterium tuberculosis (MTB) sample preparation.

[0153] FIG. 51B shows a diagram of laboratory kit contents for Mycobacterium tuberculosis (MTB) nucleic acid extraction.

[0154] FIG. 52A shows a diagram of laboratory kit contents and equipment used for Mycobacterium tuberculosis (MTB) sample preparation and preparation of H37Ra secondary culture.

[0155] FIG. 52B shows a diagram of a workflow for H37Ra cell dilution in preparationfor extraction (e.g., Seek Extraction) and molecular diagnostic testing.

[0156] FIG. 52C shows a graph of an MTB growth curve of MTB secondary culture according to hours post inoculation indicating robust secondary culture growth.

[0157] FIG. 52D shows an exemplary workflow diagram of steps for H37Ra lysis and extraction of DNA from MTB lysate.

[0158] FIG. 52E shows an exemplary workflow diagram of steps for nucleic acid elution and collection of nucleic acid using an elution buffer.

[0159] FIG. 53 shows an exemplary workflow diagram of steps for amplification (e.g., Seek Amplification).

[0160] FIG. 54A shows an exemplary instruction card including master mix recipe and workflow setup diagram for amplification (e.g., Seek Amplification).

[0161] FIG. 54B shows an exemplary instruction card including method steps for workflow setup for amplification (e.g., Seek Amplification).

[0162] FIG. 55A shows an exemplary instruction card including master mix recipe and workflow setup diagram for Real Time amplification (e.g., Seek Amplification).

[0163] FIG. 55B shows an exemplary instruction card including method steps for workflow setup for Real Time amplification (e.g., Seek Amplification) and analysis.

[0164]

[0165] FIG. 56 A shows a chart of average Ct values of MTB target genome from qPCR analysis of MTB extraction and processed eluates and positive lysis controls.

[0166] FIG. 56B shows a graph of qPCR amplification plots (HEX channel) for eluates and Bead-Beater positive lysis controls.

[0167] FIG. 57A shows a chart of Relative Amplification Yield of increasing MTB gDNA copies with increasing temperature for 30 min incubation using amplification (e.g., Seek Amplification).

[0168] FIG. 57B shows a chart of Relative Amplification Yield of gDNA at 25°C with Increasing Incubation Times using amplification (e.g., Seek Amplification).

[0169] FIG. 57C shows results of LFA detection of the MTB amplicon from amplification (e.g., Seek Amplification) of 106copies of MTB control gDNA amplified with a 30-minute 30°C incubation.

[0170] FIG. 58 shows a gel image of 10% TBE PAGE demonstrating similar amplification yields from MTB samples lysed by the processes disclosed herein (e.g., Chemical Lysis+Seek Extraction) and Bead-Beater templates.

[0171] FIG. 59A shows a chart of average Ct values from qPCR analysis of MTBextraction and processed eluates and positive lysis controls.

[0172] FIG. 59B shows an image of a gel of amplification (e.g., Seek Amplification) products on processed MTB eluates from processes described herein (e.g., Chemical Lysis+Seek Extraction) and Bead-Beater processed eluates.

[0173] FIG. 60A shows a chart of average Ct values from qPCR analysis of MTB extraction and processed eluates and positive lysis controls testing differing amount of detergent within a chemical lysis buffer.

[0174] FIG. 60B shows an image of a gel of amplification (e.g., Seek Amplification) products of MTB extraction and processed eluates and positive lysis controls testing differing amount of detergent within a chemical lysis buffer.

[0175] FIG. 60C shows a chart of average relative mean density of amplification (e.g., Seek Amplification) products of MTB extraction and processed eluates and positive lysis controls testing differing amount of detergent within a chemical lysis buffer.

[0176] FIG. 61 A shows mean density analysis graphs of PAGE gels for optimized and POC-compatible nasal swab lysis buffer (LB58) significantly outperformed the previously optimized nasal swab lysis buffer (LB55) in the Seeklt process (Extraction + Amplification +mLFA) for both RSV and H1N1 spiked nasal swab samples.

[0177] FIG. 61B shows mean density analysis graphs of mLFA strips for optimized and POC-compatible nasal swab lysis buffer (LB58) significantly outperformed the previously optimized nasal swab lysis buffer (LB55) in the Seeklt process (Extraction + Amplification +mLFA) for both RSV and H1N1 spiked nasal swab samples.

[0178] FIG. 61C shows representative PAGE (FIG. 61 A) and mLFA (FIG. 61B) images from (i) RSV-spiked swab experiment and (ii) HINl-spiked swab experiment.

[0179] FIG. 62A shows a chart of average Ct values from qPCR analysis of MTB extraction and processed eluates and positive lysis controls testing differing users operating the same protocol to demonstrate extraction reproducibility.

[0180] FIG. 62B shows an image of a gel of amplification (e.g., Seek Amplification) products of MTB extraction and processed eluates and positive lysis controls testing differing users operating the same protocol to demonstrate extraction reproducibility.

[0181] FIG. 63 shows a workflow diagram of steps for Real Time amplification (e.g., Seek Amplification).

[0182] FIG. 64A shows a graph of intercalating dye-based Real Time amplification (e.g., Seek Amplification) fluorescence plots.

[0183] FIG. 64B shows a graph of qPCR amplification fluorescence plots.

[0184] FIG. 64C shows a chart of MTB genomic RNA quantification of MTB samples using Real Time amplification (e.g., Seek Amplification) and qPCR amplification.

[0185] FIG. 64D shows a chart of time to detection in minutes of MTB samples using Real Time amplification (e.g., Seek Amplification) and qPCR amplification.

[0186] FIG. 65A - FIG. 65D show results from amplification (e.g., Seek Amplification) of MTB gDNA standards at various conditions and calculations of limit of detection (LOD). FIG. 65A shows an image of a representative 10% TBE PAGE, post-stained gel showing amplification (e.g., Seek Amplification) of MTB gDNA standards at 30°C, reacted for 30 minutes. FIG. 65B shows a chart of mean density analysis of MTB amplicon bands shown in FIG. 65A. FIG. 65C shows an image of a representative 10% TBE PAGE, post-stained gel showing amplification (e.g., Seek Amplification) of MTB gDNA standards at 35°C, reacted for 30 minutes. FIG. 65D shows a chart of mean density analysis of MTB amplicon bands shown in FIG. 65D.

[0187] FIG. 66A - FIG. 66B show results from quantitative amplification (e.g., Seek Amplification) of MTB gDNA standards. FIG. 66A shows an amplification plot of MTB genomic standards using quantitative ANINA (qANINA). FIG. 66B shows a calculated standard curve of MTB genomic standards using qANINA.

[0188] FIG. 67A - FIG. 67E show results from control MTB lysis protocols used to analyze sample quality and to calculate lysis efficiency. FIG. 67A shows a flow chart diagram of an MTB contrived sample preparation process tested. FIG. 67B shows a calculated growth curve of MTB secondary culture, measured by OD600 values by hours post inoculation. FIG. 67C shows a flow chart diagram of MTB contrived sample control preparation. FIG. 67D shows a chart of qPCR amplification and detection analysis of MTB contrived samples. FIG. 67E shows a chart comparing sample lysis efficiency of control samples (Non-treated, a negative control sample, and Heat-treated, a heat treatment lysate) versus to MTB lysis gold standard control using heat treatment + Bead-beater lysis (BB-L).

[0189] FIG. 68A - FIG. 68D show results of extraction, such as Seek Extraction, efficiency and amplification (e.g., Seek Amplification) of MTB contrived samples. FIG. 68A shows a flow chart diagram of an MTB contrived sample processed using an extraction device and extraction method, such as Seek extraction device and Seek extraction method. FIG. 68B shows a flow chart diagram illustrating steps for <=2 minute processing of any MTB sample using an extraction system, such as Seek extraction system. FIG. 68C shows a chart of extraction efficiency of MTB gDNA from MTB contrived samples. FIG. 68D shows a representative 10% TBE native PAGE gel image showing amplification (e.g., SeekAmplification) at 35 °C, reacted for 30 minutes and successful amplification of MTB gDNA target amplicon in samples containing human matrix.

[0190] FIG. 69A - FIG. 69G show results from chemical lysis (e.g., Seek chemical lysis), extraction (e.g., Seek Extraction), and amplification (e.g., Seek Amplification) of MTB contrived samples. FIG. 69A shows a flow chart diagram of a 30 minute multi-step mechanical lysis system requiring instruments, power and lab skills versus a 15 minute, 1- step MTB lysis (e.g., Seek MTB lysis) and extraction system using chemical lysis with no instruments, no power, and requiring no specific lab skills. FIG. 69B shows a chart of qPCR results comparing MTB chemical lysis (e.g., Seek MTB chemical lysis) and extraction (Chem-E) to the MTB lysis gold standard (BB-E). FIG. 69C shows a flow chart diagram of a 30 minute multi-step mechanical lysis system requiring instruments, power and lab skills, followed by extraction (e.g., Seek extraction), and amplification (e.g., Seek Amplification) and detection using a molecular lateral flow assay (mLFA) versus a 15 minute, l-step MTB lysis (e.g., Seek MTB lysis) and extraction system using chemical lysis with no instruments, no power, and requiring no specific lab skills, followed by extraction (e.g., Seek extraction), and amplification (e.g., Seek Amplification) and detection using a molecular lateral flow assay (mLFA). FIG. 69D shows a chart of PAGE detection results of MTB amplicons shown as MTB amplicon mean density relative to no template control (NTC). FIG. 69E shows a chart of mLFA detection results of MTB amplicons shown as mLFA test line mean density relative to no template control (NTC). FIG. 69F shows an image of PAGE analysis of amplification (e.g., Seek Amplification) at 35°C, reacted for 30 minutes and used to calculate the values in FIG. 69D. FIG. 69G shows an image of LFA detection post amplification (e.g., Seek Amplification) at 35°C, reacted for 30 minutes and used to calculate the values in FIG.69E.

[0191] FIG. 70A - FIG. 70C shows results of a real time amplification method (qANINA or qSeeklt) used for quantification of MTB in contrived samples. FIG. 70A shows a flow chart diagram of control samples prepared by various lysis systems compared to MTB Lysis + Extraction system disclosed herein (e.g., Seek MTB lysis). Samples were treated via real-time amplification (e.g., Seek Amplification) (qANINA. FIG. 70B show a chart of detection time of processed MTB samples using qANINA. FIG. 70C show a chart of quantification of MTB copies in processed MTB samples using qANINA.

[0192] FIG. 71A - FIG. 71C shows results from PCR spin column clean up of chemically lysed MTB contrived samples (using methods described herein) analyzed by qPCR for comparison to extraction (e.g., Seek extraction) and qANINA quantificationresults. FIG. 71A shows a flow chart diagram of control samples prepared by various lysis systems compared to MTB Lysis (e.g., Seek MTB lysis). Lysed samples undergo PCR spin column clean up and qPCR. FIG. 71B shows a chart of qPCR detection of processed MTB samples. FIG. 71C shows a chart of qPCR quantification of processed MTB samples.

[0193] FIG. 72A - FIG. 72D show results testing chemical lysis efficiency calculated by two parallel methods of sample extract! on / clean up and amplification. FIG. 72A shows a flow chart diagram comparing lysis method and extract! on / clean up method by either qANINA or qPCR. FIG. 72B shows a chart of qANINA detection time of processed MTB samples. FIG. 72C shows a chart of qPCR detection as average Ct values of processed MTB samples. FIG. 72D shows a chart of MTB lysis efficiency of chemical lysis buffer (e.g., Seek chemical lysis buffer) verified by qANINA and by qPCR.

[0194] FIG. 73A show steps for processing MTB-suspected samples at Point-of-Care within an exemplary instruction card for MTB extraction (e.g., Seek Extraction).

[0195] FIG. 73B show steps for processing and detection of MTB-suspected samples at Point-of-Care within an exemplary instruction card for MTB methods disclosed herein (e.g., Seeklt).

[0196] FIG. 74A shows Lateral Flow Analysis (LFA) strips of MTB amplicons.

[0197] FIG. 74B depicts a mean density analysis graph showing specific amplification (e.g., Seek Amplification) detection on mLFA strips.

[0198] FIG. 75 depicts a housing comprising a port, a substrate, a partially rounded bottom, external threads, exit radii, an incoming edge, and an outgoing edge.

[0199] FIG. 76A depicts nanophotometer readings of the concentration of sample eluates from devices disclosed herein (e.g., System z (v8)) compared to earlier device prototypes (e.g., v3 and System y.3 (v7.3)).

[0200] FIG. 76B depicts qPCR analysis to detect human GAPDH gene in blood extraction eluates from devices disclosed herein (e.g., System z (v8)) compared to earlier device prototypes (e.g., v3 and System y.3 (v7.3)).

[0201] FIG. 77A shows a PAGE gel results of amplification (e.g., Seek Amplification) samples, showing optimized nasal swab lysis buffer outperforms tissue lysis buffer with lysis and extraction of RSV RNA and is compatible with amplification (e.g., Seek Amplification).

[0202] FIG. 77B depicts the mean density analysis of LFA test line showing successful LFA detection of amplified RSV RNA extracted from RSV virions using optimized nasal swab lysis buffer and extraction devices disclosed herein (e.g., Seek extraction device).

[0203] FIG. 78A shows a PAGE gel results of amplification (e.g., Seek Amplification)samples showing that RSV-spiked nasal swab samples can be successfully lysed, extracted and amplified using tools disclosed herein (e.g., Seeklt Tools, such as Seek Extraction Device and Seek Amplification), and that Nasal Swab Lysis Buffer treatment effectively lyses the RSV virions in presence of human nasal swab matrix.

[0204] FIG. 78B depicts a mean density analysis of LFA test line showing successful LFA detection of amplified RSV RNA extracted from RSV-spiked nasal swabs using nasal swab lysis buffer and devices disclosed herein (e.g., Seek extraction device).

[0205] FIG. 79A shows a PAGE gel results of amplification (e.g., Seek Amplification) samples showing that H1N1 -spiked buffer can be successfully and reproducibly lysed, extracted and amplified using tools disclosed herein (e.g., Seeklt Tools, such as Seek Extraction Device and Seek Amplification), and that nasal swab lysis buffer effectively lyses H1N1 virions compared to the no treatment samples.

[0206] FIG. 79B depicts a mean density analysis of LFA test line showing successful LFA detection of amplified H1N1 RNA extracted from H1N1 virions using optimized nasal swab lysis buffer and devices disclosed herein (e.g., Seek extraction device).

[0207] FIG. 80 shows a PAGE gel results of amplification (e.g., Seek Amplification) samples showing that H1N1 -spiked nasal swab matrix can be successfully and reproducibly lysed, extracted and amplified using tools disclosed herein (e.g., Seeklt Tools, such as Seek Extraction Device and Seek Amplification).

[0208] FIG. 81 depicts different versions of extraction devices (e.g., Seek Extraction Device, System z (v8) disclosed herein, previous version System y (v7), and subversions of System z disclosed herein (e.g., v8.6))

[0209] FIG. 82 shows extraction yield from nanophotometer readings and eluate qualities (260 / 280 ratios) of the sample eluates from devices disclosed herein comprising an incoming edge with a slope (e.g., System z.6 (v8.6); see FIG. 75) compared to devices disclosed herein that do not comprise an incoming edge with a slope (e.g., System z.3 (v8.3)). Also depicted are qPCR results detecting Ng-2e region of the sample eluates from devices disclosed herein comprising an incoming edge with a slope (e.g., v8.6; see FIG. 75) compared to devices disclosed herein that do not comprise an incoming edge with a slope (e.g., v8.3), PAGE gel showing detected Ng amplicons, and mLFA showing detected Ng amplicons. Commercial kit extracted Ng sample was used at positive template control (PTC) and water is used as NTC.

[0210] FIG. 83A shows a mean density analysis of PAGE gel results, showing LB58- lysed RSV-spiked nasal swab samples processed with devices disclosed herein demonstrating the highest amplification yield for amplification (Seek Amplification).

[0211] FIG. 83B shows RT-qPCR analysis showing that LB58-lysed RSV-spiked nasal swab samples led to extraction of higher copies of qPCR-detectable RSV RNA.

[0212] FIG. 84A shows a PAGE gel of RSV-spiked nasal swab samples treated with LB58 and processed with an extraction device disclosed herein (Seek Extraction device) showed the highest yield with amplification (Seek Amplification) than the other tested buffers.

[0213] FIG. 84B shows mean density analysis graph, showing RSV-spiked nasal swab samples treated with LB58 and processed with an extraction device disclosed herein (Seek Extraction device) showed the highest yield with amplification (Seek Amplification) than the other tested buffers.

[0214] FIG. 84C shows mean density analysis of mLFA test line showing significantly higher LFA detection of amplified RSV RNA extracted from RSV-spiked nasal swabs using LB58 and an extraction device disclosed herein (Seek Extraction device).

[0215] FIG. 84D shows RT-qPCR analysis showing that LB58-lysed RSV-spiked nasal swab samples led to extraction of higher copies of qPCR-detectable RSV RNA.

[0216] FIG. 85 depicts a housing (e.g., second channel) comprising a port (or second opening), a substrate, a partially rounded bottom, external threads, exit radii, an incoming edge, and an outgoing edge.

[0217] FIG. 86 depicts a cylindrical housing comprising a port (or second opening), a substrate wrapped around the surface of the cylindrical housing, external threads, exit radii, and an outgoing angle.

[0218] FIG. 87 shows a non-limiting example of a WSSV field kit contents (e.g., SeekIT Field kit) including devices disclosed herein (e.g., version 10 Seek Extraction device).

[0219] FIG. 88 shows a non-limiting example of WSSV field kit process (e.g., SeekIT Field kit) using devices disclosed herein (e.g., version 10 Seek Extraction device).

[0220] FIG. 89 shows a non-limiting example of an extraction protocol for field kit process (e.g., SeekIT Field kit) using devices disclosed herein (e.g., version 10 Seek Extraction device).

[0221] FIG. 90 shows a non-limiting example of an amplification and detection protocol for WSSV field kit process (e.g., SeekIT Field kit).

[0222] FIG. 91 shows WSSV amplicons from WSSV field kit process (e.g., SeekIT Field kit) using devices disclosed herein (e.g., version 10 Seek Extraction device) visualized on mLFA strips.

[0223] FIG. 92 shows graphs comparing the results of WSSV field kit process (e.g.,SeekIT Field kit) using devices disclosed herein (e.g., version 10 Seek Extraction device) and a AAHL lab process for detection of WSSV.

[0224] FIG. 93 shows the results of WSSV-Infected shrimp tissue processed using the devices disclosed herein (e.g., Seek Extraction device v8.6.2 or vlO) with no variation in steps and similar binding membrane size. 6 replicates of ~50 mg tissue were used and no difference in steps were noted. Processed DNA was measured on Tecan spectrophotometer for assessing extracted DNA yield (left bar plot) and quality (middle bar plot). qPCR analysis was carried out to detect the number of WSSV copies extracted from each sample (right bar plot).DETAILED DESCRIPTIONOVERVIEW

[0225] Nucleic acid detection at point-of-care is a specific and sensitive diagnostic technology that can help diagnose infectious diseases, cancer, antibiotic-resistant bacteria, and other illness. Recognized herein is a need for rapid nucleic acid extraction from a biological sample, wherein the extracted nucleic acids can be further processed to produce a diagnosis. Recognized herein are systems and methods which provide for rapidly extracting nucleic acids from a biological sample for additional processing.

[0226] The present disclosure provides systems, methods and kits for processing a biological sample. For instance, biological samples as described herein may comprise nucleic acids. Recognized herein is a need for processing a nucleic acid molecule that overcomes current hurdles in the field, for instance the aforementioned technical problems.

[0227] Recognized herein is a need for an isothermal cost-effective nucleic acid amplification technology (NAAT) that specifically amplifies single-stranded and doublestranded nucleic acid target sequence already bound to detection probe in reaction. Furthermore, recognized herein is a need for a method that does not require thermal melting and can be done in a point-of-need setting without requiring access to an incubator or power source.

[0228] The present disclosure provides systems and methods for extraction, isolation, amplification, and / or detection of a target nucleic acid sequence. The present disclosure provides simplified and streamlined sample processing, such as extraction, isolation, amplification, and detection of a target nucleic acid sequence. For instance, the methods, devices, systems, and kits disclosed herein can be useful as molecular diagnostic technologies configured for deployment in field or true point-of-care (PoC) scenarios, instrument-freescenarios, use by anyone, deployed anywhere, and / or easily configured for any disease target. For instance, the methods, devices, systems, and kits disclosed herein can be useful as molecular diagnostic technologies configured for deployment in field or in near point-of-need (PON) scenarios, use with low to medium training, deployed anywhere, with rapid and sensitivity results, and / or easily configured for any disease target. The present disclosure can also be understood more readily by reference to the following detailed description of the disclosure and the Examples included therein.

[0229] The systems or devices herein may further comprise a coupler fluidly connected to the isolation system (e.g., isolation chamber). The coupler may comprise an opening to the isolation system (e.g., isolation chamber) and is configured to engage a means for preventing access to the isolation system (e.g., isolation chamber). For example, the coupler may be configured to engage a cap, a seal, a plug, or a vial so as to prevent access to the isolation system (e.g., an isolation chamber).

[0230] The present disclosure also provides a simplified and streamlined sample processing methods, devices, systems, and / or kits capable of extracting nucleic acids, such as genomic nucleic acid (gNA) (e.g., genomic DNA or RNA), in high concentration while minimizing protein interference and other contaminants that could disrupt amplification and detection processes. The sample processing can also incorporate isothermal (e.g., ambient temperature) amplification and detection of target nucleic acids. This disclosed sample processing can refer to Seek Extraction or Seeklt Extraction, among other extraction methods, systems, devices and / or kits disclosed herein. Similarly, Seek Extraction, Seeklt Extraction, and similar language can refer to any of the extraction methods, devices, systems, and / or kits disclosed herein.SYSTEMS

[0231] This disclosure provides methods, devices, systems, and / or kits for processing a biological sample. For instance, the present disclosure provides an innovative sample-to- answer molecular detection platform that includes DNA extraction, amplification and detection platform which overcomes the limitations of existing molecular diagnostics. Examples of limitations that may be overcome by the methods, systems and kits of the present disclosure include equipment requirements, reliance on trained technicians, temperature controls, complex experiment design, incompatibility with developing technology, etc. The sample-to-answer system described herein, can refer to Seeklt system or Seeklt molecular diagnostics platform, among other extraction / amplification / detectionmethods, systems, devices and / or kits disclosed herein. Similarly, Seeklt system or Seeklt molecular diagnostics platform, and similar language can refer to any of the methods, devices, systems, and / or kits disclosed herein. The sample-to-answer systems disclosed herein incorporate a sample processing system, as described in this disclosure (e.g., Seeklt Extraction or Seek Extraction) with isothermal (e.g., ambient temperature) amplification described in this disclosure (e.g., Seeklt Amplification or Seek Amplification), and incorporate detection of target nucleic acids as disclosed herein. The amplification system can further incorporate the primers and probe designed fot Annexing Isothermal Nucleotide Amplification (ANINA). This system is capable of working across a variety of sample types and can be easily adapted to detect or screen a wide variety of diseases or conditions. Its versatility make it particularly suited for Point of Care, or non-laboratory applications, and readily deployable to wherever the user is located.

[0232] The present disclosure provides a system of processing a nucleic acid from a biological sample. In some embodiments, the system comprises a first channel comprising a first opening, wherein said first channel is configured to couple thereto a biological sample. In some embodiments, the system comprises a second channel comprising: (i) a cellulose substrate coupled thereto; and (ii) a second opening. In some embodiments, the second opening comprises an incline having a slope. In some embodiments, upon a coupling of the second opening to the first opening, the biological sample is transferred from the first channel to the second channel. In some embodiments, the system comprises a third channel comprising: (i) an elution solution; and (ii) a third opening, wherein upon a coupling of the second opening to the third opening. In some embodiments, the elution solution is transferred from the third channel to the second channel. In some embodiments, the system comprises a housing comprising a cellulose substrate coupled to the housing. In some embodiments, the system comprises a port configured to (i) receive the biological sample and (ii) provide the biological sample to the cellulose substrate. In some embodiments, the port comprises an incline having a slope of about 1° to about 50°. In some embodiments, the second opening comprises an incline having a slope of about 1° to about 50°. In some embodiments, the cellulose substrate has a surface area of about 0.1 to about 1.7 square inches (in2). In some embodiments, the cellulose substrate has a surface area of about 0.6 to about 0.7 in2. In some embodiments, the cellulose substrate has a surface area of about 0.4 to about 0.5 in2. In some embodiments, the system comprises binding unit configured to bind to the nucleic acid. In some embodiments, the system comprises an amplification unit configured to amplify the nucleic acid of the lysate. In some embodiments, the amplification unit does not comprise athermocycler or incubator. In some embodiments, the amplifying is performed using an annexing probe. In some embodiments, the system further comprises an elution unit comprising an elution buffer. In some embodiments, the amplifying is performed using two or more primers.

[0233] The present disclosure features devices, systems, compositions, and methods for processing a nucleic acid molecule. A nucleic acid molecule can be isolated, amplified, and / or detected. Methods and / or systems as described herein may comprise isolating singlestranded and / or double-stranded nucleic acid molecules, such as the exemplary devices, systems, compositions, and methods depicted in the figures disclosed herein. Methods and / or systems as described herein may comprise amplifying single-stranded and / or double-stranded amplicons comprising a target sequence, such as the exemplary devices, systems, compositions, and methods depicted in the figures disclosed herein. Methods and / or systems as described herein may comprise detecting single-stranded and / or double-stranded amplicons comprising a target sequence, such as the exemplary devices, systems, compositions, and methods depicted in the figures disclosed herein. In aspects described herein, are composition, primer systems, and methods useful for isothermal (e.g., ambient temperature) nucleotide amplification.

[0234] Without wishing to limit the present invention to any theory or mechanism, it is believed that aspects of the present invention are advantageous. For example, the configuration described herein may provide rapid (e.g., less than 20 minutes), user-friendly, affordable, portable, enclosed, equipment-free (e.g., no centrifuge) devices and systems that are able to process multiple sample types and perform multiple test types. Further, configurations of the present invention can provide for physical separation of contaminants (e.g., lysis buffer debris). For example, the systems and devices may be configured to use combinations of filtration components to physically separate contaminants from the sample instead of reagents. Additionally, the use of open channels (e.g., tubes) between chamber and / or vials described herein advantageously allows for less force to be required to move liquid around the system or device. Furthermore, the present invention provides both positive and negative pressure within the systems and devices described herein to allow for fluid to flow in a continuous circuit. None of the presently known prior references or work has the unique inventive technical feature of the present invention.

[0235] The present disclosure provides a kit comprising (i) any one of the systems as disclosed herein and (ii) instructions for use. In some embodiments, the instructions designate a treatment of a subject in need thereof. In some embodiments, the instructions designate atreatment of a viral infection. In some embodiments, the instructions designate a treatment of RSV. In some embodiments, the instructions designate a treatment of White Spot Syndrome Virus (WSSV). In some embodiments, the instructions designate a treatment of a bacterial infection. In some embodiments, the instructions designate a treatment of a Neisseria gonorrhoeae infection.

