WO2023122648A1

WO2023122648A1 - Devices, systems, and methods for detecting target nucleic acids

Info

Publication number: WO2023122648A1
Application number: PCT/US2022/082117
Authority: WO
Inventors: Sarah Jane SHAPIRO; Benjamin Andrew BLIZARD; Philip You Fai LEE; Jesus Ching; Janice Sha CHEN; Jacob LESINSKI
Original assignee: Mammoth Biosciences, Inc.
Priority date: 2021-12-23
Filing date: 2022-12-21
Publication date: 2023-06-29

Abstract

Disclosed herein are devices, systems and methods for detecting a target nucleic acid in a biological sample.

Description

DEVICES, SYSTEMS, AND METHODS FOR DETECTING TARGET NUCLEIC ACIDS

CROSS-REFERENCE

[0001] This application claims priority to and the benefit of U.S. Provisional Application No. 63/293,508, filed December 23, 2021, which application is incorporated herein by reference in its entirety.

STATEMENT AS TO FEDERALLY-SPONSORED RESEARCH

[0002] This invention was made with government support under Contract No. N66001-21-C- 4048 awarded by the Department of Defense, Defense Advanced Research Projects Agency (DARPA). The US government has certain rights in the invention.

REFERENCE TO AN ELECTRONIC SEQUENCE LISTING

[0003] The contents of the electronic sequence listing (MABI_001_00WO_SeqList_ST26.xml; Size: 163,080 bytes; and Date of Creation: December 20, 2022) are herein incorporated by reference in its entirety.

BACKGROUND

[0004] Various communicable diseases can easily spread from an individual or environment to an individual. The detection of the ailments, especially at the early stages of infection, may provide guidance on treatment or intervention to reduce the progression or transmission of the ailment.

[0005] Traditional nucleic acid-based molecular testing methods, such as PCR or sequencing, can be useful for detecting diseases but they typically require elaborate and costly instrumentation, and/or specialized laboratory materials. For example, the use of external instrumentation imposes tremendous economic barriers for the access of such testing methods. Further, dependence upon a small number of instruments to run tests presents a potentially significant bottleneck when an outbreak demands surge capacity and increased throughput. Additionally, instrumentation dependence complicates the access of test devices to clinical sites where logistic constraints preclude transportation of bulky associated equipment or infrastructure requirements are absent.

[0006] Thus, there is a need for a rapid nucleic acid-based molecular testing method that is affordable and does not require elaborate instrumentation. SUMMARY

[0007] In one aspect, disclosed herein is a device, comprising: a) a sample chamber configured to receive a biological sample including a target nucleic acid; and b) a plurality of detection chambers fluidically connected to the sample chamber via one or more capillary channels, thereby enabling a fluid volume of the biological sample to flow from the sample chamber to at least one detection chamber from the plurality of detection chambers by capillary action, wherein the at least one detection chamber includes a detection reagent having a programmable nuclease, a guide nucleic acid, and a reporter, and wherein the reporter is capable of being cleaved upon binding of the guide nucleic acid to a segment of the target nucleic acid.

[0008] In some cases, the sample chamber further comprises a lysis buffer. In some cases, the device further comprises a lysis buffer storage chamber fluidically connected to the sample chamber. In some cases, the device further comprises a lysis chamber fluidically connected to the sample chamber, wherein the lysis chamber comprises a lysis buffer. In some cases, the lysis buffer comprises an enzyme that disrupts cell membranes. In some cases, the lysis buffer has a pH range of 1 to 14. In some cases, the lysis buffer has a pH range of about 1 to about 13. In some cases, the lysis buffer has a pH range of at least about 1. In some cases, the lysis buffer has a pH range of at most about 13. In some cases, the lysis buffer has a pH range of about 1 to about 3, about 1 to about 5, about 1 to about 7, about 1 to about 9, about 1 to about 11, about 1 to about 13, about 3 to about 5, about 3 to about 7, about 3 to about 9, about 3 to about 11, about 3 to about 13, about 5 to about 7, about 5 to about 9, about 5 to about 11, about 5 to about 13, about 7 to about 9, about 7 to about 11, about 7 to about 13, about 9 to about 11, about 9 to about 13, or about 11 to about 13. In some cases, the lysis buffer has a pH range of about 1, about 3, about 5, about 7, about 9, about 11, or about 13. In some cases, the lysis chamber further comprises a neutralization buffer that is capable of neutralize the lysis buffer.

[0009] In some cases, the sample chamber is capable of being hermetically sealed from an external environment. In some cases, the sample chamber is configured to receive the biological sample from a syringe or swab. In some cases, the one or more capillary channels are branched and connected to the plurality of detection chambers. In some cases, the one or more capillary channels are configured to create substantially the same fluid volume in the plurality of detection chambers. In some cases, each detection chamber from the plurality of detection chambers is a standalone physical compartment. In some cases, each detection chamber from the plurality of detection chambers is located in a region of one of the capillary channels. In some cases, each detection chamber from the plurality of detection chambers is located at the end of one of the capillary channels. In some cases, each detection chamber from the plurality of detection chambers has substantially equivalent volume. In some cases, the plurality of detection chambers have different volumes. In some cases, the plurality of detection chambers are circular, elongated, or hexagonal. In some cases, the at least one detection chamber from the plurality of detection chambers comprises a hydrophobic or porous substrate. In some cases, the hydrophobic or porous substrate is configured to create resistance with presence of the fluid volume of the biological sample in the at least one detection chamber, thereby directing the biological sample to flow to an unfilled detection chamber. In some cases, the at least one detection chamber from the plurality of detection chambers comprises an optically transparent surface. In some cases, the at least one detection chamber from the plurality of the detection chambers is configured to hold from 1 pL to 1 pL of fluid. In some cases, the at least one detection chamber from the plurality of the detection chambers is configured to hold fluid of about 1 pL to about 1,000,000 pL. In some cases, the at least one detection chamber from the plurality of the detection chambers is configured to hold fluid of at least about 1 pL. In some cases, the at least one detection chamber from the plurality of the detection chambers is configured to hold fluid of at most about 1,000,000 pL. In some cases, the at least one detection chamber from the plurality of the detection chambers is configured to hold fluid of about 1 pL to about 10 pL, about 1 pL to about 100 pL, about 1 pL to about 1,000 pL, about 1 pL to about 10,000 pL, about 1 pL to about 100,000 pL, about 1 pL to about 1,000,000 pL, about 10 pL to about 100 pL, about 10 pL to about 1,000 pL, about 10 pL to about 10,000 pL, about 10 pL to about 100,000 pL, about 10 pL to about 1,000,000 pL, about 100 pL to about 1,000 pL, about 100 pL to about 10,000 pL, about 100 pL to about 100,000 pL, about 100 pL to about 1,000,000 pL, about 1,000 pL to about 10,000 pL, about 1,000 pL to about 100,000 pL, about 1,000 pL to about 1,000,000 pL, about 10,000 pL to about 100,000 pL, about 10,000 pL to about 1,000,000 pL, or about 100,000 pL to about 1,000,000 pL. In some cases, the at least one detection chamber from the plurality of the detection chambers is configured to hold fluid of about 1 pL, about 10 pL, about 100 pL, about 1,000 pL, about 10,000 pL, about 100,000 pL, or about 1,000,000 pL.

[0010] Also disclosed is a method for detecting a target nucleic acid in a biological sample, comprising loading the biological sample to the sample chamber of the device disclosed herein, such that the fluid volume of the biological sample flows via the one or more capillary channels to the plurality of detection chambers by capillary action, such that the fluid volume of the biological sample contacts the detection reagent in at least one detection chamber, and such that a detectable signal is generated by cleavage of the reporter upon binding of the guide nucleic acid to the segment of the target nucleic acid, indicating the presence of the target nucleic acid. In some cases, the method further comprises quantifying the detectable signal, thereby quantifying an amount of the target nucleic acid present in the biological sample.

[0011] In another aspect, disclosed herein is a device, comprising: a plurality of detection chambers arranged as an array and configured to contact a biological sample and retain a fluid volume of the biological sample, wherein at least one detection chamber from the plurality of detection chambers includes a detection reagent having a programmable nuclease, a guide nucleic acid, and a reporter, and wherein the reporter is capable of being cleaved upon binding of the guide nucleic acid to a segment of the target nucleic acid. In some cases, the device further comprises a sample chamber fluidically connected to the plurality of detection chambers. In some cases, the sample chamber further comprises a lysis buffer. In some cases, the lysis buffer comprises an enzyme that disrupts cell membranes. In some cases, the lysis buffer has a pH range of 1 to 14. In some cases, the lysis buffer has a pH range of about 1 to about 13. In some cases, the lysis buffer has a pH range of at least about 1. In some cases, the lysis buffer has a pH range of at most about 13. In some cases, the lysis buffer has a pH range of about 1 to about 3, about 1 to about 5, about 1 to about 7, about 1 to about 9, about 1 to about 11, about 1 to about 13, about 3 to about 5, about 3 to about 7, about 3 to about 9, about 3 to about 11, about 3 to about 13, about 5 to about 7, about 5 to about 9, about 5 to about 11, about 5 to about 13, about 7 to about 9, about 7 to about 11, about 7 to about 13, about 9 to about 11, about 9 to about 13, or about 11 to about 13. In some cases, the lysis buffer has a pH range of about 1, about 3, about 5, about 7, about 9, about 11, or about 13. In some cases, the sample chamber further comprises a neutralization buffer that is capable of neutralize the lysis buffer.

[0012] In some cases, the sample chamber is capable of being hermetically sealed from an external environment. In some cases, the sample chamber is configured to receive the biological sample from a syringe or swab. In some cases, each detection chamber from the plurality of detection chambers is a standalone physical compartment. In some cases, each detection chamber from the plurality of detection chambers is a microfluidic structure, column, or microwell. In some cases, each detection chamber from the plurality of detection chambers has substantially equivalent volume. In some cases, the plurality of detection chambers have different volumes. In some cases, the plurality of detection chambers are circular, elongated, or hexagonal. In some cases, at least one detection chamber from the plurality of detection chambers is coated with the detection reagent. In some cases, the at least one detection chamber from the plurality of detection chambers comprises a hydrophobic or porous substrate. In some cases, the hydrophobic or porous substrate is configured to create resistance with presence of the fluid volume of the biological sample in the at least one detection chamber, thereby directing the biological sample to flow to an unfilled detection chamber. In some cases, the at least one detection chamber from the plurality of detection chambers comprises an optically transparent surface. In some cases, the at least one detection chamber from the plurality of the detection chambers is configured to hold from 1 pL to 1 pL of fluid. In some cases, the at least one detection chamber from the plurality of the detection chambers is configured to hold fluid of about 1 pL to about 1,000,000 pL. In some cases, the at least one detection chamber from the plurality of the detection chambers is configured to hold fluid of at least about 1 pL. In some cases, the at least one detection chamber from the plurality of the detection chambers is configured to hold fluid of at most about 1,000,000 pL. In some cases, the at least one detection chamber from the plurality of the detection chambers is configured to hold fluid of about 1 pL to about 10 pL, about 1 pL to about 100 pL, about 1 pL to about 1,000 pL, about 1 pL to about 10,000 pL, about 1 pL to about 100,000 pL, about 1 pL to about 1,000,000 pL, about 10 pL to about 100 pL, about 10 pL to about 1,000 pL, about 10 pL to about 10,000 pL, about 10 pL to about 100,000 pL, about 10 pL to about 1,000,000 pL, about 100 pL to about 1,000 pL, about 100 pL to about 10,000 pL, about 100 pL to about 100,000 pL, about 100 pL to about 1,000,000 pL, about 1,000 pL to about 10,000 pL, about 1,000 pL to about 100,000 pL, about 1,000 pL to about 1,000,000 pL, about 10,000 pL to about 100,000 pL, about 10,000 pL to about 1,000,000 pL, or about 100,000 pL to about 1,000,000 pL. In some cases, the at least one detection chamber from the plurality of the detection chambers is configured to hold fluid of about 1 pL, about 10 pL, about 100 pL, about 1,000 pL, about 10,000 pL, about 100,000 pL, or about 1,000,000 pL.

[0013] Also disclosed is a method for detecting a target nucleic acid in a biological sample, comprising contacting the biological sample with the device disclosed herein, such that the fluid volume of the biological sample contacts the detection reagent in at least one detection chamber, and such that a detectable signal is generated by cleavage of the reporter upon binding of the guide nucleic acid to the segment of the target nucleic acid, indicating the presence of the target nucleic acid. In some cases, the method further comprises quantifying the detectable signal, thereby quantifying an amount of the target nucleic acid present in the biological sample. [0014] In another aspect, disclosed herein is a device, comprising: a) a sample chamber configured to receive a biological sample including a target nucleic acid; and b) a detection chamber fluidically connected to the sample chamber via a first channel and a second channel; wherein the first channel is configured to receive a flow of a first fluid and the second channel is configured to receive a flow of a second fluid, wherein the first fluid is an aqueous fluid, and the second fluid is immiscible with the first fluid, wherein the first and second channels collectively form at least one junction, which is configured to produce a plurality of aqueous droplets surrounded by the second fluid flowing through the second channel, wherein at least one aqueous droplet includes the biological sample and a detection reagent having a programmable nuclease, a guide nucleic acid, and a reporter, and wherein the reporter is capable of being cleaved upon binding of the guide nucleic acid to a segment of the target nucleic acid.

[0015] In some cases, the sample chamber further comprises a lysis buffer. In some cases, the device further comprises a lysis buffer storage chamber fluidically connected to the sample chamber. In some cases, the device further comprises a lysis chamber fluidically connected to the sample chamber, wherein the lysis chamber comprises a lysis buffer. In some cases, the lysis buffer comprises an enzyme that disrupts cell membranes. In some cases, the lysis buffer has a pH range of 1 to 14. In some cases, the lysis buffer has a pH range of about 1 to about 13. In some cases, the lysis buffer has a pH range of at least about 1. In some cases, the lysis buffer has a pH range of at most about 13. In some cases, the lysis buffer has a pH range of about 1 to about 3, about 1 to about 5, about 1 to about 7, about 1 to about 9, about 1 to about 11, about 1 to about 13, about 3 to about 5, about 3 to about 7, about 3 to about 9, about 3 to about 11, about 3 to about 13, about 5 to about 7, about 5 to about 9, about 5 to about 11, about 5 to about 13, about 7 to about 9, about 7 to about 11, about 7 to about 13, about 9 to about 11, about 9 to about 13, or about 11 to about 13. In some cases, the lysis buffer has a pH range of about 1, about 3, about 5, about 7, about 9, about 11, or about 13. In some cases, the lysis chamber further comprises a neutralization buffer that is capable of neutralize the lysis buffer.

[0016] In some cases, the sample chamber is capable of being hermetically sealed from an external environment. In some cases, the sample chamber is configured to receive the biological sample from a syringe or swab. In some cases, the detection chamber is a standalone physical compartment. In some cases, the detection chamber is configured to receive the plurality of aqueous droplets. In some cases, the device comprises a plurality of detection chambers. In some cases, each detection chamber from the plurality of detection chambers has substantially equivalent volume. In some cases, the plurality of detection chambers have different volumes. In some cases, the detection chamber is circular, elongated, or hexagonal. In some cases, the detection chamber comprises a hydrophobic or porous substrate. In some cases, the hydrophobic or porous substrate is configured to create resistance with presence of the fluid volume of the biological sample in the detection chamber, thereby directing the biological sample to flow to an unfilled detection chamber. In some cases, the detection chamber comprises an optically transparent surface. In some cases, the at least one detection chamber from the plurality of the detection chambers is configured to hold from 1 pL to 1 pL of fluid. In some cases, the at least one detection chamber from the plurality of the detection chambers is configured to hold fluid of about 1 pL to about 1,000,000 pL. In some cases, the at least one detection chamber from the plurality of the detection chambers is configured to hold fluid of at least about 1 pL. In some cases, the at least one detection chamber from the plurality of the detection chambers is configured to hold fluid of at most about 1,000,000 pL. In some cases, the at least one detection chamber from the plurality of the detection chambers is configured to hold fluid of about 1 pL to about 10 pL, about 1 pL to about 100 pL, about 1 pL to about 1,000 pL, about 1 pL to about 10,000 pL, about 1 pL to about 100,000 pL, about 1 pL to about 1,000,000 pL, about 10 pL to about 100 pL, about 10 pL to about 1,000 pL, about 10 pL to about 10,000 pL, about 10 pL to about 100,000 pL, about 10 pL to about 1,000,000 pL, about 100 pL to about 1,000 pL, about 100 pL to about 10,000 pL, about 100 pL to about 100,000 pL, about 100 pL to about 1,000,000 pL, about 1,000 pL to about 10,000 pL, about 1,000 pL to about 100,000 pL, about 1,000 pL to about 1,000,000 pL, about 10,000 pL to about 100,000 pL, about 10,000 pL to about 1,000,000 pL, or about 100,000 pL to about 1,000,000 pL. In some cases, the at least one detection chamber from the plurality of the detection chambers is configured to hold fluid of about 1 pL, about 10 pL, about 100 pL, about 1,000 pL, about 10,000 pL, about 100,000 pL, or about 1,000,000 pL.

[0017] Also disclosed is a method for detecting a target nucleic acid in a biological sample, comprising loading the biological sample to the sample chamber of the device disclosed herein, such that the first fluid comprising the biological sample flows to the detection chamber via the first channel of the device, wherein the first fluid is an aqueous fluid; such that the second fluid flows to the detection chamber via the second channel; such that the plurality of aqueous droplets surrounded by the second fluid are produced and flow through the second channel, wherein at least one aqueous droplet comprises the biological sample and the detection reagent; and such that a detectable signal is generated by cleavage of the reporter upon binding of the guide nucleic acid to the segment of the target nucleic acid, indicating the presence of the target nucleic acid. In some cases, the method further comprises quantifying the detectable signal, thereby quantifying an amount of the target nucleic acid present in the biological sample.

[0018] In another aspect, disclosed herein is a device, comprising: a sample chamber configured to receive a biological sample including a target nucleic acid, wherein the sample chamber is configured to produce a plurality of aqueous droplets dispersed in an immiscible fluid by sonication or homogenization, wherein at least one aqueous droplet from the plurality of aqueous droplets includes the biological sample and a detection reagent having a programmable nuclease, a guide nucleic acid, and a reporter, and wherein the reporter is capable of being cleaved upon binding of the guide nucleic acid to a segment of the target nucleic acid. In some cases, the sample chamber further comprises a lysis buffer. In some cases, the device further comprises a lysis buffer storage chamber fluidically connected to the sample chamber. In some cases, the device further comprises a lysis chamber fluidically connected to the sample chamber, wherein the lysis chamber comprises a lysis buffer. In some cases, the lysis buffer comprises an enzyme that disrupts cell membranes. In some cases, the lysis buffer has a pH range of 1 to 14. In some cases, the lysis buffer has a pH range of about 1 to about 13. In some cases, the lysis buffer has a pH range of at least about 1. In some cases, the lysis buffer has a pH range of at most about 13. In some cases, the lysis buffer has a pH range of about 1 to about 3, about 1 to about 5, about 1 to about 7, about 1 to about 9, about 1 to about 11, about 1 to about 13, about 3 to about 5, about 3 to about 7, about 3 to about 9, about 3 to about 11, about 3 to about 13, about 5 to about 7, about 5 to about 9, about 5 to about 11, about 5 to about 13, about 7 to about 9, about 7 to about 11, about 7 to about 13, about 9 to about 11, about 9 to about 13, or about 11 to about 13. In some cases, the lysis buffer has a pH range of about 1, about 3, about 5, about 7, about 9, about 11, or about 13. In some cases, the lysis chamber further comprises a neutralization buffer that is capable of neutralize the lysis buffer.

[0019] In some cases, the sample chamber is capable of being hermetically sealed from an external environment. In some cases, the sample chamber is configured to receive the biological sample from a syringe or swab. In some cases, the device further comprises a detection chamber fluidically connected to the sample chamber. In some cases, the detection chambers comprises the detection reagent. In some cases, the detection chambers is a standalone physical compartment. In some cases, the detection chamber is configured to receive the plurality of aqueous droplets. In some cases, the device comprises a plurality of detection chambers. In some cases, each detection chamber from the plurality of detection chambers has substantially equivalent volume. In some cases, the plurality of detection chambers have different volumes. In some cases, the detection chamber is circular, elongated, or hexagonal. In some cases, the detection chamber comprises a hydrophobic or porous substrate. In some cases, the hydrophobic or porous substrate is configured to create resistance with presence of the fluid volume of the biological sample in the detection chamber, thereby directing the biological sample to flow to an unfilled detection chamber. In some cases, the detection chamber comprises an optically transparent surface. In some cases, the at least one detection chamber from the plurality of the detection chambers is configured to hold from 1 pL to 1 pL of fluid. In some cases, the at least one detection chamber from the plurality of the detection chambers is configured to hold fluid of about 1 pL to about 1,000,000 pL. In some cases, the at least one detection chamber from the plurality of the detection chambers is configured to hold fluid of at least about 1 pL. In some cases, the at least one detection chamber from the plurality of the detection chambers is configured to hold fluid of at most about 1,000,000 pL. In some cases, the at least one detection chamber from the plurality of the detection chambers is configured to hold fluid of about 1 pL to about 10 pL, about 1 pL to about 100 pL, about 1 pL to about 1,000 pL, about 1 pL to about 10,000 pL, about 1 pL to about 100,000 pL, about 1 pL to about 1,000,000 pL, about 10 pL to about 100 pL, about 10 pL to about 1,000 pL, about 10 pL to about 10,000 pL, about 10 pL to about 100,000 pL, about 10 pL to about 1,000,000 pL, about 100 pL to about 1,000 pL, about 100 pL to about 10,000 pL, about 100 pL to about 100,000 pL, about 100 pL to about 1,000,000 pL, about 1,000 pL to about 10,000 pL, about 1,000 pL to about 100,000 pL, about 1,000 pL to about 1,000,000 pL, about 10,000 pL to about 100,000 pL, about 10,000 pL to about 1,000,000 pL, or about 100,000 pL to about 1,000,000 pL. In some cases, the at least one detection chamber from the plurality of the detection chambers is configured to hold fluid of about 1 pL, about 10 pL, about 100 pL, about 1,000 pL, about 10,000 pL, about 100,000 pL, or about 1,000,000 pL.

[0020] Also disclosed is a method for detecting a target nucleic acid in a biological sample, comprising: a) loading the biological sample to the sample chamber of the device disclosed herein; b) loading the second fluid immiscible with the first fluid in the sample chamber; and c) producing the plurality of aqueous droplets dispersed in the second fluid by sonication or homogenization, such that a detectable signal is generated by cleavage of the reporter upon binding of the guide nucleic acid to a segment of the target nucleic acid, thereby indicating the presence of the target nucleic acid. In some cases, the method further comprises quantifying the detectable signal, thereby quantifying an amount of the target nucleic acid present in the biological sample.

[0021] In another aspect, disclosed herein is a device, comprising: a) a volume configured to receive a biological sample including a target nucleic acid via a top opening of the device; and b) a plurality of stacked detection layers, wherein at least one detection layer from the plurality of detection layers includes a porous substrate coated with or bound to a detection reagent having a programmable nuclease, a guide nucleic acid, and a reporter, and wherein the reporter is capable of being cleaved upon binding of the guide nucleic acid to a segment of the target nucleic acid. Also disclosed is a device, comprising: a) a volume configured to receive a biological sample including a target nucleic acid and a detection reagent via a top opening of the device; and b) a plurality of stacked detection layers, wherein at least one detection layer from the plurality of detection layers includes a porous substrate coated with or bound to an affinity ligand targeting nucleic acids, wherein the detection reagent has a programmable nuclease, a guide nucleic acid, and a reporter, and wherein the reporter is capable of being cleaved upon binding of the guide nucleic acid to a segment of the target nucleic acid.

[0022] In some cases, the affinity ligand specifically binds the target nucleic acid. In some cases, the affinity ligand binds nucleic acids non-specifically. In some cases, a detection layer from the plurality of detection layers binds uncleaved reporter. In some cases, the porous substrate comprises a polymer matrix, a bead, or a nanostructure. In some cases, the polymer matrix is hydrogel. In some cases, the bead is a conducting or non-conducting bead. In some cases, the nanostructure is a wire mesh.

[0023] In some cases, the volume further comprises a lysis buffer. In some cases, the device further comprises a lysis buffer storage chamber fluidically connected to the volume. In some cases, the device further comprises a lysis chamber fluidically connected to the volume, wherein the lysis chamber comprises a lysis buffer. In some cases, the lysis buffer comprises an enzyme that disrupts cell membranes. In some cases, the lysis buffer has a pH range of 1 to 14. In some cases, the lysis buffer has a pH range of about 1 to about 13. In some cases, the lysis buffer has a pH range of at least about 1. In some cases, the lysis buffer has a pH range of at most about 13. In some cases, the lysis buffer has a pH range of about 1 to about 3, about 1 to about 5, about 1 to about 7, about 1 to about 9, about 1 to about 11, about 1 to about 13, about 3 to about 5, about 3 to about 7, about 3 to about 9, about 3 to about 11, about 3 to about 13, about 5 to about 7, about 5 to about 9, about 5 to about 11, about 5 to about 13, about 7 to about 9, about 7 to about 11, about 7 to about 13, about 9 to about 11, about 9 to about 13, or about 11 to about 13. In some cases, the lysis buffer has a pH range of about 1, about 3, about 5, about 7, about 9, about 11, or about 13. In some cases, the lysis chamber further comprises a neutralization buffer that is capable of neutralize the lysis buffer.

[0024] In some cases, the volume is capable of being hermetically sealed from an external environment. In some cases, the volume is configured to receive the biological sample from a syringe or swab. In some cases, the device comprises an optically transparent surface. In some cases, the reporter is conjugated to horseradish peroxidase (HRP).

[0025] Also disclosed is a method for detecting a target nucleic acid in a biological sample, comprising a) loading the biological sample to the volume of the device via the top opening, such that the biological sample flows through the plurality of stacked detection layers of the device; b) detecting a detectable signal, wherein the detectable signal is generated by cleavage of the reporter upon binding of the guide nucleic acid to the segment of the target nucleic acid, thereby indicating the presence of the target nucleic acid. In some cases, the method further comprises loading the detection reagent such that the detection reagent flows through the plurality of stacked detection layers of the device. In some cases, the reporter is conjugated to horseradish peroxidase (HRP). In some cases, the method further comprises contacting a cleavage reporter with a HRP substrate, thereby generating an optical signal change. In some cases, the HRP substrate is a chromogenic substrate. In some cases, the chromogenic substrate is selected from the group consisting of 3,3',5,5'-Tetramethylbenzidine (TMB), 3,3'-Diaminobenzidine (DAB), and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS). In some cases, the HRP substrate is a chemiluminescent substrate. In some cases, the chemiluminescent substrate is luminol.

[0026] In another aspect, disclosed herein is a point-of-need device comprising: a sample chamber configured to receive a first volume of a biological sample; a sample volume generator configured to generate a plurality of sample volumes from the first volume of the biological sample, wherein a first sample volume of the plurality of sample volumes comprises a plurality of nucleic acids, a plurality of programmable nuclease complexes, and a plurality of reporters, wherein a molar ratio of the plurality of programmable nuclease complexes to the plurality of nucleic acids in the first sample volume is at least 1 : 1; wherein the plurality of nucleic acids in the first sample volume comprise a target nucleic acid, wherein a first programmable nuclease complex in the plurality of programmable nuclease complexes binds to the target nucleic acid to activate the programmable nuclease complex to cleave a first reporter in the plurality of reporters, wherein the signal is indicative of cleavage of the first reporter and of a presence a target nucleic acid in the biological sample. [0027] In some cases, the molar ratio of the plurality of programmable nuclease complexes to the plurality of nucleic acids in the first sample volume is at least 2: 1, 3: 1, 4: 1, 5: 1, 6: 1, 7: 1, 8: 1, 9: 1 or 10: 1. In some cases, the molar ratio of the plurality of programmable nuclease complexes to the plurality of nucleic acids in the first sample volume is about 1 to about 500. In some cases, the molar ratio of the plurality of programmable nuclease complexes to the plurality of nucleic acids in the first sample volume is at least about 1. In some cases, the molar ratio of the plurality of programmable nuclease complexes to the plurality of nucleic acids in the first sample volume is at most about 500. In some cases, the molar ratio of the plurality of programmable nuclease complexes to the plurality of nucleic acids in the first sample volume is about 1 to about 2, about 1 to about 3, about 1 to about 4, about 1 to about 5, about 1 to about 10, about 1 to about 20, about 1 to about 50, about 1 to about 100, about 1 to about 200, about 1 to about 500, about 2 to about 3, about 2 to about 4, about 2 to about 5, about 2 to about 10, about 2 to about 20, about 2 to about 50, about 2 to about 100, about 2 to about 200, about 2 to about 500, about 3 to about 4, about 3 to about 5, about 3 to about 10, about 3 to about 20, about 3 to about 50, about 3 to about 100, about 3 to about 200, about 3 to about 500, about 4 to about 5, about 4 to about 10, about 4 to about 20, about 4 to about 50, about 4 to about 100, about 4 to about 200, about 4 to about 500, about 5 to about 10, about 5 to about 20, about 5 to about 50, about 5 to about 100, about 5 to about 200, about 5 to about 500, about 10 to about 20, about 10 to about 50, about 10 to about 100, about 10 to about 200, about 10 to about 500, about 20 to about 50, about 20 to about 100, about 20 to about 200, about 20 to about 500, about 50 to about 100, about 50 to about 200, about 50 to about 500, about 100 to about 200, about 100 to about 500, or about 200 to about 500. In some cases, the molar ratio of the plurality of programmable nuclease complexes to the plurality of nucleic acids in the first sample volume is about 1, about 2, about 3, about 4, about 5, about 10, about 20, about 50, about 100, about 200, or about 500.

[0028] In some cases, the programmable nuclease complex comprises a programmable nuclease and a guide nucleic acid. In some cases, the sample volume generator comprises a branched microfluidic structure, a column with a plurality of stacked layers, a plurality of microwells, or a water-in-oil droplet generator. In some cases, the water-in-oil droplet generator comprises a first channel and a second channel coupled to one another at a junction. In some cases, the water-in-oil droplet generator comprises an emulsification chamber.

[0029] In some cases, the device disclosed herein comprises an illumination source configured to illuminate the reporter. In some cases, the illumination source is a broad spectrum light source. In some cases, the illumination source produces an illumination with a bandwidth of less than 5 nm. In some cases, the illumination source is a light emitting diode. In some cases, the light emitting diode produces white light, blue light, or green light. In some cases, the device comprises a detector configured to detect a detectable signal produced by the reporter. In some cases, the detectable signal is selected from a group consisting of an optical, fluorescence, magnetic, electrical, chemical, or electrochemical signal. In some cases, the detector is a camera or a photodiode. In some cases, the detector has a detection bandwidth of less than 100 nm, less than 75 nm, less than 50 nm, less than 40 nm, less than 30 nm, less than 20 nm, less than 10 nm, or less than 5 nm. In some cases, the device further comprises an optical filter configured to be placed before the detector. In some cases, the detectable signal is a fluorescence signal. In some cases, the detector is a fluorimeter. In some cases, the detectable signal is an electrochemical signal. In some cases, the detector is an electrode. In some cases, the biological sample is blood, serum, plasma, saliva, urine, or any combination thereof. In some cases, the device is a point-of-need device. In some cases, the device is handheld. In some cases, the device is disposable.

[0030] In some cases, the programmable nuclease comprises an RuvC catalytic domain. In some cases, the programmable nuclease is a type V CRISPR/Cas effector protein. In some cases, the type V CRISPR/Cas effector protein is a Casl2 protein. In some cases, the Casl2 protein comprises a Casl2a polypeptide, a Casl2b polypeptide, a Casl2c polypeptide, a Casl2d polypeptide, a Casl2e polypeptide, a C2c4 polypeptide, a C2c8 polypeptide, a C2c5 polypeptide, a C2cl0 polypeptide, and a C2c9 polypeptide. In some cases, the programmable nuclease has at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 97%, or at least 99% sequence identity to any one of SEQ ID NO: 1 - SEQ ID NO: 72. In some cases, the programmable nuclease is selected from SEQ ID NO: 1 - SEQ ID NO: 72. In some cases, the type V CRIPSR/Cas effector protein is a Casl4 protein. In some cases, the Casl4 protein comprises a Casl4a polypeptide, a Casl4b polypeptide, a Casl4c polypeptide, a Casl4d polypeptide, a Casl4e polypeptide, a Casl4f polypeptide, a Cast 4g polypeptide, a Casl4h polypeptide, a Casl4i polypeptide, a Casl4j polypeptide, or a Cast 4k polypeptide. In some cases, the type V CRIPSR/Cas effector protein is a Cas protein. In some cases, the programable nuclease comprises a HEPN cleaving domain. In some cases, the programmable nuclease is a type VI CRISPR/Cas effector protein. In some cases, the type VI CRISPR/Cas effector protein is a Casl3 protein. In some cases, the Casl3 protein comprises a Casl3a polypeptide, a Cast 3b polypeptide, a Cast 3c polypeptide, a Cast 3c polypeptide, a Cast 3d polypeptide, or a Casl3e polypeptide. In some cases, the target nucleic acid is from a virus. In some cases, the virus comprises a respiratory virus. In some cases, the respiratory virus is an upper respiratory virus. In some cases, the virus comprises an influenza virus. In some cases, the influenza virus comprises an influenza A virus, influenza B virus, or a combination thereof. In some cases, the virus comprises a coronavirus. In some cases, the target nucleic acid is from SARS-CoV-2. In some cases, the target nucleic acid is from an N gene, an E gene, an S gene, or a combination thereof. In some cases, the guide nucleic acid is a guide RNA. In some cases, the device further comprises a control nucleic acid. In some cases, the control nucleic acid is in the at least one detection chamber. In some cases, the control nucleic acid is RNaseP. In some cases, the reporter comprises a single stranded reporter comprising a detection moiety. In some cases, the detection moiety is a fluorophore, a FRET pair, a fluor ophore/quencher pair, or an electrochemical reporter molecule. In some cases, the detection moiety produces a detectable signal upon cleavage of the reporter. In some cases, the detectable signal is a colorimetric signal, a fluorescence signal, an amperometric signal, or a potentiometric signal.

INCORPORATION BY REFERENCE

[0031] All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference.

BRIEF DESCRIPTION OF THE DRAWINGS

[0032] The novel features of the invention are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present invention will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the invention are utilized, and the accompanying drawings of which:

[0033] FIG. 1 shows schematically the detection of the presence or absence of a target nucleic acid in a sample using the methods disclosed herein.

[0034] FIG. 2A shows a schematic of an exemplary device including a plurality of capillary channels, and FIGs. 2B, 2C, and 2D show exemplary detection chambers of the device disclosed herein.

[0035] FIGs. 3A and 3B show a schematic of an exemplary flow fractionation junction of the device disclosed herein. [0036] FIG. 4A shows a schematic of an exemplary device including a plurality of microwells prior to the addition of the biological sample, and FIG. 4B shows the plurality of microwells after a volume of the biological sample is retained in each microwell.

[0037] FIG. 5A shows a schematic of an exemplary device including a plurality of detection chambers, and FIG. 5B shows a side view of the device, including a top chamber surface and a bottom chamber surface.

[0038] FIG. 6A shows a schematic of an exemplary device, including at least one junction for droplet production, and FIG. 6B shows an alternative configuration of the junction for droplet production.

[0039] FIG. 7 shows a schematic of an exemplary device that can be used to create an emulsion.

[0040] FIG. 8 shows a schematic of an exemplary device that can use flow filtration for detecting the target nucleic acid.

DETAILED DESCRIPTION

Overview

[0041] Disclosed herein are devices, systems, and methods for detecting a target nucleic acid in a biological sample. Briefly, methods can include sample preparation, incubation with a programmable nuclease, and/or detection (e.g., readout) steps. In some cases, there can be an optional amplification step after the same preparation step. In some cases, the sample preparation and amplification step(s) can be carried out within a device described herein or, alternatively, can be carried out prior to introduction into the device. In some cases, the incubation and detection steps can be performed sequentially (one after another) or concurrently (at the same time). In some cases, the incubation and detection steps can be carried out within the same chamber of the device.

