Compositions, methods and kits to detect Herpes Simplex virus nucleic acids

1. A method for determining the presence or absence of Herpes Simplex Virus 1 (HSV-1) or Herpes Simplex Virus 2 (HSV-2) in a sample, said method comprising:

(1) contacting a sample, said sample suspected of containing HSV-1 or HSV-2, with at least two oligomers for amplifying a target region of an HSV-1 target nucleic acid and at least two oligomers for amplifying a target region of an HSV-2 target nucleic acid,

wherein the at least two amplification oligomers for amplifying a target region of an HSV-1 target nucleic acid comprise

(a) a first amplification oligomer comprising a first target-hybridizing sequence that is from about 15 to about 27 contiguous nucleotides contained in the sequence of SEQ ID NO:31 and that includes at least the sequence of SEQ ID NO:30; and

(b) a second amplification oligomer comprising a second target-hybridizing sequence that is from about 15 to about 27 contiguous nucleotides contained in the sequence of SEQ ID NO:33 and that includes at least the sequence of SEQ ID NO:32;

and wherein the at least two amplification oligomers for amplifying a target region of an HSV-2 target nucleic acid comprise

(c) a third amplification oligomer comprising a third target-hybridizing sequence that is from about 15 to about 27 contiguous nucleotides (i) contained in the sequence of SEQ ID NO:49 and that includes at least the sequence of SEQ ID NO:48 or (ii) contained in the sequence of SEQ ID NO:43 and that includes at least the sequence of SEQ ID NO:42; and

(d) a fourth amplification oligomer comprising a fourth target-hybridizing sequence that is from about 15 to about 27 contiguous nucleotides (i) contained in the sequence of SEQ ID NO:51 and that includes at least the sequence of SEQ ID NO:50 or (ii) contained in the sequence of SEQ ID NO:45 and that includes at least the sequence of SEQ ID NO:44;

(2) performing an in vitro multiplex nucleic acid amplification reaction, wherein any HSV-1 or HSV-2 target nucleic acid present in said sample is used as a template for generating an HSV-1 or HSV-2 amplification product, respectively; and

(3) detecting the presence or absence of the HSV-1 amplification product and the presence or absence of the HSV-1 amplification product, thereby indicating the presence or absence of HSV-1 and HSV-2 in said sample.

2. The method of claim 1 , wherein the first target-hybridizing sequence has the sequence of SEQ ID NO: 20 or SEQ ID NO: 6, and/or the second target-hybridizing sequence has the sequence of SEQ ID NO: 7 or SEQ ID NO: 9.

3. The method of claim 1 , wherein the third target-hybridizing sequence has the sequence of SEQ ID NO: 24 and/or the fourth target hybridizing sequence has the sequence of SEQ ID NO: 25.

4. The method of claim 1 , wherein the third target-hybridizing sequence has the sequence of SEQ ID NO:14 and/or the fourth target hybridizing sequence has the sequence of SEQ ID NO:15.

5. The method of claim 1 , wherein

(a) the first and second target-hybridizing sequences respectively have the nucleotide sequences of

(i) SEQ ID NO:20 and SEQ ID NO:7;

(ii) SEQ ID NO:6 and SEQ ID NO:7; or

(iii) SEQ ID NO: 6 and SEQ ID NO: 9; and

(b) the third and fourth target-hybridizing sequences respectively have the nucleotide sequences of

(i) SEQ ID NO:24 and SEQ ID NO:25; or

SEQ ID NO:14 and SEQ ID NO:15.

6. The method of claim 1 , wherein the first amplification oligomer is a promoter primer or promoter provider further comprising a promoter sequence located 5′ to the first target-hybridizing sequence, and/or the third amplification oligomer is a promoter primer or promoter provider further comprising a promoter sequence located 5′ to the third target-hybridizing sequence.

7. The method of claim 6 , wherein the promoter sequence is a T7 promoter sequence.

8. The method of claim 1 , further comprising purifying the HSV-1 or HSV-2 target nucleic acid from other components in the sample before step (1).

9. The method of claim 8 , wherein the purifying step comprises contacting the sample with:

(a) at least one first capture probe oligomer comprising a target-hybridizing sequence, wherein (i) the target-hybridizing sequence is SEQ ID NO: 4 or SEQ ID NO: 18; or (ii) the target-hybridizing sequence is from about 15 to about 30 contiguous nucleotides contained in the sequence of SEQ ID NO:76 and includes at least the sequence of SEQ ID NO:75; or (iii) the target-hybridizing sequence is from about 15 to about 30 contiguous nucleotides contained in the sequence of SEQ ID NO:74 and includes at least the sequence of SEQ ID NO:73;

and

(b) at least one second capture probe oligomer comprising a target-hybridizing sequence wherein (i) the target-hybridizing sequence is SEQ ID NO:4, SEQ ID NO:18, SEQ ID NO:70, or SEQ ID NO:72; or (ii) the target-hybridizing sequence is SEQ ID NO:3, SEQ ID NO:17, SEQ ID NO:69, or SEQ ID NO:71; or (iii) the target-hybridizing sequence is from about 15 to about 30 contiguous nucleotides contained in the sequence of SEQ ID NO:76 and includes at least the sequence of SEQ ID NO:75; or (iv) the target-hybridizing sequence is from about 15 to about 30 contiguous nucleotides contained in the sequence of SEQ ID NO:74 and includes at least the sequence of SEQ ID NO:75.