[0236] Any feature or combination of features described herein are included within the scope of the present invention provided that the features included in any such combination are not mutually inconsistent as will be apparent from the context, this specification, and the knowledge of one of ordinary skills in the art. Additional advantages and aspects of the present invention are apparent in the following detailed description and claims.

[0237] An additional aspect of the present disclosure provides systems and methods comprising a first channel. In some embodiments, a first channel comprises a first opening. In some embodiments, a first channel comprises a biological sample as described herein. In some embodiments, a first channel receives a biological sample. In some embodiments, the first channel receives, through the first opening, a biological sample. Suitable channels include, but are not limited to, beakers, bottles, burettes, containers, cylinders, vials, tubes, and any other channel.

[0238] In some embodiments, a housing comprises the second channel. In some embodiments, the housing comprises a port. In some embodiments, the port comprises a second opening. For instance, as depicted in FIG. 50A, housing 3000 may comprise a port 3001 and a binding chamber 3002 which comprises a cellulose substrate 3003. The port can also comprise a connector 3004, such as to connect the housing to a channel.

[0239] In some embodiments, the system comprises a particulate filter. In some embodiments, the first channel comprises a particulate filter. In some embodiments, the particulate filter may filter a biological sample. In some embodiments, the particulate filter may filter a biological sample prior to a providing of the biological sample to the first channel. In some embodiments, the particulate filter may filter a biological sample prior to a providing of the biological sample to the system. In some embodiments, a particulate filter has a pore size of about 1 pm to about 500 pm. In some embodiments, a particulate filter has a pore size of about 1 pm to about 2 pm, about 1 pm to about 5 pm, about 1 pm to about 10 pm, about 1 pm to about 25 pm, about 1 pm to about 50 pm, about 1 pm to about 100 pm, about 1 pm to about 200 pm, about 1 pm to about 300 pm, about 1 pm to about 400 pm, about 1 pm to about 500 pm, about 2 pm to about 5 pm, about 2 pm to about 10 pm, about 2 pm to about 25 pm, about 2 pm to about 50 pm, about 2 pm to about 100 pm, about 2 pm toabout 200 pm, about 2 pm to about 300 pm, about 2 pm to about 400 pm, about 2 pm to about 500 pm, about 5 pm to about 10 pm, about 5 pm to about 25 pm, about 5 pm to about 50 pm, about 5 pm to about 100 pm, about 5 pm to about 200 pm, about 5 pm to about 300 pm, about 5 pm to about 400 pm, about 5 pm to about 500 pm, about 10 pm to about 25 pm, about 10 pm to about 50 pm, about 10 pm to about 100 pm, about 10 pm to about 200 pm, about 10 pm to about 300 pm, about 10 pm to about 400 pm, about 10 pm to about 500 pm, about 25 pm to about 50 pm, about 25 pm to about 100 pm, about 25 pm to about 200 pm, about 25 pm to about 300 pm, about 25 pm to about 400 pm, about 25 pm to about 500 pm, about 50 pm to about 100 pm, about 50 pm to about 200 pm, about 50 pm to about 300 pm, about 50 pm to about 400 pm, about 50 pm to about 500 pm, about 100 pm to about 200 pm, about 100 pm to about 300 pm, about 100 pm to about 400 pm, about 100 pm to about 500 pm, about 200 pm to about 300 pm, about 200 pm to about 400 pm, about 200 pm to about 500 pm, about 300 pm to about 400 pm, about 300 pm to about 500 pm, or about 400 pm to about 500 pm. In some embodiments, a particulate filter has a pore size of about 1 pm, about 2 pm, about 5 pm, about 10 pm, about 25 pm, about 50 pm, about 100 pm, about 200 pm, about 300 pm, about 400 pm, or about 500 pm. In some embodiments, a particulate filter has a pore size of at least about 1 pm, about 2 pm, about 5 pm, about 10 pm, about 25 pm, about 50 pm, about 100 pm, about 200 pm, about 300 pm, or about 400 pm. In some embodiments, a particulate filter has a pore size of at most about 2 pm, about 5 pm, about 10 pm, about 25 pm, about 50 pm, about 100 pm, about 200 pm, about 300 pm, about 400 pm, or about 500 pm. The particulate filter can retain particles of the biological sample when the biological sample is transferred from the first channel to the second channel, such as to improve the quality and / or concentration of extracted analytes from the biological sample.

[0240] In some embodiments, a first channel receives a lysis solution. As described herein, a lysis solution provided herein can lyse any biological samples as described herein. A lysis solution may include any solution which can lyse a biological sample. As described herein, a lysis solution provided herein can lyse biological samples described herein to provide analytes of the biological sample for binding to a cellulose substrate described herein.

[0241] In some embodiments, the second opening comprises an incline having a slope of about 45°. In some embodiments, the second opening comprises an incline having a slope of about 3°. In some embodiments, the first channel further comprises a filtration device. In some embodiments, the filtration device is configured to filter the biological sample prior to the transfer of the biological sample from the first channel to the second channel. In some embodiments, the first channel further comprises a lysis solution. In some embodiments, theprocessing comprises an extraction of an analyte from the biological sample. In some embodiments, the processing comprises a nucleic acid extraction. In some embodiments, the nucleic acid comprises a DNA or an RNA or both. In some embodiments, the processing comprises binding a plurality of nucleic acids to the cellulose substrate. In some embodiments, the processing further comprises eluting at least a portion of the bound plurality of nucleic acids into the elution solution. In some embodiments, a detection of amplified extracted nucleic acids determines the presence or absence of a target sequence. In some embodiments, the target sequence is a nucleic acid sequence of a virus or a bacteria. In some embodiments, the target sequence is a DNA sequence or RNA sequence or both. In some embodiments, the DNA sequence is related to a genetic trait. In some embodiments, the DNA sequence or RNA sequence is mammalian gDNA or genomic RNA. In some embodiments, amplification is performed via a quantitative polymerase chain reaction (qPCR), PCR, or isothermal amplification. In some embodiments, the isothermal amplification is RPA or ANINA. In some embodiments, the amplified extracted nucleic acids have a CQ value that is less than or almost equal to a CQ value of amplified nucleic acids extracted via centrifugation. In some embodiments, a connector is configured to couple the third channel to the second channel, or wherein the connector is configured to couple the first channel to the second channel. In some embodiments, the systems further comprise a dropper cap, optionally wherein the first channel is configured to transfer the biological sample to the second channel through the dropper cap. In some embodiments, the dropper cap is configured to couple to the first channel. In some embodiments, the preceding claims, wherein the first channel is a vial, or a flexible tube. In some embodiments, the preceding claims, wherein the second channel is a vial, or a flexible tube. In some embodiments, the third channel is a vial. In some embodiments, the cellulose substrate is affixed to the second channel. In some embodiments, the second channel comprises a single chamber. In some embodiments, the first channel or the second channel comprise a particulate filter having a pore size of greater than about 10 um, and wherein the particulate filter is configured to retain particles when the biological sample is transferred from the first channel to the second channel in (b). In some embodiments, either the first channel or second channel comprises an adapter, wherein the adapter, when in use, couples the first channel to the second channel. In some embodiments, the adapter comprises internal threads. In some embodiments, either the first channel or the second channel comprises internal treads, wherein the internal treads, when in use, couple the first channel to the second channel. In some embodiments, either the first channel or the second channel comprises a flexible tubing, wherein the flexible tubing,when in use, couples the first channel to the second channel. In some embodiments, a first channel comprising the biological sample is configured to transfer the biological sample to a port of the second channel. In some embodiments, the first channel comprises a lysis solution. In some embodiments, the system further comprises a dropper cap, wherein, when in use, the first channel transfers the biological sample through the dropper cap to the port. In some embodiments, a connector is configured to couple the third channel to the port, wherein the third channel comprises an elution solution, and wherein the coupling of the third channel to the port transfers the elution solution to and from the second channel. In some embodiments, transferring the elution solution to and from the second channel occurs in less than about 30 seconds. In some embodiments, the second opening comprises an incline having a slope of about 45°. In some embodiments, the second opening comprises an incline having a slope of about 3°. In some embodiments, the nucleic acid comprises a DNA or an RNA or both. In some embodiments, the cellulose substrate is configured to bind a plurality of nucleic acids. In some embodiments, the housing is a bottle. In some embodiments, the cellulose substrate remains affixed to the housing. In some embodiments, the housing comprises a single chamber. In some embodiments, the system does not further comprise an actuator, a centrifuge, or a vacuum. In some embodiments, the biological sample is a biological fluid. In some embodiments, the biological sample is a tissue sample. In some embodiments, the tissue sample is a skeletal tissue, a muscle tissue, a spleen tissue, an embedded tissue or a liver tissue. In some embodiments, the tissue sample has a mass of about 5 to about 200 milligrams (mg). In some embodiments, the tissue sample has a mass of at least about 25 mg.

[0242] Provided herein, in some aspects, are systems for processing a biological sample, the system comprising: (a) a first channel comprising a first opening, wherein the first channel is configured to couple thereto a biological sample; (b) a second channel comprising: (i) a substrate coupled thereto; and (ii) a second opening, wherein the second opening is configured to couple to the first opening, and wherein upon the coupling of the second opening to the first opening, the biological sample is transferred from the first channel to the second channel; and (c) a third channel comprising: (i) an elution solution; and (ii) a third opening, wherein the third opening is configured to couple to the second opening, and wherein upon the coupling of the second opening to the third opening, the elution solution is transferred from the third channel to the second channel. In some embodiments, the first channel further comprises a lysis solution, wherein when said biological sample is a pathogenic bacterium said lysis solution comprises sodium hydroxide (NaOH) at aconcentration of at least about 200 mM, and one or more of the following: (i) triton-X 100 at a concentration of about 0.1% v / v to about 2% v / v of the composition; (ii) lysozyme at a concentration of about 10 mg / mL to about 150mg / mL of the composition; (iii) tween80 at a concentration of about 0.05 to about 0.5% of the composition; (iv) EDTA at a concentration from about 0.01 mM to about 1.0 mM of the composition; (v) Tris HC1 at a concentration from about 1 mM to about 100 mM of the composition; or (vi) Antifoam at a concentration of about 0.01% to about 2% of the composition. In some embodiments, the lysis solution comprises: (a) Tris HC1 at a concentration of about 10 millimolar (mM) to about 50 mM of the composition; (b) NaCl at a concentration of about 200 mM to about 400 mM of the composition; (c) triton x-100 at a concentration of about 0.1% to about 5% of the composition; and (d) TCEP at a concentration of about 10 mM to about 50 mM of the composition. In some embodiments, the first channel further comprises a chemical lysis solution or an enzymatic lysis solution.

[0243] Provided herein, in some aspects, are systems for preparation of a nucleic acid from a biological sample, the system comprising a housing comprising: (a) a substrate affixed to the housing; and (b) a port, wherein the port is configured to receive the biological sample, wherein the port is configured to provide the biological sample to the substrate. In some embodiments, the port is further configured to receive a lysis solution, wherein when said biological sample is a pathogenic bacterium said lysis solution comprises sodium hydroxide (NaOH) at a concentration of at least about 200 mM, and one or more of the following: (i) triton-X 100 at a concentration of about 0.1% v / v to about 2% v / v of the composition; (ii) lysozyme at a concentration of about 10 mg / mL to about 150mg / mL of the composition; (iii) tween80 at a concentration of about 0.05 to about 0.5% of the composition; (iv) EDTA at a concentration from about 0.01 mM to about 1.0 mM of the composition; (v) Tris HC1 at a concentration from about 1 mM to about 100 mM of the composition; or (vi) Antifoam at a concentration of about 0.01% to about 2% of the composition. In some embodiments, the lysis solution comprises: (a) Tris HC1 at a concentration of about 10 millimolar (mM) to about 50 mM of the composition; (b) NaCl at a concentration of about 200 mM to about 400 mM of the composition; (c) triton x-100 at a concentration of about 0.1% to about 5% of the composition; and (d) TCEP at a concentration of about 10 mM to about 50 mM of the composition. In some embodiments, the port is further configured to receive a chemical lysis solution or an enzymatic lysis solution.

[0244] In some embodiments, a lysis solution has a neutral pH. In some embodiments, a lysis solution has an acidic pH. In some embodiments, the lysis solution has a pH of about 1to about 7. In some embodiments, the lysis solution has a pH of about 1 to about 2, about 1 to about 3, about 1 to about 4, about 1 to about 5, about 1 to about 6, about 1 to about 7, about 2 to about 3, about 2 to about 4, about 2 to about 5, about 2 to about 6, about 2 to about 7, about 3 to about 4, about 3 to about 5, about 3 to about 6, about 3 to about 7, about 4 to about 5, about 4 to about 6, about 4 to about 7, about 5 to about 6, about 5 to about 7, or about 6 to about 7. In some embodiments, the lysis solution has a pH of about 1, about 2, about 3, about 4, about 5, about 6, or about 7. In some embodiments, the lysis solution has a pH of at least about 1, about 2, about 3, about 4, about 5, or about 6. In some embodiments, a lysis solution has a pH of at most about 2, about 3, about 4, about 5, about 6, or about 7. In some embodiments, a lysis solution has a pH of about 7.5.

[0245] In some embodiments, a lysis solution has an alkaline pH. In some embodiments, the lysis solution has a pH of about 7 to about 14. In some embodiments, the lysis solution has a pH of about 7 to about 8, about 7 to about 9, about 7 to about 10, about 7 to about 11, about 7 to about 12, about 7 to about 13, about 7 to about 14, about 8 to about 9, about 8 to about 10, about 8 to about 11, about 8 to about 12, about 8 to about 13, about 8 to about 14, about 9 to about 10, about 9 to about 11, about 9 to about 12, about 9 to about 13, about 9 to about 14, about 10 to about 11, about 10 to about 12, about 10 to about 13, about 10 to about 14, about 11 to about 12, about 11 to about 13, about 11 to about 14, about 12 to about 13, about 12 to about 14, or about 13 to about 14. In some embodiments, the lysis solution has a pH of about 7, about 8, about 9, about 10, about 11, about 12, about 13, or about 14. In some embodiments, the lysis solution has a pH of at least about 7, about 8, about 9, about 10, about 11, about 12, or about 13. In some embodiments, the lysis solution has a pH of at most about 8, about 9, about 10, about 11, about 12, about 13, or about 14. In some embodiments, a lysis solution has a pH of about 8. In some embodiments, the lysis buffer is a chemical lysis buffer. In some embodiments, the chemical lysis buffer is an acidic lysis buffer. In some embodiments, the chemical lysis buffer is a neutral lysis buffer. In some embodiments, the chemical lysis buffer is an alkaline lysis buffer. In some embodiments, the lysis buffer is an enzymatic lysis buffer. In some embodiments, the lysis buffer comprises a chemical lysis buffer and an enzymatic lysis buffer. In some embodiments, the lysis buffer uses sequential lysis with enzymatic lysis buffer used first, followed by used of a chemical lysis buffer. In some embodiments, the biological sample and the chemical lysis solution or enzymatic lysis solution are mixed prior to coupling to the first channel in (a).

[0246] In some embodiments, a lysis solution comprises salts, sodium acetate, sodium chloride, sodium hydroxide, Tris, Tris HC1, NaCl, polysorbate (e.g., Tween 20), Triton X-100, water, SDS, sodium dodecyl, glucose, DTT, guanidine hydrochloride, proteinase K, or any combination thereof. In some embodiments, the lysis solution comprises salts. In some embodiments, the lysis buffer comprises Tris HC1. Table 1 provides examples of lysis buffers that can be used with any one of the systems and methods disclosed herein.

[0247] The present disclosure provides systems, methods, devices, and kits for amplification, isolation, and / or detection of a biological sample. In some embodiments, the device comprises a system for isolating nucleic acid. In some embodiments, the device comprises a system for amplifying a target region of a nucleic acid molecule, such as any one of the systems described herein. In some embodiments, the device comprises a detection system for detecting the target nucleic acid. In some embodiments, the kit comprises an isolation / extract! on system for isolating nucleic acid. In some embodiments, the kit comprises a system for amplifying a target region of a nucleic acid molecule, such as any one of the systems described herein. In some embodiments, the kit comprises a detection system for detecting the target nucleic acid.

[0248] The present invention also features a system or device comprising an isolation system (e.g., isolation chamber) having a binding component capable of binding nucleic acid disposed therein, an amplification system (e.g., amplification chamber), and a detection system (e.g., detection chamber, detection component, means of detection, a detection unit, etc.). The amplification system (e.g., amplification chamber) may be fluidly connected to the isolation system (e.g., isolation chamber), e.g., via a channel, a plurality of channels, etc. The detection system (e.g., detection chamber, detection component) may be fluidly connected to the amplification system (e.g., amplification chamber), e.g., via a channel, a plurality of channels, etc.

[0249] For example, the present invention features a system or device comprising an isolation system (e.g., isolation chamber) having a binding component capable of binding nucleic acid disposed therein and a detection system (e.g., detection chamber, detection component, means of detection, a detection unit, etc.). In some embodiments, the detection system is fluidly connected to the isolation system (e.g., isolation chamber), e.g., via a channel, a plurality of channels, a tube, a plurality of tubes, other appropriate connection components, etc.

[0250] The present invention also features a system or device comprising an isolation system (e.g., isolation chamber) having a binding component capable of binding nucleic acid disposed therein, an amplification system (e.g., amplification chamber), and a detection system (e.g., detection chamber, detection component). The system may further comprise adetection buffer chamber fluidly connected to the amplification system (e.g., amplification chamber), e.g., via one or more channels. The detection buffer chamber may also be fluidly connected to the detection system (e.g., detection chamber, detection component), e.g., via one or more channels.

[0251] The systems and devices herein may further comprise at least one means for aliquoting a fluid, e.g., an aliquoting valve or the like. As an example, the aliquoting valve may separate the isolation chamber from either one or both of the amplification chamber or the detection buffer chamber.Isolation / Extraction

[0252] Provided in some embodiments herein is a system for processing a biological sample. In some embodiments, the processing comprises isolating a nucleic acid from a biological sample. In some embodiments, the system comprises a channel. In some embodiments, the system comprises a first channel. In some embodiments, the first channel comprises a first opening. In some embodiments, the first channel is configured to receive a biological sample. In some embodiments, the first channel is configured to receive, via the first opening, a biological sample. In some embodiments, the system comprises a second channel. In some embodiments, the second channel comprises a substrate. In some embodiments, the second channel comprises a substrate comprising cellulose. In some embodiments, the second channel comprises a cellulose substrate. In some embodiments, the second channel comprises a second opening. In some embodiments, the second channel comprises a cellulose substrate coupled to the first channel and a second opening. In some embodiments, the system comprises a second opening configured to couple to the first opening. In some embodiments, the system transfers a biological sample from the first channel to the second channel. In some embodiments, the second channel comprises a nucleic acid binding substrate adhered to the side or bottom of a well, wherein the nucleic acid binding substrate is configured as a nucleic acid binding agent for a system of nucleic acid extraction. In some embodiments, the second channel comprises a cellulose substrate adhered to the side or bottom of a tube, wherein the cellulose substrate is configured as a nucleic acid binding agent for a system of nucleic acid extraction. In some embodiments, the second channel comprises a cellulose substrate adhered to the side or bottom of a well, wherein the cellulose substrate is configured as nucleic acid binding agent for a system of nucleic acid extraction. In some embodiments, the biological sample is processed in about 90 minutes or less, in about 80 minutes or less, in about 70 minutes or less, in about 60 minutes or less, in about 50 minutes or less, in about 45 minutes or less, in about 40 minutes or less, in about 35minutes or less, in about 30 minutes or less, in about 25 minutes or less, in about 20 minutes or less, or in about 15 minutes or less. In some embodiments, the biological sample is processed in about 45 minutes or less. In some embodiments, the biological sample is processed in about 30 minutes or less. In some embodiments, the biological sample is processed in about 15 minutes or less.

[0253] For instance, the system may transfer a biological sample from the first channel to the second channel upon the coupling of the second opening to the first opening. In some embodiments, the system comprises a third channel. In some embodiments, the third channel comprises a third opening. In some embodiments, the system comprises an elution solution. For instance, in some embodiments, the third channel of the system comprises an elution solution. In some embodiments, the third channel comprises a third opening and an elution solution. In some embodiments, the third channel comprises a third opening configured to couple to the second opening. In some embodiments, the system transfers the elution solution from the third channel to the second channel. For instance, the system may transfer a biological sample from the second channel to the third channel upon coupling of the third opening to the second opening. In some embodiments, the second channel is configured to transfer elution solution received from the second channel to the third channel, such as upon coupling of the third opening and the second opening. In some embodiments, the first channel receives a lysis solution (e.g., see FIG. 25A). In some embodiments, the first channel already contains a lysis solution (e.g., see FIG. 25B). In some embodiments, the first channel receives a biological sample (e.g., see FIG. 25B). In some embodiments, the first channel transfers the biological sample to a second channel (e.g., see FIG. 25C). In some embodiments, the first channel receives a biological sample, followed by receiving a lysis solution and then transferring the lysed biological solution to a second channel, (e.g., see FIG. 26A). In some embodiments, a housing receives a lysed biological solution from a channel and transfers the lysate from the housing back to the channel which is then discarded (e.g., see FIG. 26B). In some embodiments, the housing receives an elution solution from a channel, followed by transferring the eluate back to the channel which now has analytes extracted from the biological sample (e.g., see FIG. 25C). In some embodiments, the first channel transfers an extracted nucleic acid sample into a second channel containing a lyophilized amplification pellet or bead and rehydrating the said pellet to start amplification of a dual-labelled amplified target nucleic acid sequence (e.g., dual-labelled WSSV target DNA amplicons) (e.g., see FIG. 27). In some embodiments, detection (e.g., detecting a DNA amplicon) comprises a Lateral Flow Analysis (LFA) (e.g., see FIG. 28A). In someembodiments, a first channel containing an amplified nucleic acid (e.g., dual-labelled amplicon solution) from a processed biological sample is diluted with detection buffer added from a buffer packet, an LFA strip is added into the diluted amplicon solution in the first channel and the LFA results are then interpreted to detect presence of target nucleotide sequence (e.g., see FIG. 28B). In some embodiments, molecular lateral flow analysis is performed on the processed biological sample (e.g., molecular lateral flow analysis for human saliva samples spiked with EBV).

[0254] System, methods and kits for processing a biological sample as described herein may entail isolating and / or extracting nucleic acid molecules from a biological sample. For example, systems described herein can be used to isolate / extract a target nucleic acid sequence from a biological sample. Provided in some embodiments herein is a system for the preparation of nucleic acid from a biological sample. In some embodiments, the system comprises a housing. In some embodiments, the housing comprises a port. In some embodiments, the port comprises an opening. In some embodiments, the housing comprises a substrate. In some embodiments, the substrate comprises cellulose. In some embodiments, the substrate is a cellulose substrate. In some embodiments, the substrate is affixed to the housing. In some embodiments, the system comprises a housing comprising a port and a substrate. In some embodiments, the port is configured to receive a biological sample. In some embodiments, the port is configured to provide the biological sample to the cellulose substrate. In some embodiments, the housing comprises one or more channels as disclosed herein. Methods and systems for isolating and / or extracting nucleic acid molecules from a biological sample described herein can comprise a pestle (e.g., for grinding tissue), a sample tube base (e.g., made with soft plastic that can be squeezed easily), a sample tube cap (e.g., with inserted pre-filter), a lysis Buffer container (e.g., pre-filled with tissue lysis buffer), a lysate Vial with attached cap, a device as described herein (e.g., see FIG. 50A), and / or an Eluate Vial with attached cap (e.g., containing elution buffer).

[0255] The present disclosure provides a system comprising a binding membrane. In some embodiments, the system is as depicted in, e.g., FIGS. 75, 81, and 85. In some embodiments, the system as described has a binding membrane comprising a cellulose substrate. The binding membrane, e.g., cellulose substrate, may be disposed at a surface area of about 0.1 to about 2 in2. The binding membrane, e.g., cellulose substrate, may be disposed at a surface area of about 0.4 to about 0.5 in2. The binding membrane, e.g., cellulose substrate, may be disposed at a surface area of about 0.41 in2. The binding membrane, e.g., cellulose substrate, may be disposed at a surface area of about 0.408 in2.

[0256] For instance, as depicted in FIG. 48, a workflow process, hereinafter (“System A”) may comprise: inserting a biological sample into a tube 3101 mechanically lysing (e.g., pestling) the biological sample for about 30 seconds 3102, adding a lysis solution as described herein to the tube and mixing the mechanically lysed biological sample and lysis elution solution 3103 to further lyse the biological sample, coupling a dropper cap onto the tube and rotating the tube over a housing, comprising a cellulose substrate, to transfer the lysed biological sample through the dropper cap into the housing 3104, laying the housing flat for a period of about 0 to about 30 seconds such as to allow the binding of nucleic acids of the biological sample to the cellulose substrate of the housing 3105, inverting the housing to discard unbound biological sample and lysate from the housing 3106, coupling a connector to the second housing such as to couple the housing to a vial comprising an elution buffer 3107, rotating the vial 180° to transfer the elution buffer into the housing 3108, laying the housing flat for a time period of about 0 to about 30 seconds 3109, inverting the housing over the vial to transfer eluate from the housing to the vial 3110, discarding the housing 3111, and storing the extracted nucleic acids 3112.

[0257] In some embodiments, samples are processed according to the workflow, which is depicted in FIG. 49 (e.g., “Seek Extraction”). In some embodiments, Seek Extraction comprises: collecting a biological or environmental sample, mixing the biological sample with a lysis solution, transferring the lysate to a lysate vial, pouring the contents of the lysate vial into an extraction unit, pouring the lysate solution back into the lysate vial, discarding the lysate vial, pouring an elution solution into the extraction unit to produce an eluate, and pouring the eluate into an elution vial, thereby extracting and purifying analytes from the biological sample.

[0258] The present disclosure provides a system comprising a binding membrane. The system may be cylindrical. The cylindrical shape of the system may enable greater coverage of the system with the binding membrane. For instance, the system may comprise the binding membrane disposed along a surface of the system. For instance, the system may comprise a binding membrane disposed along a perimeter of the system. In some embodiments, the binding membrane is a cellulose substrate. An example of such a system can be found at FIG. 86. The binding membrane, e.g., cellulose substrate, may be disposed at a surface area of about 0.1 to about 2 in2. The binding membrane, e.g., cellulose substrate, may be disposed at a surface area of about 0.1 to about 1.6 in2. The binding membrane, e.g., cellulose substrate, may be disposed at a surface area of about 0.6 to about 0.7 in2. The binding membrane, e.g., cellulose substrate, may be disposed at a surface area of about 0.69 in2. Thebinding membrane, e.g., cellulose substrate, may be disposed at a surface area of about 0.693 in2. The binding membrane, e.g., cellulose substrate, may be disposed at a surface area of up to about 2 in2. The binding membrane, e.g., cellulose substrate, may be disposed at a surface area of up to about 1.4 in2. The binding membrane, e.g., cellulose substrate, may be disposed at a surface area of up to about 1.438 in2.

[0259] The cylindrical system may comprise an opening with an angle. For instance, the angle may be at least about 1° to about 5°. An example of such an opening is depicted in FIG. 86. An example system as depicted in FIG. 86 may have an angle of about 3°.