[0042] FIG. 1 illustrates schematically the detection of the presence or absence of a target nucleic acid in a sample. Briefly, nucleic acids 110 (including target nucleic acid and nontarget nucleic acid) in a sample can be prepared. A small volume of the nucleic acids 110 can be generated using the device 120 described herein for a subsequent reaction. The small volume of the nucleic acids 130 can contact a programmable nuclease 140, a guide nucleic acid 150, and a reporter nucleic acid 160. The small reaction volume can isolate a small number of the target nucleic acid 130 that is outnumbered by the programmable nuclease 140, a guide nucleic acid 150, and a reporter nucleic acid 160, and thus increase the probability of the target nucleic acid 130 reacting with the programmable nuclease 140, guide nucleic acid 150, and/or reporter nucleic acid 160. The programmable nuclease 140 can be a Cas protein with trans collateral cleavage activity. As illustrated in 170, the programmable nuclease 140 can be activated upon binding to a guide nucleic acid 150 and a target sequence 130 reverse complementary to a region of the guide nucleic acid 150. The activated programmable nuclease can cleave a reporter nucleic acid 160, thereby producing a detectable signal indicative of the presence of the target nucleic acid 130. Thus, if the sample contains the target nucleic acid, a detectable signal is produced 140. In some embodiments, multiplexing detection for multiple different target nucleic acids may be achieved by providing different programmable nucleases, different guide nucleic acids reverse complementary to different target nucleic acid sequences, and/or different reporters in different small volumes of a plurality of small volumes.

[0043] The devices, systems, and methods disclosed herein can be used to generate small volumes of the nucleic acids in order to reduce or avoid nonspecific binding of the programmable nuclease to non-target nucleic acids in the sample. By reducing the number of nucleic acids in the reaction in a small confined volumes (e.g., single digit microliter to attoliter) of the sample, the nonspecific binding of the programmable nuclease to non-target nucleic acids can also be reduced, thereby improving the specificity and/or speed of the reaction. In some cases, the methods disclosed herein do not require amplification or predilution of the biological sample. Here, various devices, systems, and methods for creating a plurality of small reaction volumes to enable direct detection of the target are disclosed. In some cases, the device can be a small (e.g., handheld) device and/or require low power and complexity.

Definitions

[0044] The singular forms “a”, “an”, and “the” are used herein to include plural references unless the context clearly dictates otherwise. Accordingly, unless the contrary is indicated, the numerical parameters set forth in this application are approximations that may vary depending upon the desired properties sought to be obtained by the present invention.

[0045] The term “about” and its grammatical equivalents in relation to a reference numerical value and its grammatical equivalents as used herein can include a range of values plus or minus 10% from that value, such as a range of values plus or minus 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, or 1% from that value. For example, the amount “about 10” includes amounts from 9 to 11.

[0046] As used herein, the phrase “and/or” should be understood to mean “either or both” of the elements so conjoined, i.e., elements that are conjunctively present in some cases and disjunctively present in other cases. Multiple elements listed with “and/or” should be construed in the same fashion, i.e., “one or more” of the elements so conjoined. Other elements may optionally be present other than the elements specifically identified by the “and/or” phrase, whether related or unrelated to those elements specifically identified. Thus, as a non-limiting example, a reference to “A and/or B”, when used in conjunction with open- ended language such as “comprising” or “including” can refer, in one embodiment, to A only (optionally including elements other than B); in another embodiment, to B only (optionally including elements other than A); in yet another embodiment, to both A and B (optionally including other elements); etc.

[0047] As used herein, the term, “or” should be understood to have the same meaning as “and/or” as defined above. For example, when separating items in a list, “or” or “and/or” shall be interpreted as being inclusive, i.e., the inclusion of at least one, but also including more than one, of a number or list of elements, and, optionally, additional unlisted items. Only terms clearly indicated to the contrary, such as “only one of’ or “exactly one of,” or, when used in the claims, “consisting of,” will refer to the inclusion of exactly one element of a number or list of elements. In general, the term “or” as used herein shall only be interpreted as indicating exclusive alternatives (i.e. “one or the other but not both”) when preceded by terms of exclusivity, such as “either,” “one of,” “only one of,” or “exactly one of.” “Consisting essentially of,” when used in the claims, shall have its ordinary meaning as used in the field of patent law.

[0048] The term “point-of-need device” refers to a diagnostic device used to identify the nature or cause of a medical condition wherever the test subject is. For example, the point-of- need device can be used at a healthcare facility or at home/office of the test subject.

[0049] The term “chamber” refers to a specific part of the device disclosed herein, which may or may not have a standalone physical compartment. For example, a “detection chamber” is a standalone physical compartment (e.g., microwell), which is fluidically connected to other parts of the device. In another example, a “detection chamber” is not a standalone physical compartment and located in a region of another physical compartment, e.g., located at the end or along the path of a channel. In some cases, a plurality of detection chambers are located in a physical compartment large enough to encompass the plurality of detection chambers.

[0050] The term “immiscible” refers to the resistance to mixing of at least two phases or fluids under a given condition or set of conditions (e.g., temperature and/or pressure) such that the at least two phases or fluids persist or remain at least partially separated even after the phases have undergone some type of mechanical or physical agitation. Phases or fluids that are immiscible are typically physically and/or chemically discernible, or they may be separated at least to a certain extent.

[0051] The term, “target nucleic acid,” as used herein, refers to a nucleic acid that is selected as the nucleic acid for editing, binding, hybridization or any other activity of or interaction with a nucleic acid, protein, polypeptide, or peptide described herein. A target nucleic acid may comprise RNA, DNA, or a combination thereof. A target nucleic acid may be single-stranded (e.g., single-stranded RNA or single-stranded DNA) or double-stranded (e.g., double-stranded DNA).

[0052] The term, “target sequence,” as used herein, in the context of a target nucleic acid, refers to a nucleotide sequence found within a target nucleic acid. Such a nucleotide sequence can, for example, hybridize to a respective length portion of a guide nucleic acid.

[0053] Unless otherwise indicated, open terms for example “contain,” “containing,” “include,” “including,” and the like mean comprising.

[0054] Unless otherwise indicated, some embodiments herein contemplate numerical ranges. When a numerical range is provided, unless otherwise indicated, the range includes the range endpoints. Unless otherwise indicated, numerical ranges include all values and sub ranges therein as if explicitly written out.

Devices

[0055] Disclosed herein are devices for detecting a target nucleic acid in a biological sample. In some cases, the device can create a plurality of small reaction volumes by utilizing capillary channels, microwells, and/or droplet generations. The plurality of small reaction volumes can have the same volume or different volumes. The target nucleic acid in the biological sample can contact a programmable nuclease, a guide nucleic acid, and a reporter (e.g., a labeled detector nucleic acid) in the plurality of small reaction volumes. The programmable nuclease can be activated to cleave the reporter nucleic acid, thereby producing a detectable signal indicative of the presence of the target nucleic acid. The plurality of small reaction volumes can isolate a smaller number of the target nucleic acid and increase the molecular ratio of the programmable nuclease, guide nucleic acid, and/or reporter to the target nucleic acid, thereby improving the probability of the target nucleic acid reacting with the programmable nuclease and/or guide nucleic acid. The plurality of small reaction volumes can also reduce or avoid nonspecific binding of the programmable nuclease and guide nucleic acid to any non-target nucleic acids in the sample, and thus improve the accuracy and/or sensitivity of the detection of the target nucleic acid. [0056] The device for detecting a target nucleic acid in a biological sample can include a plurality of capillary channels. FIG. 2A shows a schematic of such a device 200 including a plurality of capillary channels. The device 200 includes a sample chamber 210 configured to receive a biological sample (not shown) including a plurality of nucleic acids which may include a target nucleic acid. The biological sample can be finger-prick blood, urine, fecal matter from a fecal swab, a nasal swab sample, a cheek swab sample, a wound swab sample, and/or a complex sample collected by any other collection method or device.

[0057] The device 200 further includes a plurality of detection chambers 230 fluidically connected to the sample chamber 210. In the exemplary embodiment shown in FIG, 2A, there are a total of 32 detection chambers 230 in the device 200, each connected to the sample chamber 210 via one capillary channel 220, thereby enabling a fluid volume of the biological sample to flow from the sample chamber 210 to the detection chamber 230 by capillary action, pressure-driven flow, or the like. Each capillary channel 220 can include multiple segments or branches that connect the sample chamber 210 to the detection chamber 230. An exemplary flow fractionation junction 300 can be configured as shown in FIGs. 3 A and 3B and split fluids from one channel into three. For example, two detection chambers 230 can connect to the sample chamber 210 via two capillary channels 220 that branch at a junction and share the same segment before reaching the two detection chambers 230. Here, the device 200 has a branched arrangement, including: 1) 4 first-level capillary channel segments starting from the sample chamber 210; 2) 8 second-level capillary channel segments that further divide the first-level capillary channel segments; 3) 16 third-level capillary channel segments that further divide the second-level capillary channel segments; 4) 32 fourth-level capillary channel segments that further divide the third-level capillary channel segments and connect to the 32 detection chambers 230. Although this embodiment shows and describes 32 detection chambers, any suitable number of detection chambers can be used. In some embodiments, for example, a device can include 2, 4, 8, 16, 32, 64, 256, or more detection chambers. Similarly, any suitable number of capillary channels, segments, and levels can be used.

[0058] Each detection chamber 230 can include a detection reagent composition (not shown) having at least a programmable nuclease, a guide nucleic acid, and/or a reporter (e.g., a labeled detector nucleic acid), and wherein the reporter is capable of being cleaved by the programmable nuclease upon binding of the guide nucleic acid to a segment of the target nucleic acid. For instance, the detection reagent 240 including the programmable nuclease, guide nucleic acid, and/or reporter can be located at the detection chamber 230 and contact the target nucleic acid in the biological sample at the detection chamber 230. Alternatively, or in combination, certain component(s) of the detection reagent 240 can be mixed with the target nucleic acid in the biological sample (e.g., either prior to entering the device or at the sample chamber 210), and can contact the remaining components of the detection reagent composition within the capillary channels 220 and/or at the detection chamber 230. In some cases, the programmable nuclease is mixed with the biological sample, and the guide nucleic acid and reporter are located at the detection chamber 230. In some cases, the programmable nuclease and reporter are mixed with the biological sample, and the guide nucleic acid is located at the detection chamber 230. In some cases, the programmable nuclease and guide nucleic acid are mixed with the biological sample, and the reporter is located at the detection chamber 230. In some cases, the reporter is mixed with the biological sample, and the programmable nuclease and guide nucleic acid are located at the detection chamber 230. In some cases, the reporter and guide nucleic acid are mixed with the biological sample, and the programmable nuclease is located at the detection chamber 230. In some cases, the guide nucleic acid is mixed with the biological sample, and the programmable nuclease and reporter are located at the detection chamber 230. In some cases, the programmable nuclease, guide nucleic acid, and reporter are mixed with the biological sample before reaching the detection chamber 230.

[0059] The devices disclosed herein are configured to provide a sufficient number of programmable nuclease complexes (e.g., the programmable nuclease and guide nucleic acid) to enable an excess molecular ratio of the programmable nuclease to target nucleic acid at the detection location (e.g., detection chamber 230) and/or maximize the interactions between the programmable nuclease to target nucleic acid. In some cases, the molecular ratio of the programmable nuclease to target nucleic acid at the detection location is at least about 1 :5, 1 :4, 1 :3, 1 :2, 1 : 1, 2: 1, 3: 1, 4: 1, 5: 1, 6: 1, 7: 1, 8: 1, 9: 1, 10: 1, 20: 1, 30: 1, 40: 1, or 50: 1. For example, the molecular ratio of the programmable nuclease to target nucleic acid at the detection location can be from 1 : 1 to 10: 1.

[0060] In another aspect, the devices disclosed herein are configured to provide an excess molecular ratio of the reporter to programmable nuclease at the detection location (e.g., detection chamber 230) to maximize the sensitivity of the detection method (e.g., fluorescent, photonic, or electronic readouts). In some cases, the molecular ratio of the reporter to programmable nuclease at the detection location is at least about 10: 1, 100: 1, 1,000: 1, 2,000: 1, 5,000: 1, 10,000: 1, 20,000: 1, 50,000: 1, 100,000: 1, 200,000: 1, 500,000: 1, 1,000,000: 1, 2,000,000: 1, 5,000,000: 1, or 10,000,000: 1 (e.g., for fluorescent readout). For example, the molecular ratio of the reporter to programmable nuclease at the detection location can be from 10,000: 1 to 1,000,000: 1 (e.g., for fluorescent readout).

[0061] The detection reagent 240, including programmable nucleases, guide nucleic acids, and/or reporters (e.g., labeled detector nucleic acid), may be suspended in solution or immobilized on a surface/region (e.g., hydrophobic or porous region) of the device disclosed herein.

[0062] In one example, the detection reagent 240 including the reporter, programmable nuclease, and/or guide nucleic acid can be immobilized on the surface of a chamber in a device as disclosed herein, such as on the surface of the detection chamber 230 as illustrated in FIG. 2B. The target nucleic acid in the biological sample can react with the detection reagent 240 at the detection chamber 230 located at the end of a capillary channel 220. In this case, the readout may be detected using a fluorescence, optical (e.g., colorimetric), magnetic, electrical, chemical, and/or electrochemical detector or sensor. For example, the emitted detectable signal (e.g., fluorescence or optical signal) of cleaved reporter oligonucleotides may be monitored using a detector or sensor, such as a fluorimeter or detection camera (not shown) positioned in the detection chamber 230 or directly above/below the detection chamber 230. The readout (e.g., emitted fluorescence or optical signal) may reach the fluorimeter or detection camera (not shown) via a transparent or translucent material(s) that allows light to pass in and out of the chamber. The detection can be relative to the plane of capillary motion (e.g., perpendicular, obtuse, or in-plane). Similarly, a detector or sensor for electrical, chemical, electrochemical, or magnetic readout can be located in the detection chamber 230 or embedded in a material contacting the detection chamber 230.

[0063] The target nucleic acid can be detected without physical compartmentalization of the biological sample in the device. For example, the detection chamber 230 is not limited to a certain physical structure, such as a chamber with physical walls. Any region of the device that allows the detection of the reaction between the detection reagent 240 and target nucleic acid can be configured as the detection chamber 230. In one example, the detection reagent 240 is immobilized on a surface of the detection chamber 230 that is located at the end of the capillary channel 220, as illustrated in FIG. 2C. Here, the detection chamber 230 is located at one terminal of the capillary channel 220.

[0064] In another example, the detection reagent 240 is immobilized at the detection chamber 230, which is located in a region (e.g., hydrophobic or porous region) of the capillary channel 220, as illustrated in FIG. 2D. The detection chamber 230 can retain the reaction mixture (e.g., the target nucleic acid and/or detection reagent 240) at a surface of the capillary channel 220, a matrix material (e.g., hydrogel, wire-framed mesh, low cross-linked gel), and/or a protrusion along a surface of the capillary channel 220 (e.g., for increased surface area). For example, co-polymerization of the programmable nuclease, guide nucleic acid, and/or the reporter into the polymer matrix may result in a higher density of reporter/unit volume or reporter/unit area, may result in less undesired release of the reporter (e.g., during an assay, a measurement, or on the shelf), and thus may cause less background signal than other immobilization strategies (e.g., conjugation to a pre-formed hydrogel, bead, etc.). The capillary channel 220 can be sufficiently long to allow the detection of a small subset of the target nucleic acids without physically compartmentalizing the target nucleic acids.

[0065] The readout may be detected locally at or near the detection chamber 230 by one or more detectors (not shown) for optical, fluorescence, magnetic, electrical, chemical, or electrochemical readout. The detectors can be located in the detection chamber 230 (or a region of the capillary channel 220), directly above or below the detection chamber 230, and/or embedded in a material contacting the detection chamber 230. For example, the reporter cleavage may be linked to a colorimetric reaction and the color change can be monitored using a photosensor (e.g., charged-coupled device (CCD) camera or image sensor) located in the detection chamber 230 (or a region of the capillary channel 220) making contact with the flow/flux of the sample or embedded in at least one surface of the detection chamber 230. In another example, a signal change (e.g., increase or decrease) in light absorbance, can be detected by a photosensor located in the detection chamber 230 (or a region of the capillary channel 220) between before and after the cleavage of the reporter. In another example, the emitted fluorescence of cleaved reporter may be monitored using a fluorimeter comprising fluorescence excitation means (e.g., CO2, laser, and/or light emitting diodes (LEDs)) and/or fluorescence detection means (e.g., photodiode array, phototransistor, or others). In some cases, a signal change in emission wavelength can be generated by the cleavage of the reporter. For example, the cleavage of the reporter may allow the fluorophore to emit fluorescence at a particular wavelength and thus changing the fluorescence readout of the reaction. The fluorimeter can be located in the detection chamber 230 (or a region of the capillary channel 220) making contact with the flow/flux of the sample or embedded in at least one surface of the detection chamber 230. In another example, the reporter cleavage may change (e.g., increase/decrease) the intensity of an electrochemical signal or increase/decrease the diffusion constant of an electroactive moiety in the reporter, and the signal change may be measured by one or more detectors (e.g., electrodes) located in the detection chamber 230 (or a region of the capillary channel 220) making contact with the flow/flux of the sample or embedded in at least one surface of the detection chamber 230. In another example, an electrochemical signal change, such as a decrease in the current produced by a ferrocene (Fc), or other electroactive mediator moieties conjugated to the individual nucleotides of nucleic acid molecules (ssRNA, ssDNA, or ssRNA/DNA hybrid molecules) immobilized on a surface of the detection chamber 230 (or a region of the capillary channel 220), can be generated by the cleavage of the reporter. Without the presence of target nucleic acid, the programmable nuclease complex remains inactive, and a high current caused by the electroactive moieties can be recorded. When the target nucleic acid flows in the detection chamber 230, the activated programmable nuclease complex non- specifically degrades the immobilized Fc-conjugated nucleic acid molecules and decrease the number of electroactive molecules and, thus, leads to a decrease in recorded current. In another example, the reporter cleavage may generate a calorimetric signal change that may be measured by one or more calorimeters located in the detection chamber 230 (or a region of the capillary channel 220) making contact with the flow/flux of the sample or embedded in at least one surface of the detection chamber 230.

[0066] The plurality of detection chambers 230 can include two or more detection reagents 240, thereby enabling multiplexed detection of two or more target nucleic acids. Multiplexing may include assaying for two or more target nucleic acids in a sample. Multiplexing can be spatial multiplexing wherein multiple different target nucleic acids are detected from the same sample at the same time, but the reactions are spatially separated. For example, multiple different target nucleic acids are detected at different detection chambers 230, which are fluidically connected to the sample chamber 210 (FIG. 2B), located at the end of the capillary channels 220 (FIG. 2C), or located in different regions of the capillary channel 220 (FIG. 2D). Often, the multiple target nucleic acids are detected using the same programmable nuclease, but different guide nucleic acids. The multiple target nucleic acids sometimes are detected using different programmable nucleases. Sometimes, multiplexing can be single reaction multiplexing wherein multiple different target nucleic acids are detected in a single reaction volume. Often, at least two different programmable nucleases are used in single reaction multiplexing. For example, multiplexing can be enabled by immobilization of multiple categories of reporters within a device, to enable detection of multiple target nucleic acids.

[0067] In addition to, or instead of capillary channels, microwells can be used to create a plurality of small reaction volumes of the biological sample. A device for detecting a target nucleic acid in a biological sample can include a plurality of microwells. FIGs. 4A and 4B show a schematic of such a device 400, according to an embodiment. The device 400 is configured to provide a sufficient number of programmable nuclease complexes (e.g., the programmable nuclease and guide nucleic acid) to enable an excess molecular ratio of the programmable nuclease to target nucleic acid at the detection location (e.g., microwell 420) and/or maximize the interactions between the programmable nuclease to target nucleic acid. The microwells 420 in device 400 can have a similar dimension and/or topology as the detection chambers 230 in device 200 in FIG. 2A. Also similar to the detection chambers 230, each microwell 420 can include a detection reagent (not shown) having a programmable nuclease, a guide nucleic acid, and a labeled detector nucleic acid, and wherein the labeled detector nucleic acid is capable of being cleaved upon binding of the guide nucleic acid to a segment of the target nucleic acid. Programmable nucleases, guide nucleic acids, and/or reporters (e.g., labeled detector nucleic acid) may be suspended in solution or immobilized on a surface/region (e.g., hydrophobic or porous region) of a microwell 420. Alternatively, certain component(s) of the detection reagent can be mixed with the target nucleic acid in the biological sample 430 (e.g., prior to entering the device 400), and can contact the remaining components of the detection reagent composition at the microwell 420.

[0068] Also similar to the detection chambers 230, the plurality of microwells 420 are not limited to a certain physical structure and the target nucleic acid can be detected without physical compartmentalization. For example, the microwell 420 can retain the reaction mixture on a surface of the microwell plate 410, a matrix material (e.g., hydrogel, wireframed mesh, low cross-linked gel), and/or a protrusion along a surface of microwell plate 410, with or without a compartmentalized (“well-like”) physical structure. In some cases, the plurality of microwells 420 can include two or more detection reagents, thereby enabling multiplexed detection of two or more target nucleic acids. In some cases, a hydrophobic or porous substrate can be utilized on the surface of the microwells 420 to retain the fluid volume of the biological sample.

[0069] Although this embodiment shows and describes a 45-well microwell plate, any suitable number of microwells can be used. In some embodiments, for example, a device can include a 6-well, 12-well, 24-well, 48-well, 96-well, or 384-well plate. The microwells 420 in device 400 can have the volume of a well from a standard culture plate. In one example, the microwell plate 410 can have the size of a 24-well plate, with a 0.5-1.0 mL volume for each microwell 420. In another example, the microwell plate 410 can have the size of a 96- well plate, with a 0.1-0.2 mL volume for each microwell 420. A biological sample 430 including a target nucleic acid can be collected in a sample chamber or a separate container (not shown) before flown to the device 400 via a channel (not shown) and made contact with the microwells 420. A small volume of the sample is retained in the microwells 440.

[0070] The readout may be detected locally at or near the microwell 420 by one or more detectors (not shown) for optical, fluorescence, magnetic, electrical, chemical, or electrochemical readout. The detectors can be located in the microwell 420, directly above or below the microwell 420, and/or embedded in a material contacting the microwell 420. For example, the reporter cleavage may be linked to a colorimetric reaction and the color change can be monitored using a photosensor (e.g., charged-coupled device (CCD) camera or image sensor) located in the microwell 420 making contact with the flow/flux of the sample or embedded in at least one surface of the microwell 420. In another example, a signal change (e.g., increase or decrease) in light absorbance, can be detected by a photosensor located in the microwell 420 or embedded in at least one surface of the microwell 420 between before and after the cleavage of the reporter. In another example, the emitted fluorescence of cleaved reporter may be monitored using a fluorimeter comprising fluorescence excitation means (e.g., CO2, laser and/or light emitting diodes (LEDs)) and/or fluorescence detection means (e.g., photodiode array, phototransistor, or others). In some cases, a signal change in emission wavelength can be generated by the cleavage of the reporter. For example, the cleavage of the reporter may allow the fluorophore to emit fluorescence at a particular wavelength and thus changing the fluorescence readout of the reaction. The fluorimeter can be located in the microwell 420 making contact with the flow/flux of the sample or embedded in at least one surface of the microwell 420. In another example, the reporter cleavage may change (e.g., increase/decrease) the intensity of an electrochemical signal or increase/decrease the diffusion constant of an electroactive moiety in the reporter, and the signal change may be measured by one or more detectors (e.g., electrodes) located in the microwell 420 making contact with the flow/flux of the sample or embedded in at least one surface of the microwell 420. In another example, an electrochemical signal change, such as a decrease in the current produced by a ferrocene (Fc), or other electroactive mediator moi eties conjugated to the individual nucleotides of nucleic acid molecules (ssRNA, ssDNA, or ssRNA/DNA hybrid molecules) immobilized on a surface of the microwell 420, can be generated by the cleavage of the reporter. Without the presence of target nucleic acid, the programmable nuclease complex remains inactive, and a high current caused by the electroactive moieties can be recorded. When the target nucleic acid flows in the microwell 420, the activated programmable nuclease complex non-specifically degrades the immobilized Fc-conjugated nucleic acid molecules and decrease the number of electroactive molecules and, thus, leads to a decrease in recorded current. In another example, the reporter cleavage may generate a calorimetric signal change that may be measured by one or more calorimeters located in the microwell 420 making contact with the flow/flux of the sample or embedded in at least one surface of the microwell 420.

[0071] FIG. 5A shows the top view of another embodiment of a device with a plurality of detection chambers 520. A biological sample including a target nucleic acid can be collected in a sample chamber (not shown) or a separate container (not shown) before added to the device via a channel (not shown) and made contact with the microwells. The device 500 is configured to provide a sufficient number of programmable nuclease complexes (e.g., the programmable nuclease and guide nucleic acid) to enable an excess molecular ratio of the programmable nuclease to target nucleic acid at the detection location (e.g., detection chambers 520) and/or maximize the interactions between the programmable nuclease to target nucleic acid. Unlike the microwells in FIGs. 4A and 4B, the device 500 does not use physical microwells to retain the small volume of the biological sample; instead it uses hydrophilic or porous substrate to retain the biological sample. The device 500 shows 21 detection chambers 520 with the hydrophilic or porous substrate 540 and 560, each of which can be used to retain the biological sample. As shown in the side view of device 500 in FIG. 5B, the plurality of detection chambers 520 are sandwiched or disposed between two chamber surfaces, including a top chamber surface 530 and a bottom chamber surface 550. As illustrated in FIG. 5B, the top chamber surface 530 is coated with the hydrophilic or porous substrate 540 and the bottom chamber surface 550 is coated with the hydrophilic or porous substrate 560. The chamber surfaces and hydrophilic surface coating can retain a fluid volume of the biological sample 570 between the chamber surfaces.

[0072] Each of the detection chambers 520 can include a detection reagent having a programmable nuclease, a guide nucleic acid, and a labeled detector nucleic acid, and wherein the labeled detector nucleic acid is capable of being cleaved upon binding of the guide nucleic acid to a segment of the target nucleic acid. Programmable nucleases, guide nucleic acids, and/or reporters (e.g., labeled detector nucleic acid) may be suspended in solution or immobilized on a surface. For example, the detection reagent (not shown) can be immobilized on the top chamber surface 530 and bottom chamber surface 550, as illustrated in FIG. 5B. Alternatively, certain component(s) of the detection reagent can be mixed with the target nucleic acid in the biological sample (e.g., prior to entering the device 500), and can contact the remaining components of the detection reagent composition at the detection chambers 520. The detection chambers 520 are not limited to a certain physical structure and the target nucleic acid can be detected without physical compartmentalization. For example, the detection chamber 520 can retain the reaction mixture on a surface of the device 500, a matrix material (e.g., hydrogel, wire-framed mesh, low cross-linked gel), and/or a protrusion along a surface of device 500, with or without a compartmentalized physical structure. In some cases, the plurality of detection chambers 520 can include two or more detection reagents, thereby enabling multiplexed detection of two or more target nucleic acids.

[0073] The readout may be detected locally at or near the detection chamber 520 by one or more detectors (not shown) for optical, fluorescence, magnetic, electrical, chemical, or electrochemical readout. The detectors can be located in the detection chamber 520, directly above or below the detection chamber 520, and/or embedded in a material contacting the detection chamber 520. For example, the reporter cleavage may be linked to a colorimetric reaction and the color change can be monitored using a photosensor (e.g., charged-coupled device (CCD) camera or image sensor) located in the detection chamber 520 making contact with the flow/flux of the sample or embedded in at least one surface of the detection chamber 520. In another example, a signal change (e.g., increase or decrease) in light absorbance, can be detected by a photosensor located in the detection chamber 520 between before and after the cleavage of the reporter. In another example, the emitted fluorescence of cleaved reporter may be monitored using a fluorimeter comprising fluorescence excitation means (e.g., CO2, laser and/or light emitting diodes (LEDs)) and/or fluorescence detection means (e.g., photodiode array, phototransistor, or others). In some cases, a signal change in emission wavelength can be generated by the cleavage of the reporter. For example, the cleavage of the reporter may allow the fluorophore to emit fluorescence at a particular wavelength and thus changing the fluorescence readout of the reaction. The fluorimeter can be located in the detection chamber 520 making contact with the flow/flux of the sample or embedded in at least one surface of the detection chamber 520. In another example, the reporter cleavage may change (e.g., increase/decrease) the intensity of an electrochemical signal or increase/decrease the diffusion constant of an electroactive moiety in the reporter, and the signal change may be measured by one or more detectors (e.g., electrodes) located in the detection chamber 520 making contact with the flow/flux of the sample or embedded in at least one surface of the detection chamber 520. In another example, an electrochemical signal change, such as a decrease in the current produced by a ferrocene (Fc), or other electroactive mediator moieties conjugated to the individual nucleotides of nucleic acid molecules (ssRNA, ssDNA, or ssRNA/DNA hybrid molecules) immobilized on a surface of the detection chamber 520, can be generated by the cleavage of the reporter. Without the presence of target nucleic acid, the programmable nuclease complex remains inactive, and a high current caused by the electroactive moieties can be recorded. When the target nucleic acid flows in the detection chamber 520, the activated programmable nuclease complex non-specifically degrades the immobilized Fc-conjugated nucleic acid molecules and decrease the number of electroactive molecules and, thus, leads to a decrease in recorded current. In another example, the reporter cleavage may generate a calorimetric signal change that may be measured by one or more calorimeters located in the detection chamber 520 making contact with the flow/flux of the sample or embedded in at least one surface of the detection chamber 520.

[0074] The device for detecting a target nucleic acid in a biological sample can include at least one junction configured to produce a plurality of aqueous droplets. FIG. 6A shows a schematic of such a device 600 including at least one junction for droplet production, according to an embodiment. The device 600 is configured to provide a sufficient number of programmable nuclease complexes (e.g., the programmable nuclease and guide nucleic acid) to enable an excess molecular ratio of the programmable nuclease to target nucleic acid at a detection location (not shown) and/or maximize the interactions between the programmable nuclease to target nucleic acid. The device 600 includes or defines a first channel 630 and a second channel 610, collectively forming a junction 660. As an alternative shown in FIG. 6B, the first channel 630 and second channel 610 may meet at another type or shape of junction (e.g., T-junction) 660.

[0075] In operation, the first channel 630 may transport an aqueous fluid 640, which can include the biological sample and a detection reagent, along the first channel 630 into junction 660. Here, the detection reagent can include a programmable nuclease, a guide nucleic acid, and a labeled detector nucleic acid, and the labeled detector nucleic acid can be capable of being cleaved upon binding of the guide nucleic acid to a segment of the target nucleic acid. The first channel 630 may be fluidically connected to a sample chamber (not shown) configured to receive the biological sample including the target nucleic acid. In some cases, the first channel 630 may be fluidically connected to a reservoir (not shown) containing the detection reagent. A second fluid 620 (e.g., oil) that is immiscible with the aqueous fluid 640 can be delivered to the junction 660 from the second channel 610. The second fluid 620 can comprise an oil, such as a fluorinated oil, that includes a fluorosurfactant for stabilizing the resulting droplets, for example, inhibiting subsequent coalescence of the resulting droplets 650. [0076] Upon meeting of the aqueous fluid 640 from the first channel 630 and the second fluid 620 from the second channel 610 at the channel junction 660, the aqueous fluid 640 can be partitioned as discrete droplets 650 in the second fluid 620 and flow away from the junction 660 along the second channel 610. The second channel 610 may deliver the discrete droplets 650 to a detection chamber (not shown) fluidly coupled to the second channel 610. Alternatively, certain component(s) of the detection reagent can be mixed with the target nucleic acid in the biological sample (e.g., prior to entering the device 600), and can contact the remaining components of the detection reagent composition at the reservoir (not shown).

[0077] The detection chambers (not shown) may not be limited to a certain physical structure and the target nucleic acid can be detected without physical compartmentalization. For example, the detection chamber can retain the reaction mixture on a surface of the device 600, a matrix material (e.g., hydrogel, wire-framed mesh, low cross-linked gel), and/or a protrusion along a surface of device 600, with or without a compartmentalized physical structure.

[0078] The readout may be detected locally at or near the second channel 610 by one or more detectors (not shown) for optical, fluorescence, magnetic, electrical, chemical, or electrochemical readout. The detectors can be located in the second channel 610, directly above or below the second channel 610, and/or embedded in a material contacting the second channel 610. For example, the reporter cleavage may be linked to a colorimetric reaction and the color change can be monitored using a photosensor (e.g., charged-coupled device (CCD) camera or image sensor) located in the second channel 610 making contact with the flow/flux of the sample or embedded in at least one surface of the second channel 610. In another example, a signal change (e.g., increase or decrease) in light absorbance, can be detected by a photosensor located in the second channel 610 or embedded in at least one surface of the second channel 610 between before and after the cleavage of the reporter. In another example, the emitted fluorescence of cleaved reporter may be monitored using a fluorimeter comprising fluorescence excitation means (e.g., CO2, laser and/or light emitting diodes (LEDs)) and/or fluorescence detection means (e.g., photodiode array, phototransistor, or others). In some cases, a signal change in emission wavelength can be generated by the cleavage of the reporter. For example, the cleavage of the reporter may allow the fluorophore to emit fluorescence at a particular wavelength and thus changing the fluorescence readout of the reaction. The fluorimeter can be located in the second channel 610 making contact with the flow/flux of the sample or embedded in at least one surface of the second channel 610. In another example, the reporter cleavage may change (e.g., increase/decrease) the intensity of an electrochemical signal or increase/ decrease the diffusion constant of an electroactive moiety in the reporter, and the signal change may be measured by one or more detectors (e.g., electrodes) located in the second channel 610 making contact with the flow/flux of the sample or embedded in at least one surface of the second channel 610. In another example, an electrochemical signal change, such as a decrease in the current produced by a ferrocene (Fc), or other electroactive mediator moieties conjugated to the individual nucleotides of nucleic acid molecules (ssRNA, ssDNA or ssRNA/DNA hybrid molecules) immobilized on a surface of the second channel 610, can be generated by the cleavage of the reporter. Without the presence of target nucleic acid, the programmable nuclease complex remains inactive, and a high current caused by the electroactive moieties can be recorded. When the target nucleic acid flows in the second channel 610, the activated programmable nuclease complex non- specifically degrades the immobilized Fc-conjugated nucleic acid molecules and decrease the number of electroactive molecules and, thus, leads to a decrease in recorded current. In another example, the reporter cleavage may generate a calorimetric signal change that may be measured by one or more calorimeters located in the second channel 610 making contact with the flow/flux of the sample or embedded in at least one surface of the second channel 610.

[0079] As will be appreciated, the channel segments described herein may be coupled to any of a variety of different fluid sources or receiving components, including reservoirs, tubing, manifolds, or fluidic components of other systems. As will be appreciated, the device 600 may have other geometries. For example, the device can have more than one channel junctions. For example, the device can have 2, 3, 4, or 5 channels each carrying fluids that meet at a channel junction. Fluid may be directed flow along one or more channels or reservoirs via one or more fluid flow units. A fluid flow unit can comprise compressors (e.g., providing positive pressure), pumps (e.g., providing negative pressure), actuators, and the like to control flow of the fluid. Fluid may also or otherwise be controlled via applied pressure differentials, centrifugal force, electrokinetic pumping, vacuum, capillary or gravity flow, or the like.

[0080] A device for detecting a target nucleic acid in a biological sample can include emulsification. FIG. 7 shows a schematic of such a device 700 that can be used to create an emulsion, according to an embodiment. The device 700 is configured to provide a sufficient number of programmable nuclease complexes (e.g., the programmable nuclease and guide nucleic acid) to enable an excess molecular ratio of the programmable nuclease to target nucleic acid at a detection location and/or maximize the interactions between the programmable nuclease to target nucleic acid. For example, a first fluid 720 (e.g., aqueous fluid) containing the biological sample and a detection reagent can be mixed a second fluid 710 (e.g., oil) that is immiscible with water, thereby producing a plurality of aqueous droplets 730 surrounded by the immiscible fluid 710. In some cases, the dispersion or emulsification of the two fluids 710 and 720 can be done by sonication (e.g., using ultrasound), shaking, or homogenization. The detection reagent can include a programmable nuclease, a guide nucleic acid, and a labeled detector nucleic acid, wherein the labeled detector nucleic acid is capable of being cleaved upon binding of the guide nucleic acid to a segment of the target nucleic acid.

