Assay for detection of human parvovirus nucleic acid
Nucleic acid oligomers specific for human parvovirus genomic DNA are disclosed. An assay for amplifying and detecting human parvovirus genotypes 1, 2 and 3 nucleic acid in biological specimens is disclosed. Compositions for amplifying and detecting the presence of human parvovirus genotypes 1, 2 and 3 genomic DNA in human biological specimens are disclosed.
1. A method for the detection of human parvovirus from a sample comprising the steps of:
a) obtaining a sample suspected of containing human parvovirus genotype 1, genotype 2, or genotype 3;
b) contacting the sample with an amplification oligomer combination comprising:
i) at least one primer oligomer member comprising a target-binding sequence that is SEQ ID NO:48 or SEQ ID NO:50;
ii) a first promoter-based oligomer member that is SEQ ID NO:73; and
iii) a second promoter-based oligomer member that is SEQ ID NO:78;
c) performing an isothermal amplification reaction on the sample to generate an amplicon from a human parvovirus in the sample or from an amplicon thereof; and
d) detecting the amplicon with a detection probe oligomer; wherein the presence of an amplicon as determined by the detecting step indicates that one or more of human parvovirus genotypes 1, 2 and 3 are present in the sample.
2. The method of claim 1 , wherein the at least one primer oligomer member comprises the target-binding sequence that is SEQ ID NO:50.
3. The method of claim 1 , wherein the at least one primer oligomer member comprises the target-binding sequence that is SEQ ID NO:48.
4. The method of claim 3 , wherein the at least one primer oligomer member is SEQ ID NO:47.
5. The method of claim 1 , wherein the at least one primer oligomer member comprises a 5′ tag sequence.
6. The method of claim 1 , wherein the at least one primer member is selected from the group consisting of SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:50, and combinations thereof.
7. The method of claim 1 , wherein the detection probe oligomer is selected from the group consisting of SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:31, SEQ ID NO:32, SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, and SEQ ID NO:46.
8. The method of claim 1 , further comprising the step of contacting the sample with a target capture oligomer.
9. The method of claim 8 , wherein the target capture oligomer comprises a 3′ tail portion and a target-binding sequence selected from the group consisting of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:53, and combinations thereof.
10. The method of claim 9 , wherein the target capture oligomer is SEQ ID NO:52.
11. A method for the detection of human parvovirus from a sample comprising the steps of:
a) obtaining a sample suspected of containing human parvovirus genotype 1, genotype 2, or genotype 3;
b) contacting the sample with an amplification oligomer combination comprising at least one primer oligomer member and at least one promoter-based oligomer member, wherein the at least one primer oligomer member and the at least one promoter-based oligomer member hybridize to opposing strands of a human parvovirus genotype 1, 2 or 3 nucleic acid or amplicon thereof for transcription mediated amplification of the target nucleic acid or amplicon thereof between the hybridized primer and promoter-based oligomer members, wherein the at least one promoter-based oligomer member is a first promoter-based oligomer member that is SEQ ID NO:76 and a second promoter-based oligomer member that is SEQ ID NO:81;
c) performing an isothermal amplification reaction on the sample to generate an amplicon from a human parvovirus in the sample or from an amplicon thereof; and
d) detecting the amplicon with a detection probe oligomer; wherein the presence of an amplicon as determined by the detecting step indicates that one or more of human parvovirus genotypes 1, 2 and 3 are present in the sample.
12. The method of claim 11 , wherein the detection probe oligomer is selected from the group consisting of SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:31, SEQ ID NO:32, SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, and SEQ ID NO:46.
13. The method of claim 11 , further comprising the step of contacting the sample with a target capture oligomer.
14. The method of claim 13 , wherein the target capture oligomer comprises a 3′ tail portion and a target-binding sequence selected from the group consisting of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:53, and combinations thereof.
15. A method for the detection of human parvovirus from a sample comprising the steps of:
a) obtaining a sample suspected of containing human parvovirus genotype 1, genotype 2, or genotype 3;
b) contacting the sample with an amplification oligomer combination comprising at least one primer oligomer member and at least one promoter-based oligomer member, wherein the at least one primer oligomer member and the at least one promoter-based oligomer member hybridize to opposing strands of a human parvovirus genotype 1, 2 or 3 nucleic acid or amplicon thereof for transcription mediated amplification of the target nucleic acid or amplicon thereof between the hybridized primer and promoter-based oligomer members, wherein
i) the at least one promoter-based oligomer member is selected from the group consisting of SEQ ID NOS:58, 63, 67, 68, 73, 78, 82, and combinations thereof; or
ii) the at least one primer oligomer member is SEQ ID NO:47 and the at least one promoter-based oligomer member is selected from the group consisting of SEQ ID NOs:73, 76, 78, 81, and combinations thereof;
c) performing an isothermal amplification reaction on the sample to generate an amplicon from a human parvovirus in the sample or from an amplicon thereof; and
d) detecting the amplicon with a detection probe oligomer; wherein the presence of an amplicon as determined by the detecting step indicates that one or more of human parvovirus genotypes 1, 2 and 3 are present in the sample.
16. The method of claim 15 , wherein the detection probe oligomer is selected from the group consisting of SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:31, SEQ ID NO:32, SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, and SEQ ID NO:46.
17. The method of claim 15 , further comprising the step of contacting the sample with a target capture oligomer.
18. The method of claim 17 , wherein the target capture oligomer comprises a 3′ tail portion and a target-binding sequence selected from the group consisting of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:53, and combinations thereof.
19. A method for the detection of human parvovirus from a sample comprising the steps of:
a) obtaining a sample suspected of containing human parvovirus genotype 1, genotype 2, or genotype 3;
b) contacting the sample with an amplification oligomer combination comprising:
i) at least one primer oligomer member that is SEQ ID NO:47;
ii) a first promoter-based oligomer member comprising a target binding sequence that is SEQ ID NO:75; and
iii) a second promoter-based oligomer member comprising a target binding sequence that is SEQ ID NO:80;
wherein the target binding sequence of each of the first and second promoter-based oligomer members is joined at its 5′ end to a promoter sequence;
c) performing an isothermal amplification reaction on the sample to generate an amplicon from a human parvovirus in the sample or from an amplicon thereof; and
d) detecting the amplicon with a detection probe oligomer; wherein the presence of an amplicon as determined by the detecting step indicates that one or more of human parvovirus genotypes 1, 2 and 3 are present in the sample.