Compositions, methods and kits to detect herpes simplex virus nucleic acid

Patent metadata

Field	Value
Publication number	US-2016208345-A1
Application number	US-201514944532-A
Country	US
Kind code	A1
Filing date	Nov 18, 2015
Priority date	Apr 21, 2010
Publication date	Jul 21, 2016
Grant date	—

Abstract

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.

First claim

1 .- 93 . (canceled)

94 . A method for specifically detecting a Herpes Simplex Virus 2 (HSV-2) target nucleic acid in a sample comprising the steps of:
(a) providing a sample suspected of containing at least a HSV-2 target nucleic acid; (b) contacting said sample with at least two amplification oligomers, wherein a first amplification oligomer comprises a target hybridizing sequence 15 to 45 nucleotides in length and configured to target a sequence in a region of the HSV-2 US8.5 ORF corresponding to
nucleotides 113 to 144 of SEQ ID NO:2
and wherein a second amplification oligomers comprises a target hybridizing sequence 15 to 45 nucleotides in length and configured to target a sequence in a region of the HSV-2 US8.5 ORF corresponding to
nucleotides 172 to 200 of SEQ ID NO:2; and
(c) performing a nucleic acid detection reaction that detects an amplification product to determine whether a HSV target nucleic acid is present in said sample.

95 . The method of claim 94 , wherein said first amplification oligomer comprises, consists or consists essentially of a target hybridizing sequence configured to target a sequence in a region corresponding to nucleotides 113 to 130 or nucleotides 124 to 144 of SEQ ID NO:2; preferably,
wherein said amplification oligomer configured to target a sequence in a region corresponding to nucleotides 113 to 130 comprises, consists or consists essentially of the sequence set forth in SEQ ID NO:11; or wherein said amplification oligomer configured to target a sequence in a region corresponding to nucleotides 124 to 144 comprises, consists or consists essentially of the sequence set forth in SEQ ID NO: 12.

96 . The method of claim 94 , wherein said second amplification oligomers comprises, consists or consists essentially of a target hybridizing sequence configured to target a sequence in a region corresponding to nucleotides 172 to 193 or nucleotides 180 to 200 of SEQ ID NO:2; preferably,
wherein said second amplification oligomer configured to target a sequence in a region corresponding to nucleotides 172 to 193 comprises, consists or consists essentially of the sequence set forth in SEQ ID NO: 16; or wherein said second amplification oligomer configured to target a sequence in a region corresponding to nucleotides 180 to 200 comprises, consists or consists essentially of the sequence set forth in SEQ ID NO: 18.

97 . The method of claim 96 , wherein said second amplification oligomers further comprises a 5′ promoter sequence; preferably,
wherein the promoter is a T7 promoter; and/or
wherein said second amplification oligomers consists essentially of the sequence set forth in SEQ ID NOS: 15 or 17.

98 . The method of claim 94 , wherein said detection step comprises contacting an amplification product with a detection probe configured to detect a sequence in a region corresponding to nucleotides 148 to 169 of SEQ ID NO:2; preferably,
wherein said detection probe is configured to target a sequence in a region corresponding to nucleotides 150 to 169 of SEQ ID NO:2; preferably, wherein said detection probe configured to target a sequence in a region corresponding to nucleotides 150 to 169 of SEQ ID NO:2 comprises, consists or consists essentially of the sequence set forth in SEQ ID NO: 20; or wherein said detection probe is configured to target a sequence in a region corresponding to nucleotides 148 to 167 of SEQ ID NO:2, preferably, wherein said detection probe configured to target a sequence in a region corresponding to nucleotides 148 to 167 of SEQ ID NO:2 comprises, consists or consists essentially of the sequence set forth in SEQ ID NO: 19.

99 . The method of claim 94 , further comprising the step of contacting said sample with a target capture oligomer; preferably, wherein said target capture oligomer is configured to hybridize to a US8.5 nucleic acid from HSV-2; preferably,
wherein said target capture oligomer comprises a polyd(T) and/or a poly(A) tail.