[0081] The readout may be detected locally at or near the device 700 by one or more detectors (not shown) for optical, fluorescence, magnetic, electrical, chemical, or electrochemical readout. The detectors can be located in the immiscible fluid 710, in close proximity to the immiscible fluid 710, and/or embedded in a material contacting the immiscible fluid 710. For example, the reporter cleavage may be linked to a colorimetric reaction and the color change can be monitored using a photosensor (e.g., charged-coupled device (CCD) camera or image sensor) located in the immiscible fluid 710 making contact with the sample, in close proximity to the immiscible fluid 710, or embedded in at least one surface of the device 700. In another example, a signal change (e.g., increase or decrease) in light absorbance, can be detected by a photosensor located in the immiscible fluid 710 making contact with the sample or embedded in at least one surface of the device 700 between before and after the cleavage of the reporter. In another example, the emitted fluorescence of cleaved reporter may be monitored using a fluorimeter comprising fluorescence excitation means (e.g., CO2, laser and/or light emitting diodes (LEDs)) and/or fluorescence detection means (e.g., photodiode array, phototransistor, or others). In some cases, a signal change in emission wavelength can be generated by the cleavage of the reporter. For example, the cleavage of the reporter may allow the fluorophore to emit fluorescence at a particular wavelength and thus changing the fluorescence readout of the reaction. The fluorimeter can be located in the immiscible fluid 710 making contact with the sample, in close proximity to the immiscible fluid 710, or embedded in at least one surface of the device 700. In another example, the reporter cleavage may change (e.g., increase/decrease)the intensity of an electrochemical signal or increase/ decrease the diffusion constant of an electroactive moiety in the reporter, and the signal change may be measured by one or more detectors (e.g., electrodes) located in the immiscible fluid 710 making contact with the sample, in close proximity to the immiscible fluid 710, or embedded in at least one surface of the device 700. In another example, an electrochemical signal change, such as a decrease in the current produced by a ferrocene (Fc), or other electroactive mediator moi eties conjugated to the individual nucleotides of nucleic acid molecules (ssRNA, ssDNA or ssRNA/DNA hybrid molecules) immobilized on a surface of the device 700, can be generated by the cleavage of the reporter. Without the presence of target nucleic acid, the programmable nuclease complex remains inactive, and a high current caused by the electroactive moieties can be recorded. When the target nucleic acid flows in the immiscible fluid 710 and device 700, the activated programmable nuclease complex non-specifically degrades the immobilized Fc-conjugated nucleic acid molecules and decrease the number of electroactive molecules and, thus, leads to a decrease in recorded current. In another example, the reporter cleavage may generate a calorimetric signal change that may be measured by one or more calorimeters located in the immiscible fluid 710 making contact with the sample or embedded in at least one surface of the device 700.

[0082] A device for detecting a target nucleic acid in a biological sample can include flow filtration. FIG. 8 shows a schematic of such a device 800 that can use flow filtration for detecting the target nucleic acid, according to an embodiment. The device 800 is configured to provide a sufficient number of programmable nuclease complexes (e.g., the programmable nuclease and guide nucleic acid) to enable an excess molecular ratio of the programmable nuclease to target nucleic acid at a detection location and/or maximize the interactions between the programmable nuclease to target nucleic acid. In some cases, the biological sample may be diluted (e.g., using any of the devices disclosed above) prior to entering the device 800, in order to reduce the number of nucleic acids in the sample and/or reduce the chance of non-specific binding of the nucleic acids.

[0083] The device 800 defines a top opening 810, a volume 830 for receiving the biological sample, and one or more stacked detection layers 820. Each of the stacked detection layers 820 can comprise a porous substrate, such as polymer matrix (e.g., hydrogel), beads (e.g., solid, porous, conducting, non-conducting), and/or nanostructures (e.g., wire "es). The porous polymer matrix, beads, and/or nanostructures can be used to isolate nucleic acids and/or allow for interactions between the detection reagent and biological sample. In some cases, the polymer matrix, beads, and/or nanostructures can be conjugated with the detection reagent (e.g., programmable nuclease, guide nucleic acid, and/or the reporter). The porous polymer matrix, beads, and/or nanostructures can be embedded into the detection layers 820 to prevent the migration of the detection reagent within the column while still allowing free flow of fluids around the beads. [0084] Co-polymerization of the detection reagent (e.g., programmable nuclease, guide nucleic acid, and/or the reporter) into the porous polymer matrix, beads, and/or nanostructures may result in a higher density of reporter/unit volume or reporter/unit area than other immobilization methods utilizing surface immobilization (e.g., onto beads, after matrix polymerization, etc.). Co-polymerization of the programmable nuclease, guide nucleic acid, and/or the reporter into the porous polymer matrix, beads, and/or nanostructures may result in less undesired release of the reporter (e.g., during an assay, a measurement, or on the shelf), and thus may cause less background signal, than other immobilization strategies (e.g., conjugation to a pre-formed hydrogel, bead, etc.). In at least some instances this may be due to better incorporation of reporters into the porous polymer matrix, beads, and/or nanostructures as a co-polymer and fewer “free” reporter molecules retained on the hydrogel via non-covalent interactions or non-specific binding interactions.

[0085] The biological sample is added to the volume 830 via the top opening 810, flows through the stacked detection layers 820, reacts with a detection reagent deposited in the stacked detection layers 820, and optionally can be discharged through the bottom opening 840 after the flow filtration. In another embodiment, the top opening 810 can be fluidically connected to a sample chamber (not shown) configured to receive the biological sample before reaching the device 800. In some embodiments, the volume 830 can contain a sample processing reagent (e.g. lysis buffer). The biological sample can be collected and/or processed at the volume 830 before flowing (e.g., by gravity) into a plurality of stacked detection layers 820. For enabling multiplexed detection of multiple target nucleic acids, each detection layer 820 can include a detection reagent for detecting a target nucleic acid. As shown in this embodiment, the device 800 includes five stacked detection layers 820 for detecting five different target nucleic acids. Although this embodiment shows and describes five stacked detection layers, any suitable number of detection layers can be used. In some embodiments, for example, a device can include one, two, three, four, six, or more stacked detection layers. In some embodiments, the stacked detection layers 820 can include a semi-permeable membrane between each layer that enables free flow of nucleic acids but prevents the migration of the detection reagents within the column between layers.

[0086] The detection reagent can include a programmable nuclease, a guide nucleic acid, and a labeled detector nucleic acid, wherein the labeled detector nucleic acid is capable of being cleaved upon binding of the guide nucleic acid to a segment of the target nucleic acid.

The readout may be detected locally at or near the stacked detection layers 820 by one or more detectors (not shown) for optical, fluorescence, magnetic, electrical, chemical, or electrochemical readout. The detectors can be located in the stacked detection layers 820, in close proximity to the stacked detection layers 820, and/or embedded in a material contacting the stacked detection layers 820. For example, the reporter cleavage may be linked to a colorimetric reaction and the color change can be monitored using a photosensor (e.g., charged-coupled device (CCD) camera or image sensor) located in the stacked detection layers 820, in close proximity to the stacked detection layers 820, and/or embedded in a material contacting the stacked detection layers 820. In another example, a signal change (e.g., increase or decrease) in light absorbance, can be detected by a photosensor located in the stacked detection layers 820, in close proximity to the stacked detection layers 820, and/or embedded in a material contacting the stacked detection layers 820 between before and after the cleavage of the reporter. In another example, the emitted fluorescence of cleaved reporter may be monitored using a fluorimeter comprising fluorescence excitation means (e.g., CO2, laser and/or light emitting diodes (LEDs)) and/or fluorescence detection means (e.g., photodiode array, phototransistor, or others). In some cases, a signal change in emission wavelength can be generated by the cleavage of the reporter. For example, the cleavage of the reporter may allow the fluorophore to emit fluorescence at a particular wavelength and thus changing the fluorescence readout of the reaction. The fluorimeter can be located in the stacked detection layers 820, in close proximity to the stacked detection layers 820, and/or embedded in a material contacting the stacked detection layers 820. In another example, the reporter cleavage may change (e.g., increase/decrease) the intensity of an electrochemical signal or increase/decrease the diffusion constant of an electroactive moiety in the reporter, and the signal change may be measured by one or more detectors (e.g., electrodes) located in the stacked detection layers 820, in close proximity to the stacked detection layers 820, and/or embedded in a material contacting the stacked detection layers 820. In another example, an electrochemical signal change, such as a decrease in the current produced by a ferrocene (Fc), or other electroactive mediator moieties conjugated to the individual nucleotides of nucleic acid molecules (ssRNA, ssDNA or ssRNA/DNA hybrid molecules) immobilized on a surface of the stacked detection layers 820, can be generated by the cleavage of the reporter. Without the presence of target nucleic acid, the programmable nuclease complex remains inactive, and a high current caused by the electroactive moieties can be recorded. When the target nucleic acid flows in the stacked detection layers 820, the activated programmable nuclease complex non- specifically degrades the immobilized Fc-conjugated nucleic acid molecules and decrease the number of electroactive molecules and, thus, leads to a decrease in recorded current. In another example, the reporter cleavage may generate a calorimetric signal change that may be measured by one or more calorimeters located in the stacked detection layers 820, in close proximity to the stacked detection layers 820, and/or embedded in a material contacting the stacked detection layers 820.

[0087] In some cases, a stacked detection layer 820 can include one or more detectors (e.g., electrodes) in a cross-sectional area perpendicular to the flow/flux of the sample (e.g., essentially acts as a “disk” of detectors). In some cases, one or more detectors (e.g., electrodes) can be intercalated within each stacked detection layer 820. In some cases, one or more detectors (e.g., electrodes) are embedded in the porous substrate, including a polymer matrix (e.g., hydrogel), beads (e.g., solid, porous, conducting, non-conducting, etc.) or nanostructures (e.g., wire meshes), to form a closed circuit, where changes in resistance, etc. can be used as a readout for detection.

Readout

[0088] Readout process may be used in conjunction with any of the devices disclosed herein, such as (a) fluorescence readout and/or (b) electrochemical readout. The emitted fluorescence of cleaved reporter oligo nucleotides may be monitored using a fluorimeter positioned directly above the detection and incubation chamber. The fluorimeter may be a commercially available instrument, the optical sensor of a mobile phone or smart phone, or a custom-made optical array comprising of fluorescence excitation means, e.g. CO2, other, laser and/or light emitting diodes (LEDs), and fluorescence detection means e.g. photodiode array, phototransistor, or others. A device may comprise a chamber comprising transparent or translucent materials that allow light to pass in and out of the chamber. For example, the detection chambers 230 in FIG. 2A, the microwells 420 in FIG. 4A, and/or the detection chambers 520 in FIG. 5A can include such transparent or translucent materials that allow light to pass through.

[0089] The fluorescence detection and excitation may be multiplexed, wherein, for example, fluorescence detection involves exciting and detecting more than one fluorophore in the detection chamber. The fluorimeter itself may be multichannel, in which detecting and exciting light at different wavelengths, or more than one fluorimeter may be used in tandem, and their position above the detection chamber be modified by mechanical means, such as a motorized mechanism using micro or macro controllers and actuators (electric, electronic, and/or piezo-electric).

[0090] Two electrochemical detection variations are described herein, using integrated working, counter and reference electrodes in the detection chamber. The first electrochemical detection variation can increase in signal. The progress of the cleavage reaction catalyzed by the programmable nuclease may be detected using a streptavidin-biotin coupled reaction. The top surface of the detection chamber may be functionalized with nucleic acid molecules (ssRNA, ssDNA or ssRNA/DNA hybrid molecules) conjugated with a biotin moiety. The bottom surface of the detection chamber operates as an electrode, comprising of working, reference, and counter areas, manufactured (or screen-printed) from carbon, graphene, silver, gold, platinum, boron-doped diamond, copper, bismuth, titanium, antimony, chromium, nickel, tin, aluminum, molybdenum, lead, tantalum, tungsten, steel, carbon steel, cobalt, indium tin oxide (ITO), ruthenium oxide, palladium, silver-coated copper, carbon nano-tubes, or other metals. The bottom surface of the detection chamber may be coated with streptavidin molecules. In the absence of any biotin molecules, the current measured by a connected electrochemical analyzer (commercial, or custom-made) is low. When the pre- complexed programmable nuclease mix with amplified target flows in the detection chamber, and is activated at a higher temperature, for example at 37°C, cleavage of the single-stranded nucleic acid (ssNA) linker releases biotin molecules that can diffuse onto the streptavidin- coated bottom surface of the detection chamber. Because of the interaction of biotin and streptavidin molecules, an increase in the current is read by a coupled electrochemical analyzer. In some cases, reporter cleavage may increase the intensity of an electrochemical signal (e.g., a potentiometric signal from a square wave or cyclic voltammogram). Reporter cleavage may increase the diffusion constant of an electroactive moiety in the reporter, which can lead to an increase of an electrochemical signal. Thus, in some cases, electrochemical signal increase proportional to the degree of transcollateral reporter cleavage.

[0091] Some experiments may be sensitive to small changes in cleaved reporter concentration, allowing low concentrations of target nucleic acid to be detected or distinguished. An electrochemical assay (an assay that utilizes electrochemical detection) may be capable to detecting less than 100 nM target nucleic acid. An electrochemical assay may be capable to detecting less than 10 nM target nucleic acid. An electrochemical assay may be capable to detecting less than 1 nM target nucleic acid. An electrochemical assay may be capable to detecting less than 100 pM target nucleic acid. An electrochemical assay may be capable to detecting less than 10 pM target nucleic acid. An electrochemical assay may be capable to detecting less than 1 pM target nucleic acid. An electrochemical assay may be capable to detecting less than 100 fM target nucleic acid. An electrochemical assay may be capable to detecting less than 50 fM target nucleic acid. An electrochemical assay may be capable to detecting less than 10 fM target nucleic acid. An electrochemical assay may be capable to detecting less than 1 fM target nucleic acid. In some cases, an electrochemical detection may be more sensitive than fluorescence detection. In some cases, a assay with electrochemical detection may have a lower detection limit than a assay that utilizes fluorescence detection.

[0092] In some cases, an electrochemical reaction may require low reporter concentrations. In some cases, an electrochemical reaction may require low reporter concentrations. An electrochemical reaction may require less than 10 pM reporter.

[0093] An electrochemical reaction may require less than 1 mM reporter. An electrochemical reaction may require less than 100 nM reporter. An electrochemical reaction may require less than 10 nM reporter. An electrochemical reaction may require less than 1 nM reporter. An electrochemical reaction may require less than 100 pM reporter. An electrochemical reaction may require less than 10 pM reporter. An electrochemical reaction may require less than 1 pM reporter.

[0094] Other types of signal amplification that use enrichment may also be used apart from biotin-streptavidin excitation. Non-limiting examples are: (1) glutathione, glutathione S- transferase, (2) maltose, maltose-binding protein, and (3) chitin, chitin-binding protein.

[0095] The second electrochemical detection variation can decrease in signal. The progress of the programmable nuclease cleavage reaction may be monitored by recording the decrease in the current produced by a ferrocene (Fc), or other electroactive mediator moi eties, conjugated to the individual nucleotides of nucleic acid molecules (ssRNA, ssDNA or ssRNA/DNA hybrid molecules) immobilized on the bottom surface of the detection chamber. In the absence of the amplified target, the programmable nuclease complex remains inactive, and a high current caused by the electroactive moieties is recorded. When the programmable nuclease complex with guides flows in the detection chamber and is activated by the matching nucleic acid target at 37°C, the programmable nuclease complex non-specifically degrades the immobilized Fc-conjugated nucleic acid molecules. This cleavage reaction decreases the number of electroactive molecules and, thus, leads to a decrease in recorded current.

[0096] The electrochemical detection may also be multiplexed. This is achieved by the addition of one or more working electrodes in the incubation and detection chamber. The electrodes can be plain, or modified, as described above for the single electrochemical detection method.

[0097] Electrochemiluminescence in a combined optical and electrochemical readout method. The optical signal may be produced by luminescence of a compound, such as tripropyl amine (TP A) generated as an oxidation product of an electroactive product, such as ruthenium bipyridine, [Ru (py)³]²⁺. [0098] A number of different programmable nuclease proteins may be multiplexed by: (1) separate fluidic paths (parallelization of channels), mixed with the same sample, for each of the proteins, or (2) switching to digital (two-phase) microfluidics, where each individual droplet contains a separate reaction mix. The droplets could be generated from single or double emulsions of water and oil. The emulsions are compatible with programmable nuclease reaction, and optically inert.

[0099] The following methods may be used to couple the readout of the Cas reaction to invertase activity. First, colorimetry using a camera, standalone, or an integrated mobile phone optical sensor. The amount of fructose and glucose is linked to a colorimetric reaction. Two examples are: (a) 3, 5 -Dinitrosalicylic acid (DNS), and (b) formazan dye thiazolyl blue. The color change can be monitored using a CCD camera, or the image sensor of a mobile phone. Second, an amperometry using a conventional glucometer, or an electrochemical analyzer. The top of the chamber surface can be coated with single stranded nucleic acid that is conjugated to the enzyme invertase (Inv). The target-activated programmable nuclease complex cleaves the invertase enzyme from the oligo (ssRNA, ssDNA or ssRNA/DNA hybrid molecule), and invertase is then available to catalyze the hydrolysis of sucrose. The mixture can be mixed and the glucose produced may be detected colorimetrically, as previously described, electrochemically. The enzyme glucose oxidase can catalyze the oxidation of glucose to hydrogen peroxide and D -glucono- 5 -lactone.

Programmable Nucleases

[0100] Disclosed herein are programmable nucleases and uses thereof, e.g., detection and editing of target nucleic acids. In some cases, a programmable nuclease is capable of being activated when complexed with the guide nucleic acid and the target nucleic acid segment. A programmable nuclease can be capable of being activated when complexed with a guide nucleic acid and the target sequence. The programmable nuclease can be activated upon binding of the guide nucleic acid to its target nucleic acid and can non-specifically degrade a non-target nucleic acid in its environment. The programmable nuclease has trans cleavage activity once activated. A programmable nuclease can be a Cas protein (also referred to, interchangeably, as a Cas nuclease or Cas effector protein). A guide nucleic acid (e.g., crRNA) and Cas protein can form a CRISPR enzyme.

[0101] The systems and methods of the present disclosure can be implemented using a device that is compatible with a plurality of programmable nucleases. The device can comprise a plurality of programmable nuclease probes comprising the plurality of programmable nucleases and one or more corresponding guide nucleic acids. The plurality of programmable nuclease probes can be the same. Alternatively, the plurality of programmable nuclease probes can be different. For example, the plurality of programmable nuclease probes can comprise different programmable nucleases and/or different guide nucleic acids associated with the programmable nucleases.

[0102] As used herein, a programmable nuclease generally refers to any enzyme that can cleave nucleic acid. The programmable nuclease can be any enzyme that can be or has been designed, modified, or engineered by human contribution so that the enzyme targets or cleaves the nucleic acid in a sequence-specific manner. Programmable nucleases can include, for example, zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and/or RNA-guided nucleases such as the bacterial clustered regularly interspaced short palindromic repeat (CRISPR)-Cas (CRISPR-associated) nucleases or Cpfl. Programmable nucleases can also include, for example, PfAgo and/or NgAgo.

[0103] ZFNs can cut genetic material in a sequence- specific matter and can be designed, or programmed, to target specific viral targets. A ZFN is composed of two domains: a DNA- binding zinc-finger protein linked to the Fokl nuclease domain. The DNA-binding zinc-finger protein is fused with the non-specific Fokl cleave domain to create ZFNs. The protein will typically dimerize for activity. Two ZFN monomers form an active nuclease; each monomer binds to adjacent half- sites on the target. The sequence specificity of ZFNs is determined by ZFPs. Each zinc-finger recognizes a 3 -bp DNA sequence, and 3-6 zinc-fingers are used to generate a single ZFN subunit that binds to DNA sequences of 9-18 bp. The DNA-binding specificities of zinc-fingers is altered by mutagenesis. New ZFPs are programmed by modular assembly of pre-characterized zinc fingers.

[0104] Transcription activator-like effector nucleases (TALENs) can cut genetic material in a sequence-specific matter and can be designed, or programmed, to target specific viral targets. TALENs contain the Fokl nuclease domain at their carboxyl termini and a class of DNA binding domains known as transcription activator- like effectors (TALEs). TALENs are composed of tandem arrays of 33-35 amino acid repeats, each of which recognizes a single base-pair in the major groove of target viral DNA. The nucleotide specificity of a domain comes from the two amino acids at positions 12 and 13 where Asn-Asn, Asn-Ile, His-Asp and Asn-Gly recognize guanine, adenine, cytosine and thymine, respectively. That pattern allows one to program TALENs to target various nucleic acids.

[0105] Several programmable nucleases are consistent with the methods and devices of the present disclosure. For example, Cas proteins are programmable nucleases used in the methods and systems disclosed herein. Cas proteins can include any of the known Classes and Types of CRISPR/Cas enzymes. Programmable nucleases disclosed herein include Class 1 Cas proteins, such as the Type I, Type IV, or Type III Cas proteins. Programmable nucleases disclosed herein also include the Class 2 Cas proteins, such as the Type II, Type V, and Type VI Cas proteins. Programmable nucleases included in the devices disclosed herein and methods of use thereof include a Type V or Type VI Cas proteins.

[0106] In some instances, the programmable nuclease is a Type V Cas protein. In general, a Type V Cas effector protein comprises a RuvC domain, but lacks an HNH domain. In most instances, the RuvC domain of the Type V Cas effector protein comprises three patrial RuvC domains (RuvC-I, RuvC-II, and RuvC-III, also referred to herein as subdomains). In some instances, the three RuvC subdomains are located within the C-terminal half of the Type V Cas effector protein. In some instances, none of the RuvC subdomains are located at the N terminus of the protein. In some instances, the RuvC subdomains are contiguous. In some instances, the RuvC subdomains are not contiguous with respect to the primary amino acid sequence of the Type V Cas protein, but form a ruvC domain once the protein is produced and folds. In some instances, there are zero to about 50 amino acids between the first and second RuvC subdomains. In some instances, there are zero to about 50 amino acids between the second and third RuvC subdomains. In some instances, the Cas effector is a Casl4 effector. In some instances, the Casl4 effector is a Casl4a, Casl4al, Casl4b, Casl4c, Casl4d, Casl4e, Casl4f, Cas 14g, Casl4h, or Casl4u effector. In some instances, the Cas effector is a CasPhi effector. In some instances, the Cas effector is a Casl2 effector. In some instances, the Casl2 effector is a Casl2a, Casl2b, Casl2c, Casl2d, Casl2e, or Casl2j effector.

[0107] In some instances, the Type V Cas protein comprises a Casl4 protein. Casl4 proteins may comprise a bilobed structure with distinct amino-terminal and carboxy-terminal domains. The amino- and carboxy-terminal domains may be connected by a flexible linker. The flexible linker may affect the relative conformations of the amino- and carboxyl-terminal domains. The flexible linker may be short, for example less than 10 amino acids, less than 8 amino acids, less than 6 amino acids, less than 5 amino acids, or less than 4 amino acids in length. The flexible linker may be sufficiently long to enable different conformations of the amino- and carboxy-terminal domains among two Cas 14 proteins of a Cas 14 dimer complex (e.g., the relative orientations of the amino- and carboxy-terminal domains differ between two Casl4 proteins of a Casl4 homodimer complex). The linker domain may comprise a mutation which affects the relative conformations of the amino- and carboxyl-terminal domains. The linker may comprise a mutation which affects Casl4 dimerization. For example, a linker mutation may enhance the stability of a Cast 4 dimer.

[0108] In some instances, the amino-terminal domain of a Cast 4 protein comprises a wedge domain, a recognition domain, a zinc finger domain, or any combination thereof. The wedge domain may comprise a multi-strand P-barrel structure. A multi-strand P-barrel structure may comprise an oligonucleotide/oligosaccharide-binding fold that is structurally comparable to those of some Casl2 proteins. The recognition domain and the zinc finger domain may each (individually or collectively) be inserted between P-barrel strands of the wedge domain. The recognition domain may comprise a 4-a-helix structure, structurally comparable but shorter than those found in some Cast 2 proteins. The recognition domain may comprise a binding affinity for a guide nucleic acid or for a guide nucleic acid-target nucleic acid heteroduplex. In some cases, a REC lobe may comprise a binding affinity for a PAM sequence in the target nucleic acid. The amino-terminal may comprise a wedge domain, a recognition domain, and a zinc finger domain. The carboxy -terminal may comprise a RuvC domain, a zinc finger domain, or any combination thereof. The carboxy -terminal may comprise one RuvC and one zinc finger domain.

[0109] Casl4 proteins may comprise a RuvC domain or a partial RuvC domain. The RuvC domain may be defined by a single, contiguous sequence, or a set of partial RuvC domains that are not contiguous with respect to the primary amino acid sequence of the Casl4 protein. In some instances, a partial RuvC domain does not have any substrate binding activity or catalytic activity on its own. A Casl4 protein of the present disclosure may include multiple partial RuvC domains, which may combine to generate a RuvC domain with substrate binding or catalytic activity. For example, a Casl4 may include 3 partial RuvC domains (RuvC-I, RuvC-II, and RuvC-III, also referred to herein as subdomains) that are not contiguous with respect to the primary amino acid sequence of the Cast 4 protein, but form a RuvC domain once the protein is produced and folds. A Casl4 protein may comprise a linker loop connecting a carboxy terminal domain of the Cast 4 protein with the amino terminal domain of the Cas 14 protein, and wherein the carboxy terminal domain comprises one or more RuvC domains and the amino terminal domain comprises a recognition domain.

[0110] Casl4 proteins may comprise a zinc finger domain. In some instances, a carboxy terminal domain of a Casl4 protein comprises a zinc finger domain. In some instances, an amino terminal domain of a Cas 14 protein comprises a zinc finger domain. In some instances, the amino terminal domain comprises a wedge domain (e.g., a multi -P-barrel wedge structure), a zinc finger domain, or any combination thereof. In some cases, the carboxy terminal domain comprises the RuvC domains and a zinc finger domain, and the amino terminal domain comprises a recognition domain, a wedge domain, and a zinc finger domain.

[OHl] In some instances, the Type V Cas protein is a Cas protein. A Cas protein can function as an endonuclease that catalyzes cleavage at a specific sequence in a target nucleic acid. A programmable Cas nuclease may have a single active site in a RuvC domain that is capable of catalyzing pre-crRNA processing and nicking or cleaving of nucleic acids. This compact catalytic site may render the programmable Cas nuclease especially advantageous for genome engineering and new functionalities for genome manipulation.

[0112] In some instances, the programmable nuclease is a Type VI Cas protein. In some embodiments, the Type VI Cas protein is a programmable Cas 13 nuclease. The general architecture of a Cas 13 protein includes an N-terminal domain and two HEPN (higher eukaryotes and prokaryotes nucleotide-binding) domains separated by two helical domains. The HEPN domains each comprise aR-X4-H motif. Shared features across Casl3 proteins include that upon binding of the crRNA of the guide nucleic acid to a target nucleic acid, the protein undergoes a conformational change to bring together the HEPN domains and form a catalytically active RNase. Thus, two activatable HEPN domains are characteristic of a programmable Casl3 nuclease of the present disclosure. However, programmable Casl3 nucleases also consistent with the present disclosure include Cas 13 nucleases comprising mutations in the HEPN domain that enhance the Cas 13 proteins cleavage efficiency or mutations that catalytically inactivate the HEPN domains. Programmable Cast 3 nucleases consistent with the present disclosure also Casl3 nucleases comprising catalytic components. In some instances, the Cas effector is a Cas 13 effector. In some instances, the Cas 13 effector is a Cas 13 a, a Cas 13b, a Cas 13c, a Cas 13d, or a Cas 13e effector protein.

[0113] In some embodiments, a programmable nuclease as disclosed herein is an RNA- activated programmable RNA nuclease. In some embodiments, a programmable nuclease as disclosed herein is a DNA-activated programmable RNA nuclease. In some embodiments, a programmable nuclease is capable of being activated by a target RNA to initiate trans cleavage of an RNA reporter and is capable of being activated by a target DNA to initiate trans cleavage of an RNA reporter, such as a Type VI CRISPR/Cas enzyme (e.g., a Cas 13 nuclease). For example, Casl3a of the present disclosure can be activated by a target RNA to initiate trans cleavage activity of the Cast 3a for the cleavage of an RNA reporter and can be activated by a target DNA to initiate trans cleavage activity of the Casl3a for trans cleavage of an RNA reporter. An RNA reporter can be an RNA-based reporter. In some embodiments, the Casl3a recognizes and detects ssDNA to initiate transcleavage of RNA reporters. Multiple Casl3a isolates can recognize, be activated by, and detect target DNA, including ssDNA, upon hybridization of a guide nucleic acid with the target DNA. For example, Lbu- Casl3a and Lwa-Casl3a can both be activated to transcollaterally cleave RNA reporters by target DNA. Thus, Type VI CRISPR/Cas enzyme (e.g., a Casl3 nuclease, such as Casl3a) can be DNA-activated programmable RNA nucleases, and therefore can be used to detect a target DNA using the methods as described herein. DNA-activated programmable RNA nuclease detection of ssDNA can be robust at multiple pH values. For example, target ssDNA detection by Cast 3 can exhibit consistent cleavage across a wide range of pH conditions, such as from a pH of 6.8 to a pH of 8.2. In contrast, target RNA detection by Casl3 can exhibit high cleavage activity of pH values from 7.9 to 8.2. In some embodiments, a DNA- activated programmable RNA nuclease that also is capable of being an RNA-activated programmable RNA nuclease, can have DNA targeting preferences that are distinct from its RNA targeting preferences. For example, the optimal ssDNA targets for Cast 3a have different properties than optimal RNA targets for Cast 3 a. As one example, gRNA performance on ssDNA can not necessarily correlate with the performance of the same gRNAs on RNA. As another example, gRNAs can perform at a high level regardless of target nucleotide identity at a 3’ position on a target RNA sequence. In some embodiments, gRNAs can perform at a high level in the absence of a G at a 3’ position on a target ssDNA sequence. Furthermore, target DNA detected by Cast 3 disclosed herein can be directly taken from organisms or can be indirectly generated by nucleic acid amplification methods, such as PCR and LAMP or any amplification method described herein. Key steps for the sensitive detection of a target DNA, such as a target ssDNA, by a DNA-activated programmable RNA nuclease, such as Casl3a, can include: (1) production or isolation of DNA to concentrations above about 0.1 nM per reaction for in vitro diagnostics, (2) selection of a target sequence with the appropriate sequence features to enable DNA detection as these features are distinct from those required for RNA detection, and (3) buffer composition that enhances DNA detection.

[0114] The detection of a target DNA by a DNA-activated programmable RNA nuclease can be connected to a variety of readouts including fluorescence, lateral flow, electrochemistry, or any other readouts described herein. Multiplexing of programmable DNA nuclease, such as a Type V CRISPR-Cas protein, with a DNA-activated programmable RNA nuclease, such as a Type VI protein, with a DNA reporter and an RNA reporter, can enable multiplexed detection of target ssDNAs or a combination of a target dsDNA and a target ssDNA, respectively. Multiplexing of different RNA-activated programmable RNA nucleases that have distinct RNA reporter cleavage preferences can enable additional multiplexing. Methods for the generation of ssDNA for DNA-activated programmable RNA nuclease-based diagnostics can include (1) asymmetric PCR, (2) asymmetric isothermal amplification, such as RPA, LAMP, SDA, etc. (3) NEAR for the production of short ssDNA molecules, and (4) conversion of RNA targets into ssDNA by a reverse transcriptase followed by RNase H digestion. Thus, DNA-activated programmable RNA nuclease detection of target DNA is compatible with the various systems, kits, compositions, reagents, and methods disclosed herein. For example target ssDNA detection by Casl3a can be employed in a DETECTR assay disclosed herein.

[0115] In some cases, the programmable nuclease can be Casl3. Sometimes the Cast 3 can be Cast 3 a, Cast 3b, Cast 3 c, Cast 3d, or Casl3e. In some cases, the programmable nuclease can be Mad7 or Mad2. In some cases, the programmable nuclease can be Casl2. Sometimes the Cast 2 can be Cast 2a, Cast 2b, Cast 2c, Cast 2d, or Casl2e. In some cases, the programmable nuclease can be Csml, Cas9, C2c4, C2c8, C2c5, C2cl0, C2c9, or CasZ. Sometimes, the Csml can also be also called smCmsl, miCmsl, obCmsl, or suCmsl. Sometimes Casl3a can also be also called C2c2. Sometimes CasZ can also be called Casl4a, Cast 4b, Cast 4c, Casl4d, Casl4e, Casl4f, Cast 4g, or Casl4h. Sometimes, the programmable nuclease can be a type V CRISPR-Cas system. In some cases, the programmable nuclease can be a type VI CRISPR-Cas system. Sometimes the programmable nuclease can be a type III CRISPR-Cas system. In some cases, the programmable nuclease can be from at least one of Leptotrichia shahii (Lsh), Listeria seeligeri (Lse), Leptotrichia buccalis (Lbu), Leptotrichia wadeu (Lwa), Rhodobacter capsulatus (Rea), Herbinix hemicellulosilytica (Hhe), Paludibacter propionicigenes (Ppr), Lachnospiraceae bacterium (Lba), [Eubacterium] rectale (Ere), Listeria newyorkensis (Lny), Clostridium aminophilum (Cam), Prevotella sp. (Psm), Capnocytophaga canimorsus (Cea, Lachnospiraceae bacterium (Lba), Bergeyella zoohelcum (Bzo), Prevotella intermedia (Pin), Prevotella buccae (Pbu), Alistipes sp. (Asp), Riemerella anatipestifer (Ran), Prevotella aurantiaca (Pau), Prevotella saccharolytica (Psa), Prevotella intermedia (Pin2), Capnocytophaga canimorsus (Cea), Porphyromonas gulae (Pgu), Prevotella sp. (Psp), Porphyromonas gingivalis (Pig), Prevotella intermedia (Pin3), Enterococcus italicus (Ei), Lactobacillus salivarius (Ls), or Thermus thermophilus (Tt). Sometimes the Casl3 is at least one of LbuCasl3a, LwaCasl3a, LbaCasl3a, HheCasl3a, PprCasl3a, EreCasl3a, CamCasl3a, or LshCasl3a. The trans cleavage activity of the CRISPR enzyme can be activated when the crRNA is complexed with the target nucleic acid. The trans cleavage activity of the CRISPR enzyme can be activated when the guide nucleic acid comprising a tracrRNA and crRNA are complexed with the target nucleic acid. In some embodiments, the target nucleic acid can be RNA or DNA.

[0116] In some embodiments, the programmable nuclease comprises a Casl2 protein, wherein the Cast 2 enzyme binds and cleaves double stranded DNA and single stranded DNA. In some embodiments, programmable nuclease comprises a Cast 3 protein, wherein the Cast 3 enzyme binds and cleaves single stranded RNA. In some embodiments, programmable nuclease comprises a Casl4 protein, wherein the Casl4 enzyme binds and cleaves both double stranded DNA and single stranded DNA.

[0117] Table 1 provides illustrative amino acid sequences of programmable nucleases having trans-cleavage activity. In some instances, programmable nucleases described herein comprise an amino acid sequence that is at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 98%, at least 99%, or 100% identical to any one of SEQ ID Nos: 1-72. The programmable nuclease may consist of an amino acid sequence that is at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to any one or SEQ ID Nos: 1-72. The programmable nuclease may comprise at least about 50, at least about 100, at least about 150, at least about 200, at least about 250, at least about 300, at least about 350, at least about 400, at least about 450, at least about 500 consecutive amino acids of any one of SEQ ID NOs: 1-72.

Table 1: Amino Acid Sequences of Exemplary Programmable Nucleases

[0118] In some cases, the effector proteins comprise a RuvC domain (e.g., a partial RuvC domain). In some instances, the RuvC domain may be defined by a single, contiguous sequence, or a set of partial RuvC domains that are not contiguous with respect to the primary amino acid sequence of the protein. An effector protein of the present disclosure may include multiple partial RuvC domains, which may combine to generate a RuvC domain with substrate binding or catalytic activity. For example, an effector protein may include three partial RuvC domains (RuvC-I, RuvC-II, and RuvC-III, also referred to herein as subdomains) that are not contiguous with respect to the primary amino acid sequence of the effector protein, but form a RuvC domain once the protein is produced and folds. In some cases, effector proteins comprise a recognition domain with a binding affinity for a guide nucleic acid or for a guide nucleic acid-target nucleic acid heteroduplex. In some instances, the effector protein does not comprise a zinc finger domain. In some instances, the effector protein does not comprise an HNH domain.