[0260] The cylindrical system comprising a binding membrane may be used in diagnostic applications for animal samples. For instance, the system may be used to detect a disease or disorder in an animal subject in need thereof. An example of a workflow using the cylindrical system as described herein is described at FIGs. 87-90 and Example 24. The subject may be an aquatic animal. For instance, the subject may be a shrimp. The aquatic animal may be tested for an infectious illness. For instance, the aquatic animal may be tested for a viral infection, such as White Spot Syndrome Virus (WSSV). The aquatic animal may be tested for a bacterial infection. The subject may be a land animal. For instance, the subject may be a domesticated animal, such as a cow, pig, sheep, goat, dog, cat, or chicken. The land animal may be tested for an infectious illness. For instance, the land animal may be tested for a viral infection, such as African Swine Fever (ASF). The land animal may be tested for a bacterial infection. As an example, results of the system when used with shrimp samples have been shown at Examples 6 and 11.

[0261] Systems as described herein, e.g., the cylindrical system (e.g., FIG. 86) can be used with any of the other systems described herein. For instance, systems as described herein can be used with any of the systems for amplification as described herein. For instance, systems as described herein can be used with any of the systems for detection as described herein. For instance, systems as described herein can be used with any of the computing systems as described herein. Systems as described herein, e.g., the cylindrical system can be used with any of the biological samples described herein. Systems as described herein, e.g., the cylindrical system can be used with any of the buffers described herein.

[0262] The systems and devices described herein may further comprise either one or both of: a sample chamber (e.g., a first chamber) or an elution chamber (e.g., a second chamber). Both chambers may be fluidly connected to the first end of the isolation chamber, e.g., via a channel (e.g., a first channel and a second channel). In some embodiments, both chambers may be fluidly connected to the first end of the isolation chamber via a single channel. Inother embodiments, both chambers may be fluidly connected to the first end of the isolation chamber via two channels. In embodiments where the device comprises both a sample chamber and an elution chamber, the chambers are disposed on opposite sides of the first end of the isolation chamber. The sample chamber may further comprise a first coupler comprising an opening to the sample chamber and configured to engage a means for preventing access to the sample chamber through the first coupler, e.g., a cap, a seal, a plug, or a vial. Likewise, the elution chamber may further comprise a second coupler comprising an opening to the elution chamber and configured to engage at least a means for preventing access to the elution chamber through the second coupler, e.g., a cap, a seal, a plug, or a vial.

[0263] An additional aspect of the present disclosure provides systems and methods provides for a second channel. Suitable channels include, but are not limited to, beakers, bottles, burettes, containers, cylinders, vials, tubes, pipettes, syringes, adapters or connectors, and any other channel. In some embodiments, the second channel is a vial (see for example FIG. 86)

[0264] In some embodiments, a second channel comprises a second opening. In some embodiments, a second channel receives a biological sample as described herein from a first channel as described herein. In some embodiments, a second channel, by a second opening, receives a biological sample from a first channel. In some embodiments, a second channel receives, by a second opening, a lysis solution from the first channel. In some embodiments, a second channel can receive, by a second opening, an elution solution from the third channel. In some embodiments a second channel can discard, by a second opening, lysate. In some embodiments a second channel can transfer, by the second opening, eluate to the third channel.

[0265] In some embodiments, a second channel comprises a substrate. In some embodiments, a substrate is a cellulose substrate. In some embodiments, a substrate is within a chamber of a second channel. In some embodiments, analytes of a lysed biological sample bind to the substrate upon transfer of the biological sample from a first channel to a second channel comprising the substrate. In some embodiments, a portion of the biological sample comprises sample (e.g., nucleic acids, analytes, or other target materials) which binds to a substrate. In some embodiments, a substrate is permanently affixed to a second channel. In some embodiments, a substrate (e.g., cellulose beads) wraps around a chamber of a second channel (see for example FIG. 86). The substrate can retain particles of a biological sample, as described herein, such as to increase the quality and / or concentration of extracted analytes from the biological sample. In some embodiments, the substrate has an area of about .1, about.2, about .3, about .4, about .5, about .6, about .7, or about .8 square inches. For example, the device depicted in FIG. 85 (e.g., version 8) can have a substrate with an area of -0.408 square inches. In some embodiments, the substrate has an area of about .1, about .2, about .3, about .4, about .5, about .6, about .7, about .8, about .9, about 1, about 1.1, about 1.2, about 1.3, about 1.4, about 1.5, about 1.6, about 1.7, about 1.8, about 1.9, or about 2 square inches. For example, the device depicted in FIG. 86 (e.g., version 10) can have a substrate with an area of - 1.438 square inches.

[0266] In some embodiments, a housing comprises the second channel. In some embodiments, the housing comprises a port. In some embodiments, the port comprises a second opening. For instance, as depicted in FIG. 50A, housing 3000 may comprise a port 3001 and a binding chamber 3002 which comprises a cellulose substrate 3003. The port can also comprise a connector 3004, such as to connect the housing to a channel.

[0267] As depicted in FIG. 50B, a workflow process for nucleic acid extraction and sample preparation using an extraction device such as that depicted in FIG. 50A, hereinafter (“System A”) may comprise: inserting a biological sample into a tube 331, pestling the biological sample for about 30 seconds 332, adding an elution solution as described herein to the tube and mixing the pestled biological sample and elution solution 333 to lyse the biological sample, coupling a dropper cap onto the tube and rotating the tube over a housing comprising a cellulose substrate to transfer the lysed biological sample through the dropper cap into the housing 334, laying the housing flat for a period of about 30 seconds such as to allow the binding of nucleic acids of the biological sample to the cellulose substrate of the housing 335, inverting the housing to discard unbound biological sample and lysate from the housing 336, coupling a connector to the second housing such as to couple the housing to a vial comprising an elution buffer 337, rotating the vial 180° to transfer the elution buffer into the housing 338, laying the housing on its side for a time period of about 30 seconds 339, inverting the housing over the vial to transfer eluate from the housing to the vial 330, discarding the housing 3300, and storing the extracted nucleic acids 3301.

[0268] In some embodiments, a first channel transfers, via a first opening, a biological sample to a second channel through a second opening. In some embodiments, an opening of a first channel couples to a second opening of a second channel, such as to transfer a biological sample and / or a lysis solution from the first channel to the second channel. In some embodiments, a first channel comprises an adapter. In some embodiments, a second channel comprises an adapter. In some embodiments, an adapter couples a first and second openings. In some embodiments, an adapter is an external thread on a channel. In some embodiments, afirst channel comprises internal tread. In some embodiments, a second channel comprises internal tread. In some embodiments, an internal thread couples a first channel to a second channel via a first and second opening. In some embodiments, a first channel comprises flexible tubing. In some embodiments, a second channel comprises flexible tubing. In some embodiments, a flexible tubing couples the first and second channel. In some embodiments, an adapter is a Luer locking mechanism between the first and second channel. In some embodiments, the first channel is a female Luer lock connector, and the second channel is a male Luer lock connector. In some embodiments, the first channel is a male Luer lock connector, and the second channel is a female Luer lock connector. In some embodiments, the pathway between the first and second channel comprises a particulate filter.

[0269] In some embodiments, a dropper cap is positioned between a first and second channel. In some embodiments, a first channel transfers a biological sample as described herein through a dropper cap into a second channel. In some embodiments, a dropper cap comprises a particulate filter as described herein.

[0270] In some embodiments, a first opening of a first channel is inverted over a second channel, such as to transfer a biological sample as described herein from the first channel to the second channel. In some embodiments, a first opening of a first channel is rotated 180°, such as to invert the first opening of the first channel over a second channel. In some embodiments, gravity transfers a biological sample from a first channel to a second channel. In some embodiments, a force exerted onto a first channel transfers from the first channel to a second channel.

[0271] In some embodiments, a second channel disposes of lysate. In some embodiments, disposed lysate comprises lysis solution. In some embodiments, disposed lysate comprises a portion of the biological sample which does not bind to a substrate of a second channel. In some embodiments, a second channel transfers, as described herein, unbound lysate to a first channel, thereby disposing the unbound lysate.

[0272] In some embodiments, the systems and methods described herein comprise an actuator. In some embodiments an actuator exerts a force onto a biological sample to transfer the biological sample between channels as described herein. In some embodiments, an actuator is a pump, a bulb, a syringe, or any other actuator, such as a pipette. In some embodiments, the systems and methods described herein do not comprise an actuator. In some embodiments, systems as described herein use gravity to exert force on the biological sample. For instance, in some embodiments, systems as described herein use gravity to transfer the biological subject between channels.

[0273] In some embodiments, the systems and methods described herein comprise a centrifuge. In some embodiments, a biological sample is centrifuged to separate analytes of the biological sample from the biological sample. In some embodiments, the systems and methods described herein do not comprise a centrifuge. In some embodiments, systems as described herein do not comprise a centrifuge to separate analytes of the biological sample. In some embodiments, systems and methods as described herein that do not comprise a centrifuge are used to perform nucleic acid processing in about ten minutes or less. In some embodiments, systems and methods as described herein that do not comprise a centrifuge are used to perform nucleic acid processing in about 10 minutes, 9 minutes, 8 minutes, 7 minutes, 6 minutes, 5 minutes, 4 minutes, 3 minutes, 2 minutes, 1 minute, or less.

[0274] An additional aspect of the present disclosure provides systems and methods provides for a third channel. Suitable channels include, but are not limited to, pipettes, beakers, bottles, burettes, containers, cylinders, vials, tubes, syringes, adaptors, connectors, or any other channel (see for example FIG. 86).

[0275] The third channel can comprise a third opening. The third channel can couple to, via the third opening, the second channel. In some embodiments, the third channel comprises a connector. In some embodiments, the second channel comprises a connector. In some embodiments, a connector couples the second and third channels.

[0276] In some embodiments, a third channel comprises an elution solution. In some embodiments, a third channel couples to a second channel, as described herein, such as to transfer an elution solution from the third channel to the second channel. In some embodiments, a third channel is inverted over a second channel, such as to transfer an elution solution from the third channel to the second channel. In some embodiments, a third opening of a third channel is rotated 180°, such as to invert the third opening of a third channel over a second channel.

[0277] In some embodiments, an elution solution elutes analytes bound to a substrate. In some embodiments, an elution solution elutes a portion of the analytes bound to a substrate. In some embodiments, the elution solution elutes at least a portion of the analytes bound to a substrate. In some embodiments, the elution solution elutes all analytes bound to a substrate. In some embodiments, an eluate comprises analytes of a biological sample.

[0278] In some embodiments, eluate is transferred from a second channel to a third channel. In some embodiments, a second channel is coupled to a third channel, as described herein, to transfer eluate from the second channel to the third channel. In some embodiments, a second channel is inverted over a third channel to transfer, via gravity, eluate from thesecond channel to the third channel. In some embodiments, a second opening of a second channel is rotated 180°, such as to invert the second opening of the second channel over a third channel.

[0279] In some embodiments, the second opening comprises an incline having a slope. In some embodiments, the port comprises an incline having a slope. In some embodiments, an incoming edge of the port and / or second opening comprises an incline having a slope (e.g., see FIG. 75 depicting an incoming edge with a slope). In some embodiments, an outgoing angle of the port and / or second opening comprises an incline having a slope (e.g., see FIG. 86 depicting an outgoing angle with a slope). The system may comprise an incoming edge (see FIG. 75 and FIG. 85), a side radius (see FIG. 85), and a bottom radius (see FIG. 85). In some embodiments, the slope allows fluid to flow more readily (e.g., not get trapped as it leaves the sample vial). For example, see FIG. 75 depicting a housing comprising a port (e.g., an opening comprising an incline having a slope) and FIG. 82 depicting improvements to, for example, extraction yield in a device comprising an incoming edge with a slope compared to a device that does not comprise an incoming edge with a slope. In some embodiments, the second opening or port comprises an incline having a slope of about 1° to about 10°, about 1° to about 70°, about 10° to about 70°, about 20° to about 70°, about 25° to about 65°, about 30° to about 60°, about 31° to about 59°, about 31° to about 59°, about 31° to about 59°, about 32° to about 58°, about 33° to about 57°, about 34° to about 56°, about 35° to about 55°, about 36° to about 54°, about 37° to about 53°, about 38° to about 52°, about 391° to about 51°, about 40° to about 50°, about 41° to about 49°, about 42° to about 48°, about 43° to about 47°, or about 44° to about 46°. In some embodiments, the second opening or port comprises an incline having a slope of about 40° to about 50°. In some embodiments, the second opening or port comprises an incline having a slope of about 1°, about 2°, about 3°, about 4°, about 5°, about 6°, about 7°, about 8°, about 9°, about 10°, about 15°, about 20°, about 25°, about 30°, about 35°, about 40°, about 41°, about 42°, about 43°, about 44°, about 45°, about 46°, about 47°, about 48°, about 49°, about 50°, about 55°, about 60°, about 65°, or about 70°. In some embodiments, the second opening or port comprises an incline having a slope of about 45°. In some embodiments, the second opening or port comprises an incline having a slope of about 3°. In some embodiments, upon a coupling of the second opening to the first opening, the biological sample is transferred from the first channel to the second channel.

[0280] In some embodiments, the second opening comprises a bottom radius (see FIG. 55). In some embodiments, the second opening comprises a side radius (see FIG. 85). Insome embodiments, the port comprises a bottom radius. In some embodiments, the comprises has a side radius. In some embodiments, the side radius and / or bottom radius can refer to the exit radii (see FIG. 75). In some embodiments, the bottom radius is about .1 inches, about .125 inches, about .15 inches, about .2 inches, about .25 inches, about .3 inches, about .35 inches, about .4 inches, about .45 inches, about .5 inches, about .55 inches, about .6 inches, about .65 inches, about .7 inches, about .75 inches, about .8 inches, about .85 inches, about .9 inches, about .95 inches, about 1 inch, or about 1.5 inch. In some embodiments, the bottom radius is about .125 inches. In some embodiments, the bottom radius is about .95 inches. In some embodiments, the bottom radius is about 1 inch. In some embodiments, the side radius is about .1 inches, about .125 inches, about .15 inches, about .2 inches, about .25 inches, about .3 inches, about .35 inches, about .4 inches, about .45 inches, about .5 inches, about .55 inches, about .6 inches, about .65 inches, about .68 inches, about .7 inches, about .75 inches, about .8 inches, about .85 inches, about .9 inches, about .95 inches, about 1 inch, or about 1.5 inch. In some embodiments, the side radius is about .125 inches. In some embodiments, the side radius is about .68 inches. In some embodiments, the side radius is about .9 inches.

[0281] In some embodiments, the devices disclosed herein comprise a rounded bottom (see FIG. 81). In some embodiments, the devices disclosed herein comprise a flat bottom (see FIG. 81). In some embodiments, the second opening comprises internal threads. In some embodiments, the port comprises internal threads. In some embodiments, the second opening comprises external threads (see FIG. 75). In some embodiments, the port comprises external threads (see FIG. 75). In some embodiments, the second opening comprises an outgoing edge. In some embodiments, the port comprises an outgoing edge. For example, see FIG. 75. In some embodiments, the outgoing edge is about .1 inches, about .125 inches, about .15 inches, about .2 inches, about .25 inches, about .3 inches, about .35 inches, about .4 inches, about .45 inches, about .5 inches, about .55 inches, about .6 inches, about .65 inches, about .7 inches, about .75 inches, about .8 inches, about .85 inches, about .9 inches, about .95 inches, about 1 inch, about 1.5 inches, about 2 inches, about 3 inches, about 4 inches, or about 5 inches.

[0282] An additional aspect of the present disclosure provides systems and methods which extract nucleic acids from a biological sample as described herein. Examples of protocols used for extraction of nucleic acids with systems and methods as described herein may be found at, for instance, Schnepp, Bruce C., et al., Characterization ofAdeno- Associated Virus Genomes Isolated from Human Tissues. J. 79 Virology 23 (December,2005) (DOI: 10.1128 / JVI.79.23.14793-14803.2005) and Jackson, D. P., et al., Tissue Extraction ofDNA andRNA and analysis by polymerase chain reaction, 43 J. Clin. Pathol.499-504 (1990) (DOI: 10.1136 / jcp.43.6.499), which are hereby incorporated by reference in its entirety. In some embodiments, nucleic acids extracted from a biological sample are amplified. Suitable amplification methods and / or systems include, but are not limited to, polymerase chain reaction (PCR), quantitative PCR (qPCR), isothermal amplification, or any other amplification technique. In some embodiments, an isothermal amplification comprises recombinase polymerase amplification (RPA). In some embodiments, an isothermal (e.g., ambient temperature) amplification comprises ANINA. In some embodiments, an isothermal (e.g., ambient temperature) amplification comprises Seek Amplification.

[0283] In some embodiments, amplified nucleic acids determine the presence of a target sequence in a sample. A target sequence can indicate the presence of a disease. In some embodiments, a target sequence is a nucleic acid sequence of a virus. In some embodiments, a target sequence a target sequence is a nucleic acid sequence of African Swine Fever Virus. In some embodiments, a target sequence is a nucleic acid sequence of White Spot Syndrome Virus. In some embodiments, a target sequence is a nucleic acid sequence of Respiratory Syncytial Virus (RSV). In some embodiments, a target sequence is a nucleic acid sequence of Influenza A virus (H1N1). In some embodiments, a target sequence is a nucleic acid sequence of Influenza. In some embodiments, a target sequence is a nucleic acid sequence of Epstein-Barr Virus (EBV).

[0284] A target sequence can indicate the presence of a disease or disorder. For example, the disease or disorder may be an infection. In some embodiments, a target sequence is a nucleic acid sequence of a virus. In some embodiments, a target sequence is a nucleic acid sequence of a bacteria. In some embodiments, a target sequence is a nucleic acid sequence of a bacteria that causes a sexually transmitted infection or sexually transmitted disease. In some embodiments, a target sequence is a nucleic acid sequence of a gonorrhea bacteria. In some embodiments, a target sequence is a nucleic acid sequence of an HIV virus. In some embodiments, a target sequence is a nucleic acid sequence of a herpes virus. In some embodiments, a target sequence is a nucleic acid sequence of chlamydia bacteria. In some embodiments, a target sequence is a nucleic acid sequence of a syphilis bacteria.

[0285] A target sequence can indicate a presence of a genetic trait. In some embodiments, a target sequence is a nucleic acid sequence which indicates the presence of a genetic trait. In some embodiments, a target sequence is a nucleic acid sequence which indicates the presenceof photic sneeze. In some embodiments, a target sequence is a nucleic acid sequence which indicates the presence of alcohol flush.

[0286] In some embodiments, extracted nucleic acids have an average yield of at about 100 ng / mg of tissue to about 2000 ng / mg of tissue. In some embodiments, extracted nucleic acids have an average yield of about 300 ng / mg of tissue to about 1500 ng / mg of tissue. In some embodiments, extracted nucleic acids have an average yield of at least 150 ng / mg. In some embodiments, extracted nucleic acids have an average yield of about 300 ng / mg. In some embodiments, extracted nucleic acids have an average yield of about 400 ng / mg of tissue. In some embodiments, extracted nucleic acids have an average yield of about 500 ng / mg of tissue. In some embodiments, extracted nucleic acids have an average yield of about 600 ng / mg of tissue. In some embodiments, extracted nucleic acids have an average yield of about 700 ng / mg of tissue. In some embodiments, extracted nucleic acids have an average yield of about 800 ng / mg of tissue. In some embodiments, extracted nucleic acids have an average yield of about 900 ng / mg of tissue. In some embodiments, extracted nucleic acids have an average yield of about 1000 ng / mg of tissue. In some embodiments, extracted nucleic acids have an average yield of about 1100 ng / mg of tissue. In some embodiments, extracted nucleic acids have an average yield of about 1200 ng / mg of tissue. In some embodiments, extracted nucleic acids have an average yield of about 1300 ng / mg of tissue. In some embodiments, extracted nucleic acids have an average yield of about 1400 ng / mg of tissue. In some embodiments, extracted nucleic acids have an average yield of about 1500 ng / mg of tissue.

[0287] The quality of extracted nucleic acids can be measured. In some embodiments, the quality of the nucleic acid may be quantified. For instance, the quality may be quantified via a 260 / 280 ratio. In some embodiments, the extracted nucleic acids have a 260 / 280 ratio of about 1 to about 10. In some embodiments, the extracted nucleic acids have a 260 / 280 ratio of at least 1.4. In some embodiments, the extracted nucleic acids have a 260 / 280 ratio of at least about 1.5. In some embodiments, the extracted nucleic acids have a 260 / 280 ratio of at least about 1.6. In some embodiments, the extracted nucleic acids have a 260 / 280 ratio of at least about 1.7. In some embodiments, the extracted nucleic acids have a 260 / 280 ratio of at least about 1.8. In some embodiments, the extracted nucleic acids have a 260 / 280 ratio of at least about 1.9. In some embodiments, the extracted nucleic acids have a 260 / 280 ratio of at least about 2. Nucleic acids extracted by the systems and methods described herein can be amplified with any quality.

[0288] An additional aspect of the present disclosure provides systems and methodswhich rapidly process a biological sample as described herein. In some embodiments, the systems and methods described herein process a biological sample in about 10 seconds to about 10 minutes. In some embodiments, the systems and methods described herein process a biological sample in about ten minutes or less. In some embodiments, the systems and methods described herein process a biological sample in about 1 minute to about 10 minutes. In some embodiments, the systems and methods described herein process a biological sample in about 1 minute to about 8 minutes. In some embodiments, the systems and methods described herein process a biological sample in about 5 minutes or less. In some embodiments, the systems and methods described herein process a biological sample in about 4 minutes or less. In some embodiments, the systems and methods described herein process a biological sample in about 3 minutes or less. In some embodiments, the systems and methods described herein process a biological sample in about 2 minutes or less. In some embodiments, the systems and methods described herein process processes a biological sample in about 1 minute or less. In some embodiments, the systems and methods described herein process processes a biological sample in about 10 minutes, about 9 minutes, about 8 minutes, about 7 minutes, about 6 minutes, about 5 minutes, about 4 minutes, about 3 minutes, about 2 minutes, about 1 minute, or less. In some embodiments, the systems and methods described herein process processes a biological sample in about 1 minutes, about 59 seconds, about 55 seconds, about 50 seconds, about 45 seconds, about 40 seconds, about 35 seconds, about 30 seconds, about 25 seconds, about 20 seconds, about 15 seconds, about 10 seconds, or less.

[0289] In some embodiments, the systems and methods described herein take about 1 minute to complete. In some embodiments, the systems and methods described herein take less than 1 minute to complete. In some embodiments, the systems and methods described herein take about 2 minutes to complete. In some embodiments, the systems and methods described herein take less than 5 minutes to complete. In some embodiments, the systems and methods described herein take about 20 minutes to complete. In other embodiments, the systems and methods described herein take about 10 to 40 minutes, or about 10 to 35 minutes, or about 10 to 30 minutes, or about 10 to 25 minutes, or about 10 to 20 minutes, or about 10 to 15 minutes, or about 15 to 40 minutes, or about 15 to 35 minutes, or about 15 to 30 minutes, or about 15 to 25 minutes, or about 15 to 20 minutes, or about 20 to 40 minutes, or about 20 to 35 minutes, or about 20 to 30 minutes, or about 20 to 25 minutes, or about 25 to 40 minutes, or about 25 to 35 minutes, or about 25 to 30 minutes, or about 30 to 40 minutes, or about 30 to 35 minutes, or about 35 to 40 minutes to complete. In furtherembodiments, the systems and methods described herein take about 10 minutes, about 15 minutes, about 20 minutes, about 25 minutes, about 30 minutes, about 35 minutes, or about 40 minutes to complete.

[0290] In some embodiments, a lysis buffer as described herein lyses the biological sample as described herein in less than about 1 minute. In some embodiments, a lysis buffer as described herein lyses the biological sample as described herein in less than about 30 seconds. In some embodiments, a biological sample is prepared prior to the addition of the lysis solution to the first channel. In some embodiments, a pestle prepares the biological sample. In some embodiments, the pestle prepares the biological sample by homogenizing the biological sample. In some embodiments, the pestle homogenizes the biological sample for less than about 1 minute. In some embodiments, the pestle homogenizes the biological sample for less than about 30 seconds. In some embodiments, solid beads, made of glass or metal, can be used inside the sample vial to lyse the samples more effectively.

[0291] An additional aspect of the present disclosure provides systems and methods provides for the rapid transfer of a biological sample as described herein from a first channel to a second channel. In some embodiments, transfer of a biological sample from a first channel to a second channel occurs in less than about 1 minute. In some embodiments, transfer of a biological sample from a first channel to a second channel occurs in less than about 30 seconds. In some embodiments, transfer of a biological sample from a first channel to a second channel occurs in less than about 10 seconds. In some embodiments, transfer of a biological sample from a first channel to a second channel occurs upon the inversion of a first channel over a second channel coupled thereto.

[0292] In some embodiments, a lysed biological sample is not incubated in a second channel before immediately moving to the next step. In some embodiments, a lysed biological sample is incubated in a second channel. In some embodiments, incubation can increase the amount of nucleic acids which bind to the cellulose substrate. In some embodiments, a second channel is rotated to lie flat to incubate a lysed biological sample. In some embodiments, a second channel is rested at room temperature to incubate a lysed biological sample. In some embodiments, a second channel is rotated to lie flat and rested at room temperature to incubate a lysed sample. In some embodiments, a lysed sample is incubated for a period of time of about 1 second to about 1 minute. In some embodiments, a lysed biological sample is incubated in the second chamber for a period of time of less than about 30 seconds.

[0293] In some embodiments, an elution solution and analytes bound to a substrate arenot incubated before immediately moving to the next step. In some embodiments, an elution solution and analytes bound to a substrate are incubated. In some embodiments, incubating an elution solution and analytes bound to a substrate can increase the quantity of analytes eluted. In some embodiments, a second channel is rotated to lie flat to incubate an elution solution and analytes bound to a substrate. In some embodiments, the second channel is rested at room temperature to incubate an elution solution and analytes bound to a substrate. In some embodiments, a second channel is rotated to lay flat and rested at room temperature to incubate an elution solution and analytes bound to a substrate. In some embodiments, an elution solution and analytes are incubated for a period of time of about 1 second to about 1 minute. In some embodiments, the elution solution and analytes are incubated for a period of time of less than about 30 seconds.

[0294] For instance, as depicted in FIG. 48, a workflow process, hereinafter (“System A”) may comprise: inserting a biological sample into a tube 3101 mechanically lysing (e.g., pestling) the biological sample for about 30 seconds 3102, adding a lysis solution as described herein to the tube and mixing the mechanically lysed biological sample and lysis solution 3103 to further lyse the biological sample, coupling a dropper cap onto the tube and rotating the tube over a housing, comprising a cellulose substrate, to transfer the lysed biological sample through the dropper cap into the housing 3104, laying the housing flat for a period of about 0 to about 30 seconds such as to allow the binding of nucleic acids of the biological sample to the cellulose substrate of the housing 3105, inverting the housing to discard unbound biological sample and lysate from the housing 3106, coupling a connector to the second housing such as to couple the housing to a vial comprising an elution buffer 3107, rotating the vial 180° to transfer the elution buffer into the housing 3108, laying the housing flat for a time period of about 0 to about 30 seconds 3109, inverting the housing over the vial to transfer eluate from the housing to the vial 3110, discarding the housing 3111, and storing the extracted nucleic acids 3112.

