# US 2021/0340622 A1 · Polynucleotides for amplification and detection of sars-cov-2

> Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt

- Number: US 2021/0340622 A1
- Document ID: US20210340622A1
- Status: Published application
- Kind: A1
- Application number: 17/325,390
- Filed: 2021-05-20
- Published: 2021-11-04
- Earliest claimed: 2020-03-23
- Assignees: Talis Biomedical Corporation
- Applicants: Talis Biomedical Corporation
- Inventors: Nadya Andini; Kathy Chiu; Xuewen Jiang; Hédia Maamar
- Web page: https://patentgrep.com/patent/US20210340622A1

## CPC

- C12Q 1/6876: Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q 1/701: {Specific hybridization probes}
- C12Q 1/6813: Hybridisation assays
- C12Q 1/6844: Nucleic acid amplification reactions
- C12Q 1/6853: using modified primers or templates
- C12Q 1/70: involving virus or bacteriophage {(immunoassay for viruses G01N33/56983)}
- C12Q 2521/101: DNA polymerase
- C12Q 2521/107: RNA dependent DNA polymerase,(i.e. reverse transcriptase)
- C12Q 2531/119: Strand displacement amplification [SDA]
- C12Q 2600/112: Disease subtyping, staging or classification
- Y02A 50/30: Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change
- 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
- Y02A: TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE

## Abstract

Disclosed herein are primers and probes related to the detection of SARS-CoV-2 via nucleic acid amplification testing (NAAT), for example to amplify and determine the presence of SARS-CoV-2 in test samples and/or to diagnose Covid-19. Specifically, the present disclosure describes primers and probes that bind to the N gene, ORF1ab, or E gene of SARS-CoV-2 coronavirus for detection via loop mediated isothermal amplification (LAMP) and molecular beacon hybridization.

## Claims

### Claim at position 1

-30. (canceled)

### Claim 31

A composition comprising SEQ ID NO: 49, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, and SEQ ID NO: 54.

### Claim 32 (depends on 31)

The composition of claim 31, further comprising a molecular beacon comprising a fluorophore, a quencher and a polynucleotide.

### Claim 33 (depends on 32)

The composition of claim 32, wherein the polynucleotide comprises a sequence selected from the group consisting of: nucleotides 5-22 of SEQ ID NO: 75, nucleotides 5-22 of SEQ ID NO: 76, nucleotides 5-22 of SEQ ID NO: 80, nucleotides 5-22 of SEQ ID NO: 81, nucleotides 4-22 of SEQ ID NO: 82, nucleotides 6-28 of SEQ ID NO: 83, nucleotides 6-25 of SEQ ID NO: 84, and nucleotides 3-23 of SEQ ID NO: 85.

### Claim 34 (depends on 33)

The composition of claim 33, wherein the polynucleotide comprises a sequence selected from the group consisting of: SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 80, SEQ ID NO: 81, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, and SEQ ID NO: 85.

### Claim 35 (depends on 34)

The composition of claim 34, wherein the polynucleotide consists a sequence selected from the group consisting of: SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 80, SEQ ID NO: 81, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, and SEQ ID NO: 85.

### Claim 36 (depends on 32)

The composition of claim 32, wherein the fluorophore is FAM and the quencher is BHQ1.

### Claim 37 (depends on 32)

The composition of claim 32, wherein the fluorophore is ATTO 565 or Alexa 594 and the quencher is BHQ1 or BHQ2.

### Claim 38 (depends on 31)

The composition of claim 31, further comprising an intercalating dye.

### Claim 39 (depends on 31)

The composition of claim 31, further comprising a strand displacement DNA polymerase and a reverse transcriptase.

### Claim 40

A composition comprising a set of polynucleotides selected from the group consisting of: Set-5 and Set-9.

