Assay for detection of human parvovirus nucleic acid
View Patent ↗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. An amplification oligomer combination for amplifying human parvovirus comprising:
a) at least one primer oligomer member comprising a nucleobase sequence 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; and
b) at least one promoter-based oligomer member comprising a nucleobase sequence that is selected from the group consisting of;
wherein said amplification oligomer combination is configured to generate from GenBank Accession No. DQ225149.1 gi:77994407 an amplicon that is from about 150 nucleobases in length to about 180 nucleobases in length.
2. The amplification oligomer combination of claim 1 , wherein a second of said at least one promoter-based oligomer member comprises a nucleobase sequence that is selected from the group consisting of SEQ ID NO:23, SEQ ID NO:56, SEQ ID NO:61. SEQ ID NO:66, SEQ ID NO:72, SEQ ID NO:81 and combinations thereof.
3. The amplification oligomer combination of claim 1 , wherein (i) said at least one promoter based oligomer member is a first promoter-based oligomer member comprising a nucleobase sequence consisting of SEQ ID NO:76 and a second promoter-based oligomer member comprising a nucleobase sequence consisting of SEQ ID NO:81; or (ii) said at least one promoter based oligomer member is a first promoter-based oligomer member comprising a nucleobase sequence consisting of SEQ ID NO:73 and a second promoter-based oligomer member comprising a nucleobase sequence consisting of SEQ ID NO:78; or (iii) said at least one primer oligomer member comprises a nucleobase sequence consisting of SEQ ID NO:50 and said at least one promoter-based oligomer member comprises a nucleobase sequence selected from the group comprising SEQ ID NOS:73, 76, 78, 81 and combinations thereof; or (iv) said at least one primer oligomer member comprises a nucleobase sequence consisting of SEQ ID NO:47 and said at least one promoter-based oligomer member comprises a nucleobase sequence selected from the group comprising SEQ ID NOS:73, 76, 78, 81 and combinations thereof.
4. A method for the detection of human parvovirus from a sample comprising the steps of:
a) contacting a biological sample with an amplification oligomer combination that is configured for amplifying human parvovirus genotypes 1, 2 and 3, wherein said amplification oligomer combination is (i) at least one primer oligomer member, and (ii) at least one promoter-based oligomer member,
wherein the at least one primer member in (i) comprises a nucleobase sequence that is selected from the group consisting of SEQ ID NOS:47, 48, 49, 50 and combinations thereof, and
wherein the at least one promoter-based oligomer member in (ii) comprises a nucleobase sequence that is selected from the group consisting of;
b) performing an isothermal amplification reaction, wherein the at least one primer oligomer member and the at least one promoter-based oligomer member in step a) generate an amplicon from a human parvovirus nucleic acid; and
c) performing a detection reaction to detect the presence or absence of an amplicon from step b), wherein detecting the presence of an amplicon indicates that the sample contained one or more of a human parvovirus genotype 1, 2 or 3.
5. The method of claim 4 , wherein a second promoter-based oligomer member comprises a target binding sequence selected from the group consisting of SEQ ID NO:24, SEQ ID NO:57; SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:70, SEQ ID NO:75, SEQ ID NO:80 and combinations thereof.
6. The method of claim 5 , wherein said at least one promoter based oligomer member is a first promoter-based oligomer member comprising a target binding sequence comprising a nucleobase sequence consisting of SEQ ID NO:75 and a second promoter-based oligomer member comprising a target binding sequence consisting of SEQ ID NO:80.
7. The method of claim 4 , wherein said at least one promoter based oligomer member is a first promoter-based oligomer member comprising a nucleobase sequence consisting of SEQ ID NO:76 and a second promoter-based oligomer member comprising a nucleobase sequence consisting of SEQ ID NO:81.
8. The method of claim 4 , wherein a second promoter-based oligomer member comprises a target binding sequence that consists of SEQ ID NO:24, 57, 60, 62, 70, 75 or 80, and further comprises an internal tag sequence.
9. The method of claim 8 , wherein said second promoter based oligomer comprises a nucleobase sequence consisting of SEQ ID NOS:58, 63, 67, 68, 73, 78, or 82.
