# US 2021/0340636 A1 · Assays for the Detection of SARS-CoV-2

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- Number: US 2021/0340636 A1
- Document ID: US20210340636A1
- Status: Published application
- Kind: A1
- Application number: 17/374,333
- Filed: 2021-07-13
- Published: 2021-11-04
- Earliest claimed: 2020-03-31
- Assignees: DiaSorin S.p.A.
- Applicants: DiaSorin S.p.A.
- Inventors: Chiara Brambati; Simone Bocchetta; Giulia Minnucci
- Web page: https://patentgrep.com/patent/US20210340636A1

## CPC

- C12Q 1/701: {Specific hybridization probes}
- C12Q 2600/156: Polymorphic or mutational markers
- 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

The present invention is directed to methods for assaying for the presence of SARS-CoV-2 in a sample, including a clinical sample, and to oligonucleotides, reagents, and kits useful in such assays. In particular, the present invention is directed to such assays that are rapid, accurate and specific for the detection of SARS-CoV-2.

## Claims

### Claim 1

A detectably labeled oligonucleotide that is capable of specifically hybridizing to a SARS-CoV-2 polynucleotide, wherein the nucleotide sequence of said detectably labeled oligonucleotide that is capable of specifically hybridizing to said SARS-CoV-2 polynucleotide is able to hybridize to an oligonucleotide having a nucleotide sequence that consists essentially of the nucleotide sequence atggtgtt, or aatggtgtt, or the respective complements thereof, aacaccat and aacaccatt.

### Claim 2 (depends on 1)

The detectably labeled oligonucleotide of claim 1, wherein said oligonucleotide is able to hybridize to an oligonucleotide having a nucleotide sequence that consists essentially of the nucleotide sequence atggtgtt.

### Claim 3 (depends on 1)

The detectably labeled oligonucleotide of claim 1, wherein said oligonucleotide is able to hybridize to an oligonucleotide having a nucleotide sequence that consists essentially of the nucleotide sequence aatggtgtt.

### Claim 4 (depends on 1)

The detectably labeled oligonucleotide of claim 1, wherein said oligonucleotide is able to hybridize to an oligonucleotide having a nucleotide sequence that consists essentially of the nucleotide sequence aacaccat.

### Claim 5 (depends on 1)

The detectably labeled oligonucleotide of claim 1, wherein said oligonucleotide is able to hybridize to an oligonucleotide having a nucleotide sequence that consists essentially of the nucleotide sequence aacaccatt.

### Claim 6 (depends on 5)

The detectably labeled oligonucleotide of claim 5, wherein said oligonucleotide consists essentially of the nucleotide sequence of SEQ ID NO:153.

### Claim 7

A kit for detecting the presence of SARS-CoV-2 in a clinical sample, wherein said kit comprises:
(A) one or more oligonucleotide primers capable of amplifying a portion of a SARS-CoV-2 polynucleotide; and
(B) a detectably labeled oligonucleotide that is capable of specifically hybridizing to said amplified portion of said SARS-CoV-2 polynucleotide, wherein the nucleotide sequence of said detectably labeled oligonucleotide that is capable of specifically hybridizing to said SARS-CoV-2 polynucleotide is able to hybridize to an oligonucleotide having a nucleotide sequence that consists essentially of the nucleotide sequence atggtgtt, or aatggtgtt, or the respective complements thereof, aacaccat and aacaccatt.

### Claim 8 (depends on 7)

The kit of claim 7, wherein said kit permits the detection of the N501Y polymorphism of the S gene of SARS-CoV-2.

### Claim 9 (depends on 7)

The kit of claim 7, wherein said kit is a multi-chambered, fluidic device.

### Claim 10 (depends on 7)

The kit of claim 7, wherein said detectably labeled oligonucleotide is a TaqMan probe, a molecular beacon probe, a scorpion primer-probe, or a HyBeacon probe.

### Claim 11 (depends on 7)

The kit of claim 7, wherein said detectably labeled oligonucleotide is fluorescently labeled.

