Compositions, methods and kits to detect herpes simplex virus nucleic acids
View Patent ↗The disclosed invention is related to methods, compositions, kits and isolated nucleic acid sequences for targeting Herpes Simplex Virus (HSV) nucleic acid (eg. HSV-1 and/or HSV-2 nucleic acid). Compositions include amplification oligomers, detection probe oligomers and/or target capture oligomers. Kits and methods comprise at least one of these oligomers.
1. A method for specifically detecting a Herpes Simplex Virus-1 (HSV-1) target nucleic acid in a sample comprising the steps of:
(a) providing a sample suspected of containing at least a HSV-1 target nucleic acid;
(b) contacting said sample with at least two amplification oligomers, wherein a first of said amplification oligomers comprises a target hybridizing sequence 15 to 25 nucleotides in length and configured to target a sequence in a region of the HSV-1 US8.5 ORF corresponding to nucleotides 124 to 156 of SEQ ID NO:1, and wherein a second of said amplification oligomers comprises a target hybridizing sequence comprising SEQ ID NO:10; and
(c) performing a nucleic acid detection reaction with a detection probe configured to detect a sequence in a region corresponding to nucleotides 173 to 196 of SEQ ID NO:1 that detects an amplification product to determine whether a HSV-1 target nucleic acid is present in said sample.
2. The method of claim 1 , wherein said first of said amplification oligomers comprises a target hybridizing sequence wherein said target hybridizing sequence consists of SEQ ID NO:7, or wherein said target hybridizing sequence consists of SEQ ID NO:8.
3. The method of claim 1 , wherein said second of said amplification oligomers further comprises a 5′ promoter sequence.
4. The method of claim P, wherein said detection is real-time detection.
5. The method of claim 1 , wherein said detection probe has a sequence consisting of SEQ ID NO:13, or consisting of SEQ ID NO: 14.
6. The method of claim 1 , further comprising the step of contacting said sample with a target capture oligomer.
7. The method of claim 6 , wherein said target capture oligomer is configured to hybridize to a US8.5 nucleic acid from HSV-1 and HSV-2.
8. The method of claim 6 , wherein said target capture oligomer comprises a target hybridizing sequence consisting of SEQ ID NO:3, or SEQ ID NO:5.
9. The method of claim 1 , wherein said amplification product is produced in an isothermal amplification reaction, a transcription mediated amplification reaction, or a strand displacement amplification reaction.
10. The method of claim 1 , wherein said amplification product is an RNA amplification product.
11. The method of claim 1 wherein the first of said amplification oligomers comprises a target hybridizing sequence consisting of SEQ ID NOS:7, or 8; and wherein the second of said amplification oligomers comprises a target hybridizing sequence consisting of SEQ ID NO:10 joined at its 5′ end to a promoter sequence; and wherein step (c) is performed using a detection probe oligomer the sequence of which consists of SEQ ID NO:13 or SEQ ID NO:14.
12. A composition for use in a Herpes Simplex Virus-1 (HSV-1) target nucleic acid amplification assay comprising at least two amplification oligomers capable of stably hybridizing to a HSV-1 US8.5 target nucleic acid, wherein the at least two amplification oligomers comprise first amplification oligomers and second amplification oligomers, wherein the first amplification oligonucleotides comprise a target binding sequence consisting of SEQ ID NO:7 or 8, and the second amplification oligonucleotides comprise a target binding sequence consisting of SEQ ID NO:10 joined at its 5′ end to a promoter sequence, wherein pairs of the first and second amplification oligonucleotides can hybridize to opposing strands of HSV-1 nucleic acid for transcription mediated amplification of the US8.5 target nucleic acid between hybridized pairs of the first and second amplification oligonucleotides.
13. The composition of claim 12 , wherein the sequence of the second amplification oligomer consists of SEQ ID NO:9.
14. The composition of claim 12 , further comprising a detection probe oligomer, the sequence of which consists of SEQ ID NO:13 or SEQ ID NO:14.
15. The composition of claim 14 , wherein at least one nucleotide in the detection probe oligomer sequence further comprises a modification selected from the group consisting of: 2′ methoxy substitutions and 2′ halide substitutions.
16. The composition of claim 12 , further comprising a target capture oligomer.
17. The composition of claim 16 , wherein said target capture oligomer is configured to hybridize to a US8.5 nucleic acid from HSV-1 and HSV-2.
18. The composition of claim 16 , wherein said target capture oligomer comprises a target binding region consisting of SEQ ID NO:3, or SEQ ID NO:5.
19. A kit comprising the composition of claim 12 , and optionally a set of instructions for using same.
20. The method of claim 1 , wherein the second of said amplification oligomers comprises a-sequence consisting of SEQ ID NO:9.
21. The method of claim 5 , wherein at least one nucleotide in the detection probe oligomer sequence further comprises a modification selected from the group consisting of: 2′ methoxy substitutions and 2′ halide substitutions.
22. The method of claim 21 , wherein the 2′ halide substitution is a 2′-F substitution.
23. The composition of claim 15 , wherein the 2′ halide substitution is a 2′-F substitution.