[0295] In some embodiments, samples are processed according to the workflow, which is depicted in FIG. 49 (“Seek Extraction” can refer to any extraction method, system, etc., disclosed herein). In some embodiments, Seek Extraction comprises: collecting a biological or environmental sample, mixing the biological sample with a lysis solution, transferring the lysate to a lysate vial, pouring the contents of the lysate vial into an extraction unit, pouring the lysate solution back into the lysate vial, discarding the lysate vial, pouring an elution solution into the extraction unit to produce an eluate, and pouring the eluate into an elution vial, thereby extracting and purifying analytes from the biological sample.

[0296] In some embodiments, samples are processed according to the workflow, examples of which are depicted in FIG. 26A-FIG. 26C (“Seek Extraction” can refer to any extraction method, system, etc., disclosed herein). In some embodiments, Seek Extraction comprises attaching a Seek Extraction unit (comprising a binding substrate) vertically to a lysate vial containing a lysis solution of a biological or environmental sample, inverting the connected system to a position where the extraction unit is on the bottom, letting the lysate solution drop into the extraction unit via gravity and bind the analyte to the substrate, inverting the connected system again (by 180°) such that the lysate vial is on the bottom, letting the lysate solution drop back into the lysate vial via gravity, detaching the Seek Extraction Unit from the lysate vial, attaching the Seek Extraction unit vertically to an elute vial comprising an elution solution, inverting the connected system to a position where the extraction unit is on the bottom, letting the elution solution to drop into the extraction unit via gravity and eluting the analyte from the substrate, creating an eluate, inverting the connected system again (by 180°) such that the elute vial is on the bottom, letting the elution solution to drop back into the elute vial via gravity, thereby extracting and purifying analytes from the biological or environmental sample into the eluate in the elute vial.

[0297] In some embodiments, samples are pre-processed before moving to the sample processing workflow, depicted in FIG. 26A- FIG. 26C (“Seek Extraction” can refer to any extraction method, system, etc. disclosed herein). In some embodiments, Seek Extraction comprises: collecting a solid biological or environmental sample in a sample vial, mechanically lysing the sample with a pestle or metal bead, mixing the biological sample with a lysis solution, adding a cap containing a filtration substrate to the sample vial, transferring the lysate to a lysate vial by squeezing the sample vial. In some embodiments, the sample vial is discarded in an appropriate manner after transferring the contents to a lysate vial.

[0298] In some embodiments, samples are pre-processed according to the workflow, which is depicted in FIG 25B before moving to the sample processing workflow, depicted in FIG. 26A- FIG. 26C (“Seek Extraction” can refer to any extraction method, system, etc. disclosed herein). In some embodiments, Seek Extraction comprises collecting a swab sample from a biological or environmental specimen and mixing the swab sample with a lysis solution contained in a lysate vial and then discarding the swab in an appropriate manner. In some embodiments, the sample vial is discarded in an appropriate manner after transferring the contents to a lysate vial.

[0299] In some embodiments, samples are pre-processed according to the workflow,which is depicted in FIG 25C before moving to the sample processing workflow, depicted in FIG. 26A- FIG. 26C (“Seek Extraction” can refer to any extraction method, system, etc. disclosed herein). In some embodiments, Seek Extraction comprises collecting a fluid biological or environmental sample in a sample vial and transferring the sample to a lysate vial containing a lysis solution. In some embodiments, Seek Extraction comprises collecting a fluid biological or environmental sample in a sample vial containing a lysis solution, adding a cap containing a filtration substrate to the sample vial, and transferring the lysate to a lysate vial by squeezing the sample vial. In some embodiments, the sample vial is discarded in an appropriate manner after transferring the contents to a lysate vial.

[0300] In some instances, the target source is a human. In embodiments in which the target source is a human subject, one or more biological samples are collected from the human subject in which the one or more biological samples are appropriate for a target diagnostic test. The sample collection system may comprise one or more flocked swabs, one or more sample vials, one or more pestles, one or more capillary tubes, one or more syringes with needles, one or more devices, or any combination thereof. The one or more flocked swabs may be used for swab samples such as buccal, throat, nasal, nasopharyngeal, cervical, or vaginal samples. The one or more sample vials may be used for collecting tissue or solid organ samples, such as spleen, skin; and body fluid samples such as saliva, urine, or whole blood. The one or more pestles may be used for solid tissue grinding. The one or more capillary tubes may be used for whole blood collection, for instance, at a point-of-care setting. The one or more syringes with needles may be used for whole blood collection, for instance, at a point-of-care setting. The one or more devices may be used for blood collection, for instance, at a home setting or in a point-of-care setting. Following sample collection, the one or more biological samples may be processed as appropriate (e.g., tissue grinding) or may proceed without further processing. The one or more biological samples may be processed for nucleic acid extraction with application of an appropriate lysis buffer from a lysis buffer packet (a lysis buffer packet can comprise buffers as disclosed herein). The one or more biological samples plus lysis buffer may be transferred to a lysate vial. Nucleic acid (NA) extraction products from the one or more biological samples can be eluted to an eluate comprising the eluted NA sample which may then be transferred to one or more elution vials. Biological material remaining outside of the one or more elution vials may be transferred to a waste disposal bag.Buffers

[0301] The present disclosure provides a buffer for use with any one of the systems ormethods as described herein. For instance, the system may comprise any one of the devices as described herein. In some embodiments, the sample comprises a biological or an environmental sample and / or a lysis buffer. The sample may be added either directly or indirectly to the isolation chamber or the first chamber. In embodiments in which the sample is indirectly added to said chambers, a first vial may be used.

[0302] In some embodiments, the first vial can be made with a material, e.g., a flexible material, such that the first vial may be used as an actuator itself to transfer liquid into or out of the device. In such cases, there might not be an actuator inside the device itself, e.g., an internal actuator. The first vial can attach fluidly to the device either directly or by using an adaptor cap or unit. In some embodiments, the first vial is configured to house a lysis buffer before the addition of the biological sample. The first vial may or may not house the lysis buffer before the addition of a biological sample. The first vial can also be part of an acquisition system, e.g., a vial to collect a saliva or blood sample.

[0303] In some embodiments, the first vial may be used to lyse the sample (e.g., a biological or environmental sample) outside of the device by mechanical or chemical methods or some combination thereof. Then, the lysate may be transferred into the device by squeezing it (e.g., with a drip tube). In some embodiments, the vial can have a cap or adaptor unit to fluidly connect to the device. In some embodiments, the adaptor may further comprise a filter element to filter out specific components of the lysate from entering the device.

[0304] In some embodiments, after the binding step, the first vial may be used as a waste vial to get the lysate out of the device. In some embodiments, the waste vial can be a separate vial from the first vial. The vials can attach fluidly to the device either directly or by using an adaptor cap or unit.

[0305] In some embodiments, an additional second or third vial may be used and may contain an elution buffer (e.g., an elution vial). In some embodiments, the elution buffer may comprise an amplification reaction buffer, which can perform the dual role of eluting DNA / RNA from the binding membrane and then mixing with separate amplification components and starting an amplification reaction. The elution vial can attach fluidly with the device either directly or using a cap or adaptor. The elution vial may be made with a material, e.g., a flexible material, such that the elution vial may be used as an actuator itself to transfer liquid (e.g., the elution buffer) into or out of the device so it can elute the DNA / RNA from the binding component.

[0306] Buffers as described herein can be used with any of the systems, method or kits as described herein. Systems as described herein may further comprise one or more actuatorsinside or outside (e.g., an internal actuator or an external actuator). The one or more actuators may be configured to move a fluid through each of the aforementioned chambers. The fluid may be a buffer. For instance, the devices and systems described herein may comprise multiple aliquoting systems. Each aliquoting system may be fluidly connected to an amplification chamber and / or detection chamber (e.g., detection units). In other embodiments, the devices and systems described herein may comprise a single aliquoting system that is attached to multiple amplification chambers and / or detection chambers (e.g., detection units). An aliquoting system as described herein may be fluidly connected to any buffer as described herein.

[0307] The present disclosure also features lysis buffers for use with the methods and / or systems of isolating and / or extracting described herein. Lysis buffers are well known to one of ordinary skill in the art. A lysis buffer may comprise, for example, a solution that comprises a buffering agent and a salt (or a combination of salts). In some embodiments, the lysis buffer comprises a solution that comprises one or more buffering agents and one or more salts. In some embodiments, the lysis buffer further comprises a chelating agent. In some embodiments, the lysis buffer comprises a detergent. In some embodiments, the lysis buffer further comprises antifoaming agents. In some embodiments, the lysis buffer further comprises additional additives, e.g., DNA binding enhancers, chaotropic agents, enzymes (Proteinase K, Protease, Pronase, etc.), or a combination thereof. Commercially available lysis buffers are also within the scope of the present disclosure. In some embodiments, the systems and devices herein are not depending on the pH of the lysis buffer. As a non-limiting example, a lysis buffer may comprise Tris and NaCl. Another non-limiting example includes a lysis buffer comprising PBS.

[0308] In some embodiments, a first channel receives a lysis solution. As described herein, a selected lysis solution provided herein can lyse any biological samples as described herein. A lysis solution may include any solution which can lyse a biological sample. As described herein, a lysis solution provided herein can lyse biological samples described herein to provide analytes of the biological sample for binding to a cellulose substrate described herein.

[0309] In some embodiments, a lysis solution has a neutral pH. In some embodiments, a lysis solution has an acidic pH. In some embodiments, the lysis solution has a pH of about 1 to about 7. In some embodiments, the lysis solution has a pH of about 1 to about 2, about 1 to about 3, about 1 to about 4, about 1 to about 5, about 1 to about 6, about 1 to about 7, about 2 to about 3, about 2 to about 4, about 2 to about 5, about 2 to about 6, about 2 to about 7, about3 to about 4, about 3 to about 5, about 3 to about 6, about 3 to about 7, about 4 to about 5, about 4 to about 6, about 4 to about 7, about 5 to about 6, about 5 to about 7, or about 6 to about 7. In some embodiments, the lysis solution has a pH of about 1, about 2, about 3, about 4, about 5, about 6, or about 7. In some embodiments, the lysis solution has a pH of at least about 1, about 2, about 3, about 4, about 5, or about 6. In some embodiments, a lysis solution has a pH of at most about 2, about 3, about 4, about 5, about 6, or about 7. In some embodiments, a lysis solution has a pH of about 7.5.

[0310] In some embodiments, a lysis solution has an alkaline pH. In some embodiments, the lysis solution has a pH of about 7 to about 14. In some embodiments, the lysis solution has a pH of about 7 to about 8, about 7 to about 9, about 7 to about 10, about 7 to about 11, about 7 to about 12, about 7 to about 13, about 7 to about 14, about 8 to about 9, about 8 to about 10, about 8 to about 11, about 8 to about 12, about 8 to about 13, about 8 to about 14, about 9 to about 10, about 9 to about 11, about 9 to about 12, about 9 to about 13, about 9 to about 14, about 10 to about 11, about 10 to about 12, about 10 to about 13, about 10 to about 14, about 11 to about 12, about 11 to about 13, about 11 to about 14, about 12 to about 13, about 12 to about 14, or about 13 to about 14. In some embodiments, the lysis solution has a pH of about 7, about 8, about 9, about 10, about 11, about 12, about 13, or about 14. In some embodiments, the lysis solution has a pH of at least about 7, about 8, about 9, about 10, about 11, about 12, or about 13. In some embodiments, the lysis solution has a pH of at most about 8, about 9, about 10, about 11, about 12, about 13, or about 14. In some embodiments, a lysis solution has a pH of about 8. In some embodiments, a chemical lysis buffer has a lysis solution with an alkaline pH. In some embodiments, a chemical lysis buffer comprises NaOH. In some embodiments, NaOH concentration in the alkaline lysis buffer solution is between about 0.2 M to about 2.0 M. In some embodiments, NaOH concentration in the alkaline lysis buffer solution is between about 0.2 M to about 1.0 M. In some embodiments, NaOH concentration in the alkaline lysis buffer solution is between about 0.5 M to about 1.5 M. In some embodiments, NaOH concentration in the alkaline lysis buffer solution is between about 0.4 M to about 0.6 M. In some embodiments, NaOH concentration in the alkaline lysis buffer solution is about 0.1 M, 0.2 M, 0.25 M, 0.3 M, 0.35 M, 0.4 M, 0.45 M, 0.5 M, 0.55 M, 0.6 M, 0.65 M, 0.7 M, 0.75 M, 0.8 M, 0.85 M, 0.9 M, 0.95 M, 1.0 M, 1.05 M, 1.1 M, 1.15 M, 1.2 M, 1.25 M, 1.3 M, 1.35 M, 1.4 M, 1.45 M, 1.5 M, 1.6 M, 1.7 M, 1.8 M, 1.9 M, or 2 M. In some embodiments, NaOH concentration in the alkaline lysis buffer solution is about 1.0 M. In some embodiments, NaOH concentration in the alkaline lysis buffer solution is about 0.5 M. In some embodiments, a chemical lysis buffer comprises adetergent. In some embodiments, the detergent is a nonionic surfactant. In some embodiments, the detergent is a poly(ethylene glycol) derivative. In some embodiments, the detergent is an octoxynol. In some embodiments, the detergent is a long-chain octoxynol. In some embodiments, the long-chain octoxynol is selected from octoxynol-9, octoxynol-10, octoxynol-11, octoxynol-12, octoxynol-13, octoxynol-16, octoxynol-20, octoxynol-25, octoxynol-30, octoxynol-33, octoxynol-40, or octoxynol-70. In some embodiments, the detergent is an octoxynol-9. In some embodiments, the detergent comprises Triton-X 100. In some embodiments, the detergent is the IUPAC name 2-[4-(2,4,4-trimethylpentan-2- yl)phenoxy]ethanol. In some embodiments, the detergent comprises Tween80. In some embodiments, Tween80 is at a concentration of about 0.025% v / v to about 0.5% v / v. In some embodiments, Tween80 is at a concentration of about 0.025% v / v, about 0.05% v / v, about 0.075% v / v, about 0.1% v / v, about 0.2% v / v, about 0.3% v / v, about 0.4% v / v, or about 0.5% v / v. In some embodiments, the detergent comprises Tween20. In some embodiments, the detergent comprises Cetyltrimethylammonium bromide (CTAB). In some embodiments, the detergent comprises SDS. In some embodiments, Triton-X 100 is present at a concentration of about 0.5% to about 2%. In some embodiments, Triton-X 100 is present at a concentration of about 1.0% to about 1.5%. In some embodiments, Triton-X 100 is present at a concentration of about 0.025% v / v to about 0.5% v / v. In some embodiments, Tween80 is at a concentration of about 0.025% v / v, about 0.05% v / v, about 0.075% v / v, about 0.1% v / v, about 0.2% v / v, about 0.3% v / v, about 0.4% v / v, or about 0.5% v / v, about 1% v / v, about 1.5% v / v, or about 2% v / v. In some embodiments, Triton-X 100 is present at a concentration of about 1.25%. In some embodiments, a chemical lysis buffer comprises an antifoam reagent. In some embodiments, the antifoam reagent is Commercial (Pond) Antifoam. In some embodiments, the antifoam reagent is present at a concentration of about 0% to about 2.0%. In some embodiments, the antifoam reagent is present at a concentration of about 0.05% to about 2.0%. In some embodiments, the antifoam reagent is present at a concentration of about 0.5%. In some embodiments, the antifoam reagent is present at a concentration of about 1.0%. In some embodiments, the antifoam reagent is present at a concentration of about 1.5%. In some embodiments, the antifoam reagent is present at a concentration of about 2.0%. In some embodiments, the lysis buffer is an enzymatic buffer. In some embodiments, the enzymatic buffer comprises lysozyme at a concentration of about 10 mg / mL - 150 mg / mL and one or more detergents. In some embodiments, the enzymatic buffer comprises lysozyme at a concentration of about 10 mg / mL - 150mg / mL and either Tween80 (0.05%-0.5%) or Tween80+Triton-X 100: 0.05% + 0.05%. In some embodiments,the enzymatic buffer comprises lysozyme at a concentration of about 50mg / mL and Tween80 (0.05%). In some embodiments, the enzymatic buffer comprises lysozyme at a concentration of about 50mg / mL, Tween80 (0.05%), and Triton-X 100 (0.05%). In some embodiments, the enzymatic buffer comprises lysozyme at a concentration of about lOmg / mL, about 20mg / mL, about 30mg / mL, about 40mg / mL, about 50mg / mL, about 60mg / mL, about 70mg / mL, about 80mg / mL, about 90mg / mL, about lOOmg / mL, about HOmg / mL, about 120mg / mL, about 130mg / mL, about 140mg / mL, or about 150mg / mL. In some embodiments, the enzymatic buffer comprises mutanolysin at about 10 units / uL. In some embodiments, the enzymatic buffer comprises lipase at about 10 units / uL. In some embodiments, the enzymatic buffer comprises esterase at about 1 mg / mL. In some embodiments, a dilution solution is added to the biological sample prior to coupling to the first channel in (a). In some embodiments, the dilution solution comprises a Tris-EDTA buffer. In some embodiments of systems described herein, the system comprises the alkaline lysis buffer solution, and wherein after the first channel is coupled to the biological sample in (a) the alkaline lysis buffer solution comprises: i) sodium hydroxide at a concentration of between about 0.1 M to about 1.0 M, ii) Triton-X 100 at a concentration of between about 0.25% to about 1.5%, iii) an antifoam reagent at a concentration between about 0.025% to about 1.0%, iv) Tris at a concentration of between about 0.5 mM to about 10 mM, v) EDTA as a concentration of between about 0.1 mM to about 1.0 mM, and vi) the biological sample. In some embodiments of systems described herein, the system comprises the alkaline lysis buffer solution, and wherein after the first channel is coupled to the biological sample in (a) the alkaline lysis buffer solution comprises: i) sodium hydroxide at a concentration of about 0.5 M, ii) Triton-X 100 at a concentration of about 0.75%, iii) an antifoam reagent at a concentration about 0.5%, iv) Tris at a concentration of about 5 mM, v) EDTA as a concentration of about 0.5 mM, and vi) the biological sample.

[0311] In some embodiments, a lysis solution comprises salts, sodium acetate, sodium chloride, sodium hydroxide, Tris, Tris HC1, NaCl, polysorbate (e.g., Tween 20), Triton-X 100, water, SDS, sodium dodecyl, glucose, DTT, guanidine hydrochloride, antifoam reagent, Tween80, Cetyltrimethylammonium bromide (CTAB), lysozyme, proteinase K, Mutanolysin, lipase, esterase, Sodium Metaperiodate, Hydrogen Peroxide, Sodium Hypochlorite, or Calcium Hypochlorite, or any combination thereof. In some embodiments, the lysis solution refers to the lysis buffer. In some embodiments, the lysis solution comprises salts. In some embodiments, the lysis buffer and / or lysis solution comprises Tris HC1. In some embodiments, the lysis buffer comprises Tris HC1 at a concentration of at least about 1millimolar (mM), about 5 mM, about 10 mM, about 15 mM, about 20 mM, about 25 mM, about 30 mM, about 50 mM, about 100 mM, about 150 mM, about 200 mM, about 250 mM, about 300 mM, about 350 mM, about 400 mM, about 450 mM, about 500 mM, about 550 mM, about 600 mM, about 650 mM, about 700 mM, about 750 mM, about 800 mM, about 850 mM, about 900 mM, about 950 mM, or about 1000 mM. In some embodiments, the lysis buffer comprises sodium chloride (NaCl) at a concentration of at least about 100 millimolar (mM), about 150 mM, about 200 mM, about 250 mM, about 300 mM, about 350 mM, about 400 mM, about 450 mM, about 500 mM, about 550 mM, about 600 mM, about 650 mM, about 700 mM, about 750 mM, about 800 mM, about 850 mM, about 900 mM, about 950 mM, or about 1000 mM. In some embodiments, the lysis buffer comprises sodium hydroxide (NaOH) at a concentration of at least about 100 millimolar (mM), about 150 mM, about 200 mM, about 250 mM, about 300 mM, about 350 mM, about 400 mM, about 450 mM, about 500 mM, about 550 mM, about 600 mM, about 650 mM, about 700 mM, about 750 mM, about 800 mM, about 850 mM, about 900 mM, about 950 mM, or about 1000 mM. In some embodiments, the lysis buffer comprises sodium hydroxide (NaOH) at a concentration of at least about 200 millimolar (mM).

[0312] In some embodiments, said chemical lysis solution or said enzymatic lysis solution comprises sodium hydroxide (NaOH) at a concentration of at least about 100 millimolar (mM), about 150 mM, about 200 mM, about 250 mM, about 300 mM, about 350 mM, about 400 mM, about 450 mM, about 500 mM, about 550 mM, about 600 mM, about 650 mM, about 700 mM, about 750 mM, about 800 mM, about 850 mM, about 900 mM, about 950 mM, or about 1000 mM. In some embodiments, said chemical lysis solution or said enzymatic lysis solution comprises sodium hydroxide (NaOH) at a concentration of at least about 200 millimolar (mM).

[0313] In some embodiments, the lysis buffer and / or lysis solution comprises a reducing agent. In some embodiments, the reducing agent comprises DTT. In some embodiments, the lysis buffer and / or lysis solution comprises DTT at a concentration of at least about 1 millimolar (mM), about 5 mM, about 10 mM, about 15 mM, about 20 mM, about 25 mM, about 30 mM, about 35 mM, or about 40 mM. In some embodiments, the reducing agent comprises TCEP. In some embodiments, the lysis buffer and / or lysis solution comprises TCEP at a concentration of at least about 1 millimolar (mM), about 5 mM, about 10 mM, about 15 mM, about 20 mM, about 25 mM, about 30 mM, about 35 mM, about 40 mM, about 50 mM, about 60 mM, about 70 mM, about 80 mM, about 90 mM, or about 100 mM. In some embodiments, the lysis buffer and / or lysis solution comprises PBS. In someembodiments, the lysis buffer and / or lysis solution comprises PBS at a concentration of at least about 1 millimolar (mM), about 5 mM, about 10 mM, about 15 mM, about 20 mM, about 25 mM, about 30 mM, about 35 mM, about 40 mM, about 50 mM, about 60 mM, about 70 mM, about 80 mM, about 90 mM, or about 100 mM.

[0314] Provided herein, in some aspects, are compositions for processing a biological sample, the composition comprising: (a) sodium hydroxide (NaOH) at a concentration of about 0.2 to about 2 molar (M) of the composition; and (b) triton-X 100 at a concentration of about 0.5% v / v to about 2% v / v of the composition. In some embodiments, the composition further comprises antifoam at a concentration of about 0.01 % v / v to about 2% v / v of the composition. In some embodiments, sodium hydroxide (NaOH) is at a concentration of about 1 molar of the composition; triton-X 100 is at a concentration of about 1.5% v / v of the composition; and antifoam is at a concentration of about 1 % v / v to about 2% v / v of the composition. Provided herein, in some aspects, are compositions for processing a biological sample, the composition comprising: (a) lysozyme at a concentration of about 10 mg / mL to about 150mg / mL; and (b) detergent, wherein the detergent comprises: (i) tween80 at a concentration of about 0.05 to about 0.5% of the composition; (ii) triton-X 100 at a concentration of about 0.05 to about 0.5% of the composition; or (iii) any combination of (i) and (ii). In some embodiments, lysozyme is at a concentration of about 50 mg / mL of the composition; and tween80 is at a concentration of about 0.05% of the composition. In some embodiments, lysozyme is at a concentration of about 50 mg / mL of the composition; tween80 is at a concentration of about 0.05% of the composition; and triton-X 100 at a concentration of about 0.05% of the composition. Provided herein, in some aspects, are compositions for processing a biological sample, the composition comprising: (a) sodium hydroxide (NaOH) at a concentration of about 0.2 molar to about 2 molar (M) of the composition; (b) triton-X 100 at a concentration of about 0.5% v / v to about 2% v / v of the composition; (c) antifoam at a concentration of about 0.01 % v / v to about 2% v / v of the composition; (d) lysozyme at a concentration of about lOmg / mL to about 150mg / mL of the composition; and (e) tween80 at a concentration of about 0.05 to about 0.5% of the composition. In some embodiments, lysozyme is at a concentration of about 50 mg / mL; tween80 is at a concentration of about 0.05% of the composition; sodium hydroxide (NaOH) is at a concentration of about 1 molar of the composition; and triton-X 100 at a concentration of about 1.5% of the composition; and antifoam is at a concentration of about 1 % v / v of the composition. Provided herein, in some aspects, are compositions for processing a biological sample, the composition comprising: (a) Tris HC1 at a concentration of about 10 millimolar(mM) to about 100 mM of the composition; (b) NaCl at a concentration of about 25 mM to about 500 mM of the composition; (c) triton x-100 at a concentration of about 0.1% to about 5% of the composition; and (d) TCEP at a concentration of about 1 mM to about 100 mM of the composition. In some embodiments, Tris HC1 is at a concentration of about 25 mM of the composition. In some embodiments, NaCl is at a concentration of about 300 mM of the composition. In some embodiments, triton x-100 is at a concentration of about 1% of the composition. In some embodiments, TCEP is at a concentration of about 20 mM of the composition.

[0315] Table 1 provides examples of lysis buffers that can be used with any one of the systems and methods disclosed herein. In some embodiments of systems and methods described herein, a lysis buffer is selected for use to extract nucleic acid from a particular biological sample. In some embodiments of systems and methods described herein, a lysis buffer is selected for use to extract nucleic acid from a biological sample for the assay and detection of a particular target nucleic acid sequence. In some embodiments of systems and methods described herein, a lysis buffer is selected for use to extract nucleic acid from a biological sample for the assay and detection of a pathogenic bacterium target nucleic acid sequence. In some embodiments of systems and methods described herein, a lysis buffer is selected for use to extract nucleic acid from a biological sample for the assay and detection of a Mycobacterium tuberculosis (MTB) target nucleic acid sequence. In some embodiments, the MTB target nucleic acid sequence resides within an MTB gDNA target region. In some embodiments, the lysis buffer is a chemical lysis buffer. In some embodiments, the chemical lysis buffer is an acidic lysis buffer. In some embodiments, the chemical lysis buffer is a neutral lysis buffer. In some embodiments, the chemical lysis buffer is an alkaline lysis buffer. In some embodiments, the lysis buffer is an enzymatic lysis buffer. In some embodiments, the lysis buffer comprises a chemical lysis buffer and an enzymatic lysis buffer. In some embodiments, the lysis buffer uses sequential lysis with enzymatic lysis buffer used first, followed by used of a chemical lysis buffer. Examples of lysis buffers and their components may be found at Table 1.Table 1. List of Lysis Buffers and Their ComponentsAmplification

[0316] Provided herein are systems for amplification, isolation, extraction, and / or detection of a biological sample. In some embodiments, the systems as described herein are for amplification, isolation, extraction, and / or detection of a target region of a nucleic acid molecule. In some embodiments, the method comprises amplifying a target nucleic acid sequence located within the target region. In some embodiments, the method comprises amplifying a target nucleic acid sequence at an ambient temperature. In some embodiments, the target region is on a single-stranded DNA. In some embodiments, the target region is on a double-stranded nucleic acid (dsDNA). In some embodiments, the target region is on an RNA. In some embodiments, the target region is on a genomic DNA (gDNA). In some embodiments, the DNA sequence or RNA sequence is animal genomic DNA or genomic RNA. In some embodiments, the DNA sequence or RNA sequence is mammalian genomic DNA or genomic RNA. The present disclosure provides system for amplifying a target nucleic acid sequence. The systems disclosed herein can utilize any components (e.g., oligonucleotides, labels, enzymes, samples, etc.), methods, devices, and / or kits disclosed herein. In some embodiments, the present disclosure provides systems for amplifying a target nucleic acid sequence at an ambient temperature. The target nucleic acid sequence can be isolated and processed from a biological sample. In some embodiments, the system comprises a first oligonucleotide (Pl). In some embodiments, the Pl binds to a strand of the target nucleic acid sequence. In some embodiments, the system comprises a second oligonucleotide (P2). In some embodiments, the P2 binds to another strand of the target nucleic acid sequence. In some embodiments, the system comprises a third oligonucleotide. In some embodiments, the third oligonucleotide binds to the target nucleic acid sequence. In some embodiments, the third oligonucleotide comprises a 3' end blocking feature that blocks extension of the third oligonucleotide by a polymerase. In some embodiments, the third oligonucleotide does not facilitate a localizing and a binding of P2 to the target nucleic acid sequence. In some embodiments, a 5' end of the third oligonucleotide and a 5' end of the Pl bind to the strand of the target nucleic acid sequence at a distance from about 3 nucleotides toabout 25 nucleotides apart. In some embodiments, the system comprises a polymerase. In some embodiments, the system comprises a DNA processing enzyme to the target nucleic acid sequence. In some embodiments, the system comprises nucleotides in an amount sufficient to support amplification of the target region. In some embodiments, the system of amplification is conducted in an absence of a denaturing of the target nucleic acid. In some embodiments, the Pl localizes and binds to the strand of the target nucleic acid sequence independently of the third oligonucleotide. In some embodiments, the P2 localizes and binds to the other strand of the target nucleic acid sequence independently of the third oligonucleotide. In some embodiments, a 5’ end of a third primer (P3) binds to the strand of the target nucleic acid sequence.