### Claim 12 (depends on 7)

The kit of claim 7, wherein said kit comprises a second detectably labeled oligonucleotide, wherein the detectable labels of said oligonucleotides are distinguishable, and wherein the nucleotide sequence of said second detectably labeled oligonucleotide is capable of specifically hybridizing to an amplified portion of said SARS-CoV-2 polynucleotide, wherein the nucleotide sequence of said second detectably labeled oligonucleotide that is capable of specifically hybridizing to said SARS-CoV-2 polynucleotide is able to specifically hybridize to an oligonucleotide having a nucleotide sequence that consists essentially of the nucleotide sequence of SEQ ID NO:7 or SEQ ID NO:8.

### Claim 13 (depends on 12)

The kit of claim 12, wherein said kit permits the detection of the D614G polymorphism of the S gene of SARS-CoV-2.

### Claim 14 (depends on 13)

The kit of claim 13, wherein said kit additionally permits the detection of the N501Y polymorphism of the S gene of SARS-CoV-2.

### Claim 15 (depends on 12)

The kit of claim 12, wherein said kit is a multi-chambered, fluidic device.

### Claim 16 (depends on 12)

The kit of claim 12, wherein said detectably labeled oligonucleotide is a TaqMan probe, a molecular beacon probe, a scorpion primer-probe, or a HyBeacon probe.

### Claim 17 (depends on 12)

The kit of claim 12, wherein the distinguishable detectable labels of said oligonucleotides are fluorescent labels.

### Claim 18

A method for detecting the presence of SARS-CoV-2 in a clinical sample, wherein said method comprises incubating said clinical sample in vitro in the presence of a detectably labeled oligonucleotide that is capable of specifically hybridizing to a SARS-CoV-2 polynucleotide, wherein the nucleotide sequence of said detectably labeled oligonucleotide that is capable of specifically hybridizing to said SARS-CoV-2 polynucleotide is able to specifically hybridize to an oligonucleotide having a nucleotide sequence that consists essentially of the nucleotide sequence atggtgtt, or aatggtgtt, or the respective complements thereof, aacaccat and aacaccatt; wherein said method detects the presence of SARS-CoV-2 in said clinical sample by detecting hybridization between a SARS-CoV-2 polynucleotide in said clinical sample and said detectably labeled oligonucleotide.

### Claim 19 (depends on 18)

The method of claim 18, wherein said method comprises a PCR amplification of said SARS-CoV-2 polynucleotide.

### Claim 20 (depends on 18)

The method of claim 18, wherein said detectably labeled oligonucleotide is a TaqMan probe, a molecular beacon probe, a scorpion primer-probe, or a HyBeacon probe.

### Claim 21 (depends on 18)

The method of claim 18, wherein said method comprises a LAMP amplification of said SARS-CoV-2 polynucleotide.

### Claim 22 (depends on 18)

The method of claim 18, wherein said detectably labeled oligonucleotide is fluorescently labeled.

### Claim 23 (depends on 18)

The method of claim 18, wherein said method permits the detection of the N501Y polymorphism of the S gene of SARS-CoV-2.

### Claim 24 (depends on 18)

The method of claim 18, wherein said method additionally comprises incubating said clinical sample in the presence of a second detectably labeled oligonucleotide, wherein the detectable labels of said oligonucleotides are distinguishable, and wherein the nucleotide sequence of said second detectably labeled oligonucleotide is capable of specifically hybridizing to an amplified portion of said SARS-CoV-2 polynucleotide, wherein the nucleotide sequence of said second detectably labeled oligonucleotide that is capable of specifically hybridizing to said SARS-CoV-2 polynucleotide is able to specifically hybridize to an oligonucleotide having a nucleotide sequence that consists essentially of the nucleotide sequence of SEQ ID NO:7 or SEQ ID NO:8.

### Claim 25 (depends on 24)

The method of claim 24, wherein said method permits the detection of the D614G polymorphism of the S gene of SARS-CoV-2.

### Claim 26 (depends on 25)

The method of claim 25, wherein said method additionally permits the detection of the N501Y polymorphism of the S gene of SARS-CoV-2.

### Claim 27 (depends on 24)

The method of claim 24, wherein the distinguishable detectable labels of said oligonucleotides are fluorescent labels.