[0119] Effector proteins disclosed herein may function as an endonuclease that catalyzes cleavage at a specific position e.g., at a specific nucleotide within a nucleic acid sequence) in a target nucleic acid. The target nucleic acid may be single stranded RNA (ssRNA), double stranded DNA (dsDNA) or single-stranded DNA (ssDNA). In some instances, the target nucleic acid is single-stranded DNA. In some instances, the target nucleic acid is singlestranded RNA. The effector proteins may provide cis cleavage activity, trans cleavage activity, nickase activity, or a combination thereof. Cis cleavage activity is cleavage of a target nucleic acid that is hybridized to a guide nucleic acid (e.g., a dual gRNA or a sgRNA), wherein cleavage occurs within or directly adjacent to the region of the target nucleic acid that is hybridized to guide nucleic acid. Trans cleavage activity (also referred to as transcollateral cleavage) is cleavage of ssDNA or ssRNA that is near, but not hybridized to the guide nucleic acid. Trans cleavage activity is triggered by the hybridization of guide nucleic acid to the target nucleic acid. Nickase activity is a selective cleavage of one strand of a dsDNA.

[0120] Effector proteins of the present disclosure, dimers thereof, and multimeric complexes thereof may cleave or nick a target nucleic acid within or near a protospacer adjacent motif (PAM) sequence of the target nucleic acid. In some instances, cleavage occurs within 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 nucleosides of a 5’ or 3’ terminus of a PAM sequence. A target nucleic acid may comprise a PAM sequence adjacent to a sequence that is complementary to a guide nucleic acid spacer region.

Engineered Proteins

[0121] In some instances, effector proteins disclosed herein are engineered proteins. Engineered proteins are not identical to a naturally-occurring protein. Engineered proteins may provide enhanced nuclease or nickase activity as compared to a naturally occurring nuclease or nickase. An engineered protein may comprise a modified form of a wild type counterpart protein.

[0122] In some instances, effector proteins comprise at least one amino acid change (e.g., deletion, insertion, or substitution) that reduces the nucleic acid-cleaving activity of the effector protein relative to the wild type counterpart. For example, a nuclease domain (e.g., RuvC domain) of an effector protein may be deleted or mutated relative to a wild type counterpart effector protein so that it is no longer functional or comprises reduced nuclease activity. The effector protein may have less than 90%, less than 80%, less than 70%, less than 60%, less than 50%, less than 40%, less than 30%, less than 20%, less than 10%, less than 5%, or less than 1% of the nucleic acid-cleaving activity of the wild-type counterpart. Engineered proteins may have no substantial nucleic acid-cleaving activity. Engineered proteins may be enzymatically inactive or “dead,” that is it may bind to a nucleic acid but not cleave it. An enzymatically inactive protein may comprise an enzymatically inactive domain (e.g. inactive nuclease domain). Enzymatically inactive may refer to an activity less than 1%, less than 2%, less than 3%, less than 4%, less than 5%, less than 6%, less than 7%, less than 8%, less than 9%, or less than 10% activity compared to the wild-type counterpart. A dead protein may associate with a guide nucleic acid to activate or repress transcription of a target nucleic acid sequence. In some instances, the enzymatically inactive protein is fused with a protein comprising recombinase activity.

[0123] In some instances, effector proteins comprise at least one amino acid change (e.g., deletion, insertion, or substitution) that increases the nucleic acid-cleaving activity of the effector protein relative to the wild type counterpart. The effector protein may provide at least about 20%, at least about 30%, at least about 40%, at least about 50% at least about 60%, at least about 70%, at least about 80%, at least about 90%, or about 100% more nucleic acidcleaving activity relative to that of the wild-type counterpart. The effector protein may provide at least about 2 fold, at least about 3 fold, at least about 4 fold, at least about 5 fold, at least about 6 fold, at least about 7 fold, at least about 8 fold, at least about 9 fold or at least about 10 fold more nucleic acid-cleaving activity relative to that of the wild-type counterpart.

Fusion Proteins

[0124] In some instances, an effector protein is a fusion protein, wherein the fusion protein comprises a Cas effector protein and a fusion partner protein. A fusion partner protein is also simply referred to herein as a fusion partner. The fusion partner may comprise a protein or a functional domain thereof. Non-limiting examples of fusion partners include cell surface receptor proteins, intracellular signaling proteins, transcription factors, or functional domains thereof. The fusion partner may comprise a signaling peptide, e.g., a nuclear localization signal (NLS).

[0125] In some instances, the fusion partner modulates transcription (e.g., inhibits transcription, increases transcription) of a target nucleic acid. In some instances, the fusion partner is a protein (or a domain from a protein) that inhibits transcription of a target nucleic acid, also referred to as a transcriptional repressor. Transcriptional repressors may inhibit transcription via recruitment of transcription inhibitor proteins, modification of target DNA such as methylation, recruitment of a DNA modifier, modulation of histones associated with target DNA, recruitment of a histone modifier such as those that modify acetylation and/or methylation of histones, or a combination thereof. In some instances, the fusion partner is a protein (or a domain from a protein) that increases transcription of a target nucleic acid, also referred to as a transcription activator. Transcriptional activators may promote transcription via recruitment of transcription activator proteins, modification of target DNA such as demethylation, recruitment of a DNA modifier, modulation of histones associated with target DNA, recruitment of a histone modifier such as those that modify acetylation and/or methylation of histones, or a combination thereof. [0126] In some instances, the fusion protein is a base editor. In general, a base editor comprises a deaminase. In some instances, a fusion protein that comprises a deaminase and a Cas effector protein changes a nucleobase to a different nucleobase, e.g., cytosine to thymine or guanine to adenine.

[0127] In some instances, fusion partners provide enzymatic activity that modifies a target nucleic acid. Such enzymatic activities include, but are not limited to, histone acetyltransferase activity, histone deacetylase activity, nuclease activity, methyltransferase activity, demethylase activity, DNA repair activity, DNA damage activity, deamination activity, dismutase activity, alkylation activity, depurination activity, oxidation activity, kinase activity, phosphatase activity, pyrimidine dimer forming activity, integrase activity, transposase activity, recombinase activity, polymerase activity, ligase activity, helicase activity, photolyase activity, ubiquitin ligase activity, deubiquitinating activity, adenylation activity, deadenylation activity, SUMOylating activity, deSUMOylating activity, ribosylation activity, deribosylation activity, myristoylation activity, and demyristoylation activity, and glycosylase activity. In some instances, the fusion partner comprises an RNA splicing factor.

[0128] Multimeric Complexes

[0129] In some instances, an effector protein may form a multimeric complex with another protein. In general, a multimeric complex comprises multiple programmable nucleases that non-covalently interact with one another. A multimeric complex may comprise enhanced activity relative to the activity of any one of its programmable nucleases alone. For example, a multimeric complex comprising two programmable nucleases may comprise greater nucleic acid binding affinity, cis-cleavage activity, and/or transcollateral cleavage activity than that of either of the programmable nucleases provided in monomeric form. A multimeric complex may have an affinity for a target region of a target nucleic acid and is capable of catalytic activity (e.g., cleaving, nicking or modifying the nucleic acid) at or near the target region. Multimeric complexes may be activated when complexed with a guide nucleic acid. Multimeric complexes may be activated when complexed with a guide nucleic acid and a target nucleic acid. In some instances, the multimeric complex cleaves the target nucleic acid. In some instances, the multimeric complex nicks the target nucleic acid.

[0130] In some instances, the multimeric complex is a dimer comprising two programmable nucleases of identical amino acid sequences. In some instances, the multimeric complex comprises a first programmable nuclease and a second programmable nuclease, wherein the amino acid sequence of the first programmable nuclease is at least 90%, at least 92%, at least 94%, at least 96%, at least 98% identical, or at least 99% identical to the amino acid sequence of the second programmable nuclease. In some instances, the multimeric complex is a heterodimeric complex comprising at least two programmable nucleases of different amino acid sequences. In some instances, the multimeric complex is a heterodimeric complex comprising a first programmable nuclease and a second programmable nuclease, wherein the amino acid sequence of the first programmable nuclease is less than 90%, less than 85%, less than 80%, less than 75%, less than 70%, less than 65%, less than 60%, less than 55%, less than 50%, less than 45%, less than 40%, less than 35%, less than 30%, less than 25%, less than 20%, less than 15%, or less than 10% identical to the amino acid sequence of the second programmable nuclease.

[0131] In some instances, a multimeric complex comprises at least two programmable nucleases. In some instances, a multimeric complex comprises more than two programmable nucleases. In some instances, multimeric complexes comprise at least one Type V CRISPR/Cas protein, or a fusion protein thereof. In some instances, a multimeric complex comprises two, three or four Casl4 proteins.

[0132] Thermostable Programmable Nucleases

[0133] Described herein are various embodiments of thermostable programmable nucleases. In some embodiments, a programmable nuclease is referred to as a programmable nuclease. A programmable nuclease may be thermostable. In some instances, known programmable nucleases (e.g., Casl2 nucleases) are relatively thermo-sensitive and only exhibit activity (e.g., cis and/or trans cleavage) sufficient to produce a detectable signal in a diagnostic assay at temperatures less than 40° C, and optimally at about 37° C. A thermostable protein may have enzymatic activity, stability, or folding comparable to those at 37 °C. In some instances, the trans cleavage activity (e.g., the maximum trans cleavage rate as measured by fluorescent signal generation) of a programmable nuclease in a trans cleavage assay at 40°C may be at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 100%, at least 1-fold, at least 2-fold, at least 3-fold, at least 4-fold, at least 5-fold, at least 6-fold, at least 7-fold, at least 8-fold, at least 9-fold, at least 10-fold, at least 11 -fold, at least 12-fold, at least 13 -fold, at least 14-fold, at least 15-fold, at least 20-fold, at least 25-fold, at least 30-fold, at least 35- fold, at least 40-fold, at least 45-fold, at least 50-fold or more of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 45°C may be at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 100%, at least 1-fold, at least 2- fold, at least 3-fold, at least 4-fold, at least 5-fold, at least 6-fold, at least 7-fold, at least 8- fold, at least 9-fold, at least 10-fold, at least 11 -fold, at least 12-fold, at least 13 -fold, at least

14-fold, at least 15-fold, at least 20-fold, at least 25-fold, at least 30-fold, at least 35-fold, at least 40-fold, at least 45-fold, at least 50-fold or more of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 50°C may be at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 100%, at least 1-fold, at least 2-fold, at least

3-fold, at least 4-fold, at least 5-fold, at least 6-fold, at least 7-fold, at least 8-fold, at least 9- fold, at least 10-fold, at least 11 -fold, at least 12-fold, at least 13 -fold, at least 14-fold, at least

15-fold, at least 20-fold, at least 25-fold, at least 30-fold, at least 35-fold, at least 40-fold, at least 45-fold, at least 50-fold or more of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 55°C may be at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 100%, at least 1-fold, at least 2-fold, at least 3 -fold, at least

4-fold, at least 5 -fold, at least 6-fold, at least 7-fold, at least 8-fold, at least 9-fold, at least 10- fold, at least 11-fold, at least 12-fold, at least 13-fold, at least 14-fold, at least 15-fold, at least 20-fold, at least 25-fold, at least 30-fold, at least 35-fold, at least 40-fold, at least 45-fold, at least 50-fold or more of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 60°C may be at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 100%, at least 1-fold, at least 2-fold, at least 3 -fold, at least 4-fold, at least 5-fold, at least 6-fold, at least 7-fold, at least 8-fold, at least 9-fold, at least 10-fold, at least 11-fold, at least 12-fold, at least 13-fold, at least 14-fold, at least 15-fold, at least 20- fold, at least 25-fold, at least 30-fold, at least 35-fold, at least 40-fold, at least 45-fold, at least 50-fold or more of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 65°C may be at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 100%, at least 1-fold, at least 2-fold, at least 3 -fold, at least 4-fold, at least 5-fold, at least 6-fold, at least 7-fold, at least 8-fold, at least 9-fold, at least 10-fold, at least 11-fold, at least 12-fold, at least 13-fold, at least 14-fold, at least 15-fold, at least 20- fold, at least 25-fold, at least 30-fold, at least 35-fold, at least 40-fold, at least 45-fold, at least 50-fold or more of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 70 °C, 75 °C. 80 °C, or more may be at least 50, at least 60 %, at least 65 %, at least 70 %, at least 75 %, at least 80 %, at least 85 %, at least 95 %, at least 100 %, at least 1-fold, at least 2-fold , at least 3 -fold , at least 4-fold , at least 5-fold , at least 6-fold , at least 7-fold , at least 8-fold , at least 9-fold , at least 10-fold , at least 11-fold, at least 12-fold, at least 13-fold, at least 14-fold, at least 15-fold, at least 20- fold, at least 25-fold, at least 30-fold, at least 35-fold, at least 40-fold, at least 45-fold, at least 50-fold or more of that at 37 °C.

Engineered Guide Nucleic Acids

[0134] Provided herein are compositions comprising one or more engineered guide nucleic acids. A guide nucleic acid can comprise a sequence that is reverse complementary to the sequence of a target nucleic acid. Guide nucleic acids are often referred to as a “guide RNA.” However, a guide nucleic acid may comprise deoxyribonucleotides. The term “guide RNA,” as well as crRNA and tracrRNA, includes guide nucleic acids comprising DNA bases, RNA bases, and modified nucleobases. In general, a guide nucleic acid is a nucleic acid molecule that binds to an effector protein (e.g., a Cas effector protein), thereby forming a ribonucleoprotein complex (RNP). In some instances, the engineered guide RNA imparts activity or sequence selectivity to the effector protein. In general, the engineered guide nucleic acid comprises a CRISPR RNA (crRNA) that is at least partially complementary to a target nucleic acid. In some instances, the engineered guide nucleic acid comprises a transactivating crRNA (tracrRNA), at least a portion of which interacts with the effector protein. The tracrRNA may hybridize to a portion of the guide RNA that does not hybridize to the target nucleic acid. In some instances, the crRNA and tracrRNA are provided as a single guide nucleic acid, also referred to as a single guide RNA (sgRNA). In some instances, a crRNA and tracrRNA function as two separate, unlinked molecules.

[0135] In some instances, the length of the crRNA is not greater than about 40, about 45, about 50, about 55, about 60, about 65, about 70 or about 75 linked nucleosides. In some instances, the length of the crRNA is about 30 to about 120 linked nucleosides. In some instances, the length of a crRNA is about 40 to about 100, about 40 to about 90, about 40 to about 80, about 40 to about 70, about 40 to about 60, about 40 to about 50, about 50 to about 90, about 50 to about 80, about 50 to about 70, or about 50 to about 60 linked nucleosides. In some instances, the length of a crRNA is about 40, about 45, about 50, about 55, about 60, about 65, about 70 or about 75 linked nucleosides.

[0136] In general, crRNAs comprise a spacer region that hybridizes to a target sequence of a target nucleic acid, and a repeat region that interacts with the effector protein. The repeat region may also be referred to as a “protein-binding segment.” Typically, the repeat region is adjacent to the spacer region. For example, a guide RNA that interacts with the effector protein comprises a repeat region that is 5’ of the spacer region. The spacer region of the guide RNA may comprise complementarity with (e.g., hybridize to) a target sequence of a target nucleic acid. In some cases, the spacer region is 15-28 linked nucleosides in length. In some cases, the spacer region is 15-26, 15-24, 15-22, 15-20, 15-18, 16-28, 16-26, 16-24, 16- 22, 16-20, 16-18, 17-26, 17-24, 17-22, 17-20, 17-18, 18-26, 18-24, or 18-22 linked nucleosides in length. In some cases, the spacer region is 18-24 linked nucleosides in length. In some cases, the spacer region is at least 15 linked nucleosides in length. In some cases, the spacer region is at least 16, 18, 20, or 22 linked nucleosides in length. In some cases, the spacer region comprises at least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some cases, the spacer region is at least 17 linked nucleosides in length. In some cases, the spacer region is at least 18 linked nucleosides in length. In some cases, the spacer region is at least 20 linked nucleosides in length. In some cases, the spacer region is at least 80%, at least 85%, at least 90%, at least 95% or 100% complementary to a target sequence of the target nucleic acid. In some cases, the spacer region is 100% complementary to the target sequence of the target nucleic acid. In some cases, the spacer region comprises at least 15 contiguous nucleobases that are complementary to the target nucleic acid.

[0137] A guide nucleic acid may comprise or be coupled to a tracrRNA. The tracrRNA may comprise deoxyribonucleosides in addition to ribonucleosides. The tracrRNA may be separate from but form a complex with a crRNA. The tracrRNA may be (covalently) linked to a crRNA to form a single guide RNA. In some instances, the crRNA and the tracrRNA are separate polynucleotides. A tracrRNA may comprise a repeat hybridization region and a hairpin region. The repeat hybridization region may hybridize to all or part of the sequence of the repeat of a crRNA. The repeat hybridization region may be positioned 3’ of the hairpin region. The hairpin region may comprise a first sequence, a second sequence that is reverse complementary to the first sequence, and a stem-loop linking the first sequence and the second sequence.

[0138] In some instances, the length of the tracrRNA is not greater than 50, 56, 68, 71, 73, 95, or 105 linked nucleosides. In some instances, the length of a tracrRNA is about 30 to about 120 linked nucleosides. In some instances, the length of a tracrRNA is about 50 to about 105, about 50 to about 95, about 50 to about 73, about 50 to about 71, about 50 to about 68, or about 50 to about 56 linked nucleosides. In some instances, the length of a tracrRNA is 56 to 105 linked nucleosides, from 56 to 105 linked nucleosides, 68 to 105 linked nucleosides, 71 to 105 linked nucleosides, 73 to 105 linked nucleosides, or 95 to 105 linked nucleosides. In some instances, the length of a tracrRNA is 40 to 60 nucleotides. In some instances, the length of the tracrRNA is 50, 56, 68, 71, 73, 95, or 105 linked nucleosides. In some instances, the length of the tracrRNA is 50 nucleotides.

[0139] An exemplary tracrRNA may comprise, from 5’ to 3’, a 5’ region, a hairpin region, a repeat hybridization region, and a 3’ region. In some cases, the 5’ region may hybridize to the 3’ region. In some instances, the 5’ region does not hybridize to the 3’ region. In some cases, the 3’ region is covalently linked to the crRNA (e.g., through a phosphodiester bond). In some instances, a tracrRNA may comprise an unhybridized region at the 3’ end of the tracrRNA. The unhybridized region may have a length of about 1, about 2, about 3, about 4, about 5, about 6, about 7, about 8, about 9, about 10, about 12, about 14, about 16, about 18, or about 20 linked nucleosides. In some instances, the length of the unhybridized region is 0 to 20 linked nucleosides.

[0140] In some instances, the guide RNA does not comprise a tracrRNA. In some cases, an effector protein does not require a tracrRNA to locate and/or cleave a target nucleic acid. In some instances, the crRNA of the guide nucleic acid comprises a repeat region and a spacer region, wherein the repeat region binds to the effector protein and the spacer region hybridizes to a target sequence of the target nucleic acid. The repeat sequence of the crRNA may interact with an effector protein, allowing for the guide nucleic acid and the effector protein to form an RNP complex.

[0141] In some cases, an effector protein or a multimeric complex thereof cleaves a precursor RNA (“pre-crRNA”) to produce a guide RNA, also referred to as a “mature guide RNA.” An effector protein that cleaves pre-crRNA to produce a mature guide RNA is said to have pre-crRNA processing activity. In some cases, a repeat region of a guide RNA comprises mutations or truncations relative to respective regions in a corresponding pre- crRNA.

[0142] The guide nucleic acid may bind to a target nucleic acid (e.g., a single strand of a target nucleic acid) or a portion thereof. The guide nucleic acid may bind to a target nucleic acid such as a nucleic acid from a bacterium, a virus, a parasite, a protozoa, a fungus or other agents responsible for a disease, or an amplicon thereof. The target nucleic acid may comprise a mutation, such as a single nucleotide polymorphism (SNP). A mutation may confer for example, resistance to a treatment, such as antibiotic treatment. The guide nucleic acid may bind to a target nucleic acid, such as DNA or RNA, from a cancer gene or gene associated with a genetic disorder, or an amplicon thereof, as described herein. The guide nucleic acid may comprise a first region complementary to a target nucleic acid (FR1) and a second region that is not complementary to the target nucleic acid (FR2). In some cases, FR1 is located 5’ to FR2 (FR1-FR2). In some cases, FR2 is located 5’ to FR1 (FR2-FR1).

[0143] In some cases, the guide comprises 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 linked nucleosides. In general, a guide nucleic acid comprises at least linked nucleosides. In some instances, a guide nucleic acid comprises at least 25 linked nucleosides. A guide nucleic acid may comprise 10 to 50 linked nucleosides. In some cases, the guide nucleic acid comprises or consists essentially of about 12 to about 80 linked nucleosides, about 12 to about 50, about 12 to about 45, about 12 to about 40, about 12 to about 35, about 12 to about 30, about 12 to about 25, from about 12 to about 20, about 12 to about 19 , about 19 to about 20, about 19 to about 25, about 19 to about 30, about 19 to about 35, about 19 to about 40, about 19 to about 45, about 19 to about 50, about 19 to about 60, about 20 to about 25, about 20 to about 30, about 20 to about 35, about 20 to about 40, about 20 to about 45, about 20 to about 50, or about 20 to about 60 linked nucleosides. In some cases, the guide nucleic acid has about 10 to about 60, about 20 to about 50, or about 30 to about 40 linked nucleosides.

[0144] A guide nucleic acid can comprise a sequence that is reverse complementary to the sequence of a target nucleic acid. A guide nucleic acid can include a crRNA. Sometimes, a guide nucleic acid comprises a crRNA and tracrRNA. The guide nucleic acid can bind specifically to the target nucleic acid. In some cases, the guide nucleic acid is not naturally occurring and is instead made by artificial combination of otherwise separate segments of sequence. Often, the artificial combination is performed by chemical synthesis, by genetic engineering techniques, or by the artificial manipulation of isolated segments of nucleic acids. The target nucleic acid can be designed and made to provide desired functions. In some cases, the targeting region of a guide nucleic acid is 20 nucleotides in length. The targeting region of the guide nucleic acid may have a length of at least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides in length. In some instances, the targeting region of the guide nucleic acid is 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides in length. In some cases, the targeting region of a guide nucleic acid has a length from exactly or about 12 nucleotides (nt) to about 80 nt, from about 12 nt to about 50 nt, from about 12 nt to about 45 nt, from about 12 nt to about 40 nt, from about 12 nt to about 35 nt, from about 12 nt to about 30 nt, from about 12 nt to about 25 nt, from about 12 nt to about 20 nt, from about 12 nt to about 19 nt, from about 19 nt to about 20 nt, from about 19 nt to about 25 nt, from about 19 nt to about 30 nt, from about 19 nt to about 35 nt, from about 19 nt to about 40 nt, from about 19 nt to about 45 nt, from about 19 nt to about 50 nt, from about 19 nt to about 60 nt, from about 20 nt to about 25 nt, from about 20 nt to about 30 nt, from about 20 nt to about 35 nt, from about 20 nt to about 40 nt, from about 20 nt to about 45 nt, from about 20 nt to about 50 nt, or from about 20 nt to about 60 nt. It is understood that the sequence of a polynucleotide need not be 100% complementary to that of its target nucleic acid to be specifically hybridizable or hybridizable or able to bind specifically. The guide nucleic acid can have a sequence comprising at least one uracil in a region from nucleic acid residue 5 to 20 that is reverse complementary to a modification variable region in the target nucleic acid. The guide nucleic acid, in some cases, has a sequence comprising at least one uracil in a region from nucleic acid residue 5 to 9, 10 to 14, or 15 to 20 that is reverse complementary to a modification variable region in the target nucleic acid. The guide nucleic acid can have a sequence comprising at least one uracil in a region from nucleic acid residue 5 to 20 that is reverse complementary to a methylation variable region in the target nucleic acid. The guide nucleic acid, in some cases, has a sequence comprising at least one uracil in a region from nucleic acid residue 5 to 9, 10 to 14, or 15 to 20 that is reverse complementary to a methylation variable region in the target nucleic acid.

Pooling Guide Nucleic Acids

[0145] In some instances, compositions, systems or methods provided herein comprise a pool of guide nucleic acids. A guide nucleic acid can be selected from a group of guide nucleic acids that have been tiled against the nucleic acid sequence of a strain of an infection or genomic locus of interest. The guide nucleic acid can be selected from a group of guide nucleic acids that have been tiled against the nucleic acid sequence of a strain of interest. The genomic locus of interest may belong to a viral genome, a bacterial genome, or a mammalian genome. Non-limiting examples of viral genomes are an HPV genome, an HIV genome, an influenza genome, or a coronavirus genome. Often, guide nucleic acids that are tiled against the nucleic acid of a strain of an infection or genomic locus of interest can be pooled for use in a method described herein. Often, these guide nucleic acids are pooled for detecting a target nucleic acid in a single assay. The pooling of guide nucleic acids that are tiled against a single target nucleic acid can enhance the detection of the target nucleic acid using the methods described herein. The pooling of guide nucleic acids that are tiled against a single target nucleic acid can ensure broad coverage of the target nucleic acid within a single reaction using the methods described herein. The tiling, for example, is sequential along the target nucleic acid. Sometimes, the tiling is overlapping along the target nucleic acid. In some instances, the tiling comprises gaps between the tiled guide nucleic acids along the target nucleic acid. In some instances, the tiling of the guide nucleic acids is non-sequential. In some instances, the pool of guide nucleic acids are collectively complementary to at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or 100% of the target nucleic acid. In some instances, at least a portion of the guide nucleic acids of the pool overlap in sequence. In some instances, at least a portion of the guide nucleic acids of the pool do not overlap in sequence. In some cases, the pool of guide nucleic acids comprises at least 2, at least 3, at least 4, at least 5, or at least 6 guide nucleic acids targeting different sequences of a target nucleic acid. Often, a method for detecting a target nucleic acid comprises contacting a target nucleic acid to a pool of guide nucleic acids and a programmable nuclease, wherein a guide nucleic acid of the pool of guide nucleic acids has a sequence selected from a group of tiled guide nucleic acid that correspond to nucleic acids of a target nucleic acid; and assaying for a signal produce by cleavage of at least some reporters of a population of reporters. Pooling of guide nucleic acids can ensure broad spectrum identification, or broad coverage, of a target species within a single reaction. This can be particularly helpful in diseases or indications, like sepsis, that may be caused by multiple organisms.

Reporters

[0146] In some instances, systems disclosed herein comprise a reporter. By way of nonlimiting and illustrative example, a reporter may comprise a single stranded nucleic acid and a detection moiety (e.g., a labeled single stranded RNA reporter), wherein the nucleic acid is capable of being cleaved by a programmable nuclease (e.g., a Type V CRISPR/Cas protein as disclosed herein) or a multimeric complex thereof, releasing the detection moiety, and, generating a detectable signal. As used herein, "reporter" is used interchangeably with "reporter nucleic acid" or "reporter molecule". The programmable nucleases disclosed herein, activated upon hybridization of a guide RNA to a target nucleic acid, may cleave the reporter. Cleaving the "reporter" may be referred to herein as cleaving the "reporter nucleic acid," the "reporter molecule," or the "nucleic acid of the reporter." Reporters may comprise RNA. Reporters may comprise DNA. Reporters may be double-stranded. Reporters may be singlestranded.

[0147] In some cases, the reporter comprises a detection moiety. In some instances, the reporter comprises a cleavage site, wherein the detection moiety is located at a first site on the reporter, wherein the first site is separated from the remainder of reporter upon cleavage at the cleavage site. In some cases, the detection moiety is 3' to the cleavage site. In some cases, the detection moiety is 5' to the cleavage site. Sometimes the detection moiety is at the 3' terminus of the nucleic acid of a reporter. In some cases, the detection moiety is at the 5' terminus of the nucleic acid of a reporter.

[0148] In some embodiments, the reporter may comprise a nucleic acid and a detection moiety. In some embodiments, a reporter is connected to a surface by a linkage. In some embodiments, a reporter may comprise at least one of a nucleic acid, a chemical functionality, a detection moiety, a quenching moiety, or a combination thereof. In some embodiments, a reporter is configured for the detection moiety to remain immobilized to the surface and the quenching moiety to be released into solution upon cleavage of the reporter. In some embodiments, a reporter is configured for the quenching moiety to remain immobilized to the surface and for the detection moiety to be released into solution, upon cleavage of the reporter. Often the detection moiety is at least one of a label, a polypeptide, a dendrimer, or a nucleic acid, or a combination thereof. In some embodiments, the reporter contains a label. In some embodiments, label may be FITC, DIG, TAMRA, Cy5, AF594, or Cy3. In some embodiments, the label may comprise a dye, a nanoparticle configured to produce a signal. In some embodiments, the dye may be a fluorescent dye. In some embodiments, the at least one chemical functionality may comprise biotin. In some embodiments, the at least one chemical functionality may be configured to be captured by a capture probe. In some embodiments, the at least one chemical functionality may comprise biotin and the capture probe may comprise anti-biotin, streptavidin, avidin or other molecule configured to bind with biotin. In some embodiments, the dye is the chemical functionality. In some embodiments, a capture probe may comprise a molecule that is complementary to the chemical functionality. . In some embodiments, the capture antibodies are anti-FITC, anti- DIG, anti-TAMRA, anti-Cy5, anti-AF594, or any other appropriate capture antibody capable of binding the detection moiety or conjugate. In some embodiments, the detection moiety can be the chemical functionality.

[0149] In some instances, reporters comprise a detection moiety capable of generating a signal. A signal may be a calorimetric, potentiometric, amperometric, optical (e.g., fluorescent, colorimetric, etc.), or piezo-electric signal. In some cases, the reporter comprises a detection moiety. Suitable detectable labels and/or moieties that may provide a signal include, but are not limited to, an enzyme, a radioisotope, a member of a specific binding pair, a fluorophore, a fluorescent protein, a quantum dot, and the like.

[0150] In some cases, the reporter comprises a detection moiety and a quenching moiety. In some instances, the reporter comprises a cleavage site, wherein the detection moiety is located at a first site on the reporter and the quenching moiety is located at a second site on the reporter, wherein the first site and the second site are separated by the cleavage site. Sometimes the quenching moiety is a fluorescence quenching moiety. In some cases, the quenching moiety is 5' to the cleavage site and the detection moiety is 3' to the cleavage site. In some cases, the detection moiety is 5' to the cleavage site and the quenching moiety is 3' to the cleavage site. Sometimes the quenching moiety is at the 5' terminus of the nucleic acid of a reporter. Sometimes the detection moiety is at the 3' terminus of the nucleic acid of a reporter. In some cases, the detection moiety is at the 5' terminus of the nucleic acid of a reporter. In some cases, the quenching moiety is at the 3' terminus of the nucleic acid of a reporter.

[0151] Suitable fluorescent proteins include, but are not limited to, green fluorescent protein (GFP) or variants thereof, blue fluorescent variant of GFP (BFP), cyan fluorescent variant of GFP (CFP), yellow fluorescent variant of GFP (YFP), enhanced GFP (EGFP), enhanced CFP (ECFP), enhanced YFP (EYFP), GFPS65T, Emerald, Topaz (TYFP), Venus, Citrine, mCitrine, GFPuv, destabilised EGFP (dEGFP), destabilised ECFP (dECFP), destabilised EYFP (dEYFP), mCFPm, Cerulean, T-Sapphire, CyPet, YPet, mKO, HcRed, t- HcRed, DsRed, DsRed2, DsRed-monomer, J-Red, dimer2, t-dimer2(12), mRFPl, pocilloporin, Renilla GFP, Monster GFP, paGFP, Kaede protein and kindling protein, Phycobiliproteins and Phycobiliprotein conjugates including B -Phycoerythrin, R- Phycoerythrin and Allophycocyanin. Suitable enzymes include, but are not limited to, horseradish peroxidase (HRP), alkaline phosphatase (AP), beta-galactosidase (GAL), glucose-6-phosphate dehydrogenase, beta-N-acetylglucosaminidase, CE<-glucuronidase, invertase, Xanthine Oxidase, firefly luciferase, and glucose oxidase (GO).

[0152] In some instances, the detection moiety comprises an invertase. The substrate of the invertase may be sucrose. A DNS reagent may be included in the system to produce a colorimetric change when the invertase converts sucrose to glucose. In some cases, the reporter nucleic acid and invertase are conjugated using a heterobifunctional linker via sulfo- SMCC chemistry.

[0153] Suitable fluorophores may provide a detectable fluorescence signal in the same range as 6-Fluorescein (Integrated DNA Technologies), IRDye 700 (Integrated DNA Technologies), TYE 665 (Integrated DNA Technologies), Alex Fluor 594 (Integrated DNA Technologies), or ATTO TM 633 (NHS Ester) (Integrated DNA Technologies). Non-limiting examples of fluorophores are fluorescein amidite, 6-Fluorescein, IRDye 700, TYE 665, Alex Fluor 594, or ATTO TM 633 (NHS Ester). The fluorophore may be an infrared fluorophore. The fluorophore may emit fluorescence in the range of 500 nm and 720 nm. In some cases, the fluorophore emits fluorescence at a wavelength of 700 nm or higher. In other cases, the fluorophore emits fluorescence at about 665 nm. In some cases, the fluorophore emits fluorescence in the range of 500 nm to 520 nm, 500 nm to 540 nm, 500 nm to 590 nm, 590 nm to 600 nm, 600 nm to 610 nm, 610 nm to 620 nm, 620 nm to 630 nm, 630 nm to 640 nm, 640 nm to 650 nm, 650 nm to 660 nm, 660 nm to 670 nm, 670 nm to 680 nm, 690 nm to 690 nm, 690 nm to 700 nm, 700 nm to 710 nm, 710 nm to 720 nm, or 720 nm to 730 nm. In some cases, the fluorophore emits fluorescence in the range 450 nm to 750 nm, 500 nm to 650 nm, or 550 to 650 nm.

[0154] Systems may comprise a quenching moiety. A quenching moiety may be chosen based on its ability to quench the detection moiety. A quenching moiety may be a non- fluorescent fluorescence quencher. A quenching moiety may quench a detection moiety that emits fluorescence in the range of 500 nm and 720 nm. A quenching moiety may quench a detection moiety that emits fluorescence in the range of 500 nm and 720 nm. In some cases, the quenching moiety quenches a detection moiety that emits fluorescence at a wavelength of 700 nm or higher. In other cases, the quenching moiety quenches a detection moiety that emits fluorescence at about 660 nm or about 670 nm. In some cases, the quenching moiety quenches a detection moiety that emits fluorescence in the range of 500 to 520, 500 to 540, 500 to 590, 590 to 600, 600 to 610, 610 to 620, 620 to 630, 630 to 640, 640 to 650, 650 to 660, 660 to 670, 670 to 680, 690 to 690, 690 to 700, 700 to 710, 710 to 720, or 720 to 730 nm. In some cases, the quenching moiety quenches a detection moiety that emits fluorescence in the range 450 nm to 750 nm, 500 nm to 650 nm, or 550 to 650 nm. A quenching moiety may quench fluorescein amidite, 6-Fluorescein, IRDye 700, TYE 665, Alex Fluor 594, or ATTO TM 633 (NHS Ester). A quenching moiety may be Iowa Black RQ, Iowa Black FQ or IRDye QC-1 Quencher. A quenching moiety may quench fluorescein amidite, 6-Fluorescein (Integrated DNA Technologies), IRDye 700 (Integrated DNA Technologies), TYE 665 (Integrated DNA Technologies), Alex Fluor 594 (Integrated DNA Technologies), or ATTO TM 633 (NHS Ester) (Integrated DNA Technologies). A quenching moiety may be Iowa Black RQ (Integrated DNA Technologies), Iowa Black FQ (Integrated DNA Technologies) or IRDye QC-1 Quencher (LiCor). Any of the quenching moi eties described herein may be from any commercially available source, may be an alternative with a similar function, a generic, or a non-trade name of the quenching moieties listed.

[0155] The generation of the detectable signal from the release of the detection moiety indicates that cleavage by the programmable nucleases has occurred and that the sample contains the target nucleic acid. In some cases, the detection moiety comprises a fluorescent dye. Sometimes the detection moiety comprises a fluorescence resonance energy transfer (FRET) pair. In some cases, the detection moiety comprises an infrared (IR) dye. In some cases, the detection moiety comprises an ultraviolet (UV) dye. Alternatively, or in combination, the detection moiety comprises a protein. Sometimes the detection moiety comprises a biotin. Sometimes the detection moiety comprises at least one of avidin or streptavidin. In some instances, the detection moiety comprises a polysaccharide, a polymer, or a nanoparticle. In some instances, the detection moiety comprises a gold nanoparticle or a latex nanoparticle.