100 . A method for specifically detecting a HSV-2 target nucleic acid in a sample comprising the steps of:
(a) providing a sample suspected of containing at least a HSV target nucleic acid; (b) contacting said sample with at least two amplification oligomers, wherein a first amplification oligomer comprises a target hybridizing sequence 15 to 45 nucleotides in length and containing a sequence comprising, consisting or consisting essentially of SEQ ID NOS: 11 or 12; and wherein a second amplification oligomer comprises a target hybridizing sequence 15 to 45 nucleotides in length and containing a sequence comprising, consisting or consisting essentially of SEQ ID NOS: 16 or 18; and (c) performing a nucleic acid detection reaction that detects an amplification product obtained from an amplification reaction of said amplification oligomers of step (b) and said HSV target nucleic acid, said detection reaction to determine whether a HSV-2 target nucleic acid is present in said sample, wherein said amplification product is detected using a detection probe oligomer configured to detect a sequence in a region corresponding to nucleotides 148 to 169 of SEQ ID NO:2.

101 . The method of claim 100 , wherein said detection probe is configured to target a sequence in a region corresponding to nucleotides 148 to 167 of SEQ ID NO:2; preferably,
wherein said detection probe configured to target a sequence in a region corresponding to nucleotides 148 to 167 of SEQ ID NO:2 comprises, consists or consists essentially of the sequence set forth in SEQ ID NO: 19; or wherein said detection probe is configured to target a sequence in a region corresponding to nucleotides 150 to 169 of SEQ ID NO:2; preferably, wherein said detection probe configured to target a sequence in a region corresponding to nucleotides 150 to 169 comprises, consists or consists essentially of the sequence set forth in SEQ ID NO: 20.

102 . A composition for use in a HSV-2 target nucleic acid amplification assay comprising at least two amplification oligomers capable of stably hybridizing to a HSV US8.5 target nucleic acid, wherein a first amplification oligomer comprises a target hybridizing sequence 15 to 45 nucleotides in length and configured to target a sequence in a region of the HSV US8.5 corresponding to
nucleotides 113 to 144 of SEQ ID NO:2 and wherein a second amplification oligomer comprises a target hybridizing sequence 15 to 45 nucleotides in length and configured to target a sequence in a region of the HSV US8.5 ORF corresponding to
nucleotides 172 to 200 of SEQ ID NO:2.

103 . The composition of claim 102 , wherein said first amplification oligomer comprises, consists or consists essentially of a target hybridizing sequence configured to target a sequence in a region corresponding to nucleotides 113 to 130 or nucleotides 124 to 144 of SEQ ID NO:2; preferably,
wherein said amplification oligomer configured to target a sequence in a region corresponding to nucleotides 113 to 130 comprises, consists or consists essentially of the sequence set forth in SEQ ID NO:11; or wherein said amplification oligomer configured to target a sequence in a region corresponding to nucleotides 124 to 144 comprises, consists or consists essentially of the sequence set forth in SEQ ID NO: 12.

104 . The composition of claim 102 , wherein said second amplification oligomer comprises, consists or consists essentially of a target hybridizing sequence configured to target a sequence in a region corresponding to nucleotides 172 to 193 or nucleotides 180 to 200 of SEQ ID NO:2; preferably,
wherein said second amplification oligomer configured to target a sequence in a region corresponding to nucleotides 172 to 193 comprises, consi

Assignees

• Gen Probe Inc

Inventors

• Getman Damon K
• Aiyer Aparna
• Chen Wendy

Classifications

• C12Q1/6865

  Promoter-based amplification, e.g. nucleic acid sequence amplification [NASBA], self-sustained sequence replication [3SR] or transcription-based amplification system [TAS] · CPC title

• C12Q2600/158

  Expression markers · CPC title

• C12Q1/705 Primary

  for herpetoviridae, e.g. herpes simplex, varicella zoster · CPC title