[0317] This disclosure further provides details of an ambient temperature nucleic acid amplification platform that can include a detection probe in reaction (e.g., in-reaction detection probe). This isothermal amplification platform described in this disclosure can refer to Seek Amplification or Seeklt Amplification, among other amplification methods, systems, devices and / or kits disclosed herein. Similarly, Seek Amplification, Seeklt Amplification, and similar language can refer to any of the extraction methods, devices, systems, and / or kits disclosed herein. In some embodiments in the present disclosure, the in-reaction detection probe also decreases non-specific amplification by increasing specific primer annealing or annexation, thereby becoming an annexing probe (e.g., a labelled annexing oligonucleotide). In such cases, the isothermal amplification system described in the disclosure can refer to Annexing Isothermal Nucleotide Amplification (ANINA). In some embodiments, methods and systems for amplification to further increase specificity and sensitivity by using an annexing probe approach can refer to Annexing Isothermal Nucleotide Amplification (ANINA).

[0318] Described herein are methods and / or systems for processing one or more analytes. In an aspect described herein are methods and / or systems for processing an analyte comprising: (a) binding the analyte to a channel comprising a nucleic acid binding substrate coupled thereto; (b) extracting a target nucleic acid sequence comprising a first oligonucleotide target, a second oligonucleotide target, and a third oligonucleotide target from the first analyte; (c) binding an oligonucleotide primer to a strand of the first oligonucleotide target; (d) bringing into contact with the third oligonucleotide target a third oligonucleotide, and blocking an extension of the third oligonucleotide by a DNA polymerase, wherein the third oligonucleotide does not facilitate a localizing or a binding of the oligonucleotide primer to the first oligonucleotide target; (e) using a DNA polymeraseand a DNA processing enzyme to amplify the target nucleic acid sequence; (f) providing a label to the amplified target nucleic acid sequence; and g) detecting the labeled amplified target nucleic acid sequence in real-time. In some embodiments, the target nucleic acid sequence to be amplified comprises the DNA sequence of at least two of the first oligonucleotide target, the second oligonucleotide target, and the first oligonucleotide target. In some embodiments, the target nucleic acid sequence to be amplified comprises the DNA sequence of the first oligonucleotide target, the second oligonucleotide target, and the first oligonucleotide target. In some embodiments, an oligonucleotide comprise sequence complementarity to the first oligonucleotide target. In some embodiments, a second oligonucleotide comprises sequence complementarity to the second oligonucleotide target. In some embodiments, a third oligonucleotide comprise sequence complementarity to the third oligonucleotide target. In some embodiments, a fourth oligonucleotide that comprises sequence complementarity to a fourth oligonucleotide target is used in the method for processing the analyte. In some embodiments, at least two of the first oligonucleotide, the second oligonucleotide, the third oligonucleotide, and the fourth oligonucleotide function as oligonucleotide primers during initiation of DNA replication. The DNA polymerase can begin DNA replication near the binding site of an oligonucleotide by adding nucleotides to a 3 ’-OH end of a bound primer. In some embodiments, the method further comprises: (h) binding a second oligonucleotide primer to a strand of a second oligonucleotide target, wherein a 5’ end of the third oligonucleotide and a 5' end of the second oligonucleotide primer bind to the strand of the target nucleic acid sequence at a distance of about 3 nucleotides to about 25 nucleotides apart. In some embodiments, the 5' end of the third oligonucleotide and the 3’ end of the second oligonucleotide bind to the strand of the target nucleic acid sequence with 1 or more base pair (bp) of overlap. In some embodiments, the 5' end of the third oligonucleotide and the 3’ end of the second oligonucleotide bind to the strand of the target nucleic acid sequence with 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 base pair (bp) of overlap. In some embodiments, the 5' end of the third oligonucleotide and the 3’ end of the second oligonucleotide are adjacent and bind to the strand of the target nucleic acid sequence. In some embodiments, the 5' end of the third oligonucleotide and the 3’ end of the second oligonucleotide bind to the strand of the target nucleic acid sequence with a gap in contiguous sequence of the target nucleic acid sequence of between about 1-9 bp. In some embodiments, the third oligonucleotide comprises a 3’ blocking feature that blocks nucleotide extension of the DNA polymerase. In some embodiments, the 3' end blocking feature that blocks extension of the third oligonucleotideby a DNA polymerase comprises an inverted nucleotide or a C3 -spacer. In some embodiments, the DNA processing enzyme is comprised in an enzyme mix. In some embodiments, the enzyme mix comprises a DNA polymerase or functional fragment thereof, the DNA processing enzyme, one or more nucleotides in an amount sufficient to support amplification of the target nucleic acid sequence, a single-strand binding protein, a crowding reagent, a magnesium salt or any combination thereof. In some embodiments, the DNA processing enzyme facilitates the binding of the first oligonucleotide to the first oligonucleotide target, the second oligonucleotide to the second oligonucleotide target, or the third oligonucleotide to the third oligonucleotide target. In some embodiments the target nucleic acid sequence is amplified at an ambient temperature. In some embodiments, the method of processing results in an amplified target nucleic acid sequence. In some embodiments, the method of processing results in target single-stranded (ss) amplicons. In some embodiments, the method of processing results in target double-stranded (ds) amplicons. In some embodiments, the method of processing results in target ds amplicons and target ss amplicons. In some embodiments, the first oligonucleotide, the second oligonucleotide, or the third oligonucleotide comprises a label. In some embodiments, the first oligonucleotide comprises a first label, and wherein the third oligonucleotide comprises a second label. In some embodiments, the third oligonucleotide comprises a label at or near the 5’ end. In some embodiments, the third oligonucleotide promotes the localizing and binding of the second oligonucleotide to the second oligonucleotide target of the target nucleic acid sequence. In some embodiments, the third oligonucleotide promotes annealing specificity of the first oligonucleotide primer or the second oligonucleotide primer or both to the target nucleic acid sequence. In some embodiments, the detecting in (g) is conducted at a clinical laboratory testing location or at a hospital to provide a molecular diagnostic near point-of-need (PON) test. In some embodiments, the molecular diagnostic near PON tests for a range of pathogens selected from Table 2, Table 3, Table 4, Table 5, or Table 6, or any combination thereof. In some embodiments, the molecular diagnostic near PON tests for a one or more viral pathogens selected from IAV, IBV, RSV, SARS-CoV2, HPIV, Rhinovirus, Adenovirus and one or more bacterial pathogens selected from Streptococcal sp, and Mycobacterium tuberculosis (MTB). In some embodiments, the viral pathogen is IAV and wherein the specific strain of Influenza A virus is H1N1, H5N1, or H3N7. In some embodiments, the molecular diagnostic near PON tests for a range of bacterial pathogens and is configured to identify presence of one or more antibiotic resistance genes. In some embodiments, the method is conducted at a veterinary facility or on a farm, wherein thesample is derived from an animal, and wherein the processing allows for monitoring of animal health or disease surveillance at a farm. In some embodiments, the sample is derived from a shrimp, and wherein random shrimp testing or water testing from each pond in an aquaculture farm is used to detect for presence of two or more pathogens, wherein the two or more pathogens are selected from WSSV, YHV, TSV, IMNV, IHHNV, WFSV, CMNV, and Vibrio parahaemolyticus. In some embodiments, the method is conducted near a body of water for monitoring water bodies for presence of Giardia, Cryptosporidium, Naegleria fowleri, or Cyanobacteria, or any combination thereof. In some embodiments, the method is conducted near a food production facility for monitoring meat products for presence of Salmonella sp, Listeria sp, or Chronobacter sp, or any combination thereof. In some embodiments, the label in (f) comprises a fluorescent DNA-binding dye. In some embodiments, the label in (f) comprises a quencher and FRET label. In some embodiments, the label in (f) comprises a quencher and a fluorophore, and wherein the label is attached to the oligonucleotide primer, and wherein the oligonucleotide primer is a chimeric primer comprising one or more ribonucleotides and one or more deoxyribonucleotides. In some embodiments, the quencher is attached to an internal region of the chimeric primer and wherein the fluorophore attached to the 5’ end of the chimeric primer. In some embodiments, the labeled amplified target nucleic acid sequence is detected in (g) in real-time by measuring a level of fluorescence of unquenched fluorophore. In some embodiments, amplicon length of amplified target nucleic acid sequence is gradually decreased as target nucleic acid sequence amplification proceeds. In some embodiments, the real-time detecting in (g) provides a quantitative measurement of an initial concentration of the analyte prior to target nucleic acid sequence amplification. In some embodiments, the quantitative measurement is provided in less than about 90 minutes, less than about 80 minutes, less than about 70 minutes, less than about 60 minutes, less than about 55 minutes, less than about 50 minutes, less than about 45 minutes, less than about 30 minutes, less than about 25 minutes, less than about 20 minutes, less than about 15 minutes, less than about 12 minutes, less than about 10 minutes, or less than about 5 minutes after the start of the using the DNA polymerase and the DNA processing enzyme in In some embodiments, the quantitative measurement is provided in less than about 45 minutes, less than about 30 minutes, less than about 25 minutes, less than about 20 minutes, less than about 15 minutes, less than about 12 minutes, less than about 10 minutes, or less than about 5 minutes after the start of the using the DNA polymerase and the DNA processing enzymein (e). In some embodiments, the nucleic acid binding substrate comprises cellulose.

[0319] In some embodiments, the amplification chamber may comprise one or more amplification reaction components, which may comprise enzymes and other materials to amplify the DNA / RNA target. The amplification reaction components may comprise one or more enzymes, such as a DNA / RNA polymerase, a recombinase, a single-strand binding enzyme, etc. The amplification mix may also comprise oligonucleotides, such as primers and probes. In some embodiments, the oligonucleotides aid or are required for efficient amplification of the DNA / RNA target. The amplification mix may be preloaded in the amplification chamber or can be added by the user via the aliquoting chamber. The amplification mix may comprise a liquid component, lyophilized component, or a combination thereof. The elution buffer from the previous section can include an amplification reaction buffer, which can perform the dual role of eluting DNA / RNA from the binding membrane and then mixing with separate amplification components and starting an amplification reaction. In some embodiments, the amplification reaction buffer may comprise magnesium. In other embodiments, the amplification reaction buffer contains no magnesium. In some embodiments, the elution buffer comprises an amplification reaction buffer with or without magnesium, acetate, or other amplification reagents that cannot be lyophilized. In some embodiments, an amplification of extracted nucleic acids determines presence or absence of a target sequence. In some embodiments, the amplification produces detectable amplified target sequence in less than about 60, 55, 50, 45, 40, 35, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, or 8 minutes following the start of the amplification reaction. In some embodiments, detection of detectable amplified target sequence determines the presence of a pathogenic bacterium in the biological sample. In some embodiments, a lack of detection of amplified target sequence determines the absence of a pathogenic bacterium in the biological sample. In some embodiments, detection of detectable amplified target sequence determines the presence of Mycobacterium tuberculosis in the biological sample. In some embodiments, a lack of detection of amplified target sequence determines the absence of Mycobacterium tuberculosis in the biological sample.

[0320] The amplification reaction buffer can also be added by a separate chamber, if needed, which can be kept separate from the amplification chamber until needed. In case the amplification mix is a lyophilized component, the amplification reaction buffer can also perform an additional function of a rehydration buffer, which can hydrate the lyophilized amplification components in the amplification chamber and start the amplification reaction.

[0321] An additional aspect of the present disclosure provides systems and methodsprovides for the rapid transfer of a biological sample as described herein from a first channel to a second channel. In some embodiments, transfer of a biological sample from a first channel to a second channel occurs in less than about 1 minute. In some embodiments, transfer of a biological sample from a first channel to a second channel occurs in less than about 30 seconds. In some embodiments, transfer of a biological sample from a first channel to a second channel occurs in less than about 10 seconds. In some embodiments, transfer of a biological sample from a first channel to a second channel occurs upon the inversion of a first channel over a second channel coupled thereto.

[0322] In some embodiments, a lysed biological sample is incubated in a second channel. Incubation can increase the quantities of nucleic acids which bind to the cellulose substrate. In some embodiments, a second channel is rotated to lie flat to incubate a lysed biological sample. In some embodiments, a second channel is rested at room temperature to incubate a lysed biological sample. In some embodiments, a second channel is rotated to lie flat and rested at room temperature to incubate a lysed sample. In some embodiments, a lysed sample is incubated for a period of time of about 1 second to about 1 minute. In some embodiments, a lysed biological sample is incubated in the second chamber for a period of time of less than about 30 seconds.

[0323] In some embodiments, an elution solution and analytes bound to a substrate are incubated. Incubating an elution solution and analytes bound to a substrate can increase the amount of analytes eluted. In some embodiments, a second channel is rotated to lie flat to incubate an elution solution and analytes bound to a substrate. In some embodiments, the second channel is rested at room temperature to incubate an elution solution and analytes bound to a substrate. In some embodiments, a second channel is rotated to lay flat and rested at room temperature to incubate an elution solution and analytes bound to a substrate. In some embodiments, an elution solution and analytes are incubated for a period of time of about 1 second to about 1 minute. In some embodiments, the elution solution and analytes are incubated for a period of time of less than about 30 seconds.

[0324] In some embodiments, amplified nucleic acids determine the presence of a target sequence in a sample. A target sequence can indicate the presence of a disease. In some embodiments, a target sequence is a nucleic acid sequence of a virus. In some embodiments, a target sequence is a nucleic acid sequence of African Swine Fever Virus. In some embodiments, a target sequence is a nucleic acid sequence of White Spot Syndrome Virus. In some embodiments, a target sequence is a nucleic acid sequence of Respiratory Syncytial Virus (RSV). In some embodiments, a target sequence is a nucleic acid sequence ofInfluenza. In some embodiments, a target sequence is a nucleic acid sequence of Epstein-Barr Virus (EBV).

[0325] A target sequence can indicate the presence of a disease or disorder. For example, the disease or disorder may be an infection. In some embodiments, a target sequence is a nucleic acid sequence of a virus. In some embodiments, a target sequence is a nucleic acid sequence of a bacteria. In some embodiments, a target sequence is a nucleic acid sequence of a bacteria that causes a sexually transmitted infection or sexually transmitted disease. In some embodiments, a target sequence is a nucleic acid sequence of a gonorrhea bacteria. In some embodiments, a target sequence is a nucleic acid sequence of an HIV virus. In some embodiments, a target sequence is a nucleic acid sequence of a herpes virus. In some embodiments, a target sequence is a nucleic acid sequence of chlamydia bacteria. In some embodiments, a target sequence is a nucleic acid sequence of a syphilis bacteria.

[0326] A target sequence can indicate a presence of a genetic trait. In some embodiments, a target sequence is a nucleic acid sequence which indicates the presence of a genetic trait. In some embodiments, a target sequence is a nucleic acid sequence which indicates the presence of photic sneeze. In some embodiments, a target sequence is a nucleic acid sequence which indicates the presence of alcohol flush.

[0327] The present disclosure may also feature a method of annexing isothermal (e.g., ambient temperature) nucleotide amplification for producing single-stranded and / or doublestranded amplicons of a target region of nucleic acid. The present disclosure may also feature a method of annexing isothermal nucleotide amplification for producing single-stranded and double-stranded amplicons of a target region of nucleic acid. The method may comprise introducing to a sample a system of primers as described herein, as well as an annexing oligonucleotide, and a solution comprising enzymes, dNTPs, and a buffer comprising buffering reagents, salts, and crowding reagents. Additionally, the method may comprise incubating the sample with the primers and solution at a reaction temperature for a length of time.

[0328] The present disclosure may also feature a method of asymmetric semi-nested isothermal nucleotide amplification for producing single-stranded amplicons and / or doublestranded amplicons of a target region of nucleic acid. The present disclosure may also feature a method of asymmetric semi-nested isothermal nucleotide amplification for producing single-stranded amplicons or double-stranded amplicons of a target region of nucleic acid. Without wishing to limit the present disclosure to any theory or mechanism, it is believed that to produce a certain amount (e.g., a specific ratio) of single-stranded amplicons and / ordouble-stranded amplicons, the ratio of the primers need to be adjusted.

[0329] In some embodiments, the method comprises maintaining the reaction conditions within a temperature range. In some embodiments, the temperature of the reaction admixture remains constant during the length of time of the reaction. In some embodiments, the temperature of the reaction admixture does not vary more than + / - 5° during the length of time of the reaction. In some embodiments, the method comprises maintaining the reaction conditions at a relatively constant temperature by placing the reaction admixture contained within a vessel at a location subject to ambient temperature or room temperature until the reaction has achieved sufficient amplification of the target. In some embodiments, a thermocycler is not used for the amplification reaction. In some embodiments, the doublestranded template to the target nucleic acid sequence has not been denatured by heat or by chemical denaturing prior to the reaction. In some embodiments, in-reaction target ds amplicons are not denatured by heat or by chemical denaturing during to the reaction.

[0330] In some embodiments, the method comprises incubating the reaction. In some embodiments, the incubation is not temperature controlled. In some embodiments, the incubation of the reaction is at an ambient temperature. In some embodiments, the incubation results in an isothermal reaction. In some embodiments, the incubation is done at room temperature. In some embodiments, the sample is incubated at a reaction temperature range maintained within 18-40°C for the length of time. In some embodiments, the sample is incubated at a reaction temperature range maintained within 20-37°C for the length of time. In some embodiments, the sample is incubated at a room temperature for the length of time. In some embodiments, the sample is incubated at a reaction temperature range maintained within 22-25°C for the length of time. In some embodiments, the method comprises maintaining the reaction conditions at a relatively constant temperature by placing the reaction admixture contained within a vessel in a heating block set to maintain a selected temperature until the reaction has achieved sufficient amplification of the target. In some embodiments, the heating block is set to maintain about 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, or 45°C. In some embodiments, the reaction temperature range is an isothermal range. In some embodiments, the length of time is between about 5-60 minutes. In some embodiments, the length of time is between about 20- 40 minutes. In some embodiments, the length of time is about 30 minutes. In some embodiments, the methods and / or systems described herein do not require thermal melting of double-stranded amplicons.

[0331] In some embodiments of methods and / or systems described herein, one or moreamplicons is produced at a rate of amplification during the length of time of the reaction. In some embodiments, the target ss and ds amplicons and / or the two target ds amplicons are produced at least at a linear rate of amplification. In some embodiments, the target ds amplicons and / or the two target ds amplicons are produced at an exponential rate of amplification. In some embodiments, the target ss amplicons are produced at least at a linear rate of amplification. In some embodiments, the target ss amplicons are produced at an exponential rate of amplification. In some embodiments of methods and / or systems described herein, the reaction proceeds for a length of time. In some instances, the length of time is sufficient to achieve linear amplification of a target amplicon. In some instances, the length of time is sufficient to achieve linear amplification of more than one target amplicon. In some instances, the length of time is sufficient to achieve exponential amplification of a target amplicon. In some instances, the length of time is sufficient to achieve exponential amplification of more than one target amplicon. In some embodiments, a target amplicon is a ssDNA. In some embodiments, a target amplicon is a dsDNA. In some embodiments, the length of time is between about 1-60 minutes. In some embodiments, the length of time is between about 20-40 minutes. In some embodiments, the length of time is about 30 minutes. In some embodiments, the reaction is maintained for a length of time sufficient to replicate and amplify the target nucleic acid sequence. In some embodiments, the reaction is maintained for a length of time sufficient to replicate and amplify the target nucleic acid sequence to a level that is detectable.

[0332] The present disclosure provides oligonucleotides for amplification, isolation, extraction, and / or detection of a biological sample. In some embodiments, oligonucleotides as described herein can be used in methods and / or systems for amplification as described herein. For instance, an oligonucleotide as described herein can be a primer, a target nucleic acid sequence, DNA, RNA, a single-stranded oligonucleotide, and / or a double-stranded oligonucleotide. In some embodiments, the systems or methods described herein comprise one or more oligonucleotides. Examples of amplification methods and systems that can be used with methods and systems as described herein may be found at, for instance, PCT / US2024 / 047823, which is incorporated herein by reference in its entirety. In some embodiments, oligonucleotides can localize and bind to a target nucleic acid sequence. In some embodiments, oligonucleotides can localize and bind to a strand of a target nucleic acid sequence. In some embodiments, one oligonucleotide can bind to a strand of the target nucleic acid and another oligonucleotide can bind to another strand of the target nucleic acid. In some embodiments, oligonucleotides can be complementary to a target nucleic acidsequence. In some embodiments, the oligonucleotides comprise a sequence at least about 70% identical to a region on the strand of the target nucleic acid sequence. In some embodiments, the oligonucleotides comprise a sequence at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or more identical to a region of the target nucleic acid sequence. In some embodiments, the oligonucleotides comprise a length from about 10 nucleotides to about 100 nucleotides. In some embodiments, the oligonucleotides comprise a length of about 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 nucleotides. In some embodiments, the oligonucleotides comprise a label. In some embodiments, the oligonucleotides can be a probe (e.g., an in-reaction probe) for detection of the target nucleic acid sequence. In some embodiments, the oligonucleotides can aid in on-target annealing of a different oligonucleotide (e.g., annexing oligonucleotides).

[0333] For example, the systems or methods comprise a first oligonucleotide (Pl); a second oligonucleotide (P2); a third oligonucleotide; and / or a fourth oligonucleotide. In some embodiments, oligonucleotides can be primers. In some embodiments, Pl is a primer. In some embodiments, P2 is a primer. In some embodiments, the third oligonucleotide is an annexing oligonucleotide. In some embodiments, the third oligonucleotide is an in-reaction probe. In some embodiments, the fourth oligonucleotide is an in-reaction probe. In some embodiments, the fourth oligonucleotide is a primer (P3). In some embodiments, the first oligonucleotide (Pl), the second oligonucleotide (P2), and / or the third oligonucleotide localize and bind to a strand of the target nucleic acid sequence. In some embodiments, the Pl localizes and binds to the strand of the target nucleic acid sequence independently of the third oligonucleotide. In some embodiments, the P2 localizes and binds to the other strand of the target nucleic acid sequence independently of the third oligonucleotide. In some embodiments, the third oligonucleotide comprises a 3’ end blocking feature that blocks extension of the third oligonucleotide by a polymerase. In some embodiments, the third oligonucleotide does not facilitate a localizing and a binding of the Pl or the P2 to the target nucleic acid. In some embodiments, the methods or systems for amplification further comprise using a polymerase and a DNA processing enzyme to extend the 3’ end of the Pl and the 3’ end of the P2, thereby amplifying the target nucleic acid. In some embodiments, the 5’ end of the third oligonucleotide and the 5’ end of the Pl bind to the strand o the target nucleic acid sequence at a distance of about 3 nucleotides to about 25 nucleotides apart. In some embodiments, a 5' end of the third oligonucleotide binds to the strand of the target nucleic acid sequence. In some embodiments, the 5' end of the third oligonucleotide and a 5' end of the Pl bind to a strand of the target nucleic acid sequence at a distance from about 3nucleotides to about 25 nucleotides apart.

[0334] In some embodiments, the Pl or the P2 is a nucleotide length insufficient to produce amplicons of the target nucleic acid sequence without the presence of the third oligonucleotide.

[0335] In some embodiments, the Pl and the P2 are present in molar excess relative to the target nucleic acid sequence.

[0336] In some embodiments, the Pl, the P2, the third oligonucleotide, the fourth oligonucleotide, or any combination thereof comprise a length of at least about 10 nucleotides, at least about 15 nucleotides, at least about 20 nucleotides, at least about 25 nucleotides, at least about 30 nucleotides, at least about 35 nucleotides, at least about 40 nucleotides, at least about 45 nucleotides, at least about 50 nucleotides, at least about 55 nucleotides, at least about 60 nucleotides, at least about 65 nucleotides, at least about 70 nucleotides, at least about 75 nucleotides, at least about 80 nucleotides, at least about 85 nucleotides, at least about 90 nucleotides, at least about 95 nucleotides, at least about 100 nucleotides, or more. In some embodiments, the Pl or the P2 is a nucleotide length insufficient to produce amplicons of the target region without the presence of third oligonucleotide. In some embodiments, the Pl and P2 are present in molar excess relative to the target nucleic acid sequence.

[0337] In some embodiments, the oligonucleotide comprises a 3' end blocking feature that blocks extension of a DNA polymerase. For example, the oligonucleotide can have a 3’ modification such as an inverted nucleotide, C3 -spacer, etc. which blocks 3’ extension by polymerase. In some embodiments, the 3' end blocking feature that blocks extension of a DNA polymerase comprises an inverted nucleotide, 2',3'-dideoxy-3'-aminonucleoside 5'- triphosphates, or a C3-spacer. In some embodiments, the blocking feature comprises a 3’ phosphorylation, a 3’ dideoxynucleotide (ddNTP), a 3’ amino acid, or a 3’ BHQ. Theoretically, any modification that makes the 3 ’OH of the last nucleotide in a primer unavailable for a DNA polymerase to start adding nucleotides can be a blocking feature.

