IP Library › Granted Patent US 11,332,798
Granted Patent B2
US 11,332,798 · App. 16/659,375 · Granted May 17, 2022

Compositions and methods for detecting Zika virus nucleic acid

Inventors: Kui Gao (San Diego, CA); Jeffrey M. Linnen (Poway, CA)
Assignee: GEN-PROBE INCORPORATED
C12Q1/701C12Q2600/158C12Q2600/16
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Quick Facts
Patent No.
US 11,332,798
App. No.
16/659,375
Granted
May 17, 2022
Kind
B2
Abstract

Disclosed are nucleic acid oligomers, including amplification oligomers, capture probes, and detection probes, for detection of Zika virus nucleic acid. Also disclosed are methods of specific nucleic acid amplification and detection using the disclosed oligomers, as well as corresponding reaction mixtures and kits.

Claims (50)

1. A combination of at least three oligomers for determining the presence or absence of a Zika virus nucleic acid in a sample, the oligomer combination comprising:

at least two amplification oligomers configured to amplify a target sequence corresponding to a Zika virus target nucleic acid and at least one detectably labeled probe oligomer, wherein a first amplification oligomer and a second amplification oligomer are configured to hybridize to opposite ends of the target sequence to generate amplification products;

wherein

(i) the first amplification oligomer comprises a target-hybridizing sequence that is selected from the group consisting of SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:20, SEQ ID NO:21, and SEQ ID NO:23, and the second amplification oligomer comprises a target-hybridizing sequence consisting of SEQ ID NO:125; or

(ii) the first amplification oligomer comprises a target-hybridizing sequence that is selected from the group consisting of SEQ ID NO:11, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:22, and SEQ ID NO:23, and the second amplification oligomer comprises a target-hybridizing sequence that is selected from the group consisting of SEQ ID NO:114 and SEQ ID NO:127; or

(iii) the first amplification oligomer comprises a target-hybridizing sequence that is selected from the group consisting of SEQ ID NO:12, SEQ ID NO:18, SEQ ID NO:19, and SEQ ID NO:21, and the second amplification oligomer comprises a target-hybridizing sequence consisting of SEQ ID NO:131; or

(iv) the first amplification oligomer comprises a target-hybridizing sequence that is selected from the group consisting of SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:19, and SEQ ID NO:22, and the second amplification oligomer comprises a target-hybridizing sequence consisting of SEQ ID NO:133; or

(v) the first amplification oligomer comprises a target-hybridizing sequence that is selected from the group consisting of SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:21, SEQ ID NO:22, and SEQ ID NO:23, and the second amplification oligomer comprises a target-hybridizing sequence consisting of SEQ ID NO:114;

wherein the second amplification oligomer target-hybridizing sequence is joined at its 5′ end to a T7 promoter sequence; and

wherein the at least one detectably labeled probe oligomer comprises a target-hybridizing sequence consisting of SEQ ID NO:69.

2. An amplification reaction mixture, comprising the at least three oligomers of claim 1 , wherein (i) the mixture is a buffered aqueous solution; or (ii) the mixture is a dried composition.

3. A kit comprising the at least three oligomers of claim 1 .

4. A method for determining the presence or absence of a Zika virus nucleic acid in a sample, the method comprising the steps of:

(A) contacting a sample with a combination of at least two amplification oligomers configured to amplify a target sequence corresponding to a Zika virus target nucleic acid, wherein a first amplification oligomer and a second amplification oligomer are configured to hybridize to opposite ends of the target sequence to generate amplification products;

wherein

(i) the first amplification oligomer comprises a target-hybridizing sequence that is selected from the group consisting of SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:20, SEQ ID NO:21, and SEQ ID NO:23, and the second amplification oligomer comprises a target-hybridizing sequence consisting of SEQ ID NO:125; or