### Claim 41

A method of detecting SARS-CoV-2 in a test sample, the method comprising:
(a) extracting nucleic acid from the test sample;
(b) amplifying a target sequence by reacting the nucleic acid extracted in step (a) with a reaction mixture comprising a strand displacement DNA polymerase activity, a reverse transcriptase activity, and a sequence-specific primer set, wherein said sequence-specific primer set is selected from the group consisting of: Set-5 and Set-9; and
(c) detecting the presence or absence of an amplification product from step (b);
wherein the presence of said amplification product is indicative of the presence of SARS-CoV-2 in the test sample.

### Claim 42 (depends on 41)

The method of claim 41, wherein the amplification in step (b) of the target sequence is performed between about 60° C. and about 67° C. for less than 30 minutes.

### Claim 43 (depends on 42)

The method of claim 42, wherein the amplification step is performed for less than fifteen minutes.

### Claim 44 (depends on 43)

The method of claim 43, wherein the amplification step is performed for less than twelve minutes.

### Claim 45 (depends on 44)

The method of claim 44, wherein the amplification step is performed for less than nine minutes.

### Claim 46 (depends on 41)

The method of claim 41, wherein detecting the presence or absence of the amplification product comprises hybridizing the amplification product with a probe comprising a polynucleotide attached to a label.

### Claim 47 (depends on 46)

The method of claim 46, wherein the label is a fluorophore.

### Claim 48 (depends on 47)

The method of claim 47, wherein the fluorophore is covalently attached to a terminus of the polynucleotide.

### Claim 49 (depends on 46)

The method of claim 46, wherein the labeled polynucleotide comprises a sequence selected from the group consisting: of nucleotides 5-22 of SEQ ID NO: 75, nucleotides 5-22 of SEQ ID NO: 76, nucleotides 5-22 of SEQ ID NO: 80, nucleotides 5-22 of SEQ ID NO: 81, nucleotides 4-22 of SEQ ID NO: 82, nucleotides 6-28 of SEQ ID NO: 83, nucleotides 6-25 of SEQ ID NO: 84, and nucleotides 3-23 of SEQ ID NO: 85.

### Claim 50 (depends on 49)

The method of claim 49, wherein the labeled polynucleotide comprises a sequence selected from the group consisting of: SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 80, SEQ ID NO: 81, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, and SEQ ID NO: 85.

### Claim 51 (depends on 50)

The method of claim 50, wherein the sequence-specific primer set is Set-9 and the sequence of the labeled polynucleotide is SEQ ID NO: 83.

### Claim 52 (depends on 31)

A kit comprising the composition of claim 31.

### Claim 53 (depends on 52)

The kit of claim 52, further comprising a strand displacement polymerase and a reverse transcriptase.

### Claim 54 (depends on 53)

The kit of claim 53, further comprising a molecular beacon comprising a fluorophore, a quencher, and a polynucleotide.

### Claim 55 (depends on 54)

The kit of claim 54, wherein the polynucleotide comprises a sequence selected from the group consisting of: nucleotides 5-22 of SEQ ID NO: 75, nucleotides 5-22 of SEQ ID NO: 76, nucleotides 5-22 of SEQ ID NO: 80, nucleotides 5-22 of SEQ ID NO: 81, nucleotides 4-22 of SEQ ID NO: 82, nucleotides 6-28 of SEQ ID NO: 83, nucleotides 6-25 of SEQ ID NO: 84, and nucleotides 3-23 of SEQ ID NO: 85.

### Claim 56 (depends on 55)

The kit of claim 55, wherein the polynucleotide comprises a sequence selected from the group consisting of: SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 80, SEQ ID NO: 81, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, and SEQ ID NO: 85.

### Claim 57 (depends on 56)

The kit of claim 56, wherein the polynucleotide consists a sequence selected from the group consisting of: SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 80, SEQ ID NO: 81, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, and SEQ ID NO: 85.

### Claim 58 (depends on 57)

The kit of claim 57, wherein the polynucleotide consists of SEQ ID NO: 83.