[0156] A detection moiety may be any moiety capable of generating a calorimetric, potentiometric, amperometric, optical (e.g., fluorescent, colorimetric, etc.), or piezo-electric signal. A nucleic acid of a reporter, sometimes, is protein-nucleic acid that is capable of generating a calorimetric, potentiometric, amperometric, optical (e.g., fluorescent, colorimetric, etc.), or piezo-electric signal upon cleavage of the nucleic acid. Often a calorimetric signal is heat produced after cleavage of the nucleic acids of a reporter. Sometimes, a calorimetric signal is heat absorbed after cleavage of the nucleic acids of a reporter. A potentiometric signal, for example, is electrical potential produced after cleavage of the nucleic acids of a reporter. An amperometric signal may be movement of electrons produced after the cleavage of nucleic acid of a reporter. In some cases, the detection moiety may be a conjugated conducting polymer (e.g., pi electron dense), such as polyacetylene (PA), polyaniline (PANI), polypyrrole (PPy), polythiophene (PTH), poly(para-phenylene) (PPP), poly(phenylenevinylene) (PPV), or polyfuran (PF). Often, the signal is an optical signal, such as a colorimetric signal or a fluorescence signal. An optical signal is, for example, a light output produced after the cleavage of the nucleic acids of a reporter. Sometimes, an optical signal is a change in light absorbance between before and after the cleavage of nucleic acids of a reporter. Often, a piezo-electric signal is a change in mass between before and after the cleavage of the nucleic acid of a reporter. Other methods of detection can also be used, such as optical imaging, surface plasmon resonance (SPR), and/or interferometric sensing.

[0157] The detectable signal may be a colorimetric signal or a signal visible by eye. In some instances, the detectable signal may be fluorescent, electrical, chemical, electrochemical, or magnetic. In some cases, a detectable signal (e.g., a first detectable signal) may be generated by binding of the detection moiety to the capture molecule in the detection region, where the detectable signal indicates that the sample contained the target nucleic acid. Sometimes systems are capable of detecting more than one type of target nucleic acid, wherein the system comprises more than one type of guide nucleic acid and more than one type of reporter nucleic acid. In some cases, the detectable signal may be generated directly by the cleavage event. Alternatively, or in combination, the detectable signal may be generated indirectly by the cleavage event. Sometimes the detectable signal is not a fluorescent signal. In some instances, the detectable signal may be a colorimetric or color-based signal. In some cases, the detected target nucleic acid may be identified based on its spatial location on the detection region of the support medium. In some cases, a second detectable signal may be generated in a spatially distinct location than a first detectable signal when two or more detectable signals are generated.

[0158] Often, the reporter is an enzyme-nucleic acid. The enzyme may be sterically hindered when present as in the enzyme-nucleic acid, but then functional upon cleavage from the nucleic acid by the programmable nuclease. Often, the enzyme is an enzyme that produces a reaction with an enzyme substrate. An enzyme can be invertase. Often, the substrate of invertase is sucrose and DNS reagent.

[0159] Sometimes the reporter is a substrate-nucleic acid. Often the substrate is a substrate that produces a reaction with an enzyme. Release of the substrate upon cleavage by the programmable nuclease may free the substrate to react with the enzyme.

[0160] A reporter may be attached to a solid support. The solid support, for example, is a surface. A surface can be an electrode. Sometimes the solid support is a bead. Often the bead is a magnetic bead. Upon cleavage, the detection moiety is liberated from the solid support and interacts with other mixtures. For example, the detection moiety is an enzyme, and upon cleavage of the nucleic acid of the enzyme-nucleic acid, the enzyme flows through a chamber into a mixture comprising the substrate. When the enzyme meets the enzyme substrate, a reaction occurs, such as a colorimetric reaction, which is then detected. As another example, the detection moiety is an enzyme substrate, and upon cleavage of the nucleic acid of the enzyme substrate-nucleic acid, the enzyme flows through a chamber into a mixture comprising the enzyme. When the enzyme substrate meets the enzyme, a reaction occurs, such as a calorimetric reaction, which is then detected.

[0161] In some embodiments, the reporter comprises a nucleic acid conjugated to an affinity molecule which is in turn conjugated to the fluorophore (e.g., nucleic acid - affinity molecule - fluorophore) or the nucleic acid conjugated to the fluorophore which is in turn conjugated to the affinity molecule (e.g., nucleic acid - fluorophore - affinity molecule). In some embodiments, a linker conjugates the nucleic acid to the affinity molecule. In some embodiments, a linker conjugates the affinity molecule to the fluorophore. In some embodiments, a linker conjugates the nucleic acid to the fluorophore. A linker can be any suitable linker known in the art. In some embodiments, the nucleic acid of the reporter can be directly conjugated to the affinity molecule and the affinity molecule can be directly conjugated to the fluorophore or the nucleic acid can be directly conjugated to the fluorophore and the fluorophore can be directly conjugated to the affinity molecule. In this context, “directly conjugated” indicates that no intervening molecules, polypeptides, proteins, or other moieties are present between the two moieties directly conjugated to each other. For example, if a reporter comprises a nucleic acid directly conjugated to an affinity molecule and an affinity molecule directly conjugated to a fluorophore - no intervening moiety is present between the nucleic acid and the affinity molecule and no intervening moiety is present between the affinity molecule and the fluorophore. The affinity molecule can be biotin, avidin, streptavidin, or any similar molecule.

[0162] In some cases, the reporter comprises a substrate-nucleic acid. The substrate may be sequestered from its cognate enzyme when present as in the substrate-nucleic acid, but then is released from the nucleic acid upon cleavage, wherein the released substrate can contact the cognate enzyme to produce a detectable signal. Often, the substrate is sucrose and the cognate enzyme is invertase, and a DNS reagent can be used to monitor invertase activity.

[0163] A reporter may be a hybrid nucleic acid reporter. A hybrid nucleic acid reporter comprises a nucleic acid with at least one deoxyribonucleotide and at least one ribonucleotide. In some embodiments, the nucleic acid of the hybrid nucleic acid reporter can be of any length and can have any mixture of DNAs and RNAs. For example, in some cases, longer stretches of DNA can be interrupted by a few ribonucleotides. Alternatively, longer stretches of RNA can be interrupted by a few deoxyribonucleotides. Alternatively, every other base in the nucleic acid may alternate between ribonucleotides and deoxyribonucleotides. A major advantage of the hybrid nucleic acid reporter is increased stability as compared to a pure RNA nucleic acid reporter. For example, a hybrid nucleic acid reporter can be more stable in solution, lyophilized, or vitrified as compared to a pure DNA or pure RNA reporter.

[0164] The reporter can be lyophilized or vitrified. The reporter can be suspended in solution or immobilized on a surface. For example, the reporter can be immobilized on the surface of a chamber in a device as disclosed herein. In some cases, the reporter is immobilized on beads, such as magnetic beads, in a chamber of a device as disclosed herein where they can be held in position by a magnet placed below the chamber. [0165] In some cases, the reporter is a single-stranded nucleic acid comprising deoxyribonucleotides. In some cases, the reporter nucleic acid is a single-stranded nucleic acid sequence comprising ribonucleotides. The nucleic acid of a reporter may be a singlestranded nucleic acid sequence comprising at least one ribonucleotide. In some cases, the nucleic acid of a reporter is a single-stranded nucleic acid comprising at least one ribonucleotide residue at an internal position that functions as a cleavage site. In some cases, the nucleic acid of a reporter comprises at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, or at least 10 ribonucleotide residues at an internal position. In some cases, the nucleic acid of a reporter comprises from 2 to 10, from 3 to 9, from 4 to 8, or from 5 to 7 ribonucleotide residues at an internal position. In some cases, the reporter may comprise from 3 to 10, from 4 to 10, from 5 to 10, from 6 to 10, from 7 to 10, from 8 to 10, from 9 to 10, from 2 to 8, from 3 to 8, from 5 to 8, from 6 to 8, from 7 to 8, from 2 to 5, from 3 to 5, or from 4 to 5 ribonucleotide residues at an internal position. Sometimes the ribonucleotide residues are continuous. Alternatively, the ribonucleotide residues are interspersed in between non-ribonucleotide residues. In some cases, the nucleic acid of a reporter has only ribonucleotide residues. In some cases, the nucleic acid of a reporter has only deoxyribonucleotide residues. In some cases, the nucleic acid comprises nucleotides resistant to cleavage by the programmable nuclease described herein. In some cases, the nucleic acid of a reporter comprises synthetic nucleotides. In some cases, the nucleic acid of a reporter comprises at least one ribonucleotide residue and at least one non-ribonucleotide residue.

[0166] In some cases, the nucleic acid of a reporter comprises at least one uracil ribonucleotide. In some cases, the nucleic acid of a reporter comprises at least two uracil ribonucleotides. Sometimes the nucleic acid of a reporter has only uracil ribonucleotides. In some cases, the nucleic acid of a reporter comprises at least one adenine ribonucleotide. In some cases, the nucleic acid of a reporter comprises at least two adenine ribonucleotide. In some cases, the nucleic acid of a reporter has only adenine ribonucleotides. In some cases, the nucleic acid of a reporter comprises at least one cytosine ribonucleotide. In some cases, the nucleic acid of a reporter comprises at least two cytosine ribonucleotide. In some cases, the nucleic acid of a reporter comprises at least one guanine ribonucleotide. In some cases, the nucleic acid of a reporter comprises at least two guanine ribonucleotide. In some instances, a nucleic acid of a reporter comprises a single unmodified ribonucleotide. In some instances, a nucleic acid of a reporter comprises only unmodified ribonucleotides. In some instances, a nucleic acid of a reporter comprises only unmodified deoxyribonucleotides. [0167] In some cases, the nucleic acid of a reporter is 5 to 20, 5 to 15, 5 to 10, 7 to 20, 7 to 15, or 7 to 10 nucleotides in length. In some cases, the nucleic acid of a reporter is 3 to 20,

4 to 20, 5 to 20, 6 to 20, 7 to 20, 8 to 20, 9 to 20, 10 to 20, 13 to 20, 15 to 20, 3 to 15, 4 to 15,

5 to 15, 6 to 15, 7 to 15, 8 to 15, 9 to 15, 10 to 15, 3 to 10, 4 to 10, 5 to 10, 6 to 10, 7 to 10, 8 to 10, 9 to 10, 3 to 8, 4 to 8, 5 to 8, 6 to 8, or 7 to 8, nucleotides in length. In some cases, the nucleic acid of a reporter is 5 to 12 nucleotides in length. In some cases, the reporter nucleic acid is at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, or at least 30 nucleotides in length. In some cases, the reporter nucleic acid is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides in length. For cleavage by a programmable nuclease comprising Casl3, a reporter can be 5, 8, or 10 nucleotides in length. For cleavage by a programmable nuclease comprising Casl2, a reporter can be 10 nucleotides in length.

[0168] In some cases, systems comprise a plurality of reporters. The plurality of reporters may comprise a plurality of signals. In some cases, systems comprise at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 20, at least 30, at least 40, or at least 50 reporters. In some cases, there are 2 to 50, 3 to 40, 4 to 30, 5 to 20, or 6 to 10 different reporters.

[0169] In some instances, systems comprise a Type V CRISPR/Cas protein and a reporter nucleic acid configured to undergo transcollateral cleavage by the Type V CRISPR/Cas protein. Transcollateral cleavage of the reporter may generate a signal from the reporter or alter a signal from the reporter. In some cases, the signal is an optical signal, such as a fluorescence signal or absorbance band. Transcollateral cleavage of the reporter may alter the wavelength, intensity, or polarization of the optical signal. For example, the reporter may comprise a fluorophore and a quencher, such that transcollateral cleavage of the reporter separates the fluorophore and the quencher thereby increasing a fluorescence signal from the fluorophore. Herein, detection of reporter cleavage to determine the presence of a target nucleic acid sequence may be referred to as 'DETECTR'. In some embodiments described herein is a method of assaying for a target nucleic acid in a sample comprising contacting the target nucleic acid with a programmable nuclease, a non-naturally occurring guide nucleic acid that hybridizes to a segment of the target nucleic acid, and a reporter nucleic acid, and assaying for a change in a signal, wherein the change in the signal is produced by cleavage of the reporter nucleic acid. [0170] In the presence of a large amount of non-target nucleic acids, an activity of a programmable nuclease (e.g., a Type V CRISPR/Cas protein as disclosed herein) may be inhibited. If total nucleic acids are present in large amounts, they may outcompete reporters for the programmable nucleases. In some instances, systems comprise an excess of reporter(s), such that when the system is operated and a solution of the system comprising the reporter is combined with a sample comprising a target nucleic acid, the concentration of the reporter in the combined solution-sample is greater than the concentration of the target nucleic acid. In some instances, the sample comprises amplified target nucleic acid. In some instances, the sample comprises an unamplified target nucleic acid. In some instances, the concentration of the reporter is greater than the concentration of target nucleic acids and nontarget nucleic acids. The non-target nucleic acids may be from the original sample, either lysed or unlysed. The non-target nucleic acids may comprise byproducts of amplification. In some instances, systems comprise a reporter wherein the concentration of the reporter in a solution 1.5 fold, at least 2 fold, at least 3 fold, at least 4 fold, at least 5 fold, at least 6 fold, at least 7 fold, at least 8 fold, at least 9 fold, at least 10 fold, at least 11 fold, at least 12 fold, at least 13 fold, at least 14 fold, at least 15 fold, at least 16 fold, at least 17 fold, at least 18 fold, at least 19 fold, at least 20 fold, at least 30 fold, at least 40 fold, at least 50 fold, at least 60 fold, at least 70 fold, at least 80 fold, at least 90 fold, at least 100 fold excess of total nucleic acids. 1.5 fold to 100 fold, 2 fold to 10 fold, 10 fold to 20 fold, 20 fold to 30 fold, 30 fold to 40 fold, 40 fold to 50 fold, 50 fold to 60 fold, 60 fold to 70 fold, 70 fold to 80 fold, 80 fold to 90 fold, 90 fold to 100 fold, 1.5 fold to 10 fold, 1.5 fold to 20 fold, 10 fold to 40 fold, 20 fold to 60 fold, or 10 fold to 80 fold excess of total nucleic acids.

DETECTR Immobilization

[0171] One or more components or reagents of a programmable nuclease-based detection reaction may be suspended in solution or immobilized on a surface. Programmable nucleases, guide nucleic acids, and/or reporters may be suspended in solution or immobilized on a surface. For example, the reporter, programmable nuclease, and/or guide nucleic acid can be immobilized on the surface of a chamber in a device as disclosed herein. In some cases, the reporter, programmable nuclease, and/or guide nucleic acid can be immobilized on beads, such as magnetic beads, in a chamber of a device as disclosed herein where they are held in position by a magnet placed below the chamber. An immobilized programmable nuclease can be capable of being activated and cleaving a free-floating or immobilized reporter. An immobilized guide nucleic acid can be capable of binding a target nucleic acid and activating a programmable nuclease complexed thereto. An immobilized reporter can be capable of being cleaved by the activated programmable nuclease, thereby generating a detectable signal.

[0172] Described herein are various methods to immobilize programmable nuclease- based diagnostic reaction components to the surface of a reaction chamber or other surface (e.g., a surface of a bead). Any of the devices described herein may comprise one or more immobilized detection reagent components (e.g., programmable nuclease, guide nucleic acid, and/or reporter). In certain instances, methods include immobilization of programmable nucleases (e.g., Cas proteins or Cas enzymes), reporters, and guide nucleic acids (e.g., gRNAs). In some embodiments, various programmable nuclease-based diagnostic reaction components are modified with biotin. In some embodiments, these biotinylated programmable nuclease-based diagnostic reaction components are immobilized on surfaces coated with streptavidin. In some embodiments, the biotin-streptavidin chemistries are used for immobilization of programmable nuclease-based reaction components. In some embodiments, NHS-Amine chemistry is used for immobilization of programmable nuclease- based reaction components. In some embodiments, amino modifications are used for immobilization of programmable nuclease-based reaction components.

[0173] In some embodiments, the programmable nuclease, guide nucleic acid, or the reporter are immobilized to a device surface by a linkage or linker. In some embodiments, the linkage comprises a covalent bond, a non-covalent bond, an electrostatic bond, a bond between streptavidin and biotin, an amide bond or any combination thereof. In some embodiments, the linkage comprises non-specific absorption. In some embodiments, the programmable nuclease is immobilized to the device surface by the linkage, wherein the linkage is between the programmable nuclease and the surface. In some embodiments, the reporter is immobilized to the device surface by the linkage, wherein the linkage is between the reporter and the surface. In some embodiments, the guide nucleic acid is immobilized to the surface by the linkage, wherein the linkage is between the 5’ end of the guide nucleic acid and the surface. In some embodiments, the guide nucleic acid is immobilized to the surface by the linkage, wherein the linkage is between the 3’ end of the guide nucleic acid and the surface.

[0174] In some embodiments, the programmable nuclease, guide nucleic acid, or the reporter are immobilized to or within a polymer matrix. The polymer matrix may comprise a hydrogel. Co-polymerization of the programmable nuclease, guide nucleic acid, or the reporter into the polymer matrix may result in a higher density of reporter/unit volume or reporter/unit area than other immobilization methods utilizing surface immobilization (e.g., onto beads, after matrix polymerization, etc.). Co-polymerization of the programmable nuclease, guide nucleic acid, or the reporter into the polymer matrix may result in less undesired release of the reporter (e.g., during an assay, a measurement, or on the shelf), and thus may cause less background signal, than other immobilization strategies (e.g., conjugation to a pre-formed hydrogel, bead, etc.). In at least some instances this may be due to better incorporation of reporters into the polymer matrix as a co-polymer and fewer “free” reporter molecules retained on the hydrogel via non-covalent interactions or non-specific binding interactions.

[0175] In some embodiments, a plurality of oligomers and a plurality of polymerizable oligomers may comprise an irregular or non-uniform mixture. The irregularity of the mixture of polymerizable oligomers and unfunctionalized oligomers may allow pores to form within the hydrogel (i.e., the unfunctionalized oligomers may act as a porogen). For example, the irregular mixture of oligomers may result in phase separation during polymerization that allows for the generation of pores of sufficient size for free-floating programmable nucleases to diffuse into the hydrogel and access immobilized internal reporter molecules. The relative percentages and/or molecular weights of the oligomers may be varied to vary the pore size of the hydrogel. For example, pore size may be tailored to increase the diffusion coefficient of the programmable nucleases.

[0176] In some embodiments, the functional groups attached to the reporters and/or guide nucleic acids may be selected to preferentially incorporate the reporters and/or guide nucleic acids into the polymer matrix via covalent binding at the functional group versus other locations along the nucleic acid backbone of the reporter and/or guide nucleic acid. In some embodiments, the functional groups attached to the reporters and/or guide nucleic acids may be selected to favorably transfer free radicals from the functionalized ends of polymerizable oligomers to the functional group on the end of the reporter and/or guide nucleic acid (e.g., 5’ end), thereby forming a covalent bond and immobilizing the reporter and/or guide nucleic acid rather than destroying other parts of the reporter and/or guide nucleic acid molecules, respectively. In some embodiments, the functional group may comprise a single stranded nucleic acid, a double stranded nucleic acid, an acrydite group, a 5’ thiol modifier, a 3’ thiol modifier, an amine group, a I-Linker™ group, methacryl group, or any combination thereof. One of ordinary skill in the art will recognize that a variety of functional groups may be used depending on the desired properties of the immobilized components.

Modified Nucleic Acids [0177] In some cases, a reporter and/or guide nucleic acid can comprise one or more modifications, e.g., a vase modification, a backbone modification, a sugar modification, etc., to provide the nucleic acid with a new or enhanced feature (e.g., improved stability).

[0178] Examples of suitable modifications include modified nucleic acid backbones and non-natural intemucleoside linkages. Nucleic acids having modified backbones can include those that retain a phosphorus atom in the backbone and those that do not have a phosphorus atom in the backbone. Suitable modified oligonucleotide backbones containing a phosphorus atom therein include, for example, phosphorothioates, chiral phosphorothioates, phosphorodithioates, phosphotriesters, aminoalkylphosphotriesters, methyl and other alkyl phosphonates including 3'-alkylene phosphonates, 5'-alkylene phosphonates and chiral phosphonates, phosphinates, phosphoramidates including 3 '-amino phosphoramidate and aminoalkylphosphoramidates, phosphorodiamidates , thionophosphor amidates , thionoalkylphosphonates , thionoalkylphosphotriesters, selenophosphates and boranophosphates having normal 3'-5' linkages, 2'-5' linked analogs of these, and those having inverted polarity wherein one or more internucleotide linkages is a 3' to 3', 5' to 5' or 2' to 2' linkage. Suitable oligonucleotides having inverted polarity comprise a single 3' to 3' linkage at the 3'-most intemucleotide linkage i.e. a single inverted nucleoside residue which may be a basic (the nucleobase is missing or has a hydroxyl group in place thereof). Various salts (such as, for example, potassium or sodium), mixed salts and free acid forms are also included. Also suitable are nucleic acids having morpholino backbone structures. Suitable modified polynucleotide backbones that do not include a phosphorus atom therein have backbones that are formed by short chain alkyl or cycloalkyl internucleoside linkages, mixed heteroatom and alkyl or cycloalkyl internucleoside linkages, or one or more short chain heteroatomic or heterocyclic internucleoside linkages. These include those having morpholino linkages (formed in part from the sugar portion of a nucleoside); siloxane backbones; sulfide, sulfoxide and sulfone backbones; formacetyl and thioformacetyl backbones; methylene formacetyl and thioformacetyl backbones; riboacetyl backbones; alkene containing backbones; sulfamate backbones; methyleneimino and methylenehydrazino backbones; sulfonate and sulfonamide backbones; amide backbones; and others having mixed N, O, S and CH2 component parts.

[0179] Other suitable modifications include nucleic acid mimetics. The term "mimetic" as it is applied to polynucleotides is intended to include polynucleotides wherein only the furanose ring or both the furanose ring and the intemucleotide linkage are replaced with nonfuranose groups, replacement of only the furanose ring is also referred to in the art as being a sugar surrogate. The heterocyclic base moiety or a modified heterocyclic base moiety is maintained for hybridization with an appropriate target nucleic acid. One such nucleic acid, a polynucleotide mimetic that has been shown to have excellent hybridization properties, is referred to as a peptide nucleic acid (PNA). In PNA, the sugar-backbone of a polynucleotide is replaced with an amide containing backbone, in particular an aminoethylglycine backbone. The nucleotides are retained and are bound directly or indirectly to aza nitrogen atoms of the amide portion of the backbone. Another such mimetic is a morpholino-based polynucleotide based on linked morpholino units (morpholino nucleic acid) having heterocyclic bases attached to the morpholino ring. A further class of nucleic acid mimetic is referred to as a cyclohexenyl nucleic acid (CeNA). The furanose ring normally present in a DNA/RNA molecule is replaced with a cyclohexenyl ring. Another modification includes Locked Nucleic Acids (LNAs) in which the 2'-hydroxyl group is linked to the 4' carbon atom of the sugar ring thereby forming a 2'-C,4'-C-oxymethylene linkage thereby forming a bicyclic sugar moiety.

[0180] The nucleic acids described herein can include one or more substituted sugar moieties. Suitable polynucleotides comprise a sugar substituent group selected from: OH; F; O-, S-, or N-alkyl; O-, S-, or N-alkenyl; O-, S- or N-alkynyl; or O-alkyl-O-alkyl, wherein the alkyl, alkenyl and alkynyl may be substituted or unsubstituted C.sub.l to CIO alkyl or C2 to CIO alkenyl and alkynyl. Particularly suitable are O((CH2)_nO)_mCH3, O(CH2)_nOCH3, O(CH₂)nNH₂, O(CH₂)nCH₃, O(CH₂)nONH₂, and O(CH₂)nON((CH₂)nCH3)₂, where n and m are from 1 to about 10. Other suitable polynucleotides comprise a sugar substituent group selected from: Ci to CIO lower alkyl, substituted lower alkyl, alkenyl, alkynyl, alkaryl, aralkyl, O-alkaryl or O-aralkyl, SH, SCH₃, OCN, Cl, Br, CN, CF₃, OCF₃, SOCH3, SO2CH3, ONO2, NO2, N3, NH2, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalkylamino, substituted silyl, an RNA cleaving group, a reporter group, an intercalator, a group for improving the pharmacokinetic properties of an oligonucleotide, or a group for improving the pharmacodynamic properties of an oligonucleotide, and other substituents having similar properties.

[0181] Other suitable sugar substituent groups include methoxy (-O-CH3), aminopropoxy (— OCH₂ CH₂ CH2NH2), allyl (-CH₂-CH=CH₂), -O-allyl (-O-CH₂— CH=CH₂) and fluoro (F). 2'-sugar substituent groups may be in the arabino (up) position or ribo (down) position. A suitable 2'-arabino modification is 2'-F. Similar modifications may also be made at other positions on the oligomeric compound, particularly the 3' position of the sugar on the 3' terminal nucleoside or in 2'-5' linked oligonucleotides and the 5' position of 5' terminal nucleotide. Oligomeric compounds may also have sugar mimetics such as cyclobutyl moieties in place of the pentofuranosyl sugar.

[0182] The nucleic acids described herein may include nucleobase modifications or substitutions. A labeled detector ssDNA (and/or a guide RNA) may also include nucleobase (often referred to in the art simply as "base") modifications or substitutions. As used herein, "unmodified" or "natural" nucleobases include the purine bases adenine (A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C) and uracil (U). Modified nucleobases include other synthetic and natural nucleobases such as 5-methylcytosine (5-me-C), 5- hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl and other alkyl derivatives of adenine and guanine, 2-propyl and other alkyl derivatives of adenine and guanine, 2-thiouracil, 2-thiothymine and 2-thiocytosine, 5-halouracil and cytosine, 5- propynyl (-C=C-CH3) uracil and cytosine and other alkynyl derivatives of pyrimidine bases, 6-azo uracil, cytosine and thymine, 5-uracil (pseudouracil), 4-thiouracil, 8-halo, 8-amino, 8- thiol, 8-thioalkyl, 8-hydroxyl and other 8-substituted adenines and guanines, 5-halo particularly 5-bromo, 5 -trifluoromethyl and other 5- substituted uracils and cytosines, 7- methylguanine and 7-methyladenine, 2-F-adenine, 2-aminoadenine, 8-azaguanine and 8- azaadenine, 7-deazaguanine and 7-deazaadenine and 3 -deazaguanine and 3 -deazaadenine. Further modified nucleobases include tricyclic pyrimidines such as phenoxazine cytidineQH- pyrimido(5,4-b)(l,4)benzoxazin-2(3H)-one), phenothiazine cytidine (lH-pyrimido(5,4- b)(l,4)benzothiazin-2(3H)-one), G-clamps such as a substituted phenoxazine cytidine (e.g. 9- (2-aminoethoxy)-H-pyrimido(5,4-(b) (l,4)benzoxazin-2(3H)-one), carbazole cytidine (2H- pyrimido(4,5-b)indol-2-one), pyridoindole cytidine (Hpyrido(3',2':4,5)pyrrolo(2,3- d)pyrimidin-2-one). Heterocyclic base moieties may also include those in which the purine or pyrimidine base is replaced with other heterocycles, for example 7-deaza-adenine, 7- deazaguanosine, 2-aminopyridine, and 2-pyridone.

[0183] The nucleic acids described and referred to herein can comprise a plurality of base pairs. A base pair can be a biological unit comprising two nucleobases bound to each other by hydrogen bonds. Nucleobases can comprise adenine, guanine, cytosine, thymine, and/or uracil. In some cases, the nucleic acids described and referred to herein can comprise different base pairs. In some cases, the nucleic acids described and referred to herein can comprise one or more modified base pairs. The one or more modified base pairs can be produced when one or more base pairs undergo a chemical modification leading to new bases. The one or more modified base pairs can be, for example, Hypoxanthine, Inosine, Xanthine, Xanthosine, 7-Methylguanine, 7-Methylguanosine, 5,6-Dihydrouracil, Dihydrouridine, 5-Methylcytosine, 5-Methylcytidine, 5-hydroxymethylcytosine (5hmC), 5- formylcytosine (5fC), or 5-carboxylcytosine (5caC).

Target Nucleic Acids

[0184] Disclosed herein are compositions, systems and methods for detecting a target nucleic acid. In some instances, the target nucleic acid is a single stranded nucleic acid. Alternatively, or in combination, the target nucleic acid is a double stranded nucleic acid and is prepared into single stranded nucleic acids before or upon contacting the programmable nuclease-based detection reagents (e.g., programmable nuclease, guide nucleic acid, and/or reporter). In some embodiments, the target nucleic acid is a double stranded nucleic acid. In some embodiments, the double stranded nucleic acid is DNA. The target nucleic acid may be an RNA. The target nucleic acids include but are not limited to mRNA, rRNA, tRNA, noncoding RNA, long non-coding RNA, and microRNA (miRNA). In some instances, the target nucleic acid is complementary DNA (cDNA) synthesized from a single-stranded RNA template in a reaction catalyzed by a reverse transcriptase. In some cases, the target nucleic acid is single-stranded RNA (ssRNA) or mRNA. In some cases, the target nucleic acid is from a virus, a parasite, or a bacterium described herein.

[0185] In some cases, the target nucleic acid comprises 5 to 100, 5 to 90, 5 to 80, 5 to 70, 5 to 60, 5 to 50, 5 to 40, 5 to 30, 5 to 25, 5 to 20, 5 to 15, or 5 to 10 nucleotides in length. In some cases, the target nucleic acid comprises 10 to 90, 20 to 80, 30 to 70, or 40 to 60 nucleotides in length. In some instances, the target nucleic acid sequence can be from 10 to 95, from 20 to 95, from 30 to 95, from 40 to 95, from 50 to 95, from 60 to 95, from 10 to 75, from 20 to 75, from 30 to 75, from 40 to 75, from 50 to 75, from 5 to 50, from 15 to 50, from 25 to 50, from 35 to 50, or from 45 to 50 nucleotides in length. In some cases, the target nucleic acid comprises 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 50, 60, 70, 80, 90, or 100 nucleotides in length. In some instances, the target nucleic acid comprises at least 10, at least 20, at least 30, at least 40, at least 50, at least 60, at least 70, at least 80, at least 90, or at least 100 nucleotides in length. The target nucleic acid can be reverse complementary to a guide nucleic acid. In some cases, at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 50, 60, 70, 80, 90, or 100 nucleotides of a guide nucleic acid can be reverse complementary to a target nucleic acid.

[0186] A programmable nuclease-guide nucleic acid complex may comprise high selectivity for a target sequence. In some cases, a ribonucleoprotein may comprise a selectivity of at least 200: 1, 100: 1, 50: 1, 20: 1, 10:1, or 5: 1 for a target nucleic acid over a single nucleotide variant of the target nucleic acid. In some cases, a ribonucleoprotein may comprise a selectivity of at least 5: 1 for a target nucleic acid over a single nucleotide variant of the target nucleic acid. Leveraging programmable nuclease selectivity, some methods described herein may detect a target nucleic acid present in the sample in various concentrations or amounts as a target nucleic acid population. In some cases, the sample has at least 2 target nucleic acids. In some cases, the sample has at least 3, 5, 10, 20, 30, 40, 50, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000, or 10000 target nucleic acids. In some cases, the sample comprises 1 to 10,000, 100 to 8000, 400 to 6000, 500 to 5000, 1000 to 4000, or 2000 to 3000 target nucleic acids. In some cases, the method detects target nucleic acid present at least at one copy per 10 nontarget nucleic acids, 10² non-target nucleic acids, 10³ non-target nucleic acids, 10⁴ non-target nucleic acids, 10⁵ non-target nucleic acids, 10⁶ non-target nucleic acids, 10⁷ non-target nucleic acids, 10⁸ non-target nucleic acids, 10⁹ non-target nucleic acids, or 10¹⁰ non-target nucleic acids.

[0187] Often, the target nucleic acid may be from 0.05% to 20% of total nucleic acids in the sample. Sometimes, the target nucleic acid is 0.1% to 10% of the total nucleic acids in the sample. The target nucleic acid, in some cases, is 0.1% to 5% of the total nucleic acids in the sample. The target nucleic acid may also be 0.1% to 1% of the total nucleic acids in the sample. The target nucleic acid may be DNA or RNA. The target nucleic acid may be any amount less than 100% of the total nucleic acids in the sample. The target nucleic acid may be 100% of the total nucleic acids in the sample.

[0188] The target nucleic acid may be 0.05% to 20% of total nucleic acids in the sample. Sometimes, the target nucleic acid is 0.1% to 10% of the total nucleic acids in the sample. The target nucleic acid, in some cases, is 0.1% to 5% of the total nucleic acids in the sample. Often, a sample comprises the segment of the target nucleic acid and at least one nucleic acid comprising less than 100% sequence identity to the segment of the target nucleic acid but no less than 50% sequence identity to the segment of the target nucleic acid. For example, the segment of the target nucleic acid comprises a mutation as compared to at least one nucleic acid comprising less than 100% sequence identity to the segment of the target nucleic acid but no less than 50% sequence identity to the segment of the target nucleic acid. Often, the segment of the target nucleic acid comprises a single nucleotide mutation as compared to at least one nucleic acid comprising less than 100% sequence identity to the segment of the target nucleic acid but no less than 50% sequence identity to the segment of the target nucleic acid.

[0189] A target nucleic acid may be an amplified nucleic acid of interest. The nucleic acid of interest may be any nucleic acid disclosed herein or from any sample as disclosed herein. The nucleic acid of interest may be an RNA that is reverse transcribed before amplification. The nucleic acid of interest may be amplified then the amplicons may be transcribed into RNA.

[0190] In some instances, compositions described herein exhibit indiscriminate transcleavage of ssRNA, enabling their use for detection of RNA in samples. In some cases, target ssRNA are generated from many nucleic acid templates (RNA) in order to achieve cleavage of the FQ reporter in the DETECTR platform. Certain programmable nucleases may be activated by ssRNA, upon which they may exhibit trans-cleavage of ssRNA and may, thereby, be used to cleave ssRNA FQ reporter molecules in the DETECTR system. These programmable nucleases may target ssRNA present in the sample, or generated and/or amplified from any number of nucleic acid templates (RNA). Described herein are reagents comprising a single stranded reporter nucleic acid comprising a detection moiety, wherein the reporter nucleic acid (e.g., the ssDNA-FQ reporter described above) is capable of being cleaved by the programmable nuclease, upon generation and amplification of ssRNA from a nucleic acid template using the methods disclosed herein, thereby generating a first detectable signal.

[0191] In some instances, target nucleic acids comprise at least one nucleic acid comprising at least 50% sequence identity to the target nucleic acid or a portion thereof. Sometimes, the at least one nucleic acid comprises an amino acid sequence that is at least 60%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to an equal length portion of the target nucleic acid. Sometimes, the at least one nucleic acid comprises an amino acid sequence that is 100% identical to an equal length portion of the target nucleic acid. Sometimes, the amino acid sequence of the at least one nucleic acid is at least 60%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to the target nucleic acid. Sometimes, the target nucleic acid comprises an amino acid sequence that is less than 60%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to an equal length portion of the at least one nucleic acid.