(ii) the first amplification oligomer comprises a target-hybridizing sequence that is selected from the group consisting of SEQ ID NO:11, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:22, and SEQ ID NO:23, and the second amplification oligomer comprises a target-hybridizing sequence consisting of SEQ ID NO:127; or

(iii) the first amplification oligomer comprises a target-hybridizing sequence that is selected from the group consisting of SEQ ID NO:12, SEQ ID NO:18, SEQ ID NO:19, and SEQ ID NO:21, and the second amplification oligomer comprises a target-hybridizing sequence consisting of SEQ ID NO:131; or

(iv) the first amplification oligomer comprises a target-hybridizing sequence that is selected from the group consisting of SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:19, and SEQ ID NO:22, and the second amplification oligomer comprises a target-hybridizing sequence consisting of SEQ ID NO:133; or

(v) the first amplification oligomer comprises a target-hybridizing sequence that is selected from the group consisting of SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:21, SEQ ID NO:22, and SEQ ID NO:23, and the second amplification oligomer comprises a target-hybridizing sequence consisting of SEQ ID NO:114;

wherein the second amplification oligomer target-hybridizing sequence is joined at its 5′ end to a T7 promoter sequence;

(B) performing an in vitro nucleic acid amplification reaction, wherein any Zika virus target nucleic acid present in the sample is used as a template for generating an amplification product; and

(C) contacting the amplification reaction with at least one detectably labeled probe oligomer comprising a target-hybridizing sequence consisting of SEQ ID NO:69, wherein said contacting is performed under conditions whereby the presence or absence of the amplification product is determined, thereby determining the presence or absence of the Zika virus nucleic acid in the sample.

5. A multiplex method for determining the presence or absence of a Zika virus nucleic acid in a sample, the method comprising the steps of:

(A) contacting a sample with at least two combinations of at least two amplification oligomers, each configured to amplify a separate target sequence of a Zika virus target nucleic acid, wherein the at least two combinations of at least two amplification oligomers comprise (i) a first combination comprising the at least two amplification oligomers of claim 1 combined with (ii) a second combination of at least two amplification oligomers;

(B) performing an in vitro nucleic acid amplification reaction, wherein the at least two amplification oligomers of (i) and/or (ii) hybridize their respective target sequence present in the sample to generate an amplification product(s); and

(C) contacting the amplification reaction with at least two detectably labeled probe oligomers, wherein a first detectably labeled probe oligomer comprises a target-hybridizing sequence consisting of SEQ ID NO:69, and wherein said contacting is performed under conditions whereby the presence or absence of the amplification product(s) is determined, thereby determining the presence or absence of the Zika virus nucleic acid in the sample.

6. The combination of claim 1 , wherein the T7 promoter sequence consists of SEQ ID NO:179.

7. The combination of claim 1 , wherein the first amplification oligomer comprises the target-hybridizing sequence that is selected from the group consisting of SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:20, SEQ ID NO:21, and SEQ ID NO:23, and the second amplification oligomer comprises the target-hybridizing sequence consisting of SEQ ID NO:125.

8. The combination of claim 7 , wherein the nucleotide sequence of the second amplification oligomer is SEQ ID NO:75.

9. The combination of claim 7 , wherein the first amplification oligomer target-hybridizing sequence is selected from the group consisting of SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:20, SEQ ID NO:21, and SEQ ID NO:23.

10. The combination of claim 1 , wherein the first amplification oligomer comprises the target-hybridizing sequence that is selected from the group consisting of SEQ ID NO:11, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:22, and SEQ ID NO:23, and the second amplification oligomer comprises the target-hybridizing sequence consisting of SEQ ID NO:127.

11. The combination of claim 10 , wherein the nucleotide sequence of the second amplification oligomer is selected from the group consisting of SEQ ID NO:78 and SEQ ID NO:79.

12. The combination of claim 10 , wherein the first amplification oligomer target-hybridizing sequence is selected from the group consisting of SEQ ID NO:15, SEQ ID NO:20, and SEQ ID NO:23.