[0338] In some embodiments, the oligonucleotides comprise label for detection of an amplification product, as described herein. In some embodiments, the Pl, P2, third oligonucleotide, the fourth oligonucleotide, or any combination thereof comprises a label (such as a probe). In some embodiments, the oligonucleotide comprises a 3' end label, such as a label described herein. In some embodiments, the oligonucleotide comprises a 5' end label, such as a label described herein. In some embodiments, the label comprises a xanthene core or a derivative thereof. In some embodiments, the label comprises a fluorescein molecule(FAM). In some embodiments, the label comprises a chemical relative of fluorescein, such as Hexachlorofluorescein (HEX), Tetrachlorofluorescein (TET), Dimethoxyfluorescein (JOE). In some embodiments, the oligonucleotide comprises a 3' end or 5’ end fluorescein label, such as 6-FAM or fluorescein isothiocyanate (FITC).

[0339] In some embodiments, the first oligonucleotide (Pl) and the second oligonucleotide (P2) are primers. In some embodiments, the third oligonucleotide can be an annexing oligonucleotide (AO). In some embodiments, an annexing probe (AP) can refer to a labeled annexing oligonucleotide (AO). In some embodiments, the third oligonucleotide can be an in-reaction probe (IrP). In some embodiments, the fourth oligonucleotide can be an inreaction probe (IrP). In some embodiments, the in-reaction probe comprises any label as described herein. In some embodiments, the in-reaction probe comprises a detectable label. In some embodiments, the systems disclosed herein can comprise a fifth oligonucleotide, a sixth oligonucleotide, a seventh oligonucleotide, an eighth oligonucleotide, a ninth oligonucleotide, a tenth oligonucleotide, or more oligonucleotides. In some embodiments, the fifth oligonucleotide, the sixth oligonucleotide, the seventh oligonucleotide, the eighth oligonucleotide, the ninth oligonucleotide, or the tenth oligonucleotide can be a primer, an annexing oligonucleotide, or an in-reaction probe.

[0340] In some embodiments, the target nucleic acid sequence is a selected region of an RNA sequence from a pathogen. In some embodiments, the target nucleic acid sequence is from a pathogen listed in Table 2, Table 3, Table 4, Table 5, or Table 6. In some embodiments, the target nucleic acid sequence is amplified in the presence of human genomic DNA. In some embodiments, the template to the target nucleic acid sequence is a single copy of a viral genome, and wherein the amplified target nucleic acid sequence is amplified at about room temperature in less than about 30 minutes to a level of a detectable range. In some embodiments, the level of a detectable range is at least about 104copies / pL, 105copies / pL, 106copies / pL, 107copies / pL, or 108copies / pL. In some embodiments, the target ds amplicons are amplified and detected in real time. In some embodiments, target ds amplicons are amplified and detected in less than about 60 minutes, 55 minutes, 50 minutes, 45 minutes, 40 minutes, 35 minutes, 30 minutes, 25 minutes, 20 minutes, 15 minutes, 12 minutes, 10 minutes, 9 minutes, 8 minutes, 7 minutes, 6 minutes, 5 minutes, 4 minutes, or 3 minutes. In some embodiments, at least one primer in the primer set is less than or equal to 14 nucleotides in length. In some embodiments, at least one primer in the primer set is less than or equal to 12 nucleotides in length. In some embodiments, at least one primer in the primer set is less than or equal to 10 nucleotides in length. In some embodiments, the method furthercomprises detection of two different regions of the target nucleic acid sequence. In some embodiments, two or more distinct pathogenic variants are detected within a single amplification reaction. In some embodiments, two or more distinct disease mutations are detected within a single amplification reaction. In some embodiments, a single nucleotide polymorphism (SNP) within the target nucleic acid sequence is detected.

[0341] Provided in some embodiments herein is a system for processing a biological sample. In some embodiments, the system comprises a channel. In some embodiments, the system comprises a first channel. In some embodiments, the first channel comprises a first opening. In some embodiments, the first channel is configured to receive a biological sample. In some embodiments, the first channel is configured to receive, via the first opening, a biological sample. In some embodiments, the first channel further comprises a lysis solution. In some embodiments, the system comprises a second channel. In some embodiments, the second channel comprises a substrate. In some embodiments, the substrate comprises cellulose. In some embodiments, the second channel comprises a cellulose substrate. In some embodiments, the second channel comprises a second opening. In some embodiments, the second channel comprises a cellulose substrate coupled to the first channel and a second opening. In some embodiments, the system comprises a second opening configured to couple to the first opening. In some embodiments, the system transfers a biological sample from the first channel to the second channel. For instance, the system may transfer a biological sample from the first channel to the second channel upon the coupling of the second opening to the first opening. In some embodiments, the system comprises a third channel. In some embodiments, the third channel comprises a third opening. In some embodiments, the system comprises an elution solution. For instance, in some embodiments, the third channel of the system comprises an elution solution. In some embodiments, the third channel comprises a third opening and an elution solution. In some embodiments, the third channel comprises a third opening configured to couple to the second opening. In some embodiments, the system transfers the elution solution from the second channel to the third channel. For instance, the system may transfer a biological sample from the second channel to the third channel upon coupling of the third opening to the second opening. In some embodiments, the second channel is configured to transfer elution solution received from the second channel to the third channel, such as upon coupling of the third opening and the second opening. In some embodiments, the elution solution comprises water. In some embodiments, the elution solution comprises deionized water. In some embodiments, the elution solution comprises nuclease-free water. In some embodiments, the elution solution comprises a buffering agent.In some embodiments, the buffering agent comprises Tris at a concentration between about 5 mM to about 100 mM. In some embodiments, the pH of the elution solution is maintained between about 7.0 to about 10.0. In some embodiments, the elution solution is a Tris-EDTA (TE) buffer solution. In some embodiments, the elution solution comprises 10 mM Tris-HCl, 1 mM EDTA, pH 8.0.

[0342] In some aspects, provided herein are methods and / or systems of detection. Methods and / or systems of detection disclosed herein can use the systems and / or devices as described herein. For example, provided herein are systems, devices, methods and kits for the detection of a nucleic acid molecule. In some embodiments, the nucleic acid molecule is an amplified target nucleic acid sequence. In some embodiments, detection of the amplified target nucleic acid sequence can be accomplished by molecular lateral flow assay (mLFA) detection. Detection can be performed in a single step or in multiple steps. For example, detection buffer and solution can be added to amplification products, next read strips can be added to the detection buffer / solution and incubated for about 5-15 minutes, strips can then be read to determine the presence or absence of the target nucleic acid sequence.

[0343] In some embodiments, detecting the target ds amplicons. In some embodiments, detecting the target ss amplicons. In some embodiments, the detecting comprises analyzing reaction products using a molecular lateral flow assay (mLFA). In some embodiments, the detecting comprises analyzing reaction products using an intercalating dye or fluorophore. In some embodiments, use of FRET in the detecting. In some embodiments, the detecting comprises analyzing reaction products using a nucleic acid hybridization technique. In some embodiments, the detecting comprises analyzing reaction products using a fluorescence detection technique. In some embodiments, the detecting comprises analyzing reaction products using a colorimetric technique. In some embodiments, the detecting comprises analyzing reaction products using nucleic acid sequencing. In some embodiments, the detecting comprises analyzing reaction products using DNA fragment size discrimination. In some embodiments, an oligonucleotide probe is added to ss amplicons or ds amplicons produced from the reaction to aid in the detecting. In some embodiments, a separate oligonucleotide probe comprising a quencher is added to ss amplicons or ds amplicons produced from the reaction to aid in the detecting. In some embodiments, the detecting comprising determining a quantitative measure of an amplified reaction product comprising the target ds amplicons. In some embodiments, the detecting comprising determining a quantitative measure of an amplified reaction product comprising the target ss amplicons. In some embodiments, the target ds amplicons are amplified and detected in real time. In someembodiments, target ds amplicons are amplified and detected in less than about 60 minutes, 55 minutes, 50 minutes, 45 minutes, 40 minutes, 35 minutes, 30 minutes, 25 minutes, 20 minutes, 15 minutes, 12 minutes, 10 minutes, 9 minutes, 8 minutes, 7 minutes, 6 minutes, 5 minutes, 4 minutes, or 3 minutes. In some embodiments, target ss amplicons are amplified and detected in less than about 60 minutes, 55 minutes, 50 minutes, 45 minutes, 40 minutes, 35 minutes, 30 minutes, 25 minutes, 20 minutes, 15 minutes, 12 minutes, 10 minutes, 9 minutes, 8 minutes, 7 minutes, 6 minutes, 5 minutes, 4 minutes, or 3 minutes. In some embodiments, the method further comprises detection of two different regions of the target nucleic acid sequence. In some embodiments, two or more distinct pathogenic variants are detected within a single amplification reaction. In some embodiments, two or more distinct disease mutations are detected within a single amplification reaction. In some embodiments, a single nucleotide polymorphism (SNP) within the target nucleic acid sequence is detected.

[0344] In some embodiments, nucleic acid amplification takes about 20 minutes to complete at room temperature. In other embodiments, nucleic acid amplification takes about 10 minutes, or about 15 minutes, or about 20 minutes, or about 25 minutes, or about 30 minutes to complete at room temperature (e.g., 59° to 77°F) or above e.g., up to 98°F. Amplification of the nucleic acid is complete when at least a single copy of a nucleic acid (e.g., DNA) is amplified to a detectable range.

[0345] Using one or more LFA strips for detection, in less than 5 minutes the test is ready to read. In some embodiments, the test is ready in about 5 minutes, or about 10 minutes, or about 15 minutes, or about 20 minutes, or about 25 minutes, or about 30 minutes, or about 40 minutes, or about 60 minutes.

[0346] The devices, systems, and methods described herein may be used in various procedures, e.g., biosecurity, aquaculture, food safety, environmental testing, veterinary, home testing, clinic testing, pharmacy integration, point of care procedures in rural environments, and test to treat procedures.

[0347] The present disclosure provides labels, such as labels used in the detection of nucleic acid molecules. In some embodiments, the oligonucleotide comprises a label. In some embodiments, the label is located on a 5' end of the oligonucleotide, a 3' end of the oligonucleotide, or anywhere in between. In some embodiments, the label allows extension of a DNA polymerase. In some embodiments, the label comprises a fluorescein or derivative thereof. In some embodiments, the label comprises a xanthene core or derivative thereof. In some embodiments, the label comprises a fluorophore, or a redox molecule, or biotin, or digoxigenin. In some embodiments, the label comprises a fluorophore or biotin ordigoxigenin. In some embodiments, the label comprises a redox molecule.

[0348] A label used in the systems, devices, methods, and kits as described herein can be any known oligonucleotide label. The following are non-limiting examples of labels that can be used in the systems, devices, methods, and kits as described herein. In some embodiments, a labeled oligonucleotide (e.g., labeled annexing oligonucleotide) decreases non-specific amplification relative to an unlabeled oligonucleotide. In some embodiments, the label comprises a xanthene core or a derivative thereof. In some embodiments, an oligonucleotide labeled with a xanthene core label (e.g., xanthene core labeled annexing oligonucleotide) decreases non-specific amplification relative to an oligonucleotide labeled with a nonxanthene core label. In some embodiments, the label comprises carboxyfluorescein (FAM).Detection

[0349] The present disclosure provides detection systems for a biological sample. In some embodiments, the detection system may be used with any one of the methods, systems or kits as described herein. In some embodiments, the detection system, e.g., means of detection, detection component, or detection unit, comprises a lateral flow assay strip, electrochemical sensor, a fluorometric sensor, colorimetric sensor, or the like. In some embodiments, the detection system or unit may be housed inside the detection system, or it can be added by the user separately. In some embodiments, the detection system may further comprise a detection assay buffer, which may be preloaded inside the detection buffer vial, or it can be added by the user separately before starting the detection step.

[0350] In some embodiments, a quantitative PCR (qPCR) conducted on said biological sample results in a Ct value of at most about 20, about 25, about 30, about 31, about 32, about 33, about 34, about 35, about 40, or about 45 when said biological sample is a pathogenic bacterium. In some embodiments, a quantitative PCR (qPCR) conducted on said biological sample results in a Ct value of at most about 40 when said biological sample is a pathogenic bacterium. In some embodiments, the quantitative PCR (qPCR) conducted on said biological sample results in a Ct value of at most about 35. In some embodiments, the quantitative PCR (qPCR) conducted on said biological sample results in a Ct value of at most about 34. In some embodiments, the quantitative PCR (qPCR) conducted on said biological sample results in a Ct value of at most about 33.

[0351] In some embodiments, the detection system may be housed in a detection chamber fluidly connected to the detection buffer chamber. The connection may contain a valve mechanism or a push or pull-tab mechanism, or the device may need to be rotated at aspecific angle to allow the detection buffer to move from the detection buffer chamber to the detection chamber or detection system. This can also keep the detection system away from the assay buffer until the user needs it. In some embodiments, the detection chamber may also contain design elements to aid the flow of the assay buffer in a specific direction, or only through the detection system, and prevent the fluid from coming in contact with the detection system in manners that may affect its performance.Biological Sample

[0352] The present disclosure provides for a nucleic acid molecule extracted from a sample, such as a biological sample, in the systems disclosed herein. In some embodiments, the sample is derived from a subject. In some embodiments, the sample is a bacterial culture. In some embodiments, the sample is an animal cell culture. In some embodiments, the sample is a tissue culture. In some embodiments, the biological sample is a complex biological sample, such as a blood sample. As described herein, complex biological samples, such as blood samples, of any subject can be processed with the methods and systems provided herein. Samples used in the methods and / or systems disclosed herein can be samples as described in the systems disclosed herein. In some embodiments, systems, methods and / or kits as described herein can more efficiently process a sample as compared to other systems, methods and / or kits. For instance, the systems, methods and / or kits as described herein can more efficiently process a complex sample more efficiently as compared to other systems, methods and / or kits. A complex sample as described herein may have one or more traits that make it more difficult to process. For instance, the complex sample may be more viscous, e.g., blood. For instance, the complex sample may comprise pathogenic bacterium.

[0353] In some embodiments, a biological sample is a biological fluid. Suitable biological fluids include, but are not limited to, systemic blood, plasma, serum, lung lavage, cell lysates, menstrual blood, urine, processed tissue samples, amniotic fluid, cerebrospinal fluid, tears, saliva, semen, and any other biological fluids. In some embodiments, a biological fluid has a volume of about 1 mL to about 250 mL. In some embodiments, a biological fluid has a volume of about 1 milliliter (mL) to about 100 mL. In some embodiments, a biological fluid has a volume of about 50 mL. In some embodiments, a biological fluid has a volume of less than about 5 mL. In some embodiments, a biological fluid has a volume of about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 150, 200, or 250 mL. In some embodiments, a biological fluid has a volume of more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 150,200, or 250 mL. In someembodiments, a biological fluid has a volume of less than about 250, 200, 150, 100, 90, 80, 70, 60, 50, 45, 40, 35, 30, 25, 20, 15, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 mL.

[0354] In some embodiments, the biological sample is a mammalian sample. In some embodiments, the biological sample is a bacteria sample. In some embodiments, the biological sample comprises water. In some embodiments, the water comprises wastewater, water derived from a pond, or water derived from aquarium. In some embodiments, the wastewater is urine. In some embodiments, a water sample has a volume of about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 150, 200, or 250 mL. In some embodiments, the biological sample is a plant sample.

[0355] In some embodiments, the sample is obtained from a biological fluid, a tissue sample, a mammalian sample, an animal sample, a eukaryotic sample, a bacterial sample, a viral sample, a plant sample, a bacterial cell, a eukaryotic cell, an animal tissue, whole blood, saliva, urine, a nasal swab, a buccal swab, a tongue swab, a cervical fluid, a vaginal fluid, an animal cell, a muscle tissue, a spleen tissue, a skin tissue, or a liver tissue. In some embodiments, the biological sample is E. coli, N. gonorrhoeas, RSV, WSSV, EBV, or human genomic DNA. In some embodiments, the biological sample is derived from a subject. In some embodiments, the subject is an organism. In some embodiments, a subject is a mammal. In some embodiments, a subject is a human. In some embodiments, a subject is a mouse. In some embodiments, a subject is a swine. In some embodiments, a subject is a crustacean. In some embodiments, a subject is a shrimp. In some embodiments, a subject is a bacterial culture. In some embodiments, a subject is a plant. The present methods and systems described herein can process samples derived from any subject. In some embodiments, a nucleic acid molecule is extracted from a sample. In some embodiments, the nucleic acid molecule extracted from the sample comprises DNA or RNA. In some embodiments, the nucleic acid molecule extracted from the sample comprises dsDNA, ssDNA, circulating DNA, cell free DNA, cDNA, plasmid DNA, mRNA, miRNA, tRNA, viral RNA, siRNA, sgRNA, or any combination thereof. In some embodiments, the nucleic acid molecule extracted from the sample comprises DNA. In some embodiments, the nucleic acid molecule extracted from the sample comprises double-stranded DNA. In some embodiments, the nucleic acid molecule extracted from the sample comprises single-stranded DNA. In some embodiments, the nucleic acid molecule extracted from the sample comprises RNA. In some embodiments, reverse transcriptase and NTPs are added to the sample to reverse transcribe the RNA extracted from the sample to cDNA, wherein the cDNA becomes a template to the target nucleic acid sequence.

[0356] In some embodiments, one or more nucleic acid molecules extracted from the sample serve as one or more analytes. An analyte is a specific substance to be measured or analyzed in a sample. In some embodiments, the analyte is a target DNA sequence. In some embodiments, the analyte is a target cDNA sequence produced from reverse transcription of a target RNA sequence. In some embodiments, an extracted nucleic acid sample comprises one target analyte. In some embodiments, an extracted nucleic acid sample comprises two target analytes. In some embodiments, one or more target analytes are bound to a channel comprising a cellulose substrate coupled thereto in a method of nucleic acid extraction. In some embodiments, an oligonucleotide target is extracted from the first analyte or the second analyte. In some embodiments, the amplified target analyte is specifically detected following target amplification. In some embodiments, two or more amplified target analytes from the same sample are specifically detected following target amplification. In some embodiments, one or more nucleic acid molecules are a target for one or more oligonucleotides. In some embodiments, an oligonucleotide for use in a method, system or kit described herein has an extent of base pair complementarity to a region of target nucleic acid sequence. In some embodiments, an oligonucleotide for use in a method, system or kit described herein serves as a primer for an amplification reaction. In some embodiments, an oligonucleotide for use in a method, system or kit described herein is supplied in molar excess to an amplification reaction to allow exponential amplification of a target nucleotide sequence. In some embodiments of methods and / or systems described herein, an oligonucleotide target is extracted from a biological sample. In some embodiments, an oligonucleotide for use in a method, system or kit described herein serves as an oligonucleotide primer in an isothermal amplification reaction. In some embodiments of methods and / or systems described herein, the analyte comprises a continuous nucleic acid sequence comprising one or more oligonucleotide targets for amplification and detection. In some embodiments of methods and / or systems described herein, the analyte comprises a continuous ssDNA sequence. In some embodiments of methods and / or systems described herein, the analyte comprises a continuous dsDNA sequence. In some embodiments of methods and / or systems described herein, the analyte comprises a continuous RNA sequence.

[0357] In some embodiments described here are methods and / or systems for processing a biological sample, the method comprising: (a) coupling a biological sample to a first channel comprising a first opening; (b) coupling the first opening of the first channel to a second opening of a second channel, thereby transferring the biological sample from the first channel to the second channel, wherein the second channel has a substrate coupled thereto; (c)coupling the second opening of the second channel to a third opening of a third channel, wherein the third channel comprises an elution solution, and wherein the coupling of the second opening to the third opening transfers the elution solution to the second channel; and (d) removing the elution solution from the second channel; wherein the first channel further comprises a chemical lysis solution or an enzymatic lysis solution. In some embodiments, the substrate comprises cellulose. In some embodiments, the biological sample and the chemical lysis solution or enzymatic lysis solution are mixed prior to coupling to the first channel in (a). In some embodiments, the elution solution comprises an analyte for use in molecular diagnostic testing. In some embodiments, the method for processing a biological sample further comprises a method for processing the analyte, the method for processing the analyte comprising: (e) binding the analyte to a channel comprising a nucleic acid binding substrate coupled thereto; (f) extracting a target nucleic acid sequence comprising a first oligonucleotide target, a second oligonucleotide target, and a third oligonucleotide target from the first analyte; (g) binding an oligonucleotide primer to a strand of the first oligonucleotide target; (h) bringing into contact with the third oligonucleotide target a third oligonucleotide, and blocking an extension of the third oligonucleotide by a DNA polymerase, wherein the third oligonucleotide does not facilitate a localizing or a binding of the oligonucleotide primer to the first oligonucleotide target; (i) using a DNA polymerase and a DNA processing enzyme to amplify the target nucleic acid sequence; (j) providing a label to the amplified target nucleic acid sequence in (i); and (k) detecting the labeled amplified target nucleic acid sequence. In some embodiments, the detecting in (k) comprises detecting the labeled amplified target nucleic acid sequence in real time. In some embodiments, the method further comprises: (1) binding a second oligonucleotide primer to a strand of a second oligonucleotide target, wherein a 5’ end of the third oligonucleotide and a 5' end of the second oligonucleotide primer bind to the strand of the target nucleic acid sequence at a distance of about 3 nucleotides to about 25 nucleotides apart. In some embodiments, the 5' end of the third oligonucleotide and the 3’ end of the second oligonucleotide bind to the strand of the target nucleic acid sequence with 1 or more base pair (bp) of overlap. In some embodiments, the third oligonucleotide comprises a 3’ blocking feature that blocks nucleotide extension of the DNA polymerase. In some embodiments, the DNA processing enzyme is comprised in an enzyme mix. In some embodiments, the DNA processing enzyme facilitates the binding of the first oligonucleotide to the first oligonucleotide target, the second oligonucleotide to the second oligonucleotide target, or the third oligonucleotide to the third oligonucleotide target. In some embodiments, the target nucleic acid sequence is amplified atan ambient temperature. In some embodiments, the method of processing results in an amplified target nucleic acid sequence. In some embodiments, the third oligonucleotide promotes the localizing and binding of the second oligonucleotide to the second oligonucleotide target of the target nucleic acid sequence. In some embodiments, the third oligonucleotide promotes annealing specificity of the first oligonucleotide primer or the second oligonucleotide primer or both to the target nucleic acid sequence. In some embodiments, the detecting in (k) is conducted at a clinical laboratory testing location or at a hospital to provide a molecular diagnostic near point-of-need (PON) test. In some embodiments, the molecular diagnostic near PON tests for a range of pathogenic bacterium. In some embodiments, the molecular diagnostic near PON tests for Mycobacterium tuberculosis (MTB). In some embodiments, the method is conducted at a veterinary facility or on a farm, wherein the sample is derived from an animal, and wherein the processing allows for monitoring of animal health or disease surveillance at a farm. In some embodiments, the sample is derived from a human subject. In some embodiments, the realtime detecting in (k) provides a quantitative measurement of an initial concentration of the analyte prior to target nucleic acid sequence amplification. In some embodiments, the quantitative measurement is provided in less than about 90 minutes, less than about 80 minutes, less than about 70 minutes, less than about 60 minutes, less than about 55 minutes, less than about 50 minutes, less than about 45 minutes, less than about 30 minutes, less than about 25 minutes, less than about 20 minutes, less than about 15 minutes, less than about 12 minutes, less than about 10 minutes, or less than about 5 minutes after the start of the using the DNA polymerase and the DNA processing enzyme in (i) In some embodiments, the quantitative measurement is provided in less than about 45 minutes, less than about 30 minutes, less than about 25 minutes, less than about 20 minutes, less than about 15 minutes, less than about 12 minutes, less than about 10 minutes, or less than about 5 minutes after the start of the using the DNA polymerase and the DNA processing enzyme in (i).

[0358] In some embodiments, methods and systems and used herein can be used to determine the presence of a target sequence in a sample. A target sequence can indicate the presence of a disease. In some embodiments, a target sequence is a nucleic acid sequence of a virus. In some embodiments, a target sequence is a nucleic acid sequence of African Swine Fever Virus. In some embodiments, a target sequence is a nucleic acid sequence of White Spot Syndrome Virus. In some embodiments, a target sequence is a nucleic acid sequence of Respiratory Syncytial Virus (RSV). In some embodiments, a target sequence is a nucleic acidsequence of Influenza. In some embodiments, a target sequence is a nucleic acid sequence of Epstein-Barr Virus (EBV). In some embodiments, the method comprises testing meat products for presence of Salmonella sp, Listeria sp, Chronobacter sp. In some embodiments, the biological sample comprises a Mycobacterium. In some embodiments, the biological sample comprises Mycobacterium tuberculosis (MTB). In some embodiments, the biological sample comprises Mycobacterium avium. In some embodiments, the biological sample comprises Mycobacterium abscessus. In some embodiments, the biological sample comprises a non-tuberculous mycobacteria species. In some embodiments, the biological sample comprises Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium avium, Mycobacterium abscessus, Mycobacterium smegmatis, Francisella philomiragia, Yersinia enterocolitica, Bacillus thuringiensis, Pseudomonas aeruginosa, Moraxella catarrhalis , or Klebsiella pneumoniae, or any combination thereof.

[0359] A target sequence can indicate the presence of a disease or disorder. For example, the disease or disorder may be an infection. In some embodiments, a target sequence is a nucleic acid sequence of a virus. In some embodiments, a target sequence is a nucleic acid sequence of a bacteria. In some embodiments, a target sequence is a nucleic acid sequence of a bacteria that causes a sexually transmitted infection or sexually transmitted disease. In some embodiments, a target sequence is a nucleic acid sequence of a gonorrhea bacteria. In some embodiments, a target sequence is a nucleic acid sequence of an HIV virus. In some embodiments, a target sequence is a nucleic acid sequence of a herpes virus. In some embodiments, a target sequence is a nucleic acid sequence of chlamydia bacteria. In some embodiments, a target sequence is a nucleic acid sequence of a syphilis bacteria.

[0360] A target sequence can indicate a presence of a genetic trait. In some embodiments, a target sequence is a nucleic acid sequence which indicates the presence of a genetic trait. In some embodiments, a target sequence is a nucleic acid sequence which indicates the presence of photic sneeze. In some embodiments, a target sequence is a nucleic acid sequence which indicates the presence of alcohol flush.

[0361] In an aspect described herein, are methods and / or systems for processing a first analyte and a second analyte, wherein the first analyte and the second analyte are derived from distinct biological samples. In some embodiments, the first analyte and the second analyte are derived from extracted nucleic acid samples from different individuals. In some embodiments, the first analyte and the second analyte are derived from extracted nucleic acid samples from different human subjects. In some embodiments, the first analyte and the second analyte are derived from extracted nucleic acid samples from different animal subjectsof the same species. In some embodiments, the method uses a system or kit configured for molecular near PON diagnostic testing using extracted nucleic acid samples from different subjects. In some embodiments, the methods and / or systems are used for human applications. In some embodiments, large number of patient samples at near PON clinics, at-pharmacy testing or workplace are tested. As a non-limiting example, in some embodiments, the method comprises FluA and / or COVID-19 screening during pandemic scenario. In some embodiments, the method comprises a screening assay for studying therapeutic effects of drugs. As a non-limiting example, in some embodiments, the method comprises testing different concentrations of a new chemotherapy drug on inhibiting cancer cell growth by looking cancer. As a non-limiting example, in some embodiments, the method comprises assaying biomarkers or apoptosis markers. In some embodiments, the method comprises in vitro and in vivo research tool for a genetic analysis, such as studying mRNA expression, studying effect of siRNA or CRISPR / Cas9 knockdown. In some embodiments, the method comprises a companion diagnostic from therapeutic clinical trials to study efficacy. In some embodiments, the method comprises veterinary or farm applications. In some embodiments, the method comprises routine monitoring of animal / plant health or disease surveillance at a farm. As a non-limiting example, in some embodiments, the method comprises shrimp testing or water testing from multiple sample source in an aquaculture farm to detect for presence of WSSV. In some embodiments, the method comprises testing several sick pets or domestic animals for 1-5 diseases. In some embodiments, the method comprises environmental management or public health monitoring. In some embodiments, the method comprises surveillance of water bodies for presence of common waterborne pathogens. As a nonlimiting example, in some embodiments, the method comprises monitoring water bodies for presence of Giardia and Cryptosporidium. In some embodiments, the method comprises food / beverage applications. In some embodiments, the method comprises disease surveillance at border checkpoints imported / exported live animals or animal-based products. As a nonlimiting example, in some embodiments, the method comprises testing all imported pigs for possible infectious diseases such as ASFV during ongoing pandemic. In some embodiments, the method comprises food quality testing. As a non-limiting example, in some embodiments, the method comprises testing meat products for presence of Salmonella sp. Listeria sp. Chronobacter sp.