[0192] In some embodiments, samples comprise a target nucleic acid at a concentration of less than 1 nM, less than 2 nM, less than 3 nM, less than 4 nM, less than 5 nM, less than 6 nM, less than 7 nM, less than 8 nM, less than 9 nM, less than 10 nM, less than 20 nM, less than 30 nM, less than 40 nM, less than 50 nM, less than 60 nM, less than 70 nM, less than 80 nM, less than 90 nM, less than 100 nM, less than 200 nM, less than 300 nM, less than 400 nM, less than 500 nM, less than 600 nM, less than 700 nM, less than 800 nM, less than 900 nM, less than 1 pM, less than 2 pM, less than 3 pM, less than 4 pM, less than 5 pM, less than 6 pM, less than 7 pM, less than 8 pM, less than 9 pM, less than 10 pM, less than 100 pM, or less than 1 mM. In some embodiments, the sample comprises a target nucleic acid sequence at a concentration of 1 nM to 2 nM, 2 nM to 3 nM, 3 nM to 4 nM, 4 nM to 5 nM, 5 nM to 6 nM, 6 nM to 7 nM, 7 nM to 8 nM, 8 nM to 9 nM, 9 nM to 10 nM, 10 nM to 20 nM, 20 nM to 30 nM, 30 nM to 40 nM, 40 nM to 50 nM, 50 nM to 60 nM, 60 nM to 70 nM, 70 nM to 80 nM, 80 nM to 90 nM, 90 nM to 100 nM, 100 nM to 200 nM, 200 nM to 300 nM, 300 nM to 400 nM, 400 nM to 500 nM, 500 nM to 600 nM, 600 nM to 700 nM, 700 nM to 800 nM, 800 nM to 900 nM, 900 nM to 1 pM, 1 pM to 2 pM, 2 pM to 3 pM, 3 pM to 4 pM, 4 pM to 5 pM, 5 pM to 6 pM, 6 pM to 7 pM, 7 pM to 8 pM, 8 pM to 9 pM, 9 pM to 10 pM, 10 pM to 100 pM, 100 pM to 1 mM, 1 nM to 10 nM, 1 nM to 100 nM, 1 nM to 1 pM, 1 nM to 10 pM, 1 nM to 100 pM, 1 nM to 1 mM, 10 nM to 100 nM, 10 nM to 1 pM, 10 nM to 10 pM, 10 nM to 100 pM, 10 nM to 1 mM, 100 nM to 1 pM, 100 nM to 10 pM, 100 nM to 100 pM, 100 nM to 1 mM, 1 pM to 10 pM, 1 pM to 100 pM, 1 pM to 1 mM, 10 pM to 100 pM, 10 pM to 1 mM, or 100 pM to 1 mM. In some embodiments, the sample comprises a target nucleic acid at a concentration of 20 nM to 200 pM, 50 nM to 100 pM, 200 nM to 50 pM, 500 nM to 20 pM, or 2 pM to 10 pM. In some embodiments, the target nucleic acid is not present in the sample.

[0193] In some embodiments, samples comprise fewer than 10 copies, fewer than 100 copies, fewer than 1000 copies, fewer than 10,000 copies, fewer than 100,000 copies, or fewer than 1,000,000 copies of a target nucleic acid sequence. In some embodiments, the sample comprises 10 copies to 100 copies, 100 copies to 1000 copies, 1000 copies to 10,000 copies, 10,000 copies to 100,000 copies, 100,000 copies to 1,000,000 copies, 10 copies to 1000 copies, 10 copies to 10,000 copies, 10 copies to 100,000 copies, 10 copies to 1,000,000 copies, 100 copies to 10,000 copies, 100 copies to 100,000 copies, 100 copies to 1,000,000 copies, 1,000 copies to 100,000 copies, or 1,000 copies to 1,000,000 copies of a target nucleic acid sequence. In some embodiments, the sample comprises 10 copies to 500,000 copies, 200 copies to 200,000 copies, 500 copies to 100,000 copies, 1000 copies to 50,000 copies, 2000 copies to 20,000 copies, 3000 copies to 10,000 copies, or 4000 copies to 8000 copies. In some embodiments, the target nucleic acid is not present in the sample. [0194] A number of target nucleic acid populations are consistent with the methods and compositions disclosed herein. Some methods described herein may detect two or more target nucleic acid populations present in the sample in various concentrations or amounts. In some cases, the sample has at least 2 target nucleic acid populations. In some cases, the sample has at least 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, or 50 target nucleic acid populations. In some cases, the sample has 3 to 50, 5 to 40, or 10 to 25 target nucleic acid populations. In some cases, the method detects target nucleic acid populations that are present at least at one copy per 10¹ non-target nucleic acids, 10² non-target nucleic acids, 10³ non-target nucleic acids, 10⁴ nontarget nucleic acids, 10⁵ non-target nucleic acids, 10⁶ non-target nucleic acids, 10⁷ non-target nucleic acids, 10⁸ non-target nucleic acids, 10⁹ non-target nucleic acids, or 10¹⁰ non-target nucleic acids. The target nucleic acid populations may be present at different concentrations or amounts in the sample.

[0195] In some embodiments, target nucleic acids may activate a programmable nuclease to initiate sequence-independent cleavage of a nucleic acid-based reporter (e.g., a reporter comprising an RNA sequence, or a reporter comprising DNA and RNA). For example, a programmable nuclease of the present disclosure is activated by a target nucleic acid to cleave reporters having an RNA (also referred to herein as an "RNA reporter"). Alternatively, a programmable nuclease of the present disclosure is activated by a target RNA to cleave reporters having an RNA (also referred to herein as a "RNA reporter"). The RNA reporter may comprise a single-stranded RNA labeled with a detection moiety or may be any RNA reporter as disclosed herein.

[0196] In some embodiments, the target nucleic acid as described in the methods herein does not initially comprise a PAM sequence. However, any target nucleic acid of interest may be generated using the methods described herein to comprise a PAM sequence, and thus be a PAM target nucleic acid. A PAM target nucleic acid, as used herein, refers to a target nucleic acid that has been amplified to insert a PAM sequence that is recognized by a CRISPR/Cas system.

[0197] In some embodiments, the target nucleic acid is in a cell. In some embodiments, the cell is a single-cell eukaryotic organism; a plant cell an algal cell; a fungal cell; an animal cell; a cell an invertebrate animal; a cell a vertebrate animal such as fish, amphibian, reptile, bird, and mammal; or a cell a mammal such as a human, a non-human primate, an ungulate, a feline, a bovine, an ovine, and a caprine. In preferred embodiments, the cell is a eukaryotic cell. In preferred embodiments, the cell is a mammalian cell, a human cell, or a plant cell. [0198] In some embodiments, the target nucleic acid sequence comprises a nucleic acid sequence of a virus, a bacterium, or other pathogen responsible for a disease in a plant (e.g., a crop). Methods and compositions of the disclosure may be used to treat or detect a disease in a plant. For example, the methods of the disclosure may be used to target a viral nucleic acid sequence in a plant. A programmable nuclease of the disclosure (e.g., Casl4) may cleave the viral nucleic acid. In some embodiments, the target nucleic acid sequence comprises a nucleic acid sequence of a virus or a bacterium or other agents (e.g., any pathogen) responsible for a disease in the plant (e.g., a crop). In some embodiments, the target nucleic acid comprises RNA. The target nucleic acid, in some cases, is a portion of a nucleic acid from a virus or a bacterium or other agents responsible for a disease in the plant (e.g., a crop). In some cases, the target nucleic acid is a portion of a nucleic acid from a genomic locus, or any NA amplicon, such as a reverse transcribed mRNA or a cDNA from a gene locus, a transcribed mRNA, or a reverse transcribed cDNA from a gene locus in at a virus or a bacterium or other agents (e.g., any pathogen) responsible for a disease in the plant (e.g., a crop). A virus infecting the plant may be an RNA virus. A virus infecting the plant may be a DNA virus. Non-limiting examples of viruses that may be targeted with the disclosure include Tobacco mosaic virus (TMV), Tomato spotted wilt virus (TSWV), Cucumber mosaic virus (CMV), Potato virus Y (PVY), Cauliflower mosaic virus (CaMV) (RT virus), Plum pox virus (PPV), Brome mosaic virus (BMV) and Potato virus X (PVX).

[0199] In some cases, the target sequence is a portion of a nucleic acid from a virus or a bacterium or other agents responsible for a disease in the sample. The target sequence, in some cases, is a portion of a nucleic acid from a sexually transmitted infection or a contagious disease, in the sample. The target sequence, in some cases, is a portion of a nucleic acid from an upper respiratory tract infection, a lower respiratory tract infection, or a contagious disease, in the sample. The target sequence, in some cases, is a portion of a nucleic acid from a hospital acquired infection or a contagious disease, in the sample. The target sequence, in some cases, is a portion of a nucleic acid from sepsis, in the sample. These diseases can include but are not limited to respiratory viruses (e.g., SARS-CoV-2 (i.e., a virus that causes COVID-19), SARS-CoV-1, MERS-CoV, influenza, Adenovirus, Coronavirus HKU1, Coronavirus NL63, Coronavirus 229E, Coronavirus OC43, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), Human Metapneumovirus (hMPV), Human Rhinovirus (HRVs A, B, C), Human Enterovirus, Influenza A, Influenza A/Hl, Influenza A/H2, Influenza A/H3, Influenza A/H4, Influenza A/H5, Influenza A/H6, Influenza A/H7, Influenza A/H8, Influenza A/H9, Influenza A/H10, Influenza A/Hl 1, Influenza A/H12, Influenza A/H13, Influenza A/H14, Influenza A/H15, Influenza A/H16, Influenza A/Hl- 2009, Influenza A/Nl, Influenza A/N2, Influenza A/N3, Influenza A/N4, Influenza A/N5, Influenza A/N6, Influenza A/N7, Influenza A/N8, Influenza A/N9, Influenza A/N10, Influenza A/Nl 1, oseltamivir-resistant Influenza A, Influenza B, Influenza B - Victoria VI, Influenza B - Yamagata Yl, Influenza C, Parainfluenza Virus 1, Parainfluenza Virus 2, Parainfluenza Virus 3, Parainfluenza Virus 4, Respiratory Syncytial Virus A, Respiratory Syncytial Virus B) and respiratory bacteria (e.g., Bordetella parapertussis, Bordetella pertussis, Bordetella bronchiseptica, Bordetella holmesii, Chlamydia pneumoniae, Mycoplasma pneumoniae). Other viruses include human immunodeficiency virus (HIV), human papillomavirus (HPV), chlamydia, gonorrhea, syphilis, trichomoniasis, sexually transmitted infection, malaria, Dengue fever, Ebola, chikungunya, and leishmaniasis. Pathogens include viruses, fungi, helminths, protozoa, malarial parasites, Plasmodium parasites, Toxoplasma parasites, and Schistosoma parasites. Helminths include roundworms, heartworms, and phytophagous nematodes, flukes, Acanthocephala, and tapeworms. Protozoan infections include infections from Giardia spp., Trichomonas spp., African trypanosomiasis, amoebic dysentery, babesiosis, balantidial dysentery, Chaga's disease, coccidiosis, malaria and toxoplasmosis. Examples of pathogens such as parasitic/protozoan pathogens include, but are not limited to: Plasmodium falciparum, P. vivax, Trypanosoma cruzi and Toxoplasma gondii. Fungal pathogens include, but are not limited to Cryptococcus neoformans, Histoplasma capsulatum, Coccidioides immitis, Blastomyces dermatitidis, Chlamydia trachomatis, Chlamydia pneumoniae, Chlamydia psittaci, and Candida albicans. Pathogenic viruses include but are not limited to: respiratory viruses (e.g., adenoviruses, parainfluenza viruses, severe acute respiratory syndrome (SARS), coronavirus, MERS), gastrointestinal viruses (e.g., noroviruses, rotaviruses, some adenoviruses, astroviruses), exanthematous viruses (e.g., the virus that causes measles, the virus that causes rubella, the virus that causes chickenpox/shingles, the virus that causes roseola, the virus that causes smallpox, the virus that causes fifth disease, chikungunya virus infection); hepatic viral diseases (e.g., hepatitis A, B, C, D, E); cutaneous viral diseases (e.g., warts (including genital, anal), herpes (including oral, genital, anal), molluscum contagiosum); hemmorhagic viral diseases (e.g. Ebola, Lassa fever, dengue fever, yellow fever, Marburg hemorrhagic fever, Crimean-Congo hemorrhagic fever); neurologic viruses (e.g., polio, viral meningitis, viral encephalitis, rabies), sexually transmitted viruses (e.g., HIV, HPV, and the like), immunodeficiency virus (e.g., HIV); influenza virus; dengue; West Nile virus; herpes virus; yellow fever virus; Hepatitis Virus C; Hepatitis Virus A; Hepatitis Virus B; papillomavirus; and the like. Pathogens include, e.g., HIV virus, Mycobacterium tuberculosis, Klebsiella pneumoniae, Acinetobacter baumannii, Bacillus anthracis, Bordetella pertussis, Burkholderia cepacia, Corynebacterium diphtheriae, Coxiella burnetii, Streptococcus agalactiae, methicillin-resistant Staphylococcus aureus, Legionella longbeachae, Legionella pneumophila, Leptospira interrogans, Moraxella catarrhalis, Streptococcus pyogenes, Escherichia coli, Neisseria gonorrhoeae, Neisseria meningitidis, Neisseria elongate, Neisseria gonorrhoeae, Parechovirus, Pneumococcus, Pneumocystis jirovecii, Cryptococcus neoformans, Histoplasma capsulatum, Haemophilus influenzae B, Treponema pallidum, Lyme disease spirochetes, Pseudomonas aeruginosa, Mycobacterium leprae, Brucella abortus, rabies virus, influenza virus, cytomegalovirus, herpes simplex virus I, herpes simplex virus II, human serum parvo-like virus, respiratory syncytial virus (RSV), M. genitalium, T. Vaginalis, varicella-zoster virus, hepatitis B virus, hepatitis C virus, measles virus, adenovirus, human T-cell leukemia viruses, Epstein-Barr virus, murine leukemia virus, mumps virus, vesicular stomatitis virus, Sindbis virus, lymphocytic choriomeningitis virus, wart virus, blue tongue virus, Sendai virus, feline leukemia virus, Reovirus, polio virus, simian virus 40, mouse mammary tumor virus, dengue virus, rubella virus, West Nile virus, Plasmodium falciparum, Plasmodium vivax, Toxoplasma gondii, Trypanosoma rangeli, Trypanosoma cruzi, Trypanosoma rhodesiense, Trypanosoma brucei, Schistosoma mansoni, Schistosoma japonicum, Babesia bovis, Eimeria tenella, Onchocerca volvulus, Leishmania tropica, Mycobacterium tuberculosis, Trichinella spiralis, Theileria parva, Taenia hydatigena, Taenia ovis, Taenia saginata, Echinococcus granulosus, Mesocestoides corti, Mycoplasma arthritidis, M. hyorhinis, M. orale, M. arginini, Acholeplasma laidlawii, M. salivarium, M. pneumoniae, Enterobacter cloacae, Kiebsiella aerogenes, Proteus vulgaris, Serratia macesens, Enterococcus faecalis, Enterococcus faecium, Streptococcus intermdius, Streptococcus pneumoniae, and Streptococcus pyogenes. Often the target nucleic acid may comprise a sequence from a virus or a bacterium or other agents responsible for a disease that can be found in the sample. In some cases, the target nucleic acid is a portion of a nucleic acid from a genomic locus, a transcribed mRNA, or a reverse transcribed cDNA from a gene locus in at least one of: human immunodeficiency virus (HIV), human papillomavirus (HPV), chlamydia, gonorrhea, syphilis, trichomoniasis, sexually transmitted infection, malaria, Dengue fever, Ebola, chikungunya, and leishmaniasis. Pathogens include viruses, fungi, helminths, protozoa, malarial parasites, Plasmodium parasites, Toxoplasma parasites, and Schistosoma parasites. Helminths include roundworms, heartworms, and phytophagous nematodes, flukes, Acanthocephala, and tapeworms. Protozoan infections include infections from Giardia spp., Trichomonas spp., African trypanosomiasis, amoebic dysentery, babesiosis, balantidial dysentery, Chaga's disease, coccidiosis, malaria and toxoplasmosis. Examples of pathogens such as parasitic/protozoan pathogens include, but are not limited to: Plasmodium falciparum, P. vivax, Trypanosoma cruzi and Toxoplasma gondii. Fungal pathogens include, but are not limited to Cryptococcus neoformans, Histoplasma capsulatum, Coccidioides immitis, Blastomyces dermatitidis, Chlamydia trachomatis, and Candida albicans. Pathogenic viruses include but are not limited to immunodeficiency virus (e.g., HIV); influenza virus; dengue; West Nile virus; herpes virus; yellow fever virus; Hepatitis Virus C; Hepatitis Virus A; Hepatitis Virus B; papillomavirus; and the like. Pathogens include, e.g., HIV virus, Mycobacterium tuberculosis, Streptococcus agalactiae, methicillin- resistant Staphylococcus aureus, Staphylococcus epidermidis, Legionella pneumophila, Streptococcus pyogenes, Streptococcus salivarius, Escherichia coli, Neisseria gonorrhoeae, Neisseria meningitidis, Pneumococcus, Cryptococcus neoformans, Histoplasma capsulatum, Hemophilus influenzae B, Treponema pallidum, Lyme disease spirochetes, Pseudomonas aeruginosa, Mycobacterium leprae, Brucella abortus, rabies virus, influenza virus, cytomegalovirus, herpes simplex virus I, herpes simplex virus II, human serum parvo-like virus, respiratory syncytial virus (RSV), Alphacoronavirus, Betacoronavirus, Sarbecovirus, SARS-related virus, Gammacoronavirus, Deltacoronavirus, M. genitalium, T. vaginalis, varicella-zoster virus, hepatitis B virus, hepatitis C virus, measles virus, human adenovirus (type A, B, C, D, E, F, G), human T-cell leukemia viruses, Epstein-Barr virus, murine leukemia virus, mumps virus, vesicular stomatitis virus, Sindbis virus, lymphocytic choriomeningitis virus, wart virus, blue tongue virus, Sendai virus, feline leukemia virus, Reovirus, polio virus, simian virus 40, mouse mammary tumor virus, dengue virus, rubella virus, West Nile virus, Human Bocavirus, Plasmodium falciparum, Plasmodium vivax, Toxoplasma gondii, Trypanosoma rangeli, Trypanosoma cruzi, Trypanosoma rhodesiense, Trypanosoma brucei, Schistosoma mansoni, Schistosoma japonicum, Babesia bovis, Eimeria tenella, Onchocerca volvulus, Leishmania tropica, Mycobacterium tuberculosis, Trichinella spiralis, Theileria parva, Taenia hydatigena, Taenia ovis, Taenia saginata, Echinococcus granulosus, Mesocestoides corti, Mycoplasma arthritidis, M. hyorhinis, M. orale, M. arginini, Acholeplasma laidlawii, M. salivarium and AL pneumoniae. SARS-CoV-2 Variants include Coronavirus HKU1, Coronavirus NL63, Coronavirus 229E, Coronavirus OC43, SARS-CoV-2 85A, SARS-CoV-2 T1001I, SARS-CoV-2 3675-3677A, SARS-CoV-2 P4715L, SARS-CoV-2 S5360L, SARS-CoV-2 69-70A, SARS-CoV-2 Tyrl44fs, SARS-CoV- 2 242-244A, SARS-CoV-2 Y453F, SARS-CoV-2 S477N, SARS-CoV-2 E848K, SARS-CoV- 2 N501Y, SARS-CoV-2 D614G, SARS-CoV-2 P681R, SARS-CoV-2 P681H, SARS-CoV-2 L21F, SARS-CoV-2 Q27Stop, SARS-CoV-2 Mlfs, and SARS-CoV-2 R203fs. In some cases, the target sequence is a portion of a nucleic acid from a genomic locus, a transcribed mRNA, or a reverse transcribed cDNA from a gene locus of bacterium or other agents responsible for a disease in the sample comprising a mutation that confers resistance to a treatment, such as a single nucleotide mutation that confers resistance to antibiotic treatment.

[0200] In some instances, the target sequence is a portion of a nucleic acid from a subject having cancer. The cancer may be a solid cancer (tumor). The cancer may be a blood cell cancer, including leukemias and lymphomas. Non-limiting types of cancer that could be treated with such methods and compositions include colon cancer, rectal cancer, renal-cell carcinoma, liver cancer, bladder cancer, cancer of the kidney or ureter, lung cancer, cancer of the small intestine, esophageal cancer, melanoma, bone cancer, pancreatic cancer, skin cancer, brain cancer (e.g., glioblastoma), cancer of the head or neck, melanoma, uterine cancer, ovarian cancer, breast cancer, testicular cancer, cervical cancer, stomach cancer, Hodgkin's Disease, non-Hodgkin's lymphoma, thyroid cancer. The cancer may be a leukemia, such as, by way of non-limiting example, acute myeloid (or myelogenous) leukemia (AML), chronic myeloid (or myelogenous) leukemia (CML), acute lymphocytic (or lymphoblastic) leukemia (ALL), and chronic lymphocytic leukemia (CLL).

[0201] In some instances, the target sequence is a portion of a nucleic acid from a cancer cell. A cancer cell may be a cell harboring one or more mutations that results in unchecked proliferation of the cancer cell. Such mutations are known in the art. Non-limiting examples of antigens are ADRB3, AKAP-4,ALK, Androgen receptor, B7H3, BCMA, BORIS, BST2, CAIX, CD 179a, CD 123, CD171, CD 19, CD20, CD22, CD24, CD30, CD300LF, CD33, CD38, CD44v6, CD72, CD79a, CD79b, CD97, CEA, CLDN6, CLEC12A, CLL-1, CS-1, CXORF61, CYP1B1, Cyclin B 1, E7, EGFR, EGFRvIII, ELF2M, EMR2, EPCAM, ERBB2 (Her2/neu), ERG (TMPRSS2 ETS fusion gene), ETV6-AML, EphA2, Ephrin B2, FAP, FCAR, FCRL5, FLT3, Folate receptor alpha, Folate receptor beta, Fos-related antigen 1, Fucosyl GM1, GD2, GD3, GM3, GPC3, GPR20, GPRC5D, GloboH, HAVCR1, HMWMAA, HPV E6, IGF-I receptor, IL-13Ra2, IL-1 IRa, KIT, LAGE-la, LAIR1, LCK, LILRA2, LMP2, LY6K, LY75, LewisY, MAD-CT-1, MAD-CT-2, MAGE Al, MAGE-A1, ML-IAP, MUC1, MYCN, MelanA/MARTl, Mesothelin, NA17, NCAM, NY-BR-1, NY-ESO-1, OR51E2, OY- TES 1, PANX3, PAP, PAX3, PAX5, PCTA-l/Galectin 8, PDGFR-beta, PLAC1, PRSS21, PSCA, PSMA, Polysialic acid, Prostase, RAGE-1, ROR1, RU1, RU2, Ras mutant, RhoC, SART3, SSEA-4, SSX2, TAG72, TARP, TEM1/CD248, TEM7R, TGS5, TRP-2, TSHR, Tie 2, Tn Ag, UPK2, VEGFR2, WT1, XAGE1, and IGLL1.

[0202] In some cases, the target sequence is a portion of a nucleic acid from a control gene in a sample. In some embodiments, the control gene is an endogenous control. The endogenous control may include human 18S rRNA, human GAPDH, human HPRT1, human GUSB, human RNase P, MS2 bacteriophage, or any other control sequence of interest within the sample.

[0203] The systems and methods of the present disclosure can be used to detect one or more target sequences or nucleic acids in one or more samples. The one or more samples can comprise one or more target sequences or nucleic acids for detection of an ailment, such as a disease, cancer, or genetic disorder, or genetic information, such as for phenotyping, genotyping, or determining ancestry and are compatible with the reagents and support mediums as described herein. Generally, a sample can be taken from any place where a nucleic acid can be found. Samples can be taken from an individual/human, a non-human animal, or a crop, or an environmental sample can be obtained to test for presence of a disease, virus, pathogen, cancer, genetic disorder, or any mutation or pathogen of interest. A biological sample can be blood, serum, plasma, lung fluid, exhaled breath condensate, saliva, spit, urine, stool, feces, mucus, lymph fluid, peritoneal , cerebrospinal fluid, amniotic fluid, breast milk, gastric secretions, bodily discharges, secretions from ulcers, pus, nasal secretions, sputum, pharyngeal exudates, urethral secretions/mucus, vaginal secretions/mucus, anal secretion/mucus, semen, tears, an exudate, an effusion, tissue fluid, interstitial fluid (e.g., tumor interstitial fluid), cyst fluid, tissue, or, in some instances, any combination thereof. A sample can be an aspirate of a bodily fluid from an animal (e.g., human, animals, livestock, pet, etc.) or plant. A tissue sample can be from any tissue that can be infected or affected by a pathogen (e.g., a wart, lung tissue, skin tissue, and the like). A tissue sample (e.g., from animals, plants, or humans) can be dissociated or liquified prior to application to detection system of the present disclosure. A sample can be from a plant (e.g., a crop, a hydroponically grown crop or plant, and/or house plant). Plant samples can include extracellular fluid, from tissue (e.g., root, leaves, stem, trunk etc.). A sample can be taken from the environment immediately surrounding a plant, such as hydroponic fluid/ water, or soil. A sample from an environment can be from soil, air, or water. In some instances, the environmental sample is taken as a swab from a surface of interest or taken directly from the surface of interest. In some instances, the raw sample is applied to the detection system. In some instances, the sample is diluted with a buffer or a fluid or concentrated prior to application to the detection system. In some cases, the sample is contained in no more than about 200 nanoliters (nL). In some cases, the sample is contained in about 200 nL. In some cases, the sample is contained in a volume that is greater than about 200 nL and less than about 20 microliters (pL). In some cases, the sample is contained in no more than 20 pl. In some cases, the sample is contained in no more than 1, 5, 10, 15, 20, 25, 30, 35 40, 45, 50, 55, 60, 65, 70, 75, 80, 90, 100, 200, 300, 400, 500 pl, or any of value from 1 pl to 500 pl. In some cases, the sample is contained in from 1 pL to 500 pL, from 10 pL to 500 pL, from 50 pL to 500 pL, from 100 pL to 500 pL, from 200 pL to 500 pL, from 300 pL to 500 pL, from 400 pL to 500 pL, from 1 pL to 200 pL, from 10 pL to 200 pL, from 50 pL to 200 pL, from 100 pL to 200 pL, from 1 pL to 100 pL, from 10 pL to 100 pL, from 50 pL to 100 pL, from 1 pL to 50 pL, from 10 pL to 50 pL, from 1 pL to 20 pL, from 10 pL to 20 pL, or from 1 pL to 10 pL. Sometimes, the sample is contained in more than 500 pl.

[0204] In some instances, the sample is taken from a single-cell eukaryotic organism; a plant or a plant cell; an algal cell; a fungal cell; an animal or an animal cell, tissue, or organ; a cell, tissue, or organ from an invertebrate animal; a cell, tissue, fluid, or organ from a vertebrate animal such as fish, amphibian, reptile, bird, and mammal; a cell, tissue, fluid, or organ from a mammal such as a human, a non-human primate, an ungulate, a feline, a bovine, an ovine, and a caprine. In some instances, the sample is taken from nematodes, protozoans, helminths, or malarial parasites. In some cases, the sample may comprise nucleic acids from a cell lysate from a eukaryotic cell, a mammalian cell, a human cell, a prokaryotic cell, or a plant cell. In some cases, the sample may comprise nucleic acids expressed from a cell.

[0205] The sample used for disease testing can comprise at least one target sequence that can bind to a guide nucleic acid of the reagents described herein. In some cases, the target sequence is a portion of a nucleic acid. A nucleic acid can be from a genomic locus, a transcribed mRNA, or a reverse transcribed cDNA. A nucleic acid can be from 5 to 100, 5 to 90, 5 to 80, 5 to 70, 5 to 60, 5 to 50, 5 to 40, 5 to 30, 5 to 25, 5 to 20, 5 to 15, or 5 to 10 nucleotides in length. A nucleic acid can be from 10 to 90, from 20 to 80, from 30 to 70, or from 40 to 60 nucleotides in length. A nucleic acid sequence can be from 10 to 95, from 20 to 95, from 30 to 95, from 40 to 95, from 50 to 95, from 60 to 95, from 10 to 75, from 20 to 75, from 30 to 75, from 40 to 75, from 50 to 75, from 5 to 50, from 15 to 50, from 25 to 50, from 35 to 50, or from 45 to 50 nucleotides in length. A nucleic acid can be 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 50, 60, 70, 80, 90, or 100 nucleotides in length. The target nucleic acid can be reverse complementary to a guide nucleic acid. In some cases, at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 50, 60, 70, 80, 90, or 100 nucleotides of a guide nucleic acid can be reverse complementary to a target nucleic acid.

[0206] In some embodiments, the Coronavirus HKU1 sequence is a target of an assay. In some embodiments, the Coronavirus NL63 sequence is a target of an assay. In some embodiments, the Coronavirus 229E sequence is a target of an assay. In some embodiments, the Coronavirus OC43 sequence is a target of an assay. In some embodiments, the SARS- CoV-1 sequence is a target of an assay. In some embodiments, the MERS sequence is a target of an assay. In some embodiments, the SARS-CoV-2 sequence is a target of an assay. In some embodiments, the Respiratory Syncytial Virus A sequence is a target of an assay. In some embodiments, the Respiratory Syncytial Virus B sequence is a target of an assay. In some embodiments, the Influenza A sequence is a target of an assay. In some embodiments, the Influenza B sequence is a target of an assay. In some embodiments, the Human Metapneumovirus sequence is a target of an assay. In some embodiments, the Human Rhinovirus sequence is a target of an assay. In some embodiments, the Human Enterovirus sequence is a target of an assay. In some embodiments, the Parainfluenza Virus 1 sequence is a target of an assay. In some embodiments, the Parainfluenza Virus 2 sequence is a target of an assay. In some embodiments, the Parainfluenza Virus 3 sequence is a target of an assay. In some embodiments, the Parainfluenza Virus 4 sequence is a target of an assay. In some embodiments, the Alphacoronavirus genus sequence is a target of an assay. In some embodiments, the Betacoronavirus genus sequence is a target of an assay. In some embodiments, the Sarbecovirus subgenus sequence is a target of an assay. In some embodiments, the SARS-related virus species sequence is a target of an assay. In some embodiments, the Gammacoronavirus Genus sequence is a target of an assay. In some embodiments, the Deltacoronavirus Genus sequence is a target of an assay. In some embodiments, the Influenza B - Victoria VI sequence is a target of an assay. In some embodiments, the Influenza B - Yamagata Y1 sequence is a target of an assay. In some embodiments, the Influenza A Hl sequence is a target of an assay. In some embodiments, the Influenza A H2 sequence is a target of an assay. In some embodiments, the Influenza A H3 sequence is a target of an assay. In some embodiments, the Influenza A H4 sequence is a target of an assay. In some embodiments, the Influenza A H5 sequence is a target of an assay. In some embodiments, the Influenza A H6 sequence is a target of an assay. In some embodiments, the Influenza A H7 sequence is a target of an assay. In some embodiments, the Influenza A H8 sequence is a target of an assay. In some embodiments, the Influenza A H9 sequence is a target of an assay. In some embodiments, the Influenza A H10 sequence is a target of an assay. In some embodiments, the Influenza A Hl 1 sequence is a target of an assay. In some embodiments, the Influenza A H12 sequence is a target of an assay. In some embodiments, the Influenza A Hl 3 sequence is a target of an assay. In some embodiments, the Influenza A H14 sequence is a target of an assay. In some embodiments, the Influenza A Hl 5 sequence is a target of an assay. In some embodiments, the Influenza A Hl 6 sequence is a target of an assay. In some embodiments, the Influenza A N1 sequence is a target of an assay. In some embodiments, the Influenza A N2 sequence is a target of an assay. In some embodiments, the Influenza A N3 sequence is a target of an assay. In some embodiments, the Influenza A N4 sequence is a target of an assay. In some embodiments, the Influenza A N5 sequence is a target of an assay. In some embodiments, the Influenza A N6 sequence is a target of an assay. In some embodiments, the Influenza A N7 sequence is a target of an assay. In some embodiments, the Influenza A N8 sequence is a target of an assay. In some embodiments, the Influenza A N9 sequence is a target of an assay. In some embodiments, the Influenza A N10 sequence is a target of an assay. In some embodiments, the Influenza A Ni l sequence is a target of an assay. In some embodiments, the Influenza A/Hl-2009 sequence is a target of an assay. In some embodiments, the Human endogenous control 18S rRNA sequence is a target of an assay. In some embodiments, the Human endogenous control GAPDH sequence is a target of an assay. In some embodiments, the Human endogenous control HPRT1 sequence is a target of an assay. In some embodiments, the Human endogenous control GUSB sequence is a target of an assay. In some embodiments, the Human endogenous control RNASe P sequence is a target of an assay. In some embodiments, the Influenza A oseltamivir resistance sequence is a target of an assay. In some embodiments, the Human Bocavirus sequence is a target of an assay. In some embodiments, the SARS-CoV-2 85A sequence is a target of an assay. In some embodiments, the SARS- CoV-2 T1001I sequence is a target of an assay. In some embodiments, the SARS-CoV-2 3675-3677A sequence is a target of an assay. In some embodiments, the SARS-CoV-2 P4715L sequence is a target of an assay. In some embodiments, the SARS-CoV-2 S5360L sequence is a target of an assay. In some embodiments, the SARS-CoV-2 69-70A sequence is a target of an assay. In some embodiments, the SARS-CoV-2 Tyrl44fs sequence is a target of an assay. In some embodiments, the SARS-CoV-2 242-244A sequence is a target of an assay. In some embodiments, the SARS-CoV-2 Y453F sequence is a target of an assay. In some embodiments, the SARS-CoV-2 S477N sequence is a target of an assay. In some embodiments, the SARS-CoV-2 E848K sequence is a target of an assay. In some embodiments, the SARS-CoV-2 N501 Y sequence is a target of an assay. In some embodiments, the SARS-CoV-2 D614G sequence is a target of an assay. In some embodiments, the SARS-CoV-2 P681R sequence is a target of an assay. In some embodiments, the SARS-CoV-2 P681H sequence is a target of an assay. In some embodiments, the SARS-CoV-2 L21F sequence is a target of an assay. In some embodiments, the SARS-CoV-2 Q27Stop sequence is a target of an assay. In some embodiments, the SARS-CoV-2 Mlfs sequence is a target of an assay. In some embodiments, the SARS-CoV-2 R203fs sequence is a target of an assay. In some embodiments, the Human adenovirus - pan assay sequence is a target of an assay. In some embodiments, the Bordetella parapertussis sequence is a target of an assay. In some embodiments, the Bordetella pertussis sequence is a target of an assay. In some embodiments, the Chlamydophila pneumoniae sequence is a target of an assay. In some embodiments, the Mycoplasma pneumoniae sequence is a target of an assay. In some embodiments, the Legionella pneumophila sequence is a target of an assay. In some embodiments, the Bordetella bronchoseptica sequence is a target of an assay. In some embodiments, the Bordetella holmesii sequence is a target of an assay. In some embodiments, the Human adenovirus Type A sequence is a target of an assay. In some embodiments, the Human adenovirus Type B sequence is a target of an assay. In some embodiments, the Human adenovirus Type C sequence is a target of an assay. In some embodiments, the Human adenovirus Type D sequence is a target of an assay. In some embodiments, the Human adenovirus Type E sequence is a target of an assay. In some embodiments, the Human adenovirus Type F sequence is a target of an assay. In some embodiments, the Human adenovirus Type G sequence is a target of an assay. In some embodiments, the MERS-CoV sequence is a target of an assay. In some embodiments, the human metapneumovirus sequence is a target of an assay. In some embodiments, the human parainfluenza 1 sequence is a target of an assay. In some embodiments, the human parainfluenza 2 sequence is a target of an assay. In some embodiments, the human parainfluenza 4 sequence is a target of an assay. In some embodiments, the hCoV-OC43 sequence is a target of an assay. In some embodiments, the human parainfluenza 3 sequence is a target of an assay. In some embodiments, the RSV-A sequence is a target of an assay. In some embodiments, the RSV-B sequence is a target of an assay. In some embodiments, the hCoV-229E sequence is a target of an assay. In some embodiments, the hCoV-HKUl sequence is a target of an assay. In some embodiments, the hCoV-NL63 sequence is a target of an assay. In some embodiments, the Gammacoronavirus sequence is a target of an assay. In some embodiments, the Deltacoronavirus sequence is a target of an assay. In some embodiments, the Alphacoronavirus sequence is a target of an assay. In some embodiments, the Rhinovirus C sequence is a target of an assay. In some embodiments, the Betacoronavirus sequence is a target of an assay. In some embodiments, the Influenza A sequence is a target of an assay. In some embodiments, the Influenza B sequence is a target of an assay. In some embodiments, the SARS-CoV-2 sequence is a target of an assay. In some embodiments, the SARS-CoV-1 sequence is a target of an assay. In some embodiments, the Sarbecovirus subgenus sequence is a target of an assay. In some embodiments, the SARS-related viruses sequence is a target of an assay. In some embodiments, the MS2 sequence is a target of an assay.