13. The combination of claim 1 , wherein the first amplification oligomer comprises the target-hybridizing sequence that is selected from the group consisting of SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:21, and SEQ ID NO:23, and the second amplification oligomer comprises the target-hybridizing sequence consisting of SEQ ID NO:114.

14. The combination of claim 1 , wherein the first amplification oligomer comprises the target-hybridizing sequence that is selected from the group consisting of SEQ ID NO:12, SEQ ID NO:18, SEQ ID NO:19, and SEQ ID NO:21, and the second amplification oligomer comprises the target-hybridizing sequence consisting of SEQ ID NO:131.

15. The combination of claim 14 , wherein the nucleotide sequence of the second amplification oligomer consists of SEQ ID NO:83.

16. The combination of claim 14 , wherein the first amplification oligomer target-hybridizing sequence is SEQ ID NO:19.

17. The combination of claim 1 , wherein the first amplification oligomer comprises the target-hybridizing sequence that is selected from the group consisting of SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:19, and SEQ ID NO:22, and the second amplification oligomer comprises the target-hybridizing sequence consisting of SEQ ID NO:133.

18. The combination of claim 17 , wherein the nucleotide sequence of the second amplification oligomer consists of SEQ ID NO:86.

19. The combination of claim 17 , wherein the first amplification oligomer target-hybridizing sequence is selected from the group consisting of SEQ ID NO:11 and SEQ ID NO:19.

20. The combination of claim 1 , wherein the nucleotide sequences of the first amplification oligomer and second amplification oligomer are selected from the group consisting of

(i) SEQ ID NO:11 and SEQ ID NO:75,

(ii) SEQ ID NO:11 and SEQ ID NO:86,

(iii) SEQ ID NO:12 and SEQ ID NO:75,

(iv) SEQ ID NO:12 and SEQ ID NO:79,

(v) SEQ ID NO:14 and SEQ ID NO:79,

(vi) SEQ ID NO:20 and SEQ ID NO:75,

(vii) SEQ ID NO:20 and SEQ ID NO:78, and

(viii) SEQ ID NO:21 and SEQ ID NO:75.

Assignments (4)
RELEASE OF SECURITY INTEREST RECORDED AT REEL/FRAME 054089/0804 Recorded Apr 28, 2026
From: BANK OF AMERICA, N.A., AS COLLATERAL AGENT
To: HOLOGIC, INC., ON ITS OWN BEHALF AND AS SUCCESSOR-BY-MERGER TO FOCAL THERAPEUTICS, INC.; GEN-PROBE INCORPORATED; FAXITRON BIOPTICS, LLC; GEN-PROBE PRODESSE, INC.
Reel/Frame 075504/0575 →
SECURITY INTEREST Recorded Apr 8, 2026
From: BIOTHERANOSTICS, INC.; GEN-PROBE INCORPORATED; GEN-PROBE PRODESSE, INC.; CYTYC CORPORATION; SUROS SURGICAL SYSTEMS, INC.; GYNESONICS, INC.; BOLDER SURGICAL, LLC; FAXITRON BIOPTICS, LLC; HEALTH BEACONS, INC.; HOLOGIC, INC.
To: ROYAL BANK OF CANADA, AS COLLATERAL AGENT
Reel/Frame 075462/0440 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Apr 20, 2022
From: GAO, KUI; LINNEN, JEFFREY M.
To: GEN-PROBE INCORPORATED
Reel/Frame 059655/0417 →
SECURITY INTEREST Recorded Oct 15, 2020
From: HOLOGIC, INC.; FAXITRON BIOPTICS, LLC; FOCAL THERAPEUTICS, INC.; GEN-PROBE INCORPORATED; GEN-PROBE PRODESSE, INC.
To: BANK OF AMERICA, N.A., AS COLLATERAL AGENT
Reel/Frame 054089/0804 →