10. The method of claim 9 , wherein the target-hybridizing sequences of the first and second capture oligomers are covalently attached to a sequence or moiety that binds to an immobilized probe.

11. The method of claim 1 , wherein the detecting step (3) comprises contacting said in vitro nucleic acid amplification reaction with a first detection probe oligomer configured to specifically hybridize to the HSV-1 amplification product and a second detection probe oligomer configured to specifically hybridize to the HSV-2 amplification product under conditions whereby the presence or absence of the HSV-1 and HSV-2 amplification products are determined, thereby indicating the presence or absence of HSV-1 and HSV-2 in said sample.

12. The method of claim 11 , wherein the first detection probe oligomer comprises (i) a target-hybridizing sequence that is from about 14 to about 40 nucleotides in length and is configured to specifically hybridize to a target sequence contained within SEQ ID NO:1 from about nucleotide position 635 to about nucleotide position 683 under conditions whereby the presence or absence of the amplification product is determined; (ii) a target-hybridizing sequence that is contained in the sequence of SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:40, or SEQ ID NO:41 and includes at least the sequence of SEQ ID NO:34, SEQ ID NO:35, or SEQ ID NO:38; or (iii) a target-hybridizing sequence that is SEQ ID NO:8, SEQ ID NO:10, or SEQ ID NO:22.

13. The method of claim 11 , wherein the second detection probe oligomer comprises (i) a target-hybridizing sequence that is from about 14 to about 25 nucleotides in length and is configured to specifically hybridize to a target sequence contained within SEQ ID NO:2 from about nucleotide position 608 to about nucleotide position 632; or (ii) a target-hybridizing sequence that is contained in the sequence of SEQ ID NO:53 and includes at least the sequence of SEQ ID NO:52; or (iii) a target-hybridizing sequence consisting of SEQ ID NO:27; or (iv) a target-hybridizing sequence that is from about 14 to about 30 nucleotides in length and is configured to specifically hybridize to a target sequence contained within SEQ ID NO:2 from about nucleotide position 549 to about nucleotide position 578; or (v) a target-hybridizing sequence that is contained in the sequence of SEQ ID NO:47 and includes at least the sequence of SEQ ID NO:46; or (vi) a target-hybridizing sequence consisting of SEQ ID NO:16.

14. The method of claim 11 , wherein the first detection probe oligomer and/or the second detection probe oligomer further comprises a detectable label.

15. The method of claim 11 , wherein the first detection probe oligomer and/or the second detection probe oligomer further comprises a non-target-hybridizing sequence.

16. A composition comprising at least four oligomers for determining the presence or absence of Herpes Simplex Virus 1 (HSV-1) and Herpes Simplex Virus 2 (HSV-2) in a sample, said oligomer combination comprising:

first and second amplification oligomers for amplifying a target region of an HSV-1 target nucleic acid, wherein

(a) a first amplification oligomer comprising a first target-hybridizing sequence that is from about 15 to about 27 contiguous nucleotides contained in the sequence of SEQ ID NO:31 and that includes at least the sequence of SEQ ID NO:30; and

(b) a second amplification oligomer comprising a second target-hybridizing sequence that is from about 15 to about 27 contiguous nucleotides contained in the sequence of SEQ ID NO:33 and that includes at least the sequence of SEQ ID NO:32;

and third and fourth amplification oligomers for amplifying a target region of an HSV-2 target nucleic acid, wherein

(c) the third amplification oligomer comprises a third target-hybridizing sequence that is from about 15 to about 27 contiguous nucleotides (i) contained in the sequence of SEQ ID NO:49 and that includes at least the sequence of SEQ ID NO:48 or (ii) contained in the sequence of SEQ ID NO:43 and that includes at least the sequence of SEQ ID NO:42; and

(d) the fourth amplification oligomer comprises a fourth target-hybridizing sequence that is from about 15 to about 27 contiguous nucleotides (i) contained in the sequence of SEQ ID NO:51 and that includes at least the sequence of SEQ ID NO:50 or (ii) contained in the sequence of SEQ ID NO:45 and that includes at least the sequence of SEQ ID NO:44.

17. The composition of claim 16 , wherein the composition is a reaction mixture.

18. The composition of claim 17 , further comprising a first detection probe oligomer configured to specifically hybridize to an amplification product produced by the first and second amplification oligomers and/or a second detection probe oligomer configured to specifically hybridize to an amplification product produced by the third and fourth amplification oligomers, wherein the first detection probe oligomer and/or the second detection probe oligomer comprises a detectable label.

19. The composition of claim 17 , wherein the first detection probe oligomer and/or second detection probe oligomer further comprises a non-target-hybridizing sequence.

20. The composition of claim 17 , wherein the first amplification oligomer and/or the third amplification oligomer is a promoter primer or a promoter provider further comprising a promoter sequence located 5′ to its target-hybridizing sequence.