[0207] In some embodiments, the assay is directed to one or more target sequences. In some embodiments, a target sequence is a portion of an antimicrobial resistance (AMR) gene, such as CTX-M-1, CTX-M-2, CTX-M-25, CTX-M-8, CTX-M-9, or IMP. In some embodiments, a target sequence is a Mycobacterium tuberculosis sequence, such as a portion of IS 1081 or IS6110. In some embodiments, a target sequence is an orthopox virus sequence. In some embodiments, a target sequence is a pseudorabies virus sequence. In some embodiments, a target sequence is a Staphylococcus aureus sequence, such as a portion of gyrA or gyrB, or a portion of a S. aureus thermonuclease. In some embodiments, a target sequence is a Stenotrophomonas maltophilia sequence, such as a sequence of S. maltophilia alpha, S. maltophilia beta, or S. maltophilia gamma. In some embodiments, a target sequence is a Bordetalla sp. sequence, such as a sequence of Bordetella bronchoseplica. Bordetella holmesii. Bordetella parapertussis, or Bordetella pertussis. In some embodiments, a target sequence is a Chlamydophila pneumoniae sequence. In some embodiments, a target sequence is a Human adenovirus sequence, such as a sequence of human adenovirus Type A, Type B, Type C, Type D, Type E, Type F, or Type G. In some embodiments, a target sequence is a human bocavirus sequence. In some embodiments, a target sequence is a Legionella pneumophila sequence. In some embodiments, a target sequence is a Mycoplasma pneumoniae sequence. In some embodiments, a target sequence is an Acinetobacter spp.

(e.g., A. pitii, A. baumannii, or A. nosocomialis) sequence, such as a portion of gyrB or a 16S- 23 S ribosomal RNA intergenic spacer sequence. In some embodiments, a target sequence is a Proteus spp. (e.g. P. mirabilis, P. vulgaris, P. penneri, or P. hauseri) sequence, such as a portion of rpoD or 16S. In some embodiments, a target sequence is an Enterobacter spp. (e.g. E. nimipressuralis, E. cloacae, E. asburiae, E. hormaechei, E. kobei, E. ludwigii, or E. mori) sequence, such as a portion of dnaJ, purG, or 16S. In some embodiments, a target sequence is a. Bacillus anthracis sequence, such as a portion of pagA or capB. In some embodiments, a target sequence is a Brucella spp. sequence, such as a portion of 23 S, bcsp31, or omp2a. In some embodiments, a target sequence is a Coxiella burnetiid sequence, such as a portion of coml or IS110. In some embodiments, a target sequence is a Francisella tularensis sequence, such as a portion of 16S. In some embodiments, a target sequence is a Rickettsia spp. sequence, such as a portion of 16S, 23 S, or 782- 17K genus common antigen. In some embodiments, a target sequence is a Yersinia pestis sequence, such as a portion of pMTl, pCDl, or pPCPl. In some embodiments, a target sequence is a A. calcoaceticus sequence, such as a portion of gyrB. In some embodiments, a target sequence is a Francisella tularensis sequence, such as a portion of tul4 or fopA. In some embodiments, a target sequence is an rRNA sequence, such as a portion of 28S rRNA or 18S rRNA. In some embodiments, a target sequence is a coronavirus sequence, such as a sequence of an alphacoronavirus, betacoronavirus, deltacoronavirus, or gammacoronavirus. In some embodiments, a target sequence is a human coronavirus (hCoV) sequence, such as a sequence of hCoV-229E, hCoV-HKUl, hCoV-NL63, hCoV-OC43. In some embodiments, a target sequence is a MERS-CoV sequence. In some embodiments, the sequence is a mammarenavirus sequence, such as a sequence of a Argentinian mammarenavirus (Junin arenavirus), Lassa mammarenavirus, Lujo mammarenavirus (e.g., an L segment or S segment thereof), or Machupo mammarenavirus. In some embodiments, a target sequence is a human metapneumovirus sequence. In some embodiments, a target sequence is a human parainfluenza sequence, such as a sequence of human parainfluenza 1, human parainfluenza 2, human parainfluenza 3, or human parainfluenza 4. In some embodiments, a target sequence is an influenza A virus sequence, such as a sequence of influenza A HI, H2, H3, H4, H5, H6, H7, H8, H9, H10, Hl 1, H12, H13, H14, H15, H16, Nl, N2, N3, N4, N5, N6, N7, N8, or N9. In some embodiments, a target sequence is an influenza B sequence, such as a sequence of influenza B-Victoria VI or influenza B-Yamagata Y1. In some embodiments, a target sequence is a bacteriophage MS2 sequence. In some embodiments, a target sequence is a rhinovirus C sequence. In some embodiments, a target sequence is a respiratory syncytial virus (RSV) sequence, such as a sequence of RSV-A or RSV-B. In some embodiments, a target sequence is a Sarbecovirus sequence. In some embodiments, a target sequence is a severe acute respiratory syndrome coronavirus (SARS-CoV) sequence, such as a sequence of SARS-CoV-1 or SARS-CoV-2. In some embodiments, a target sequence is a portion of a SARS-COV-2 S gene, such as a sequence comprising 144/145 wild-type (WT), deletion (del) 144/145 (alpha variant), 156/157 WT, dell56/157 (delta variant), 241/243 WT, del241/243 (beta variant), 69/70 WT, del69/70 (alpha variant), A570 WT, A570D (alpha variant), A701 WT, A701 V (beta variant), DI 118 WT, DI 118H (alpha variant), D215 WT, D215G (beta variant), D614 WT, D614G (beta variant), D80 WT, D80A (beta variant), E484 WT, E484K (gamma variant), P681 WT, P681H (alpha variant), P681R (delta variant), S982 WT, S982A (alpha variant), T19 WT, T19R (delta variant), T716 WT, T716F (gamma variant). In some embodiments, a target sequence is a SARS-related virus sequence. In some embodiments, a target sequence is a portion of a gene selected from 16S, 23 S, ACTB, ATP5ME, ATP5MF, ATP5MG, ATP5PB, BCSP31, CAPB, CHMP2A, Clorf43, COMI, DNAJ, EMC7, FOP A, GPI, GAPDH, GUSB, GYRB, HRPT1, NDUFB3, NDUFB4, NDUFB8, OMP2A, PAGA, PRDX1, PSMB2, PSMB4, PURG, RAB7A, REEP5, RNaseP, RPL13, RPL19, RPL27A, RPL30, RPL31, RPL32, RPL37A, RPOD, RPS10, RPS27, RPS29, RPS6, SNRPD3, TUL4, VCP, VPS29, and YWHAG.

[0208] The sample used for cancer testing or cancer risk testing can comprise at least one target sequence or target nucleic acid segment that can bind to a guide nucleic acid of the reagents described herein. The target nucleic acid segment, in some cases, is a portion of a nucleic acid from a gene with a mutation associated with cancer, from a gene whose overexpression is associated with cancer, a tumor suppressor gene, an oncogene, a checkpoint inhibitor gene, a gene associated with cellular growth, a gene associated with cellular metabolism, or a gene associated with cell cycle. Sometimes, the target nucleic acid encodes for a cancer biomarker, such as a prostate cancer biomarker or non-small cell lung cancer. In some cases, the assay can be used to detect “hotspots” in target nucleic acids that can be predictive of cancer, such as lung cancer, cervical cancer, in some cases, the cancer can be a cancer that is caused by a virus. Some non-limiting examples of viruses that cause cancers in humans include Epstein-Barr virus (e.g., Burkitt’s lymphoma, Hodgkin’s Disease, and nasopharyngeal carcinoma); papillomavirus (e.g., cervical carcinoma, anal carcinoma, oropharyngeal carcinoma, penile carcinoma); hepatitis B and C viruses (e.g., hepatocellular carcinoma); human adult T-cell leukemia virus type 1 (HTLV-1) (e.g., T-cell leukemia); and Merkel cell polyomavirus (e.g., Merkel cell carcinoma). One skilled in the art will recognize that viruses can cause or contribute to other types of cancers. In some cases, the target nucleic acid is a portion of a nucleic acid that is associated with a blood fever. In some cases, the target nucleic acid segment is a portion of a nucleic acid from a genomic locus, a transcribed mRNA, or a reverse transcribed cDNA from a locus of at least one of: ALK, APC, ATM, AXIN2, BAP1, BARD1, BLM, BMPR1A, BRCA1, BRCA2, BRIP1, CASR, CDC73, CDH1, CDK4, CDKN1B, CDKN1C, CDKN2A, CEBPA, CHEK2, CTNNA1, DICER1, DIS3L2, EGFR, EPC AM, FH, FLCN, GATA2, GPC3, GREM1, HOXB13, HRAS, KIT, MAX, MEN1, MET, MITF, MLH1, MSH2, MSH3, MSH6, MUTYH, NBN, NF1, NF2, NTHL1, PALB2, PDGFRA, PHOX2B, PMS2, POLDI, POLE, POTI, PRKAR1A, PTCHI, PTEN, RAD50, RAD51C, RAD51D, RBI, RECQL4, RET, RUNX1, SDHA, SDHAF2, SDHB, SDHC, SDHD, SMAD4, SMARCA4, SMARCB1, SMARCE1, STK11, SUFU, TERC, TERT, TMEM127, TP53, TSC1, TSC2, VHL, WRN, and WTl.The sample used for genetic disorder testing can comprise at least one target sequence or target nucleic acid segment that can bind to a guide nucleic acid of the reagents described herein. In some embodiments, the genetic disorder is hemophilia, sickle cell anemia, P -thalassemia, Duchene muscular dystrophy, severe combined immunodeficiency, or cystic fibrosis. The target nucleic acid segment, in some cases, is a portion of a nucleic acid from a gene with a mutation associated with a genetic disorder, from a gene whose overexpression is associated with a genetic disorder, from a gene associated with abnormal cellular growth resulting in a genetic disorder, or from a gene associated with abnormal cellular metabolism resulting in a genetic disorder. In some cases, the target nucleic acid segment is a portion of a nucleic acid from a genomic locus, a transcribed mRNA, or a reverse transcribed cDNA from a locus of at least one of: AAVS1, ABCA4, ABCB11, ABCC8, ABCD1, ACAD9, AC ADM, ACADVL, ACAT1, ACOX1, ACSF3, ADA, ADAMTS2, ADGRG1, AGA, AGL, AGPS, AGXT, AHI1, AIRE, ALDH3A2, ALDOB, ALG6, ALK, ALKBH5, ALMS1, ALPL, AMRC9, AMT, ANGPTL3, APC, Apo(a), APOCIII, APOEs4, APOL1, APP, AQP2, AR, ARFRP1, ARG1, ARL13B, ARL6, ARSA, ARSB, ASL, ASNS, ASP A, ASS1, ATM, ATP6V1B1, ATP7A, ATP7B, ATRX, ATXN1, ATXN10, ATXN2, ATXN3, ATXN7, ATXN8OS, AXIN1, AXIN2, B2M, BACE-1, BAK1, BAP1, BARD1, BAX2, BBS1, BBS10, BBS12, BBS2, BCKDHA, BCKDHB, BCL2L2, BCS1L, BEST1, Betaglobin gene, BLM, BMPR1A, BRAFV600E, BRCA1, BRCA2, BRIP1, BSND, C282Y, C9orf72, CA4, CACNA1A, CAPN3, CASR, CBS, CC2D2A, CCR5, CDC73, CDH1, CDH23, CDK11, CDK4, CDKN1B, CDKN1C, CDKN2A, CEBPA, CEP290, CERKL, CFTR, CHCHD10, CHEK2, CHM, CHRNE, CIITA, CLN3, CLN5, CLN6, CLN8, CLRN1, CLTA, CNBP, CNGB1, CNGB3, COL1A1, COL1A2, COL27A1, COL4A3, COL4A4, COL4A5, COL7A1, CPS1, CPT1A, CPT2, CRB1, CRX, CTNNA1, CTNNB1, CTNND2, CTNS, CTSK, CYBA, CYBB, CYP11B1, CYP11B2, CYP17A1, CYP19A1, CYP27A1, DBT, DCLRE1C, DERL2, DFNA36, DFNB31, DGAT2, DHCR7, DHDDS, DICER1, DIS3L2, DLD, DMD, DMPK, DNAH5, DNAI1, DNAI2, DNM2, DNMT1, DYSF, EDA, EDN3, EDNRB, EGFR, EIF2B5, EMC2, EMC3, EMD, EMX1, EPCAM, ERCC6, ERCC8, ESCO2, ETFA, ETFDH, ETHE1, EVC, EVC2, EYS, F5, F9, FactorB, FactorXI, FAH, FAM161A, FANCA, FANCB, FANCC, FANCD1, FANCD2, FANCE, FANCF, FANCG, FANCI, FANCJ, FANCL, FANCM, FANCN, FANCP, FANCS, FBN1, FGF14, FGFR2, FGFR3, FH, FHL1, FKRP, FKTN, FLCN, FMRI, FOXP3, FSCN2, FUS, FUT8, FVIII, FXII, FXN, G6PC, GAA, GALC, GALK1, GALT, GAMT, GATA2, GBA, GBE1, GCDH, GCGR, GDNF, GFAP, GFM1, GHR, GJB1, GJB2, GLA, GLB1, GLDC, GLE1, GNE, GNPTAB, GNPTG, GNS, GPC3, GPR98, GREM1, GRHPR, GRIN2B, H2AX, HADHA, HAX1, HBA1, HBA2, HBB, HEXA, HEXB, HGSNAT, HLCS, HMGCL, HOGA1, HOXB13, HPRPF3, HPRT1, HPS1, HPS3, HRAS, HSD17B4, HSD3B2, HTT, HYAL1, HYLS1, IDS, IDUA, IFITM5, IKBKAP, IL2RG, IMPDH1, INPP5E, IRF4, ITPR1, IVD, JAG1, KCNC3, KCND3, KCNJ11, KLHL7, KRAS, LAMA2, LAMA3, LAMB3, LAMC2, LCA5, LDLR, LDLRAP1, LHX3, LIFR, LIPA, LMNA, LOXHD1, LPL, LRAT, LRP6, LRPPRC, LRRK2, MAN2B1, MAPT, MAX, MCOLN1, MECP2, MED17, MEFV, MEN1, MERTK, MESP2, MET, METexl4, MFN2, MFSD8, MITF, MKS1, MLC1, MLH1, MLH3, MMAA, MMAB, MMACHC, MMADHC, MMD, MPI, MPL, MPV17, MSH2, MSH3, MSH6, MTHFR, MTM1, MTRR, MTTP, MUT, MUTYH, MYO7A, NAGLU, NAGS, NBN, NDRG1, NDUFAF5, NDUFS6, NEB, NF1, NF2, NOTCH2, NPC1, NPC2, NPHP1, NPHS1, NPHS2, NR2E3, NTHL1, NTRK, NTRK1, OAT, OCT4, OFD1, OP A3, OTC, PAH, PALB2, PAQR8, PAX3, PC, PCCA, PCCB, PCDH15, PCSK9, PD1, PDCD1, PDE6B, PDGFRA, PDHA1, PDHB, PEX1, PEX10, PEX12, PEX13, PEX14, PEX16, PEX19, PEX2, PEX26, PEX3, PEX5, PEX6, PEX7, PFKM, PHGDH, PHOX2B, PKD1, PKD2, PKHD1, PKK, PLEKHG4, PMM2, PMP22, PMS1, PMS2, PNPLA3, POLDI, POLE, POMGNT1, POTI, POU5F1, PPM1A, PPP2R2B, PPT1, PRCD, PRKAR1A, PRKCG, PRNP, PROMI, PROP1, PRPF31, PRPF8, PRPH2, PRPS1, PSAP, PSD95, PSEN1, PSEN2, PTCHI, PTEN, PTS, PUS1, PYGM, RAB23, RAD50, RAD51C, RAD51D, RAG2, RAPSN, RARS2, RBI, RDH12, RECQL4, RET, RHO, RICTOR, RMRP, ROS1, RP1, RP2, RPE65, RPGR, RPGRIP1L, RPL32P3, RSI, RTEL1, RUNX1, SACS, SAMHD1, SCN1A, SCN2A, SDHA, SDHAF2, SDHB, SDHC, SDHD, SEL1L, SEPSECS, SERPING1, SGCA, SGCB, SGCG, SGSH, SIRT1, SLC12A3, SLC12A6, SLC17A5, SLC22A5, SLC25A13, SLC25A15, SLC26A2, SLC26A4, SLC35A3, SLC37A4, SLC39A4, SLC4A11, SLC6A8, SLC7A7, SMAD4, SMARCA4, SMARCAL1, SMARCB1, SMARCE1, SMN1, SMPD1, SNAI2, SNCA, SNRNP200, SOD1, SOXIO, SPARA7, SPTBN2, STAR, STAT3, STK11, SUFU, SUMF1, SYNE1, SYNE2, SYS1, TARDBP, TAT, TBK1, TBP, TCIRG1, TCTN3, TECPR2, TERC, TERT, TFR2, TGFBR2, TGM1, TH, TLE3, TMEM127, TMEM138, TMEM216, TMEM43, TMEM67, TMPRSS6, TOPI, TOPORS, TP53, TPP1, TRAC, TRMU, TSFM, TSPAN14, TTBK2, TTC8, TTP A, TTR, TULP1, TYMP, UBE2G2, UBE2J1, UBE3A, USH1C, USH1G, USH2A, VEGF, VHL, VPS13A, VPS13B, VPS35, VPS45, VRK1, VSX2, VWF, WDR19, WNT10A, WS2B, WS2C, XPA, XPC, XPF, YAP1, ZFYVE26, and ZNF423.

Mutations

[0209] In some instances, target nucleic acids comprise a mutation. In some instances, a sequence comprising a mutation may be modified to a wildtype sequence with a composition, system or method described herein. In some instances, a sequence comprising a mutation may be detected with a composition, system or method described herein. The mutation may be a mutation of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more nucleotides. Non-limiting examples of mutations are insertion-deletion (indel), single nucleotide polymorphism (SNP), and frameshift mutations. In some instances, guide nucleic acids described herein hybridize to a region of the target nucleic acid comprising the mutation. The mutation may be located in a non-coding region or a coding region of a gene.

[0210] In some instances, target nucleic acids comprise a mutation, wherein the mutation is a SNP. The single nucleotide mutation or SNP may be associated with a phenotype of the sample or a phenotype of the organism from which the sample was taken. The SNP, in some cases, is associated with altered phenotype from wild type phenotype. The SNP may be a synonymous substitution or a nonsynonymous substitution. The nonsynonymous substitution may be a missense substitution or a nonsense point mutation. The synonymous substitution may be a silent substitution. The mutation may be a deletion of one or more nucleotides. Often, the single nucleotide mutation, SNP, or deletion is associated with a disease such as cancer or a genetic disorder. The mutation, such as a single nucleotide mutation, a SNP, or a deletion, may be encoded in the sequence of a target nucleic acid from the germline of an organism or may be encoded in a target nucleic acid from a diseased cell, such as a maycer cell.

[0211] In some instances, target nucleic acids comprise a mutation, wherein the mutation is a deletion of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more nucleotides. The mutation may be a deletion of about 5, about 10, about 15, about 20, about 25, about 30, about 35, about 40, about 45, about 50, about 55, about 60, about 65, about 70, about 75, about 80, about 85, about 90, about 95, about 100, about 200, about 300, about 400, about 500, about 600, about 700, about 800, about 900, or about 1000 nucleotides. The mutation may be a deletion of 1 to 5, 5 to 10, 10 to 15, 15 to 20, 20 to 25, 25 to 30, 30 to 35, 35 to 40, 40 to 45, 45 to 50, 50 to 55, 55 to 60, 60 to 65, 65 to 70, 70 to 75, 75 to 80, 80 to 85, 85 to 90, 90 to 95, 95 to 100, 100 to 200, 200 to 300, 300 to 400, 400 to 500, 500 to 600, 600 to 700, 700 to 800, 800 to 900, 900 to 1000, 1 to 50, 1 to 100, 25 to 50, 25 to 100, 50 to 100, 100 to 500, 100 to 1000, or 500 to 1000 nucleotides.

[0212] In some instances, the target nucleic acid comprises at least one mutation. Nonlimiting examples of mutations are insertion-deletion (indel), single nucleotide polymorphism (SNP), and frameshift mutations. The mutation may be a deletion of one or more nucleotides. In some instances, guide nucleic acids described herein hybridize to a region of the target nucleic acid comprising the mutation. The mutation may be located in a non-coding region or a coding region of a gene. Mutations may be associated with a phenotype of the organism that is altered from a wild type phenotype.

[0213] In some instances, target nucleic acids comprise a mutation, wherein the mutation is a deletion of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more nucleotides. The mutation may be a deletion of about 5, about 10, about 15, about 20, about 25, about 30, about 35, about 40, about 45, about 50, about 55, about 60, about 65, about 70, about 75, about 80, about 85, about 90, about 95, about 100, about 200, about 300, about 400, about 500, about 600, about 700, about 800, about 900, or about 1000 nucleotides. The mutation may be a deletion of 1 to 5, 5 to 10, 10 to 15, 15 to 20, 20 to 25, 25 to 30, 30 to 35, 35 to 40, 40 to 45, 45 to 50, 50 to 55, 55 to 60, 60 to 65, 65 to 70, 70 to 75, 75 to 80, 80 to 85, 85 to 90, 90 to 95, 95 to 100, 100 to 200, 200 to 300, 300 to 400, 400 to 500, 500 to 600, 600 to 700, 700 to 800, 800 to 900, 900 to 1000, 1 to 50, 1 to 100, 25 to 50, 25 to 100, 50 to 100, 100 to 500, 100 to 1000, or 500 to 1000 nucleotides.

[0214] In some instances, mutations are associated with a disease, that is the mutation in a subject indicates that the subject is susceptible to, or suffers from, a disease, disorder, or pathological state. In some examples, a mutation associated with a disease refers to a mutation which causes the disease, contributes to the development of the disease, or indicates the existence of the disease. A mutation associated with a disease may also refer to any mutation which generates transcription or translation products at an abnormal level, or in an abnormal form, in cells affected by a disease relative to a control without the disease. Nonlimiting examples of diseases associated with mutations are hemophilia, sickle cell anemia, P-thalassemia, Duchene muscular dystrophy, severe combined immunodeficiency (SCID, also known as “bubble boy syndrome”), Huntington’s disease, cystic fibrosis, and various cancers.

[0215] The sample used for cancer testing or cancer risk testing can comprise at least one target sequence or target nucleic acid segment that can bind to a guide nucleic acid of the reagents described herein. The target nucleic acid segment, in some cases, is a portion of a nucleic acid from a gene with a mutation associated with cancer, from a gene whose overexpression is associated with cancer, a tumor suppressor gene, an oncogene, a checkpoint inhibitor gene, a gene associated with cellular growth, a gene associated with cellular metabolism, or a gene associated with cell cycle. Sometimes, the target nucleic acid encodes for a cancer biomarker, such as a prostate cancer biomarker or non-small cell lung cancer. In some cases, the assay can be used to detect “hotspots” in target nucleic acids that can be predictive of cancer, such as lung cancer, cervical cancer, in some cases, the cancer can be a cancer that is caused by a virus. Some non-limiting examples of viruses that cause cancers in humans include Epstein-Barr virus (e.g., Burkitt’s lymphoma, Hodgkin’s Disease, and nasopharyngeal carcinoma); papillomavirus (e.g., cervical carcinoma, anal carcinoma, oropharyngeal carcinoma, penile carcinoma); hepatitis B and C viruses (e.g., hepatocellular carcinoma); human adult T-cell leukemia virus type 1 (HTLV-1) (e.g., T-cell leukemia); and Merkel cell polyomavirus (e.g., Merkel cell carcinoma). One skilled in the art will recognize that viruses can cause or contribute to other types of cancers. In some cases, the target nucleic acid is a portion of a nucleic acid that is associated with a blood fever. In some instances, the mutation is located in a portion of a nucleic acid from a genomic locus, any DNA amplicon of, a reverse transcribed mRNA, or a cDNA from a locus of at least one of: ALK, APC, ATM, AXIN2, BAP1, BARD1, BLM, BMPR1A, BRCA1, BRCA2, BRIP1, CASR, CDC73, CDH1, CDK4, CDKN1B, CDKN1C, CDKN2A, CEBPA, CHEK2, CTNNA1, DICER1, DIS3L2, EGFR, EPCAM, FH, FLCN, GATA2, GPC3, GREM1, HOXB13, HRAS, system, MAX, MEN1, MET, MITF, MLH1, MSH2, MSH3, MSH6, MUTYH, NBN, NF1, NF2, NTHL1, PALB2, PDGFRA, PHOX2B, PMS2, POLDI, POLE, POTI, PRKAR1A, PTCHI, PTEN, RAD50, RAD51C, RAD51D, RBI, RECQL4, RET, RUNX1, SDHA, SDHAF2, SDHB, SDHC, SDHD, SMAD4, SMARCA4, SMARCB1, SMARCE1, STK11, SUFU, TERC, TERT, TMEM127, TP53, TSC1, TSC2, VHL, WRN, and WT1. In some instances, the mutation is associated with a blood disorder, e.g., a thalassemia or an anemia.

[0216] The sample used for genetic disorder testing can comprise at least one target sequence or target nucleic acid segment that can bind to a guide nucleic acid of the reagents described herein. In some embodiments, the genetic disorder is hemophilia, sickle cell anemia, P-thalassemia, Duchene muscular dystrophy, severe combined immunodeficiency, or cystic fibrosis. The target nucleic acid, in some cases, is from a gene with a mutation associated with a genetic disorder, from a gene whose overexpression is associated with a genetic disorder, from a gene associated with abnormal cellular growth resulting in a genetic disorder, or from a gene associated with abnormal cellular metabolism resulting in a genetic disorder. In some cases, the target nucleic acid is a nucleic acid from a genomic locus, a transcribed mRNA, or a reverse transcribed mRNA, a DNA amplicon of or a cDNA from a locus of at least one of: CFTR, FMRI, SMN1, ABCB11, ABCC8, ABCD1, ACAD9, ACADM, ACADVL, ACAT1, ACOX1, ACSF3, ADA, ADAMTS2, ADGRG1, AGA, AGL, AGPS, AGXT, AIRE, ALDH3A2, ALDOB, ALG6, ALMS1, ALPL, AMT, AQP2, ARG1, ARSA, ARSB, ASL, ASNS, ASP A, ASS1, ATM, ATP6V1B1, ATP7A, ATP7B, ATRX, BBS1, BBS10, BBS12, BBS2, BCKDHA, BCKDHB, BCS1L, BLM, BSND, CAPN3, CBS, CDH23, CEP290, CERKL, CHM, CHRNE, CIITA, CLN3, CLN5, CLN6, CLN8, CLRN1, CNGB3, COL27A1, COL4A3, COL4A4, COL4A5, COL7A1, CPS1, CPT1A, CPT2, CRB1, CTNS, CTSK, CYBA, CYBB, CYP11B1, CYP11B2, CYP17A1, CYP19A1, CYP27A1, DBT, DCLRE1C, DHCR7, DHDDS, DLD, DMD, DNAH5, DNAI1, DNAI2, DYSF, EDA, EIF2B5, EMD, ERCC6, ERCC8, ESCO2, ETFA, ETFDH, ETHE1, EVC, EVC2, EYS, F9, FAH, F AMI 61 A, FANCA, FANCC, FANCG, FH, FKRP, FKTN, G6PC, GAA, GALC, GALK1, GALT, GAMT, GBA, GBE1, GCDH, GFM1, GJB1, GJB2, GLA, GLB1, GLDC, GLE1, GNE, GNPTAB, GNPTG, GNS, GRHPR, HADHA, HAX1, HBA1„ HBA2, HBB, HEXA, HEXB, HGSNAT, HLCS, HMGCL, HOGA1, HPS1, HPS3, HSD17B4, HSD3B2, HYAL1, HYLS1, IDS, IDUA, IKBKAP, IL2RG, IVD, KCNJ11, LAMA2, LAMA3, LAMB3, LAMC2, LCA5, LDLR, LDLRAP1, LHX3, LIFR, LIPA, LOXHD1, LPL, LRPPRC, MAN2B1, MCOLN1, MED 17, MESP2, MFSD8, MKS1, MLC1, MMAA, MMAB, MMACHC, MMADHC, MPI, MPL, MPV17, MTHFR, MTM1, MTRR, MTTP, MUT, MYO7A, NAGLU, NAGS, NBN, NDRG1, NDUFAF5, NDUFS6, NEB, NPC1, NPC2, NPHS1, NPHS2, NR2E3, NTRK1, OAT, OP A3, OTC, PAH, PC, PCCA, PCCB, PCDH15, PDHA1, PDHB, PEX1, PEX10, PEX12, PEX2, PEX6, PEX7, PFKM, PHGDH, PKHD1, PMM2, POMGNT1, PPT1, PROP1, PRPS1, PSAP, PTS, PUS1, PYGM, RAB23, RAG2, RAPSN, RARS2, RDH12, RMRP, RPE65, RPGRIP1L, RSI, RTEL1, SACS, SAMHD1, SEPSECS, SGCA, SGCB, SGCG, SGSH, SLC12A3, SLC12A6, SLC17A5, SLC22A5, SLC25A13, SLC25A15, SLC26A2, SLC26A4, SLC35A3, SLC37A4, SLC39A4, SLC4A11, SLC6A8, SLC7A7, SMARCAL1, SMPD1, STAR, SUMF1, TAT, TCIRG1, TECPR2, TFR2, TGM1, TH, TMEM216, TPP1, TRMU, TSFM, TTP A, TYMP, USH1C, USH2A, VPS13A, VPS13B, VPS45, VRK1, VSX2, WNT10A, XPA, XPC, and ZFYVE26.

Samples

[0217] The systems and methods of the present disclosure can be used to detect one or more target sequences or nucleic acids in one or more samples. The one or more samples can comprise one or more target sequences or nucleic acids for detection of an ailment, such as a disease, cancer, or genetic disorder, or genetic information, such as for phenotyping, genotyping, or determining ancestry and are compatible with the reagents and support mediums as described herein. Generally, a sample can be taken from any place where a nucleic acid can be found. Samples can be taken from an individual/human, a non-human animal, or a crop, or an environmental sample can be obtained to test for presence of a disease, virus, pathogen, cancer, genetic disorder, or any mutation or pathogen of interest. A biological sample can be blood, serum, plasma, lung fluid, exhaled breath condensate, saliva, spit, urine, stool, feces, mucus, lymph fluid, peritoneal , cerebrospinal fluid, amniotic fluid, breast milk, gastric secretions, bodily discharges, secretions from ulcers, pus, nasal secretions, sputum, pharyngeal exudates, urethral secretions/mucus, vaginal secretions/mucus, anal secretion/mucus, semen, tears, an exudate, an effusion, tissue fluid, interstitial fluid (e.g., tumor interstitial fluid), cyst fluid, tissue, or, in some instances, any combination thereof. A sample can be an aspirate of a bodily fluid from an animal (e.g., human, animals, livestock, pet, etc.) or plant. A tissue sample can be from any tissue that can be infected or affected by a pathogen (e.g., a wart, lung tissue, skin tissue, and the like). A tissue sample (e.g., from animals, plants, or humans) can be dissociated or liquified prior to application to detection system of the present disclosure. A sample can be from a plant (e.g., a crop, a hydroponically grown crop or plant, and/or house plant). Plant samples can include extracellular fluid, from tissue (e.g., root, leaves, stem, trunk etc.). A sample can be taken from the environment immediately surrounding a plant, such as hydroponic fluid/ water, or soil. A sample from an environment can be from soil, air, or water. In some instances, the environmental sample is taken as a swab from a surface of interest or taken directly from the surface of interest. In some instances, the raw sample is applied to the detection system. In some instances, the sample is diluted with a buffer or a fluid or concentrated prior to application to the detection system. In some cases, the sample is contained in no more than about 200 nanoliters (nL). In some cases, the sample is contained in about 200 nL. In some cases, the sample is contained in a volume that is greater than about 200 nL and less than about 20 microliters (pL). In some cases, the sample is contained in no more than 20 pl. In some cases, the sample is contained in no more than 1, 5, 10, 15, 20, 25, 30, 35 40, 45, 50, 55, 60, 65, 70, 75, 80, 90, 100, 200, 300, 400, 500 pl, or any of value from 1 pl to 500 pl. In some cases, the sample is contained in from 1 pL to 500 pL, from 10 pL to 500 pL, from 50 pL to 500 pL, from 100 pL to 500 pL, from 200 pL to 500 pL, from 300 pL to 500 pL, from 400 pL to 500 pL, from 1 pL to 200 pL, from 10 pL to 200 pL, from 50 pL to 200 pL, from 100 pL to 200 pL, from 1 pL to 100 pL, from 10 pL to 100 pL, from 50 pL to 100 pL, from 1 pL to 50 pL, from 10 pL to 50 pL, from 1 pL to 20 pL, from 10 pL to 20 pL, or from 1 pL to 10 pL. Sometimes, the sample is contained in more than 500 pl.

[0218] In some instances, the sample is taken from a single-cell eukaryotic organism; a plant or a plant cell; an algal cell; a fungal cell; an animal or an animal cell, tissue, or organ; a cell, tissue, or organ from an invertebrate animal; a cell, tissue, fluid, or organ from a vertebrate animal such as fish, amphibian, reptile, bird, and mammal; a cell, tissue, fluid, or organ from a mammal such as a human, a non-human primate, an ungulate, a feline, a bovine, an ovine, and a caprine. In some instances, the sample is taken from nematodes, protozoans, helminths, or malarial parasites. In some cases, the sample may comprise nucleic acids from a cell lysate from a eukaryotic cell, a mammalian cell, a human cell, a prokaryotic cell, or a plant cell. In some cases, the sample may comprise nucleic acids expressed from a cell.

[0219] The sample used for phenotyping testing can comprise at least one target nucleic acid segment that can bind to a guide nucleic acid of the reagents described herein. The target nucleic acid segment, in some cases, is a portion of a nucleic acid from a gene associated with a phenotypic trait.

[0220] The sample used for genotyping testing can comprise at least one target nucleic acid segment that can bind to a guide nucleic acid of the reagents described herein. The target nucleic acid segment, in some cases, is a portion of a nucleic acid from a gene associated with a genotype.

[0221] The sample used for ancestral testing can comprise at least one target nucleic acid segment that can bind to a guide nucleic acid of the reagents described herein. The target nucleic acid segment, in some cases, is a portion of a nucleic acid from a gene associated with a geographic region of origin or ethnic group.

[0222] The sample can be used for identifying a disease status. For example, a sample is any sample described herein, and is obtained from a subject for use in identifying a disease status of a subject. The disease can be a cancer or genetic disorder. Sometimes, a method may comprise obtaining a serum sample from a subject; and identifying a disease status of the subject. Often, the disease status is prostate disease status. In any of the embodiments described herein, the device can be configured for asymptomatic, pre-symptomatic, and/or symptomatic diagnostic applications, irrespective of immunity. In any of the embodiments described herein, the device can be configured to perform one or more serological assays on a sample (e.g., a sample comprising blood).