[0362] An additional aspect of the present disclosure provides systems and methods of processing a biological sample. In some embodiments, the biological sample is derived from a subject. In some embodiments, the sample is a bacterial culture. In some embodiments, thebiological sample is a complex biological sample, such as a blood sample. As described herein, complex biological samples, such as blood samples, of any subject can be processed with the methods and systems provided herein. In some embodiments, the biological sample is a tissue sample. In some embodiments, the tissue sample is derived from an animal. In some embodiments, the tissue sample is derived from a livestock animal. In some embodiments, the tissue sample is derived from an animal from a wild population. In some embodiments, the tissue sample is derived from an animal from a setting of captivity, such as from a zoo, a research facility, or an animal husbandry facility. In some embodiments, the tissue sample is derived from a human subject. In some embodiments, the biological sample is a sample of fluid or material collected from a subject. In some embodiments, the biological sample is a respiratory tract sample. In some embodiments, the biological sample taken from a pulmonary tissue source or location to test for the presence of pulmonary tuberculosis. In some embodiments, the biological sample is taken from an extrapulmonary tissue source or location to test for the presence of extrapulmonary tuberculosis. In some embodiments, the respiratory tract sample is a sputum sample. In some embodiments, the respiratory tract sample is taken from a nasopharyngeal or oropharyngeal swab in a subject. In some embodiments, the respiratory tract sample is a bronchoalveolar lavage. In some embodiments, the respiratory tract sample is a tracheal aspirate. In some embodiments, the sample of fluid or material collected from a subject is a blood sample. In some embodiments, the sample of fluid or material collected from a subject is a whole blood sample. In some embodiments, the sample of fluid or material collected from a subject is a plasma sample. In some embodiments, the sample of fluid or material collected from a subject is a serum sample. In some embodiments, the sample of fluid or material collected from a subject is a capillary blood sample. In some embodiments, the sample of fluid or material collected from a subject is a venous blood sample. In some embodiments, the sample of fluid or material collected from a subject is a biopsied sample. In some embodiments, the sample of fluid or material collected from a subject is a stool sample. In some embodiments, the sample of fluid or material collected from a subject is an intestinal tissue biopsy. In some embodiments, the sample of fluid or material collected from a subject is a urine sample. In some embodiments, the sample of fluid or material collected from a subject is a semen sample. In some embodiments, the sample of fluid or material collected from a subject is a taken from a urethral, cervical, or vaginal swab. In some embodiments, the sample of fluid or material collected from a subject is a taken from a skin or soft tissue sample. In some embodiments, the sample of fluid or material collected from a subject is a taken from an ear swab or middleear aspirate. In some embodiments, the sample of fluid or material collected from a subject is a take from a nasal or throat swab. In some embodiments, the sample of fluid or material collected from a subject is a saliva sample. In some embodiments, the sample of fluid or material collected from a subject is a taken from a lymphatic biopsy. In some embodiments, the sample of fluid or material collected from a subject is a lymphatic fluid sample. In some embodiments, the sample of fluid or material collected from a subject is a from a pleural biopsy. In some embodiments, the sample of fluid or material collected from a subject is a pleural fluid. In some embodiments, the sample of fluid or material collected from a subject is a cerebrospinal fluid sample. In some embodiments, the sample of fluid or material collected from a subject is a taken from a bladder or renal tissue biopsy. In some embodiments, the sample of fluid or material collected from a subject is a taken from an omental or intestinal biopsy. In some embodiments, the sample of fluid or material collected from a subject is an ascitic fluid sample. In some embodiments, the sample of fluid or material collected from a subject is a synovial fluid sample. In some embodiments, the sample of fluid or material collected from a subject is a bone biopsy or bone aspirate. In some embodiments, the sample of fluid or material collected from a subject is a taken from a skin biopsy. In some embodiments, the sample of fluid or material collected from a subject is a cultured blood sample. In some embodiments, the sample of fluid or material collected from a subject is a taken from bone marrow aspirate or bone marrow biopsy. In some embodiments, the sample of fluid or material collected from a subject is a liver biopsy. In some embodiments, a biological sample is a biological fluid. Suitable biological fluids include, but are not limited to, systemic blood, plasma, serum, lung lavage, cell lysates, menstrual blood, urine, processed tissue samples, amniotic fluid, cerebrospinal fluid, mucus, tears, saliva, semen, and any other biological fluids. In some embodiments, a biological fluid has a volume of about 10 pL to about 250 mL. In some embodiments, a biological fluid has a volume of about 1 milliliter (mL) to about 100 mL. In some embodiments, a biological fluid has a volume of about 50 mL. In some embodiments, a biological fluid has a volume of less than about 5 mL. In some embodiments, a biological fluid has a volume of about 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, 1000, 1500, 2000, or 2500 pL. In some embodiments, a biological fluid has a volume of about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 150, 200, or 250 mL. In some embodiments, a biological fluid has a volume of more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 150, 200, or 250 mL. In some embodiments, a biological fluid has a volume of less than about 250, 200, 150, 100, 90, 80,70, 60, 50, 45, 40, 35, 30, 25, 20, 15, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 mL. In some embodiments, the biological sample is a tissue sample. Suitable tissue samples include, but are not limited to, a connective tissue, an epithelial tissue, a muscle tissue, a skeletal tissue, a nervous tissue, an embedded tissue, a liver tissue, a spleen tissue, a skin tissue, and any other tissue sample. In some embodiments, the tissue sample is a semi-solid. In some embodiments, the tissue sample is a solid. In some embodiments, the sample of fluid or material collected from a subject is a post-mortem tissue sample. In some embodiments, more than one biological sample are taken from the subject. In some embodiments, the biological samples are taken from the subject on more than one day. In some embodiments, the biological samples are taken from the subject on successive days of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more than 10 days in a row. In some embodiments, the biological samples are taken from the subject on alternating days of 0, 2, 4, 6, 8, 10, 12, 14, 16, 18, 20 or more than 20 days. In some embodiments, the biological samples are taken from a subject approximately daily, every other day, every three days, every four days, every five days, twice weekly, weekly, biweekly, monthly, bi-monthly, quarterly, semi-annually, or annually. In some embodiments, biological samples are taken from a group of subjects. In some embodiments, the biological sample comprises pathogenic bacterium. In some embodiments, the biological sample comprises acid-fast bacteria. In some embodiments, the biological sample comprises a Mycobacterium. In some embodiments, the biological sample comprises Mycobacterium tuberculosis (MTB). In some embodiments, the biological sample comprises Mycobacterium avium. In some embodiments, the biological sample comprises Mycobacterium abscessus. In some embodiments, the biological sample comprises a non-tuberculous mycobacteria species. In some embodiments, the biological sample comprises Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium avium, Mycobacterium abscessus, Mycobacterium smegmatis, Francisella philomiragia, Yersinia enterocolitica, Bacillus thuringiensis, Pseudomonas aeruginosa, Moraxella catarrhalis, o Klebsiella pneumoniae, or any combination thereof. In some embodiments, the biological sample does not comprise bacteria. In some embodiments, the biological sample does not comprise pathogenic bacterium. In some embodiments, the biological sample is a sample swab taken from a subject. In some embodiments, the biological sample is a sample swab is a tongue swab, a nasal swab, a buccal swab, a nasopharyngeal swab, a lung swab, a throat swab, a skin swab, a wound swab, a pus swab, a vaginal swab, a cervical swab, a urethral swab, a rectal swab, a culture swab, a forensic swab, a dry swab, a wet swab, a swab for tuberculosis. In some embodiments, the swab is mixed directly in the lysis solution in the first channel.

[0363] In some embodiment, the biological sample is a water sample. In some embodiments, the biological subject is a White Spot Syndrome Virus (WSSV) infected aquarium water. In some embodiments, a water sample is a sample of water derived from an aquarium. In some embodiments, a water sample is a sample of water derived from a pond. In some embodiments, a water sample is a sample of water derived from wastewater. In some embodiments, wastewater is water derived from urine. In some embodiments, a water sample has a volume of about 10 pL to about 250 mL. In some embodiments, a water sample has a volume of about 50 pL to 1 mL. In some embodiments, a water sample has a volume of about 50 mL. In some embodiments, a water sample has a volume of less than about 5 mL. In some embodiments, a water sample has a volume of about 0.1, 0.2, 0.5, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 150, 200, or 250 mL. In some embodiments, a water sample has a volume of more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 150, 200, or 250 mL. In some embodiments, a water sample has a volume of less than about 250, 200, 150, 100, 90, 80, 70, 60, 50, 45, 40, 35, 30, 25, 20, 15, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 mL.

[0364] In some embodiments, the biological sample is a tissue sample. Suitable tissue samples include, but are not limited to, a connective tissue, an epithelial tissue, a muscle tissue, a skeletal tissue, a nervous tissue, an embedded tissue, a liver tissue, a spleen tissue, a skin tissue, and any other tissue sample. In some embodiments, the tissue sample is a shrimp hepatopancreas. In some embodiments, a tissue sample is a shrimp tail. In some embodiments, a tissue sample is a shrimp pleopod. In some embodiments, a tissue sample is a shrimp gill(s). In some embodiments, a tissue sample is a shell covered muscle tissue. In some embodiments, a tissue sample is a formalin fixed paraffin embedded tissue. In some embodiments, the tissue sample is a biopsied tissue sample. In some embodiments, the tissue sample is a preserved tissue sample. In some embodiments, the tissue sample is on a culture slide. In some embodiments, the tissue sample is plant material, such as a leaf, bark, etc.

[0365] In some embodiments, the tissue sample is a semi-solid. In some embodiments, the tissue sample is a solid. In some embodiments, a tissue sample is a shell covered muscle tissue. In some embodiments, a tissue sample is a formalin fixed paraffin embedded tissue.

[0366] In some embodiments, the tissue sample has a mass of about 0.01 milligrams (mg) or more. In some embodiments, the tissue sample has a mass of about 200 mg or less. In some embodiments, a tissue sample has a mass of about 0.1 mg to about 500 mg. In some embodiments, a tissue sample has a mass of about 0.1 mg to about 1 mg, about 0.1 mg to about 2 mg, about 0.1 mg to about 3 mg, about 0.1 mg to about 4 mg, about 0.1 mg to about 5mg, about 0.1 mg to about 10 mg, about 0.1 mg to about 15 mg, about 0.1 mg to about 20 mg, about 0.1 mg to about 50 mg, about 0.1 mg to about 100 mg, about 0.1 mg to about 200 mg, about 1 mg to about 2 mg, about 1 mg to about 3 mg, about 1 mg to about 4 mg, about 1 mg to about 5 mg, about 1 mg to about 10 mg, about 1 mg to about 15 mg, about 1 mg to about 20 mg, about 1 mg to about 50 mg, about 1 mg to about 100 mg, about 1 mg to about 200 mg, about 2 mg to about 3 mg, about 2 mg to about 4 mg, about 2 mg to about 5 mg, about 2 mg to about 10 mg, about 2 mg to about 15 mg, about 2 mg to about 20 mg, about 2 mg to about 50 mg, about 2 mg to about 100 mg, about 2 mg to about 200 mg, about 3 mg to about 4 mg, about 3 mg to about 5 mg, about 3 mg to about 10 mg, about 3 mg to about 15 mg, about 3 mg to about 20 mg, about 3 mg to about 50 mg, about 3 mg to about 100 mg, about 3 mg to about 200 mg, about 4 mg to about 5 mg, about 4 mg to about 10 mg, about 4 mg to about 15 mg, about 4 mg to about 20 mg, about 4 mg to about 50 mg, about 4 mg to about 100 mg, about 4 mg to about 200 mg, about 5 mg to about 10 mg, about 5 mg to about 15 mg, about 5 mg to about 20 mg, about 5 mg to about 50 mg, about 5 mg to about 100 mg, about 5 mg to about 200 mg, about 10 mg to about 15 mg, about 10 mg to about 20 mg, about 10 mg to about 50 mg, about 10 mg to about 100 mg, about 10 mg to about 200 mg, about 15 mg to about 20 mg, about 15 mg to about 50 mg, about 15 mg to about 100 mg, about 15 mg to about 200 mg, about 20 mg to about 50 mg, about 20 mg to about 100 mg, about 20 mg to about 200 mg, about 50 mg to about 100 mg, about 50 mg to about 200 mg, or about 100 mg to about 200 mg. In some embodiments, a tissue sample has a mass of about 0.1 mg, about 1 mg, about 2 mg, about 3 mg, about 4 mg, about 5 mg, about 10 mg, about 15 mg, about 20 mg, about 50 mg, about 100 mg, or about 200 mg. In some embodiments, a tissue sample has a mass of at least about 0.1 mg, about 1 mg, about 2 mg, about 3 mg, about 4 mg, about 5 mg, about 10 mg, about 15 mg, about 20 mg, about 50 mg, or about 100 mg. In some embodiments, a tissue sample has a mass of at most about 1 mg, about 2 mg, about 3 mg, about 4 mg, about 5 mg, about 10 mg, about 15 mg, about 20 mg, about 50 mg, about 100 mg, or about 200 mg. In some embodiments, the tissue sample has a mass of about 15 mg, 10 mg, or 5 mg.

[0367] In some embodiments, the biological sample is a bacteria culture. In some embodiments, the bacteria culture comprises bacteria that cause infectious diseases. In some embodiments, the bacteria culture comprises antibiotic resistant strains. In some embodiments, the bacteria culture comprises strains that cause sexually transmitted diseases, such as gonorrhea or chlamydia. In some embodiments, the bacteria culture comprises syphilis.

[0368] In some embodiments, the sample is a swab sample. In some embodiments, the swab sample is a nasal swab, a buccal swab, a tongue swab, a nasopharyngeal swab, a lung swab, a throat swab, a skin swab, a wound swab, a pus swab, a vaginal swab, a cervical swab, a urethral swab, a rectal swab, a culture swab, a forensic swab, a dry swab, a wet swab, a swab for tuberculosis, a swab for STI, a swab for EBV, a swab for respiratory diseases, a swab for Influenza A, a swab for Influenza B, a swab for COVID-19, a swab for monkey pox, a MRSA swab, or a swab for RSV.

[0369] In some embodiments, the biological sample is derived from a subject. In some embodiments, the subject is an organism. In some embodiments, a subject is a mammal. In some embodiments, a subject is a human. In some embodiments, a subject is a mouse. In some embodiments, a subject is a swine. In some embodiments, a subject is a crustacean. In some embodiments, a subject is a shrimp. In some embodiments, a subject is a bacterial culture. In some embodiments, a subject is a plant. The present methods and systems described herein can process samples derived from any subject.

[0370] In some embodiments, a biological sample as described herein comprises an analyte. In some embodiments, a biological sample as described herein comprises a plurality of analytes. Suitable analytes include, but are not limited to nucleic acids, proteins, or any other analyte. In some embodiments, a nucleic acid comprises a deoxyribonucleotide (DNA) molecule. In some embodiments, a DNA molecule comprises a genomic DNA (gDNA) molecule. In some embodiments, a nucleic acid molecule comprises a ribonucleotide (RNA) molecule. The systems and methods described herein can process a biological sample comprising any type of analyte.

[0371] In some embodiments of methods and / or systems described herein, a sample is selected for amplification of a nucleotide sequence and specific primers complementary to binding sites in the target sequence are selected. In some embodiments, the sample comprises a template to a target nucleic acid sequence selected for amplification. In some embodiments, the target nucleic acid sequence is selected for amplification in order to verify the presence of the target nucleic acid in a sample. In some embodiments, the target nucleic acid sequence is selected for amplification in order to quantitate an amount of target nucleic acid in a sample. In some embodiments, the template is double-stranded DNA. In some embodiments, the template is double-stranded genomic DNA. In some embodiments, the sample comprises DNA. In some embodiments, the template can be made double-stranded. In some embodiments, the sample comprises RNA. In some embodiments, RNA in the sample is converted into single-stranded cDNA by reverse transcription. In some embodiments, single-stranded cDNA is made double-stranded. In some embodiments, the template is doublestranded cDNA.

[0372] The sample for amplification may be derived from any source. The sample may comprise tissue and / or cells from a subject. The sample may comprise cell-free nucleic acids from a subject. The sample may comprise isolated nucleic acids from a subject. The sample may comprise purified nucleic acids from a subject. The sample may comprise size fractionated nucleic acids from a subject. The sample may comprise size selected nucleic acids from a subject. In some embodiments of methods and / or systems described herein, the sample comprises nucleic acid extracted from a subject. In some embodiments, the sample comprises nucleic acid derived from the host from which the sample was taken. In some embodiments, the sample comprises genomic DNA (gDNA) derived from the host from which the sample was taken. In some embodiments, the DNA sequence or RNA sequence is animal genomic DNA or genomic RNA. In some embodiments, the DNA seq...

Claims

CLAIMSWhat is claimed is:

1. A system for processing a biological sample, the system comprising:(a) a first channel comprising a first opening, wherein said first channel is configured to couple thereto a biological sample;(b) a second channel comprising a cellulose substrate coupled thereto and a second opening, wherein the second opening comprises an incline having a slope of about 1° to about 50°, and wherein upon a coupling of the second opening to the first opening, the biological sample is transferred from the first channel to the second channel; and(c) a third channel comprising:(i) an elution solution; and(ii) a third opening, wherein upon a coupling of the second opening to the third opening, the elution solution is transferred from the third channel to the second channel.

2. The system of claim 1, wherein the second opening comprises an incline having a slope of about 3°.

3. The system of claim 1, wherein the second opening comprises an incline having a slope of about 45°.

4. The system of any one of claims 1-3, wherein the binding membrane is disposed along an inside perimeter of the second channel.

5. The system of claim 4, wherein the cellulose substrate has a surface area of about 0.1 to about 1.7 square inches (in2).

6. The system of claim 5, wherein the cellulose substrate has a surface area of about 0.6 to about 0.7 in2.

7. The system of claim 6, wherein the cellulose substrate has a surface area of about 0.4 to about 0.5 in2.

8. The system of any one of the preceding claims, wherein the first channel further comprises a filtration device.

9. The system of claim 8, wherein the filtration device is configured to filter the biological sample prior to the transfer of the biological sample from the first channel to the second channel.

10. The system of any one of the preceding claims, wherein the first channel further comprises a lysis solution.

11. The system of any one of the preceding claims, wherein the processing comprises an extraction of an analyte from the biological sample.

12. The system of any one of the preceding claims, wherein the processing comprises a nucleic acid extraction.

13. The system of claim 12, wherein the nucleic acid comprises a DNA or an RNA or both.

14. The system of any one of the preceding claims, wherein the processing comprises binding a plurality of nucleic acids to the cellulose substrate.

15. The system of claim 14, wherein the processing further comprises eluting at least a portion of the bound plurality of nucleic acids into the elution solution.

16. The system of claim 15, wherein a detection of amplified extracted nucleic acids determines the presence or absence of a target sequence.

17. The system of claim 16, wherein the target sequence is a nucleic acid sequence of a virus or a bacteria.

18. The system of claim 16, wherein the target sequence is a DNA sequence or RNA sequence or both.

19. The system of claim 18, wherein the DNA sequence is related to a genetic trait.

20. The system of claim 18, wherein the DNA sequence or RNA sequence is animal genomic DNA or genomic RNA.

21. The system of any one of claims 16-20, wherein amplification is performed via a quantitative polymerase chain reaction (qPCR), PCR, or isothermal amplification.

22. The system of claim 21, wherein the isothermal amplification is RPA or ANINA.

23. The system of any of the preceding claims, wherein a connector is configured to couple the third channel to the second channel, or wherein the connector is configured to couple the first channel to the second channel.

24. The system of any of the preceding claims, further comprising a dropper cap, optionally wherein the first channel is configured to transfer the biological sample to the second channel through the dropper cap.

25. The system of claim 24, wherein the dropper cap is configured to couple to the first channel.

26. The system of any one of the preceding claims, wherein the first channel is a vial, or a flexible tube.

27. The system of any one of the preceding claims, wherein the second channel is a vial.

28. The system of any one of the preceding claims, wherein the third channel is a vial.

29. The system of any one of the preceding claims, wherein the cellulose substrate is affixed to the second channel.

30. The system of any one of the preceding claims, wherein the second channel comprises a single chamber.

31. The system of any one of the preceding claims, wherein the first channel or the second channel comprise a particulate filter having a pore size of greater than about 10 um, and wherein the particulate filter is configured to retain particles when the biological sample is transferred from the first channel to the second channel in (b).

32. The system of any one of the preceding claims, wherein either the first channel or second channel comprises an adapter, wherein the adapter, when in use, couples the first channel to the second channel.

33. The system of claim 32, wherein the adapter comprises internal threads.

34. The system of any one of the preceding claims, wherein either the first channel or the second channel comprises internal treads, wherein the internal treads, when in use, couple the first channel to the second channel.

35. The system of any one of the preceding claims, wherein either the first channel or the second channel comprises a flexible tubing, wherein the flexible tubing, when in use, couples the first channel to the second channel.

36. The system of any one of the preceding claims, wherein a first channel comprising the biological sample is configured to transfer the biological sample to a port of the second channel.

37. The system of claim 36, wherein the first channel comprises a lysis solution.

38. The system of any one of claims 36 or 37, further comprising a dropper cap, wherein, when in use, the first channel transfers the biological sample through the dropper cap to the port.

39. The system of any one of claims 36-38, wherein a connector is configured to couple the third channel to the port, wherein the third channel comprises an elution solution, and wherein the coupling of the third channel to the port transfers the elution solution to and from the second channel.

40. The system of claim 39, wherein transferring the elution solution to and from the second channel occurs in less than about 30 seconds.

41. A system for preparation of a nucleic acid from a biological sample, the system comprising a housing comprising:(a) a cellulose substrate coupled to the housing; and(b) a port configured to (i) receive the biological sample and (ii) provide the biological sample to the cellulose substrate, wherein the port comprises an incline having a slope of about 1° to about 50°.

42. The system of claim 41, wherein the port comprises an incline having a slope of about 3°.

43. The system of claim 41, wherein the port comprises an incline having a slope of about 45°.

44. The system of any one of claims 41-43, wherein the cellulose substrate is disposed along an inside perimeter of the housing.

45. The system of claim 44, wherein the cellulose substrate has a surface area of about 0.1 to about 1.7 square inches (in2).

46. The system of claim 45, wherein the cellulose substrate has a surface area of about 0.6 to about 0.7 in2.

47. The system of claim 46, wherein the cellulose substrate has a surface area of about 0.4 to about 0.5 in2.

48. The system of claim 47, wherein the nucleic acid comprises a DNA or an RNA or both.

49. The system of claim 47 or 48, wherein the cellulose substrate is configured to bind a plurality of nucleic acids.

50. The system of any one of claims 41-49, wherein the housing is a bottle or a vial.

51. The system of any one of claims 41-50, wherein the cellulose substrate remains affixed to the housing.

52. The system of any one of claims 41-51, wherein the housing comprises a single chamber.

53. The system of any one of the preceding claims, wherein the system does not further comprise an actuator, a centrifuge, or a vacuum.

54. The system of any one of claims 1-53, wherein the biological sample is a biological fluid.

55. The system of any one of claims 1-53, wherein the biological sample is a swab sample, such as nasal swab, oral swab, tongue swab, throat swab, wound swab, vaginal swab, etc.

56. The system of any one of claims 1-53, wherein the biological sample is a tissue sample, such as skeletal, muscle, spleen, embedded (FFPE), or liver tissue.

57. The system of claim 56, wherein the tissue sample is a skeletal tissue, a muscle tissue, a spleen tissue, an embedded tissue or a liver tissue.

58. The system of claim 56 or 57, wherein the tissue sample has a mass of about 5 to about 200 milligrams (mg).

59. The system of any one of claims 56-58, wherein the tissue sample has a mass of at least about 25 mg.

60. The system of any one of claims 1-53, wherein the biological sample is an animal sample.

61. The system of any one of claims 1-53, wherein the biological sample is a bacteria sample.

62. The system of any one of claims 1-53, wherein the biological sample comprises water, such as water derived from a natural source, tap water, aquarium(s), or wastewater.

63. The system of claim 62, wherein the water comprises wastewater, water derived from a pond, or water derived from aquarium.

64. The system of any one of claims 1-53, wherein the biological sample is a plant sample.

65. A method for processing a biological sample, the method comprising:(a) coupling a biological sample to a first channel comprising a first opening;(b) coupling the first opening of the first channel to a second opening of a second channel, thereby transferring the biological sample from the first channel to the second channel, wherein the second channel has a cellulose substrate coupled thereto, and wherein the second opening comprises an incline having a slope of about 1° to about 50°;(c) coupling the second opening of the second channel to a third opening of a third channel, wherein the third channel comprises an elution solution, and wherein the coupling of the second opening to the third opening transfers the elution solution to the second channel; and(d) removing the elution solution from the second channel.

66. The method of claim 65, wherein the second opening comprises an incline having a slope of about 3°.

67. The method of claim 65, wherein the second opening comprises an incline having a slope of about 45°.

68. The method of any one of claims 65-67, wherein the binding membrane is disposed along an inside perimeter of the second channel.

69. The method of claim 68, wherein the cellulose substrate has a surface area of about 0.1 to about 1.7 square inches (in2)70. The method of claim 69, wherein the cellulose substrate has a surface area of about 0.6 to about 0.7 in2.

71. The system of claim 70, wherein the cellulose substrate has a surface area of about 0.4 to about 0.5 in2.

72. The method of claim 70 or 71, wherein subsequent to (d), the elution solution in (c) is transferred from the second channel back into the third channel.

73. The method of any one of claim 70-72, wherein the first channel further comprises a filtration device.

74. The method of claim 73, wherein the filtration device filters the biological sample prior to the transfer of the biological sample from the first channel to the second channel.

75. The method of any one of claims 65-74, wherein the first channel further comprises a lysissolution.

76. The method of any one of claims 65-75, wherein the processing comprises an extraction of an analyte from the biological sample.

77. The method of any one of claims 65-76, wherein the processing comprises a nucleic acid extraction.

78. The method of claim 77, wherein the nucleic acid comprises a DNA or an RNA or both.

79. The method of any one of claims 65-78, wherein the processing comprises binding a plurality of nucleic acids to the cellulose substrate.

