Compositions and assays to detect influenza virus A and B nucleic acids

• US 8,338,095 B2
• Filed: 05/28/2010
• Issued: 12/25/2012
• Est. Priority Date: 05/06/2005
• Status: Active Grant

• Current Assignee: Gen-Probe Incorporated (Hologic Incorporated)
• Original Assignee: Gen-Probe Incorporated (Hologic Incorporated)
• Inventors: Darby, Paul M., Getman, Damon K., Norman, Sylvia A., Pollner, Reinhold B., Marlowe, Elizabeth M.
• Primary Examiner(s): SITTON, JEHANNE SOUAYA
• Application Number:
  US12/789,897
• Publication Number:
  US 20100285450A1
• Time in Patent Office: 942 Days
• Field of Search: None
• US Class Current: 435/6.1
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 1/701 Specific hybridization probes

Abstract

Methods for detecting influenza virus A and influenza virus B nucleic acids in biological samples by using in vitro amplification and detection are disclosed. Compositions that are target-specific nucleic acid sequences and kits comprising target-specific nucleic acid oligomers for amplifying in vitro influenza virus A or influenza virus B nucleic acid and detecting amplified nucleic acid sequences are disclosed.

Claims

1. A method for amplifying and detecting influenza virus A in a sample comprising the steps of:

(a) contacting a sample suspected of containing influenza virus A nucleic acid with a combination of oligomers, said combination of oligomers comprising;

(i) a first amplification oligomer having a target specific sequence consisting essentially of SEQ ID NO;

23 or the reverse complement of SEQ ID NO;

23; and

(ii) a second amplification oligomer that is sufficiently complementary to the influenza A nucleic acid to hybridize and participate in a nucleic acid amplification reaction, the second amplification oligomer having a target specific sequence 21 to 23 bases long, wherein the target specific sequence contains SEQ ID NO;

17 or the reverse complement of SEQ ID NO;

17;

(b) performing a nucleic acid amplification reaction; and

(c) detecting an amplification product generated in step (b), thereby determining the presence or absence of influenza A virus in the sample.

2. The method of claim 1, wherein the second amplification oligomer has a target specific sequence selected from the group consisting of SEQ ID NO:

13, SEQ ID NO;

14, SEQ ID NO;

15, SEQ ID NO;

16, SEQ ID NO;

17, SEQ ID NO;

18 and the reverse complement of any one of the aforementioned sequences.

3. The method of claim 1, wherein either the first amplification oligomer or the second amplification oligomer contains a promoter sequence.

4. The method of claim 1, wherein the detecting step uses an oligonucleotide detection probe.

5. The method of claim 4, wherein the contacting step further comprises contacting the sample with the detection probe.

6. The method of claim 4, wherein the detection probe is added to the reaction after step (a).

7. The method of claim 4, wherein the target specific sequence of the detection probe is selected from the group consisting of SEQ ID NO:

25, SEQ ID NO;

26, SEQ ID NO;

27, SEQ ID NO;

28, SEQ ID NO;

29, SEQ ID NO;

30, SEQ ID NO;

31, and the reverse complement of any one of the aforementioned sequences.

8. The method of claim 4, wherein the detection probe comprises at least one detectable label.

9. The method of claim 8, wherein the detection probe is a TaqMan probe, a molecular torch or a molecular beacon.

10. The method of claim 8, wherein the detectable label is a chemiluminescent compound.

11. The method of claim 1, wherein detecting step is a real-time detection reaction.

12. The method of claim 1, wherein the detecting step uses a homogenous detection reaction.

13. The method of claim 1, wherein the nucleic acid amplification reaction is a multiplex reaction.

14. The method of claim 13, wherein the nucleic acid amplification reaction is a multiplex reaction comprising a target nucleic acid that is an internal control target sequence.

15. The method of claim 14, wherein the internal control target sequence is amplified using one or more amplification oligomers having a target specific sequence selected from the group consisting of SEQ ID NO:

61, SEQ ID NO;

62, SEQ ID NO;

64, SEQ ID NO;

66, SEQ ID NO;

67, and combinations thereof.

16. The method of claim 13, wherein the nucleic acid amplification reaction is a multiplex reaction and wherein the sample further contains a nucleic acid from influenza virus B.

17. The method of claim 1 further comprising a target capture step to separate or purify the influenza virus A nucleic acid prior to the contacting step wherein the target capture step uses a target capture probe.

18. The method of claim 17, wherein the target specific sequence of the target capture probe is selected from the group consisting of SEQ ID NO:

3, SEQ ID NO;

4, reverse complement of SEQ ID NO;

3, and the reverse complement of SEQ ID NO;

4.

19. The method of claim 18, wherein the target capture probe is selected from the group consisting of SEQ ID NO:

5 and SEQ ID NO;

6.

20. The method of claim 1, wherein the amplification reaction uses thermal cycling.

21. The method of claim 1, wherein the amplification reaction is isothermal.