[0223] In some cases, the target sequence is a portion of a nucleic acid from a virus or a bacterium or other agents responsible for a disease in the sample. The target sequence, in some cases, is a portion of a nucleic acid from a sexually transmitted infection or a contagious disease, in the sample. The target sequence, in some cases, is a portion of a nucleic acid from an upper respiratory tract infection, a lower respiratory tract infection, or a contagious disease, in the sample. The target sequence, in some cases, is a portion of a nucleic acid from a hospital acquired infection or a contagious disease, in the sample. The target sequence, in some cases, is a portion of a nucleic acid from sepsis, in the sample. These diseases can include but are not limited to respiratory viruses (e.g., SARS-CoV-2 (i.e., a virus that causes COVID-19), SARS-CoV-1, MERS-CoV, influenza, Adenovirus, Coronavirus HKU1, Coronavirus NL63, Coronavirus 229E, Coronavirus OC43, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), Human Metapneumovirus (hMPV), Human Rhinovirus (HRVs A, B, C), Human Enterovirus, Influenza A, Influenza A/Hl, Influenza A/H2, Influenza A/H3, Influenza A/H4, Influenza A/H5, Influenza A/H6, Influenza A/H7, Influenza A/H8, Influenza A/H9, Influenza A/H10, Influenza A/Hl 1, Influenza A/H12, Influenza A/Hl 3, Influenza A/Hl 4, Influenza A/Hl 5, Influenza A/Hl 6, Influenza A/Hl- 2009, Influenza A/Nl, Influenza A/N2, Influenza A/N3, Influenza A/N4, Influenza A/N5, Influenza A/N6, Influenza A/N7, Influenza A/N8, Influenza A/N9, Influenza A/N10, Influenza A/Nl 1, oseltamivir-resistant Influenza A, Influenza B, Influenza B - Victoria VI, Influenza B - Yamagata Yl, Influenza C, Parainfluenza Virus 1, Parainfluenza Virus 2, Parainfluenza Virus 3, Parainfluenza Virus 4, Respiratory Syncytial Virus A, Respiratory Syncytial Virus B) and respiratory bacteria (e.g. Bordetella parapertussis, Bordetella pertussis, Bordetella bronchiseptica, Bordetella holmesii, Chlamydia pneumoniae, Mycoplasma pneumoniae). Other viruses include human immunodeficiency virus (HIV), human papillomavirus (HPV), chlamydia, gonorrhea, syphilis, trichomoniasis, sexually transmitted infection, malaria, Dengue fever, Ebola, chikungunya, and leishmaniasis. Pathogens include viruses, fungi, helminths, protozoa, malarial parasites, Plasmodium parasites, Toxoplasma parasites, and Schistosoma parasites. Helminths include roundworms, heartworms, and phytophagous nematodes, flukes, Acanthocephala, and tapeworms. Protozoan infections include infections from Giardia spp., Trichomonas spp., African trypanosomiasis, amoebic dysentery, babesiosis, balantidial dysentery, Chaga's disease, coccidiosis, malaria and toxoplasmosis. Examples of pathogens such as parasitic/protozoan pathogens include, but are not limited to: Plasmodium falciparum, P. vivax, Trypanosoma cruzi and Toxoplasma gondii. Fungal pathogens include, but are not limited to Cryptococcus neoformans, Histoplasma capsulatum, Coccidioides immitis, Blastomyces dermatitidis, Chlamydia trachomatis, Chlamydia pneumoniae, Chlamydia psittaci, and Candida albicans. Pathogenic viruses include but are not limited to: respiratory viruses (e.g., adenoviruses, parainfluenza viruses, severe acute respiratory syndrome (SARS), coronavirus, MERS), gastrointestinal viruses (e.g., noroviruses, rotaviruses, some adenoviruses, astroviruses), exanthematous viruses (e.g., the virus that causes measles, the virus that causes rubella, the virus that causes chickenpox/shingles, the virus that causes roseola, the virus that causes smallpox, the virus that causes fifth disease, chikungunya virus infection); hepatic viral diseases (e.g., hepatitis A, B, C, D, E); cutaneous viral diseases (e.g., warts (including genital, anal), herpes (including oral, genital, anal), molluscum contagiosum); hemmorhagic viral diseases (e.g. Ebola, Lassa fever, dengue fever, yellow fever, Marburg hemorrhagic fever, Crimean-Congo hemorrhagic fever); neurologic viruses (e.g., polio, viral meningitis, viral encephalitis, rabies), sexually transmitted viruses (e.g., HIV, HPV, and the like), immunodeficiency virus (e.g., HIV); influenza virus; dengue; West Nile virus; herpes virus; yellow fever virus; Hepatitis Virus C; Hepatitis Virus A; Hepatitis Virus B; papillomavirus; and the like. Pathogens include, e.g., HIV virus, Mycobacterium tuberculosis, Klebsiella pneumoniae, Acinetobacter baumannii, Bacillus anthracis, Bordetella pertussis, Burkholderia cepacia, Corynebacterium diphtheriae, Coxiella burnetii, Streptococcus agalactiae, methicillin-resistant Staphylococcus aureus, Legionella longbeachae, Legionella pneumophila, Leptospira interrogans, Moraxella catarrhalis, Streptococcus pyogenes, Escherichia coli, Neisseria gonorrhoeae, Neisseria meningitidis, Neisseria elongate, Neisseria gonorrhoeae, Parechovirus, Pneumococcus, Pneumocystis jirovecii, Cryptococcus neoformans, Histoplasma capsulatum, Haemophilus influenzae B, Treponema pallidum, Lyme disease spirochetes, Pseudomonas aeruginosa, Mycobacterium leprae, Brucella abortus, rabies virus, influenza virus, cytomegalovirus, herpes simplex virus I, herpes simplex virus II, human serum parvo-like virus, respiratory syncytial virus (RSV), M. genitalium, T. Vaginalis, varicella-zoster virus, hepatitis B virus, hepatitis C virus, measles virus, adenovirus, human T-cell leukemia viruses, Epstein-Barr virus, murine leukemia virus, mumps virus, vesicular stomatitis virus, Sindbis virus, lymphocytic choriomeningitis virus, wart virus, blue tongue virus, Sendai virus, feline leukemia virus, Reovirus, polio virus, simian virus 40, mouse mammary tumor virus, dengue virus, rubella virus, West Nile virus, Plasmodium falciparum, Plasmodium vivax, Toxoplasma gondii, Trypanosoma rangeli, Trypanosoma cruzi, Trypanosoma rhodesiense, Trypanosoma brucei, Schistosoma mansoni, Schistosoma japonicum, Babesia bovis, Eimeria tenella, Onchocerca volvulus, Leishmania tropica, Mycobacterium tuberculosis, Trichinella spiralis, Theileria parva, Taenia hydatigena, Taenia ovis, Taenia saginata, Echinococcus granulosus, Mesocestoides corti, Mycoplasma arthritidis, M. hyorhinis, M. orale, M. arginini, Acholeplasma laidlawii, M. salivarium, M. pneumoniae, Enterobacter cloacae, Kiebsiella aerogenes, Proteus vulgaris, Serratia macesens, Enterococcus faecalis, Enterococcus faecium, Streptococcus intermdius, Streptococcus pneumoniae, and Streptococcus pyogenes. Often the target nucleic acid may comprise a sequence from a virus or a bacterium or other agents responsible for a disease that can be found in the sample. In some cases, the target nucleic acid is a portion of a nucleic acid from a genomic locus, a transcribed mRNA, or a reverse transcribed cDNA from a gene locus in at least one of: human immunodeficiency virus (HIV), human papillomavirus (HPV), chlamydia, gonorrhea, syphilis, trichomoniasis, sexually transmitted infection, malaria, Dengue fever, Ebola, chikungunya, and leishmaniasis. Pathogens include viruses, fungi, helminths, protozoa, malarial parasites, Plasmodium parasites, Toxoplasma parasites, and Schistosoma parasites. Helminths include roundworms, heartworms, and phytophagous nematodes, flukes, Acanthocephala, and tapeworms. Protozoan infections include infections from Giardia spp., Trichomonas spp., African trypanosomiasis, amoebic dysentery, babesiosis, balantidial dysentery, Chaga's disease, coccidiosis, malaria and toxoplasmosis. Examples of pathogens such as parasitic/protozoan pathogens include, but are not limited to: Plasmodium falciparum, P. vivax, Trypanosoma cruzi and Toxoplasma gondii. Fungal pathogens include, but are not limited to Cryptococcus neoformans, Histoplasma capsulatum, Coccidioides immitis, Blastomyces dermatitidis, Chlamydia trachomatis, and Candida albicans. Pathogenic viruses include but are not limited to immunodeficiency virus (e.g., HIV); influenza virus; dengue; West Nile virus; herpes virus; yellow fever virus; Hepatitis Virus C; Hepatitis Virus A; Hepatitis Virus B; papillomavirus; and the like. Pathogens include, e.g., HIV virus, Mycobacterium tuberculosis, Streptococcus agalactiae, methicillin- resistant Staphylococcus aureus, Staphylococcus epidermidis, Legionella pneumophila, Streptococcus pyogenes, Streptococcus salivarius, Escherichia coli, Neisseria gonorrhoeae, Neisseria meningitidis, Pneumococcus, Cryptococcus neoformans, Histoplasma capsulatum, Hemophilus influenzae B, Treponema pallidum, Lyme disease spirochetes, Pseudomonas aeruginosa, Mycobacterium leprae, Brucella abortus, rabies virus, influenza virus, cytomegalovirus, herpes simplex virus I, herpes simplex virus II, human serum parvo-like virus, respiratory syncytial virus (RSV), Alphacoronavirus, Betacoronavirus, Sarbecovirus, SARS-related virus, Gammacoronavirus, Deltacoronavirus, M. genitalium, T. vaginalis, varicella-zoster virus, hepatitis B virus, hepatitis C virus, measles virus, human adenovirus (type A, B, C, D, E, F, G), human T-cell leukemia viruses, Epstein-Barr virus, murine leukemia virus, mumps virus, vesicular stomatitis virus, Sindbis virus, lymphocytic choriomeningitis virus, wart virus, blue tongue virus, Sendai virus, feline leukemia virus, Reovirus, polio virus, simian virus 40, mouse mammary tumor virus, dengue virus, rubella virus, West Nile virus, Human Bocavirus, Plasmodium falciparum, Plasmodium vivax, Toxoplasma gondii, Trypanosoma rangeli, Trypanosoma cruzi, Trypanosoma rhodesiense, Trypanosoma brucei, Schistosoma mansoni, Schistosoma japonicum, Babesia bovis, Eimeria tenella, Onchocerca volvulus, Leishmania tropica, Mycobacterium tuberculosis, Trichinella spiralis, Theileria parva, Taenia hydatigena, Taenia ovis, Taenia saginata, Echinococcus granulosus, Mesocestoides corti, Mycoplasma arthritidis, M. hyorhinis, M. orale, M. arginini, Acholeplasma laidlawii, M. salivarium and M. pneumoniae. SARS-CoV-2 Variants include Coronavirus HKU1, Coronavirus NL63, Coronavirus 229E, Coronavirus OC43, SARS-CoV-2 85A, SARS-CoV-2 T1001I, SARS-CoV-2 3675-3677A, SARS-CoV-2 P4715L, SARS-CoV-2 S5360L, SARS-CoV-2 69-70A, SARS-CoV-2 Tyrl44fs, SARS-CoV- 2 242-244A, SARS-CoV-2 Y453F, SARS-CoV-2 S477N, SARS-CoV-2 E848K, SARS-CoV- 2 N501Y, SARS-CoV-2 D614G, SARS-CoV-2 P681R, SARS-CoV-2 P681H, SARS-CoV-2 L21F, SARS-CoV-2 Q27Stop, SARS-CoV-2 Mlfs, and SARS-CoV-2 R203fs. In some cases, the target sequence is a portion of a nucleic acid from a genomic locus, a transcribed mRNA, or a reverse transcribed cDNA from a gene locus of bacterium or other agents responsible for a disease in the sample comprising a mutation that confers resistance to a treatment, such as a single nucleotide mutation that confers resistance to antibiotic treatment.

[0224] In some instances, the target sequence is a portion of a nucleic acid from a subject having cancer. The cancer may be a solid cancer (tumor). The cancer may be a blood cell cancer, including leukemias and lymphomas. Non-limiting types of cancer that could be treated with such methods and compositions include colon cancer, rectal cancer, renal-cell carcinoma, liver cancer, bladder cancer, cancer of the kidney or ureter, lung cancer, cancer of the small intestine, esophageal cancer, melanoma, bone cancer, pancreatic cancer, skin cancer, brain cancer (e.g., glioblastoma), cancer of the head or neck, melanoma, uterine cancer, ovarian cancer, breast cancer, testicular cancer, cervical cancer, stomach cancer, Hodgkin's Disease, non-Hodgkin's lymphoma, thyroid cancer. The cancer may be a leukemia, such as, by way of non-limiting example, acute myeloid (or myelogenous) leukemia (AML), chronic myeloid (or myelogenous) leukemia (CML), acute lymphocytic (or lymphoblastic) leukemia (ALL), and chronic lymphocytic leukemia (CLL).

[0225] In some instances, the target sequence is a portion of a nucleic acid from a cancer cell. A cancer cell may be a cell harboring one or more mutations that results in unchecked proliferation of the cancer cell. Such mutations are known in the art. Non-limiting examples of antigens are ADRB3, AKAP-4,ALK, Androgen receptor, B7H3, BCMA, BORIS, BST2, CAIX, CD 179a, CD 123, CD171, CD 19, CD20, CD22, CD24, CD30, CD300LF, CD33, CD38, CD44v6, CD72, CD79a, CD79b, CD97, CEA, CLDN6, CLEC12A, CLL-1, CS-1, CXORF61, CYP1B1, Cyclin B 1, E7, EGFR, EGFRvIII, ELF2M, EMR2, EPCAM, ERBB2 (Her2/neu), ERG (TMPRSS2 ETS fusion gene), ETV6-AML, EphA2, Ephrin B2, FAP, FCAR, FCRL5, FLT3, Folate receptor alpha, Folate receptor beta, Fos-related antigen 1, Fucosyl GM1, GD2, GD3, GM3, GPC3, GPR20, GPRC5D, GloboH, HAVCR1, HMWMAA, HPV E6, IGF-I receptor, IL-13Ra2, IL-1 IRa, KIT, LAGE-la, LAIR1, LCK, LILRA2, LMP2, LY6K, LY75, LewisY, MAD-CT-1, MAD-CT-2, MAGE Al, MAGE-A1, ML-IAP, MUC1, MYCN, MelanA/MARTl, Mesothelin, NA17, NCAM, NY-BR-1, NY-ESO-1, OR51E2, OY- TES 1, PANX3, PAP, PAX3, PAX5, PCTA-l/Galectin 8, PDGFR-beta, PLAC1, PRSS21, PSCA, PSMA, Polysialic acid, Prostase, RAGE-1, ROR1, RU1, RU2, Ras mutant, RhoC, SART3, SSEA-4, SSX2, TAG72, TARP, TEM1/CD248, TEM7R, TGS5, TRP-2, TSHR, Tie 2, Tn Ag, UPK2, VEGFR2, WT1, XAGE1, and IGLL1.

[0226] In some cases, the target sequence is a portion of a nucleic acid from a control gene in a sample. In some embodiments, the control gene is an endogenous control. The endogenous control may include human 18S rRNA, human GAPDH, human HPRT1, human GUSB, human RNase P, MS2 bacteriophage, or any other control sequence of interest within the sample.

Multiplexing

[0227] The systems, devices, and methods described herein can be multiplexed in a number of ways. Multiplexing may include assaying for two or more target nucleic acids in a sample. Multiplexing can be spatial multiplexing wherein multiple different target nucleic acids are detected from the same sample at the same time, but the reactions are spatially separated. Often, the multiple target nucleic acids are detected using the same programmable nuclease, but different guide nucleic acids. The multiple target nucleic acids sometimes are detected using the different programmable nucleases. Sometimes, multiplexing can be single reaction multiplexing wherein multiple different target acids are detected in a single reaction volume. Often, at least two different programmable nucleases are used in single reaction multiplexing. For example, multiplexing can be enabled by immobilization of multiple categories of reporters within a device, to enable detection of multiple target nucleic acids. Multiplexing allows for detection of multiple target nucleic acids in one kit or system. In some cases, the multiple target nucleic acids comprise different target nucleic acids to a virus. In some cases, the multiple target nucleic acids comprise different target nucleic acids associated with at least a first disease and a second disease. Multiplexing for one disease can increase at least one of sensitivity, specificity, or accuracy of the assay to detect the presence of the disease in the sample. In some cases, the multiple target nucleic acids comprise target nucleic acids directed to different viruses, bacteria, or pathogens responsible for more than one disease. In some cases, multiplexing allows for discrimination between multiple target nucleic acids, such as target nucleic acids that comprise different genotypes of the same bacteria or pathogen responsible for a disease, for example, for a wild-type genotype of a bacteria or pathogen and for genotype of a bacteria or pathogen comprising a mutation, such as a single nucleotide polymorphism (SNP) that can confer resistance to a treatment, such as antibiotic treatment. For example, multiplexing methods may comprise a single assay for a microorganism species using a first programmable nuclease and an antibiotic resistance pattern in a microorganism using a second programmable nuclease. Sometimes, multiplexing allows for discrimination between multiple target nucleic acids of different influenza strains, for example, influenza A and influenza B. Often, multiplexing allows for discrimination between multiple target nucleic acids, such as target nucleic acids that comprise different genotypes, for example, for a wild-type genotype and for a mutant (e.g., SNP) genotype.

Multiplexing for multiple viral infections can provide the capability to test a panel of diseases from a single sample. For example, multiplexing for multiple diseases can be valuable in a broad panel testing of a new patient or in epidemiological surveys. Often multiplexing is used for identifying bacterial pathogens in sepsis or other diseases associated with multiple pathogens.

[0228] Furthermore, signals from multiplexing can be quantified. For example, a method of quantification for a disease panel comprises assaying for a plurality of unique target nucleic acids in a plurality of aliquots from a sample, assaying for a control nucleic acid control in another aliquot of the sample, and quantifying a plurality of signals of the plurality of unique target nucleic acids by measuring signals produced by cleavage of reporters compared to the signal produced in the second aliquot. Often the plurality of unique target nucleic acids are from a plurality of viruses in the sample. Sometimes the quantification of a signal of the plurality correlates with a concentration of a unique target nucleic acid of the plurality for the unique target nucleic acid of the plurality that produced the signal of the plurality. The disease panel can be for any disease.

[0229] In some cases, the combination of a guide nucleic acid, a programmable nuclease, and a single stranded reporter configured to detect one target nucleic acid is provided in its own reagent chamber or its own support medium. In this case, multiple reagent chambers or support mediums are provided, where each reagent chamber is designed to detect one target nucleic acid. In some cases, multiple different target nucleic acids may be detected in the same chamber or support medium.

[0230] In some instances, the multiplexed devices and methods detect at least 2 different target nucleic acids in a single reaction. In some instances, the multiplexed devices and methods detect at least 3 different target nucleic acids in a single reaction. In some instances, the multiplexed devices and methods detect at least 4 different target nucleic acids in a single reaction. In some instances, the multiplexed devices and methods detect at least 5 different target nucleic acids in a single reaction. In some cases, the multiplexed devices and methods detect at least 6, 7, 8, 9, or 10 different target nucleic acids in a single reaction.

[0231] While preferred embodiments of the present invention have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the invention. It should be understood that various alternatives to the embodiments of the invention described herein may be employed in practicing the invention. It is intended that the following claims define the scope of the invention and that methods and structures within the scope of these claims and their equivalents be covered thereby.

[0232] The various embodiments described above can be combined to provide further embodiments. All of the U.S. patents, U.S. patent application publications, U.S. patent application, foreign patents, foreign patent application and non-patent publications referred to in this specification and/or listed in the Application Data Sheet are incorporated herein by reference, in their entirety. Aspects of the embodiments can be modified, if necessary to employ concepts of the various patents, application and publications to provide yet further embodiments.

Claims

CLAIMS WHAT IS CLAIMED IS:

1. A device, comprising: a sample chamber configured to receive a biological sample including a target nucleic acid, wherein the sample chamber is configured to produce a plurality of aqueous droplets dispersed in an immiscible fluid by sonication or homogenization, wherein at least one aqueous droplet from the plurality of aqueous droplets includes the biological sample and a detection reagent having a programmable nuclease, a guide nucleic acid, and a reporter, and wherein the reporter is capable of being cleaved upon binding of the guide nucleic acid to a segment of the target nucleic acid.

2. The device of claim 1, wherein the sample chamber further comprises a lysis buffer, or wherein the device further comprises a lysis buffer storage chamber fluidically connected to the sample chamber, and/or wherein the device further comprises a lysis chamber fluidically connected to the sample chamber, wherein the lysis chamber comprises a lysis buffer.

3. The device of claim 2, wherein the lysis buffer comprises an enzyme that disrupts cell membranes.

4. The device of any one of claims 2-3, wherein the lysis buffer has a pH range of 1 to 14.

5. The device of any one of claims 2-4, wherein the lysis chamber further comprises a neutralization buffer that is capable of neutralize the lysis buffer.

6. The device of any one of claims 2-5, further comprising a detection chamber fluidically connected to the sample chamber.

7. The device of claim 6, wherein the detection chamber comprises the detection reagent.

8. The device of any one of claims 6-7, wherein the detection chamber is a standalone physical compartment.

9. The device of any one of claims 6-8, wherein the detection chamber is configured to receive the plurality of aqueous droplets.

10. The device of any one of claims 6-9, comprising a plurality of detection chambers.

11. The device of claim 10, wherein each detection chamber from the plurality of detection chambers has substantially equivalent volume or wherein the plurality of detection chambers have different volumes.

12. The device of any one of claims 6-11, wherein the detection chamber is circular, elongated, or hexagonal.

13. The device of any one of claims 6-12, wherein the detection chamber comprises a hydrophobic or porous substrate, and optionally wherein the hydrophobic or porous substrate is configured to create resistance with presence of the fluid volume of the biological sample in the detection chamber, thereby directing the biological sample to flow to an unfilled detection chamber.

14. The device of any one of claims 6-13, wherein the detection chamber comprises an optically transparent surface.

15. The device of any one of claims 6-14, wherein the detection chamber is configured to hold from 1 pL to 1 pL of fluid.

16. A method for detecting a target nucleic acid in a biological sample, comprising: a) loading the biological sample to the sample chamber of the device in any one of claims 1-15; b) loading the second fluid immiscible with the first fluid in the sample chamber; and c) producing the plurality of aqueous droplets dispersed in the second fluid by sonication or homogenization, such that a detectable signal is generated by cleavage of the reporter upon binding of the guide nucleic acid to a segment of the target nucleic acid, thereby indicating the presence of the target nucleic acid.

17. The method of claim 16, further comprising quantifying the detectable signal, thereby quantifying an amount of the target nucleic acid present in the biological sample.

18. A device, comprising: a) a volume configured to receive a biological sample including a target nucleic acid via a top opening of the device; and b) a plurality of stacked detection layers, wherein at least one detection layer from the plurality of detection layers includes a porous substrate coated with or bound to a detection reagent having a programmable nuclease, a guide nucleic acid, and a reporter, and wherein the reporter is capable of being cleaved upon binding of the guide nucleic acid to a segment of the target nucleic acid.

19. A device, comprising: a) a volume configured to receive a biological sample including a target nucleic acid and a detection reagent via a top opening of the device; and b) a plurality of stacked detection layers, wherein at least one detection layer from the plurality of detection layers includes a porous substrate coated with or bound to an affinity ligand targeting nucleic acids, wherein the detection reagent has a programmable nuclease, a guide nucleic acid, and a reporter, and wherein the reporter is capable of being cleaved upon binding of the guide nucleic acid to a segment of the target nucleic acid.

20. The device of claim 19, wherein the affinity ligand specifically binds the target nucleic acid or wherein the affinity ligand binds nucleic acids non-specifically.

21. The device of any one of claims 18-20, wherein a detection layer from the plurality of stacked detection layers binds uncleaved reporter.

22. The device of any one of claims 19-21, wherein the porous substrate comprises a polymer matrix, a bead, or a nanostructure.

23. The device of claim 22, wherein the polymer matrix is hydrogel.

24. The device of claim 22, wherein the bead is a conducting or non-conducting bead.

25. The device of claim 22, wherein the nanostructure is a wire mesh.

26. The device of any one of claims 18-25, wherein the volume further comprises a lysis buffer, wherein the device further comprises a lysis buffer storage chamber fluidically connected to the volume, and/or wherein the device further comprises a lysis chamber fluidically connected to the volume, wherein the lysis chamber comprises a lysis buffer.

27. The device of claim 26, wherein the lysis buffer comprises an enzyme that disrupts cell membranes.

28. The device of any one of claims 26-27, wherein the lysis buffer has a pH range of 1 to 14.

29. The device of any one of claims 26-28, wherein the lysis chamber further comprises a neutralization buffer that is capable of neutralize the lysis buffer.

30. The device of any one of claims 18-29, wherein the reporter is conjugated to horseradish peroxidase (HRP).

31. A method for detecting a target nucleic acid in a biological sample, comprising a) loading the biological sample to the volume of the device via the top opening in any one of claims 18-30, such that the biological sample flows through the plurality of stacked detection layers of the device; b) detecting a detectable signal, wherein the detectable signal is generated by cleavage of the reporter upon binding of the guide nucleic acid to the segment of the target nucleic acid, thereby indicating the presence of the target nucleic acid.

32. The method of claim 31, further comprising loading the detection reagent such that the detection reagent flows through the plurality of stacked detection layers of the device.

33. The method of claim 31 or 32, wherein the reporter is conjugated to horseradish peroxidase (HRP).

144

34. The method of claim 33, further comprising contacting a cleavage reporter with a HRP substrate, thereby generating an optical signal change.

35. The method of claim 34, wherein the HRP substrate is a chromogenic substrate, and optionally wherein the chromogenic substrate is selected from the group consisting of 3, 3', 5,5'- Tetramethylbenzidine (TMB), 3, 3 '-Diaminobenzidine (DAB), and 2,2'-azino-bis(3- ethylbenzothiazoline-6-sulfonic acid) (ABTS).

36. The method of claim 34, wherein the HRP substrate is a chemiluminescent substrate, and optionally wherein the chemiluminescent substrate is luminol.

37. A point-of-need device comprising: a sample chamber configured to receive a first volume of a biological sample; a sample volume generator configured to generate a plurality of sample volumes from the first volume of the biological sample, wherein a first sample volume of the plurality of sample volumes comprises a plurality of nucleic acids, a plurality of programmable nuclease complexes, and a plurality of reporters, wherein a molar ratio of the plurality of programmable nuclease complexes to the plurality of nucleic acids in the first sample volume is at least 1 : 1; wherein the plurality of nucleic acids in the first sample volume comprise a target nucleic acid, wherein a first programmable nuclease complex in the plurality of programmable nuclease complexes binds to the target nucleic acid to activate the programmable nuclease complex to cleave a first reporter in the plurality of reporters, wherein the signal is indicative of cleavage of the first reporter and of a presence a target nucleic acid in the biological sample.

38. The device of claim 37, wherein the molar ratio of the plurality of programmable nuclease complexes to the plurality of nucleic acids in the first sample volume is at least 2: 1, 3 : 1, 4: 1, 5: 1, 6: 1, 7: 1, 8: 1, 9: 1 or 10: 1.

39. The device of claim 37 or 38, wherein the programmable nuclease complex comprises a programmable nuclease and a guide nucleic acid.

40. The device of any one of claims 37-39, wherein the sample volume generator comprises a branched microfluidic structure, a column with a plurality of stacked layers, a plurality of microwells, or a water-in-oil droplet generator.

41. The device of claim 40, wherein the water-in-oil droplet generator comprises a first channel and a second channel coupled to one another at a junction.

42. The device of claim 40, wherein the water-in-oil droplet generator comprises an emulsification chamber.

43. A device, comprising: a) a sample chamber configured to receive a biological sample including a target nucleic acid; and b) a detection chamber fluidically connected to the sample chamber via a first channel and a second channel; wherein the first channel is configured to receive a flow of a first fluid and the second channel is configured to receive a flow of a second fluid, wherein the first fluid is an aqueous fluid, and the second fluid is immiscible with the first fluid, wherein the first and second channels collectively form at least one junction, which is configured to produce a plurality of aqueous droplets surrounded by the second fluid flowing through the second channel, wherein at least one aqueous droplet includes the biological sample and a detection reagent having a programmable nuclease, a guide nucleic acid, and a reporter, and wherein the reporter is capable of being cleaved upon binding of the guide nucleic acid to a segment of the target nucleic acid.

44. The device of claim 43, wherein the sample chamber further comprises a lysis buffer, or wherein the device further comprises a lysis buffer storage chamber fluidically connected to the sample chamber, and/or wherein the device further comprises a lysis chamber fluidically connected to the sample chamber, wherein the lysis chamber comprises a lysis buffer.

45. The device of any one of claims 43-44, wherein the lysis buffer comprises an enzyme that disrupts cell membranes.

46. The device of any one of claims 43-45, wherein the lysis buffer has a pH range of 1 to 14.

47. The device of any one of claims 43-46, wherein the lysis chamber further comprises a neutralization buffer that is capable of neutralize the lysis buffer.

48. The device of any one of claims 43-47, wherein the detection chamber is a standalone physical compartment.

49. The device of any one of claims 43-48, wherein the detection chamber is configured to receive the plurality of aqueous droplets.

50. The device of claim 49, comprising a plurality of detection chambers.

51. The device of claim 50, wherein each detection chamber from the plurality of detection chambers has substantially equivalent volume or wherein the plurality of detection chambers have different volumes.

52. The device of any one of claims 43-51, wherein the detection chamber is circular, elongated, or hexagonal.

53. The device of any one of claims 43-52, wherein the detection chamber comprises a hydrophobic or porous substrate, and optionally wherein the hydrophobic or porous substrate is configured to create resistance with presence of the fluid volume of the biological sample in the detection chamber, thereby directing the biological sample to flow to an unfilled detection chamber.

54. The device of any one of claims 43-53, wherein the at least one detection chamber from the plurality of the detection chambers is configured to hold from 1 pL to 1 pL of fluid.

55. A method for detecting a target nucleic acid in a biological sample, comprising loading the biological sample to the sample chamber of the device in any one of claims 37-54, such that the first fluid comprising the biological sample flows to the detection chamber via the first channel of the device, wherein the first fluid is an aqueous fluid; such that the second fluid flows to the detection chamber via the second channel; such that the plurality of aqueous droplets surrounded by the second fluid are produced and flow through the second channel, wherein at least one aqueous droplet comprises the biological sample and the detection reagent; and such that a detectable signal is generated by cleavage of the reporter upon binding of the guide nucleic acid to the segment of the target nucleic acid, indicating the presence of the target nucleic acid.

56. The method of claim 55, further comprising quantifying the detectable signal, thereby quantifying an amount of the target nucleic acid present in the biological sample.

57. A device, comprising: a) a sample chamber configured to receive a biological sample including a target nucleic acid; and b) a plurality of detection chambers fluidically connected to the sample chamber via one or more capillary channels, thereby enabling a fluid volume of the biological sample to flow from the sample chamber to at least one detection chamber from the plurality of detection chambers by capillary action, wherein the at least one detection chamber includes a detection reagent having a programmable nuclease, a guide nucleic acid, and a reporter, and wherein the reporter is capable of being cleaved upon binding of the guide nucleic acid to a segment of the target nucleic acid.

58. The device of claim 57, wherein the sample chamber further comprises a lysis buffer, wherein the device further comprises a lysis buffer storage chamber fluidically connected to the sample chamber, and/or wherein the device further comprises a lysis chamber fluidically connected to the sample chamber, wherein the lysis chamber comprises a lysis buffer.

59. The device of any one of claims 57-58, wherein the lysis buffer comprises an enzyme that disrupts cell membranes.

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60. The device of any one of claims 57-59, wherein the lysis buffer has a pH range of 1 to 14.

61. The device of any one of claims 57-60, wherein the lysis chamber further comprises a neutralization buffer that is capable of neutralize the lysis buffer.

62. The device of any one of claims 57-61, wherein the one or more capillary channels are branched and connected to the plurality of detection chambers.

63. The device of any one of claims 57-62, wherein the one or more capillary channels are configured to create substantially the same fluid volume in the plurality of detection chambers.

64. The device of any one of claims 57-63, wherein each detection chamber from the plurality of detection chambers is a standalone physical compartment.

65. The device of any one of claims 57-64, wherein each detection chamber from the plurality of detection chambers is located in a region of one of the capillary channels or wherein each detection chamber from the plurality of detection chambers is located at the end of one of the capillary channels.

66. The device of any one of claims 57-65, wherein each detection chamber from the plurality of detection chambers has substantially equivalent volume or wherein the plurality of detection chambers have different volumes.

67. The device of any one of claims 57-66, wherein the plurality of detection chambers are circular, elongated, or hexagonal.

68. The device of any one of claims 57-67, wherein the at least one detection chamber from the plurality of detection chambers comprises a hydrophobic or porous substrate, and optionally wherein the hydrophobic or porous substrate is configured to create resistance with presence of the fluid volume of the biological sample in the at least one detection chamber, thereby directing the biological sample to flow to an unfilled detection chamber.

69. The device of any one of claims 57-68, wherein the at least one detection chamber from the plurality of the detection chambers is configured to hold from 1 pL to 1 pL of fluid.

70. A method for detecting a target nucleic acid in a biological sample, comprising loading the biological sample to the sample chamber of the device in any one of claims 57-69, such that the fluid volume of the biological sample flows via the one or more capillary channels to the plurality of detection chambers by capillary action, such that the fluid volume of the biological sample contacts the detection reagent in at least one detection chamber, and such that a detectable signal is generated by cleavage of the reporter upon binding of the guide nucleic acid to the segment of the target nucleic acid, indicating the presence of the target nucleic acid.

71. The method of claim 70, further comprising quantifying the detectable signal, thereby quantifying an amount of the target nucleic acid present in the biological sample.

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72. A device, comprising: a plurality of detection chambers arranged as an array and configured to contact a biological sample and retain a fluid volume of the biological sample, wherein at least one detection chamber from the plurality of detection chambers includes a detection reagent having a programmable nuclease, a guide nucleic acid, and a reporter, and wherein the reporter is capable of being cleaved upon binding of the guide nucleic acid to a segment of the target nucleic acid.

73. The device of claim 72, further comprising a sample chamber fluidically connected to the plurality of detection chambers.

74. The device of claim 73, wherein the sample chamber further comprises a lysis buffer.

75. The device of claim 74, wherein the lysis buffer comprises an enzyme that disrupts cell membranes.

76. The device of any one of claims 74-75, wherein the lysis buffer has a pH range of 1 to 14.

77. The device of any one of claims 72-76, wherein the sample chamber further comprises a neutralization buffer that is capable of neutralize the lysis buffer.

78. The device of any one of claims 72-77, wherein each detection chamber from the plurality of detection chambers is a standalone physical compartment.

79. The device of claim 78, wherein each detection chamber from the plurality of detection chambers is a microfluidic structure, column, or microwell.

80. The device of any one of claims 72-79, wherein each detection chamber from the plurality of detection chambers has substantially equivalent volume or wherein the plurality of detection chambers have different volumes.

81. The device of any one of claims 72-80, wherein the plurality of detection chambers are circular, elongated, or hexagonal.

82. The device of any one of claims 72-81, wherein at least one detection chamber from the plurality of detection chambers is coated with the detection reagent.

83. The device of any one of claims 72-82, wherein the at least one detection chamber from the plurality of detection chambers comprises a hydrophobic or porous substrate, and optionally wherein the hydrophobic or porous substrate is configured to create resistance with presence of the fluid volume of the biological sample in the at least one detection chamber, thereby directing the biological sample to flow to an unfilled detection chamber.

84. The device of any one of claims 72-83, wherein the at least one detection chamber from the plurality of the detection chambers is configured to hold from 1 pL to 1 pL of fluid.

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85. A method for detecting a target nucleic acid in a biological sample, comprising contacting the biological sample with the device in any one of claims 72-84, such that the fluid volume of the biological sample contacts the detection reagent in at least one detection chamber, and such that a detectable signal is generated by cleavage of the reporter upon binding of the guide nucleic acid to the segment of the target nucleic acid, indicating the presence of the target nucleic acid.

86. The method of claim 85, further comprising quantifying the detectable signal, thereby quantifying an amount of the target nucleic acid present in the biological sample.

87. The device of any one of claims 1-15, 18-30, 37-54, 57-69, 72-84, comprising an illumination source configured to illuminate the reporter.

88. The device of any one of claims 1-15, 18-30, 37-54, 57-69, 72-84, 87, comprising a detector configured to detect a detectable signal produced by the reporter.

89. The device of claim 88, wherein the detectable signal is selected from a group consisting of an optical, fluorescence, magnetic, electrical, chemical, or electrochemical signal.

90. The device of any one of claims 1-15, 18-30, 37-54, 57-69, 72-84, 87, 89, wherein the biological sample is blood, serum, plasma, saliva, urine, or any combination thereof.

91. The device of any one of claims 1-15, 18-30, 37-54, 57-69, 72-84, 87, 89, 90, wherein the device is a point-of-need device, wherein the device is handheld, and/or wherein the device is disposable.

92. The device of any one of claims 1-15, 18-30, 37-54, 57-69, 72-84, 87, 89-91, wherein the programmable nuclease is a type V CRISPR/Cas effector protein or a type VI CRISPR/Cas effector protein.

93. The device of any one of claims 1-15, 18-30, 37-54, 57-69, 72-84, 87, 89-92, wherein the target nucleic acid is from a virus and optionally wherein the virus comprises a respiratory virus.

94. The device of any one of claims 1-15, 18-30, 37-54, 57-69, 72-84, 87, 89-93, further comprising a control nucleic acid, optionally wherein the control nucleic acid is in the at least one detection chamber.

95. The device of any one of claims 1-15, 18-30, 37-54, 57-69, 72-84, 87, 89-94, wherein the reporter comprises a single stranded reporter comprising a detection moiety.

96. The device of claim 95, wherein the detection moiety is a fluorophore, a FRET pair, a fluorophore/quencher pair, or an electrochemical reporter molecule.

97. The device of claim 95 or 96, wherein the detection moiety produces a detectable signal upon cleavage of the reporter.

98. The device of claim 97, wherein the detectable signal is a colorimetric signal, a fluorescence signal, an amperometric signal, or a potentiometric signal.

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