80. The method of claim 79, wherein the processing further comprises eluting at least a portion of the bound plurality of nucleic acids into the elution solution.

81. The method of claim 80, wherein a detection of amplified extracted nucleic acids determine the presence or absence of a target sequence.

82. The method of claim 81, wherein the target sequence is a nucleic acid sequence of a virus or a bacteria.

83. The method of claim 82, wherein the target sequence is a DNA sequence or RNA sequence or both.

84. The method of claim 83, wherein the DNA sequence is related to a genetic trait.

85. The method of claim 84, wherein the DNA sequence or RNA sequence is animal genomic DNA or genomic RNA.

86. The method of any one of claims 81-85, wherein the amplification is performed via a quantitative polymerase chain reaction (qPCR), PCR, or isothermal amplification.

87. The method of claim 86, wherein the isothermal amplification is RPA or ANINA.

88. The method of any of claims 65-87, wherein a connector couples the third channel to the second channel, or wherein the connector couples the first channel to the second channel.

89. The method of any of claims 65-88, wherein the first channel transfers the biological sample to the second channel through a dropper cap.

90. The method of claim 88, wherein the dropper cap couples to the first channel.

91. The method of any one of claims 65-90, wherein the first channel is a vial, or a flexible tube.

92. The method of any one of claims 65-91, wherein the second channel is a vial.

93. The method of any one claims 65-92, wherein the third channel is a vial.

94. The method of any one of claims 65-93, wherein the cellulose substrate is affixed to the second channel.

95. The method of any one of claims 65-94, wherein the second channel comprises a singlechamber.

96. The method of any one of claims 65-95, wherein the first channel or the second channel comprise a particulate filter having a pore size of greater than about 10 um, and wherein the particulate filter retains particles when the biological sample is transferred from the first channel to the second channel in (b).

97. The method of any one of claims 65-96, wherein either the first channel or second channel comprises an adapter, wherein the adapter, when in use, couples the first channel to the second channel.

98. The method of claim 97, wherein the adapter comprises internal threads.

99. The method of any one of claims 65-98, wherein either the first channel or the second channel comprises internal treads, wherein the internal treads, when in use, couple the first channel to the second channel.

100. The method of any one of claims 65-99, wherein either the first channel or the second channel comprises a flexible tubing, wherein the flexible tubing, when in use, couples the first channel to the second channel.

101. The method of any one of claims 65-100, wherein a first channel comprising the biological sample transfers the biological sample to a port of the second channel.

102. The method of claim 101, wherein the first channel comprises a lysis solution.

103. The method of any one of claims 101 or 102, wherein, when in use, the first channel transfers the biological sample through a dropper cap to the port.

104. The method of any one of claims 101-103, wherein a connector couples the third channel to the port, wherein the third channel comprises an elution solution, wherein the coupling of the third channel to the port transfers the elution solution to and from the second channel.

105. The method of claim 104, wherein transferring the elution solution to and from the second channel occurs in less than about 30 seconds.

106. A composition for processing a biological sample, the composition comprising:(a) sodium hydroxide (NaOH) at a concentration of about 0.2 to about 2 molar (M) of the composition; and(b) triton-X 100 at a concentration of about 0.25% v / v to about 2% v / v of the composition.

107. The composition of claim 106, wherein the composition further comprises antifoam at a concentration of about 0.01% v / v to about 2% v / v of the composition.

108. The composition of claim 106 or 107, wherein sodium hydroxide (NaOH) is at aconcentration of about 1 molar of the composition.

109. The composition of any one of claims 106-108, wherein triton-X 100 is at a concentration of about 1.5% v / v of the composition.

110. The composition of any one of claims 106-109, wherein antifoam is at a concentration of about 0.05 % v / v to about 2% v / v of the composition.

111. A composition for processing a biological sample, the composition comprising:(a) lysozyme at a concentration of about 10 mg / mL to about 150mg / mL; and(b) detergent, wherein the detergent comprises:(i) tween80 at a concentration of about 0.025% v / v to about 1.5% v / v of the composition;(ii) triton-X 100 at a concentration of about 0.025% v / v to about 1.5% v / v of the composition; or(iii) any combination of (i) and (ii).

112. The composition of claim 111, wherein lysozyme is at a concentration of about 50 mg / mL of the composition.

113. The composition of 111 or 112, wherein tween80 is at a concentration of about 0.05% v / v of the composition.

114. The composition of any one of claims 111-113, wherein, wherein triton-X 100 at a concentration of about 0.05% v / v of the composition.

115. A composition for processing a biological sample, the composition comprising:(a) sodium hydroxide (NaOH) at a concentration of about 0.2 molar to about 2 molar (M) of the composition;(b) triton-X 100 at a concentration of about 0.025% v / v to about 2% v / v of the composition;(c) lysozyme at a concentration of about lOmg / mL to about 150mg / mL of the composition; and(d) tween80 at a concentration of about 0.025% v / v to about 0.5% v / v of the composition.

116. The composition of claim 115, wherein lysozyme is at a concentration of about 50 mg / mL;117. The composition of claim 115 or 116, wherein tween80 is at a concentration of about 0.05% v / v of the composition.

118. The composition of any one of claims 115-117, wherein sodium hydroxide (NaOH) is at a concentration of about 0.5 molar of the composition; and triton-X 100 at a concentrationof about 1.5% of the composition.

119. The composition of any one of claims 115-118, wherein the composition further comprises antifoam at a concentration of about 0.01% v / v to about 2% v / v of the composition.

120. The composition of any one of claims 115-119, wherein antifoam is at a concentration of about 1 % v / v of the composition.

121. The composition of any one of claims 106-120, wherein the composition further comprises EDTA at a concentration from about 0.01 mM to about 1.0 mM.

122. The composition of any one of claims 106-121, wherein the composition further comprises Tris at a concentration from about 1 mM to about 100 mM.

123. A composition for processing a biological sample, the composition comprising:(a) Tris HC1 at a concentration of about 10 millimolar (mM) to about 100 mM of the composition;(b) NaCl at a concentration of about 25 mM to about 500 mM of the composition;(c) triton x-100 at a concentration of about 0.1% to about 5% of the composition; and(d) TCEP at a concentration of about 1 mM to about 100 mM of the composition.

124. The composition of claim 123, wherein the composition further comprises PBS buffer at a concentration of about 5 mM to about 100 mM of the composition.

125. The composition of claim 123 or 124, wherein Tris HC1 is at a concentration of about 25 mM of the composition.

126. The composition of any one of claims 123-125, wherein NaCl is at a concentration of about 300 mM of the composition.

127. The composition of any one of claims 123-126, wherein triton x-100 is at a concentration of about 0.5% to about 1% of the composition, and TCEP is at a concentration of about 10 mM to about 20 mM of the composition.

128. A system for processing a biological sample, the system comprising:(a) a first channel comprising a first opening, wherein the first channel is configured to couple thereto a biological sample;(b) a second channel comprising:(i) a substrate coupled thereto; and(ii) a second opening, wherein the second opening is configured to couple to the first opening, and wherein upon the coupling of the second opening to the first opening, the biological sample is transferred fromthe first channel to the second channel; and(c) a third channel comprising:(i) an elution solution; and(ii) a third opening, wherein the third opening is configured to couple to the second opening, and wherein upon the coupling of the second opening to the third opening, the elution solution is transferred from the third channel to the second channel; wherein when the sample comprises a pathogenic bacterium, said first channel further comprises a lysis solution comprising sodium hydroxide (NAOH) at a concentration of at least about 200 mM, and one or more of the following:(i) triton-X 100 at a concentration of about 0.1% v / v to about 2% v / v of the composition;(ii) lysozyme at a concentration of about 10 mg / mL to about 150mg / mL of the composition;(iii) tween80 at a concentration of about 0.025 to about 1.5% of the composition;(iv) EDTA at a concentration from about 0.01 mM to about 1.0 mM of the composition;(v) Tris HC1 at a concentration from about 1 mM to about 100 mM of the composition; or(vi) Antifoam at a concentration of about 0.01% to about 2% of the composition.

129. The system of claim 128, wherein the second opening comprises an incline having a slope of about 45°.

130. The system of claim 128, wherein the second opening comprises an incline having a slope of about 3°.

131. The system of any one of claims 128-130, wherein one or more nucleic acid analytes from lysed pathogenic bacterium present in the biological sample bind to the substrate.

132. The system of claim 131, wherein the one or more nucleic acid analytes bound to the substrate are separated from the lysis solution, and are eluted into the third channel comprising the elution solution.

133. The system of any one of claims 128-132, wherein the processing comprises an extraction of an analyte from the biological sample.

134. The system of claim 133, wherein the processing comprises a nucleic acid extraction.

135. The system of claim 134, wherein the nucleic acid comprises a DNA.

136. The system of any one of claims 134 or 135, wherein the nucleic acid comprises an RNA.

137. The system of any one of claims 128-136, wherein the processing comprises binding a plurality of nucleic acids to the substrate.

138. The system of claim 137, wherein the processing further comprises eluting at least a portion of the bound plurality of nucleic acids into the elution solution.

139. The system of any one of claims 128-138, wherein the biological sample comprises a target sequence.

140. The system of claim 139, wherein the target sequence is a nucleic acid sequence of a pathogenic bacterium.

141. The system of claim 139 or 140, wherein the target sequence is a nucleic acid sequence of an acid-fast bacteria.

142. The system of any one of claims 136-141, wherein the target sequence is a nucleic acid sequence of Mycobacterium tuberculosis.

143. The system of claim 142, wherein the target sequence comprises a conserved sequence within the Mycobacterium tuberculosis genome.

144. The system of claim 143, wherein the target sequence comprises a mutated sequence within the Mycobacterium tuberculosis genome, that leads to antibiotic resistance.

145. The system of any one of claims 128-144, wherein the substrate is affixed to the second channel.

146. The system of claim 145, wherein a detection of amplified target sequence determines the presence of a pathogenic bacterium in the biological sample.

147. The system of claim 145, wherein a lack of detection of amplified target sequence determines the absence of a pathogenic bacterium in the biological sample.

148. The system of any one of claims 142-147, wherein detection of amplified target sequence determines the presence of Mycobacterium tuberculosis in the biological sample.

149. The system of any one of claims 142-148, wherein a lack of detection of amplified target sequence determines the absence of Mycobacterium tuberculosis in the biological sample.

150. A system for preparation of a nucleic acid from a biological sample, the system comprising a housing comprising:(a) a substrate affixed to the housing; and a port, wherein the port is configured to receive the biological sample, wherein the port isconfigured to provide the biological sample to the substrate, and wherein the port is further configured to receive a lysis solution, wherein when said biological sample is a pathogenic bacterium said lysis solution or said enzymatic lysis solution comprises sodium hydroxide (NaOH) at a concentration of at least about 200 mM, and one or more of the following:(vii) triton-X 100 at a concentration of about 0.1% v / v to about 2% v / v of the composition;(viii) lysozyme at a concentration of about 10 mg / mL to about 150mg / mL of the composition;(ix) tween80 at a concentration of about 0.025 to about 1.5% of the composition;(x) EDTA at a concentration from about 0.01 mM to about 1.0 mM of the composition;(xi) Tris HC1 at a concentration from about 1 mM to about 100 mM of the composition; or(xii) Antifoam at a concentration of about 0.01% to about 2% of the composition.

151. The system of any one of claims 128-150, wherein the biological sample comprises nucleic acid.

152. The system of claim 151, wherein the nucleic acid comprises a DNA or an RNA.

153. The system of any one of claims 128-152, wherein the substrate is configured to bind a plurality of nucleic acids.

154. The system of any one of claims 128-153, wherein substrate comprises cellulose.

155. The system of any one of claims 128-154, wherein the lysis solution is a chemical lysis solution.

156. The system of claim 155, wherein the chemical lysis solution comprises an alkaline lysis buffer solution.

157. The system of claim 156, wherein the alkaline lysis buffer solution comprises sodium hydroxide or sodium acetate at a concentration of between about 0.2 M to about 2 M158. The system of claim 156 or 157, wherein the alkaline lysis buffer solution comprises sodium hydroxide at a concentration of between about 0.5 M to about 1.2 M.

159. The system of any one of claims 156-158, wherein the alkaline lysis buffer solution comprises sodium hydroxide at a concentration of about 1.0 M160. The system of any one of claims 156-159, wherein the alkaline lysis buffer solution comprises a detergent.

161. The system of claim 160, wherein the detergent comprises Triton-X 100 at a concentration of between about 0.5% to about 2.0% of the alkaline lysis buffer solution.

162. The system of claim 160 or 161, wherein the detergent comprises Triton-X 100 at a concentration of about 1.5% of the alkaline lysis buffer solution.

163. The system of any one of claims 156-162, wherein the alkaline lysis buffer solution comprises an antifoam reagent at a concentration between about 0.01% to about 2.0% of the alkaline lysis buffer solution.

164. The system of any one of claims 155-163, wherein the chemical lysis solution further comprises a chelating agent, such as EDTA at a concentration of about 0.01 mM to about 1.0 mM.

165. The system of any one of claims 155-164, wherein the chemical lysis solution further comprises an enzymatic lysis solution.

166. The system of any one of claims 128-165, wherein the lysis solution is a chemical lysis solution.

167. The system of claim 166, wherein the enzymatic lysis solution comprises lysozyme at a concentration of between about 10 mg / mL to about 150 mg / mL of the enzymatic lysis buffer solution.

168. The system of claim 166 or 167, wherein the enzymatic lysis solution comprises a detergent, such as Tween80 at a concentration of between about 0.05% to about 0.5% of the enzymatic lysis buffer solution.

169. The system of any one of claims 128-168, wherein the lysis solution effectively lyses pathogenic bacterium present in the biological sample.

170. The system of claim 169, wherein the effective lysis of the pathogenic bacterium does not require use of a mechanical lysis method.

171. The system of claim 169 or 170, wherein the pathogenic bacterium present in the biological sample comprises one or more of Mycobacterium tuberculosis complex, Mycobacterium avium, Mycobacterium abscessus, Mycobacterium smegmatis, Streptococcus pyrogenes, Streptococcus pneumoniae, Francisella philomiragia, and Bacillus thuringiensis.

172. The system of any one of claims 169-171, wherein the pathogenic bacterium present in the biological sample comprises one or more species from Mycobacterium tuberculosis complex (MT BC), including but not limited to Mycobacterium tuberculosis, Mycobacterium africanum, Mycobacterium bovis, Mycobacterium orygis, and Mycobacterium canetti.

173. The system of any one of claims 169-172, wherein the pathogenic bacterium present in the biological sample comprises Mycobacterium tuberculosis.

174. The system of any one of claims 128-173, wherein the biological sample does not comprise a detectable amount of Mycobacterium tuberculosis.

175. The system of any one of claims 169-174, wherein effective lysis of pathogenic bacterium present in the biological sample occurs in less than about 30 minutes.

176. The system of any one of claims 128-175, wherein the biological sample is processed in about 30 minutes or less.

177. The system of any one of claims 128-176, wherein the system does not further comprise an actuator, a centrifuge, or a vacuum.

178. The system of any one of claims 128-177, wherein the biological sample is a swab sample, such as oral swab, tongue swab, buccal swab, throat swab, nasal swab, wound swab, skin swab, vaginal swab, urethral swab, anal swab.

179. The system of claim 178, wherein the biological sample is an oral swab sample.

180. The system of any one of claims 128-179, wherein the biological sample is a biological fluid.

181. The system of claim 180, wherein the biological fluid is whole blood, serum, saliva, sputum, tears, lung lavage, cell lysates, menstrual blood, urine, processed swab samples, processed tissue samples, amniotic fluid, cerebrospinal fluid, tears, or semen.

182. The system of any one of claims 128-181, wherein the biological sample is a tissue sample.

183. The system of claim 182, wherein the tissue sample is a skeletal tissue, a muscle tissue, a spleen tissue, an embedded tissue, or a liver tissue.

184. The system of any one of claims 128-183, wherein the biological sample is a bacteria culture.

185. A kit comprising the system of any one of claims 1-65 or 128-184 and instructions for use.

186. The kit of claim 185, wherein the instructions designate a protocol for use as a field kit.

187. The kit of claim 185 or 186, wherein the instructions designate a detection of a bacterial infection.

188. The kit of claim 187, wherein the bacterial infection is a pathogenic bacterium infection.

189. The kit of claim 187 or 188, wherein the bacterial infection is an acid-fast bacterial infection.

190. The kit of any one of claims 187-189, wherein the bacterial infection is a tuberculosis-causing infection.

191. The kit of any one of claims 187-190, wherein the bacterial infection is a Mycobacterium tuberculosis infection.

192. The kit of any one of claims 187-191, wherein the instructions for use are written on an instruction card for isothermal, nucleic acid target sequence amplification.

193. The kit of any one of claims 187-192, wherein the instructions for use are written on an instruction card for isothermal, real time nucleic acid target sequence amplification.

194. A method for processing a biological sample, the method comprising:(a) coupling a biological sample to a first channel comprising a first opening;(b) coupling the first opening of the first channel to a second opening of a second channel, thereby transferring the biological sample from the first channel to the second channel, wherein the second channel has a substrate coupled thereto;(c) coupling the second opening of the second channel to a third opening of a third channel, wherein the third channel comprises an elution solution, and wherein the coupling of the second opening to the third opening transfers the elution solution to the second channel; and(d) removing the elution solution from the second channel; wherein when the sample comprises a pathogenic bacterium, said first channel further comprises a lysis solution comprising sodium hydroxide (NAOH) at a concentration of at least about 200 mM, and one or more of the following:(i) triton-X 100 at a concentration of about 0.1% v / v to about 2% v / v of the composition;(ii) lysozyme at a concentration of about 10 mg / mL to about 150mg / mL of the composition;(iii) tween80 at a concentration of about 0.25% v / v to about 1.5% v / v of the composition;(iv) EDTA at a concentration from about 0.01 mM to about 1.0 mM of the composition;(v) Tris HC1 at a concentration from about 1 mM to about 100 mM of the composition; or(vi) Antifoam at a concentration of about 0.01% v / v to about 2% v / v of the composition.

195. The method of claim 194, wherein the second opening comprises an incline having a slope of about 45°.

196. The method of claim 194, wherein the second opening comprises an incline having a slope of about 3°.

197. The method of any one of claims 194-196, wherein one or more nucleic acid analytes from lysed pathogenic bacterium present in the biological sample bind to the substrate.

198. The method of claim 197, wherein the one or more nucleic acid analytes bound to the substrate are separated from the lysis solution and, wherein the one or more nucleic acid analytes bound to the substrate are eluted into the third channel comprising the elution solution.

199. The method of any one of claims 194-198, wherein the processing comprises an extraction of an analyte from the biological sample.

200. The method of claim 199, wherein the processing comprises a nucleic acid extraction.

201. The method of claim 200, wherein the nucleic acid comprises a DNA.

202. The method of any one of claims 200 or 201, wherein the nucleic acid comprises an RNA.

203. The method of any one of claims 194-202 wherein the processing comprises binding a plurality of nucleic acids to the substrate.

204. The method of claim 203, wherein the processing further comprises eluting at least a portion of the bound plurality of nucleic acids into the elution solution.

205. The method of claim 204, wherein a detection of amplified extracted nucleic acids determines the presence or absence of a target sequence.

206. The method of claim 205, wherein the target sequence is a nucleic acid sequence of a pathogenic bacterium.

207. The method of claim 205 or 206, wherein the target sequence is a nucleic acid sequence of an acid-fast bacteria.

208. The method of any one of claims 205-207, wherein the target sequence is a nucleic acid sequence of Mycobacterium tuberculosis.

209. The system of claim 208, wherein the target sequence comprises a conserved sequence within the Mycobacterium tuberculosis genome.

210. The system of claim 208, wherein the target sequence comprises a mutated sequence within the Mycobacterium tuberculosis genome, that leads to antibiotic resistance.

211. The method of any one of claims 194-210, wherein the substrate is affixed to the second channel.

212. The method of any one of claims 194-211, further comprising amplification of the extracted nucleic acids.

213. The method of claim 212, wherein the amplification is performed via a quantitative polymerase chain reaction (qPCR), PCR, or isothermal amplification.

214. The method of claim 213, wherein the isothermal amplification is RPA or ANINA.

215. The method of claim 213 or 214, wherein the isothermal amplification is real time ANINA.

216. The method of any one of claims 194-215, wherein the amplification produces detectable amplified target sequence in less than about 30, 25, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, or 8 minutes following the start of the amplification reaction.

217. The method of claim 216, wherein detection of amplified target sequence determines the presence of a pathogenic bacterium in the biological sample.

218. The method of claim 217, wherein a lack of detection of amplified target sequence determines the absence of a pathogenic bacterium in the biological sample.

219. The method of any one of claims 195-218, wherein detection of amplified target sequence determines the presence of Mycobacterium tuberculosis in the biological sample.

220. The method of any one of claims 195-219, wherein a lack of detection of amplified target sequence determines the absence of Mycobacterium tuberculosis in the biological sample.

221. A method of processing a biological sample, the method comprising bringing the sample in contact with a lysis solution under conditions sufficient to lyse the biological sample in 30 minutes or less, wherein when said biological sample is a pathogenic bacterium said lysis solution comprises sodium hydroxide (NaOH) at a concentration of at least about 200 mM, and one or more of the following:(xiii) triton-X 100 at a concentration of about 0.1% v / v to about 2% v / v of the composition;(xiv) lysozyme at a concentration of about 10 mg / mL to about 150mg / mL of the composition;(xv) tween80 at a concentration of about 0.025% v / v to about 1.5% v / v of the composition;(xvi) EDTA at a concentration from about 0.01 mM to about 1.0 mM of the composition;(xvii) Tris HC1 at a concentration from about 1 mM to about 100 mM of the composition; or(xviii) Antifoam at a concentration of about 0.01% v / v to about 2% v / v of the composition.

222. The method of any one of claims 194-221, wherein the biological sample comprises nucleic acid.

223. The method of claim 222, wherein the nucleic acid comprises a DNA or an RNA.

224. The method of any one of claims 194-223, wherein the substrate binds a plurality of nucleic acids.

225. The method of any one of claims 194-224, wherein substrate comprises cellulose.

226. The method of any one of claims 194-225, wherein the lysis solution is a chemical lysis solution.

227. The method of claim 226, wherein the chemical lysis solution comprises an alkaline lysis buffer solution.

228. The method of claim 227, wherein the alkaline lysis buffer solution comprises sodium hydroxide at a concentration of between about 0.2 M to about 2 M of the alkaline lysis buffer solution.

229. The method of claim 227 or 228, wherein the alkaline lysis buffer solution comprises sodium hydroxide at a concentration of between about 0.5 M to about 1.2 M of the alkaline lysis buffer solution.

230. The method of any one of claims 227-229, wherein the alkaline lysis buffer solution comprises sodium hydroxide at a concentration of about 1 M of the alkaline lysis buffer solution.

231. The method of any one of claims 227-230, wherein the alkaline lysis buffer solution comprises a detergent.

232. The method of claim 231, wherein the detergent comprises Triton-X 100 at a concentration of between about 0.5% to about 2.0% of the alkaline lysis buffer solution.

233. The method of claim 228 or 232, wherein the detergent comprises Triton-X 100 at a concentration of about 1.5% of the alkaline lysis buffer solution.

234. The method of any one of claims 224-233, wherein the alkaline lysis buffer solution comprises an antifoam reagent at a concentration between about 0.01% to about 2.0% of the alkaline lysis buffer solution.

235. The method of any one of claims 194-234, wherein the lysis solution is an enzymatic lysis solution.

236. The method of claim 235, wherein the enzymatic lysis solution comprises lysozyme at a concentration of between about 10 mg / mL to about 150 mg / mL of the enzymatic lysis buffer solution.

237. The method of claim 236, wherein the enzymatic lysis solution comprises lysozyme ata concentration of about 50 mg / mL of the enzymatic lysis buffer solution.

238. The method of claim 236 or 237, wherein the enzymatic lysis solution comprises a detergent.

239. The method of claim 238, wherein the detergent comprises Tween80 at a concentration of between about 0.05% to about 0.5% of the enzymatic lysis buffer solution.

240. The method of claim 238 or 239, wherein the detergent comprises Tween80 at a concentration of about 0.05% of the enzymatic lysis buffer solution.

241. The method of any one of claims 238-239, wherein the detergent further comprises Triton-X 100 at a concentration of about 0.05% of the enzymatic lysis buffer solution.

242. The method of any one of claims 194-241, wherein the lysis solution comprises Tris HC1 at a concentration of about 10 millimolar (mM) to about 100 mM of the composition.

243. The method of any one of claims 194-242, wherein the lysis solution comprises NaCl at a concentration of about 25 mM to about 500 mM of the composition.

244. The method of any one of claims 194-243, wherein the lysis solution comprises triton x-100 at a concentration of about 0.1% to about 5% of the composition.

245. The method of any one of claims 194-244, wherein the lysis solution comprises TCEP at a concentration of about 1 mM to about 100 mM of the composition.

246. The method of any one of claims 242-245, wherein Tris HC1 is at a concentration of about 25 mM of the composition.

247. The method of any one of claims 243-246, wherein NaCl is at a concentration of about 300 mM of the composition.

248. The method of any one of claims 244-247, wherein triton x-100 is at a concentration of about 1% of the composition.

249. The method of any one of claims 245-248, wherein TCEP is at a concentration of about 20 mM of the composition.

250. The method of any one of claims 194-249, wherein the lysis solution effectively lyses pathogenic bacterium present in the biological sample.

251. The method of claim 250, wherein the effective lysis of the pathogenic bacterium does not require use of a mechanical lysis method.

252. The method of claim 250 or 251, wherein the pathogenic bacterium present in the biological sample comprises one or more of Mycobacterium tuberculosis, Mycobacterium avium, Mycobacterium abscessus, Mycobacterium smegmatis, Francisella philomiragia, Yersinia enterocolitica, Bacillus thuringiensis, Pseudomonas aeruginosa, Moraxella catarrhalis, o Klebsiella pneumoniae.

253. The method of any one of claims 250-252, wherein the pathogenic bacterium present in the biological sample comprises Mycobacterium tuberculosis.

254. The method of any one of claims 194-253, wherein the biological sample does not comprise a detectable amount of Mycobacterium tuberculosis.

255. The method of any one of claims 194-254, wherein effective lysis of pathogenic bacterium present in the biological sample occurs in less than about 30 minutes.

256. The method of any one of claims 194-255, wherein the biological sample is processed in about 30 minutes or less.

257. The method of any one of claims 194-256, wherein the method does not further comprise an actuator, a centrifuge, or a vacuum.

258. The method of any one of claims 194-257, wherein the biological sample is a biological fluid.

259. The method of claim 258, wherein the biological fluid is whole blood, serum, saliva, tears, lung lavage, cell lysates, menstrual blood, urine, processed tissue samples, amniotic fluid, cerebrospinal fluid, tears, saliva, or semen.

260. The method of any one of claims 194-259, wherein the biological sample is a tissue sample.

261. The method of claim 260, wherein the tissue sample is a skeletal tissue, a muscle tissue, a spleen tissue, an embedded tissue, or a liver tissue.

262. The method of any one of claims 194-259, wherein the biological sample is a bacteria culture.

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