# US 9,428,814 B2 · Methods and materials for detecting viral or microbial infections > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 9,428,814 B2 - Document ID: US9428814B2 - Status: Granted - Kind: B2 - Application number: 14/841,289 - Filed: 2015-08-31 - Published: 2015-12-17 - Granted: 2016-08-30 - Earliest claimed: 2010-02-15 - Assignees: Cascade Biosystems, Inc. - Applicants: Cascade Biosystems, Inc. - Inventors: Kenneth D. Smith; Nina Yazvenko; Mariya Smit - Web page: https://patentgrep.com/patent/US9428814B2 ## CPC - C12Q 1/689: for bacteria - C12Q 1/683: involving restriction enzymes, e.g. restriction fragment length polymorphism [RFLP] - C12Q 1/701: {Specific hybridization probes} - C12Q 1/705: {for herpetoviridae, e.g. herpes simplex, varicella zoster} - C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES ## Abstract This document provides methods and materials for detecting target nucleic acid. For example, methods and materials for detecting the presence or absence of target nucleic acid, methods and materials for detecting the amount of target nucleic acid present within a sample, kits for detecting the presence or absence of target nucleic acid, kits for detecting the amount of target nucleic acid present within a sample, and methods for making such kits are provided. ## Claims ### Claim 1 A method for assessing a mammal for an infection, said method comprising: (a) contacting a sample from said mammal with a probe nucleic acid comprising a nucleotide sequence complementary to a sequence of a target nucleic acid present within a microorganism or virus under conditions wherein, if said target nucleic acid is present in said sample, at least a portion of said target nucleic acid hybridizes to at least a portion of said probe nucleic acid to form a double-stranded portion of nucleic acid comprising a restriction endonuclease cut site, wherein said probe nucleic acid comprises a restriction endonuclease, (b) contacting said double-stranded portion of nucleic acid with a recognition restriction endonuclease having the ability to cut said double-stranded portion of nucleic acid at said restriction endonuclease cut site under conditions wherein said recognition restriction endonuclease cleaves said double-stranded portion of nucleic acid at said restriction endonuclease cut site, thereby separating a portion of said probe nucleic acid comprising said restriction endonuclease from at least another portion of said probe nucleic acid, (c) contacting said portion of said probe nucleic acid comprising said restriction endonuclease with signal expansion nucleic acid comprising an amplifying restriction endonuclease, a label, and a double-stranded portion of nucleic acid comprising a restriction endonuclease cut site of said restriction endonuclease under conditions wherein said restriction endonuclease cleaves said signal expansion nucleic acid at said restriction endonuclease cut site of said restriction endonuclease, thereby separating a first portion of said signal expansion nucleic acid from at least another portion of said signal expansion nucleic acid, wherein said first portion comprises said label, and (d) determining the presence or absence of said first portion using said label, wherein the presence of said first portion indicates that said sample contains said target nucleic acid, thereby indicating that said mammal is infected with said microorganism or virus, and wherein the absence of said first portion indicates that said sample does not contain said target nucleic acid, thereby indicating that said mammal is not infected with said microorganism or virus. ### Claim 2 (depends on 1) The method of claim 1, wherein said mammal is a human. ### Claim 3 (depends on 1) The method of claim 1, wherein said mammal is a farm animal selected from the group consisting of bovine, porcine, and equine species. ### Claim 4 (depends on 1) The method of claim 1, wherein said mammal is a dog or cat. ### Claim 5 (depends on 1) The method of claim 1, wherein said infection is a microbial infection, and wherein said target nucleic acid is present within a microorganism. ### Claim 6 (depends on 1) The method of claim 1, wherein said infection is a viral infection, and wherein said target nucleic acid is present within a virus. ### Claim 7 (depends on 1) The method of claim 1, wherein said sample comprises a nasal or throat swab sample. ### Claim 8 (depends on 1) The method of claim 1, wherein said sample is selected from the group consisting of nasal samples, throat samples, sputum samples, bronchial lavage samples, tissue samples, cellular samples, and blood samples. ### Claim 9 (depends on 1) The method of claim 1, wherein, prior to step (a), said sample was cultured to enrich the population of microorganisms or viruses, if present, within said sample. ### Claim 10 (depends on 9) The method of claim 9, wherein said sample was cultured for at least 30 minutes in the presence of enrichment medium. ### Claim 11 (depends on 1) The method of claim 1, wherein, prior to step (a), said sample was processed to remove non-nucleic acid material from said sample, thereby increasing the concentration of nucleic acid, if present, within said sample. ### Claim 12 (depends on 1) The method of claim 1, wherein said probe nucleic acid is attached to a solid support. ### Claim 13 (depends on 1) The method of claim 1, wherein step (a) and step (b) are performed in the same compartment. ### Claim 14 (depends on 1) The method of claim 1, wherein step (a) and step (b) are performed by adding said sample to a compartment comprising said probe nucleic acid and said recognition restriction endonuclease. ### Claim 15 (depends on 1) The method of claim 1, wherein said label is a fluorescent label, a radioactive label, an enzyme label, or a redox label. ### Claim 16 (depends on 1) The method of claim 1, wherein said determining step comprises determining the amount of said target nucleic acid present within said sample. ### Claim 17 (depends on 1) The method of claim 1, wherein said probe nucleic acid is single-stranded probe nucleic acid. ### Claim 18 (depends on 1) The method of claim 1, wherein said restriction endonuclease is an EcoRI endonuclease, and wherein said amplifying restriction endonuclease is an EcoRI endonuclease. ### Claim 19 (depends on 1) The method of claim 1, wherein said restriction endonuclease is a BamHI endonuclease, and wherein said amplifying restriction endonuclease is a BamHI endonuclease. ### Claim 20 (depends on 1) The method of claim 1, wherein said restriction endonuclease cut site of said restriction endonuclease is an EcoRI endonuclease cut site or a BamHI endonuclease cut site.