10. The method of claim 4 , wherein said at least one promoter based oligomer member is a first promoter-based oligomer member comprising a nucleobase sequence consisting of SEQ ID NO:73 and a second promoter-based oligomer member comprising a nucleobase sequence consisting of SEQ ID NO:78.
11. The method of claim 4 , wherein said amplicon comprises a target specific sequence that contains SEQ ID NO:100.
12. The method of claim 11 , wherein the detection step is a probe based detection step using a detection probe oligomer that specifically hybridizes a portion of SEQ ID NO:100; or wherein the detection probe oligomer specifically hybridizes to all or a portion of SEQ ID NO:33; or wherein the detection probe oligomer is SEQ ID NO:42.
13. The method of claim 4 , wherein said amplicon comprises a target specific sequence that is 95% identical to SEQ ID NO:88 and contains a nucleotide sequence that is SEQ ID NO:33.
14. The method of claim 13 , wherein said amplicon further comprises a non-target specific portion selected from the group consisting of a tag sequence, an insert sequence, SEQ ID NO:94, SEQ ID NO:95 and combinations thereof.
15. The method of claim 13 , wherein the detection step is a probe based detection step using a detection probe oligomer that specifically hybridizes a portion of SEQ ID NO:88; or wherein the detection probe oligomer sequence consists of SEQ ID NO:42.
16. The method of claim 4 , wherein the detection step is a probe based detection step using a detection probe oligomer that specifically hybridizes a portion of the amplicon; or wherein the detection probe oligomer specifically hybridizes all or a portion of SEQ ID NO:33; or wherein the detection probe oligomer sequence consists of SEQ ID NO:42.
17. The method of claim 4 , wherein the biological sample is human plasma.
18. The method of claim 4 , wherein the biological sample is a plasma pool for manufacturing therapeutic plasma derivatives.
19. The method of claim 4 , wherein before the amplifying step the sample is contacted with a target capture oligomer comprising 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; or is contacted with target capture oligomer comprising a sequence that is SEQ ID NO:52.
20. A method for the detection of human parvovirus from a sample comprising the steps of:
a) contacting a biological sample with an amplification oligomer combination that is configured for amplifying human parvovirus genotypes 1, 2 and 3, wherein said amplification oligomer combination is (i) at least one primer oligomer member, and (ii) at least one promoter-based oligomer member,
wherein said at least one primer oligomer member comprises a nucleobase sequence consisting of SEQ ID NO:50 and
said at least one promoter-based oligomer member comprises a nucleobase sequence selected from the group consisting of
b) performing an isothermal amplification reaction, wherein the the at least one primer oligomer member and the at least one promoter-based oligomer member in step a) generate an amplicon from a human parvovirus nucleic acid; and
c) performing a detection reaction to detect the presence or absence of an amplicon from step b), wherein detecting the presence of an amplicon indicates that the sample contained one or more of a human parvovirus genotype 1, 2 or 3.
21. The method of claim 20 , wherein the nucleobase sequences of said at least one promoter-based oligomer member consists of SEQ ID NOS:73 and 78.
22. The method of claim 20 , wherein SEQ ID NO:50 further comprises a 5′ tag sequence.
23. The method of claim 20 , wherein the nucleobase sequence of said at least one primer oligomer member consists of SEQ ID NO:47 and the nucleobase sequence of said at least one promoter-based oligomer member is selected from the group consisting of SEQ ID NOS:73, 76, 78, 81 and combinations thereof.
24. The method of claim 23 , wherein the nucleobase sequences of said at least one promoter-based oligomer member consist of SEQ ID NOS:73 and 78.
25. The amplification oligomer combination of claim 1 , wherein the at least one promoter based oligomer member (ii) further comprises the sequence selected from the group consisting of SEQ ID NO:23, SEQ ID NO:56, SEQ ID NO:61, SEQ ID NO:66, SEQ ID NO:72, SEQ ID NO:81 and combinations thereof.
26. The method of claim 4 , wherein the at least one promoter based oligomer member (ii) further comprises the sequence selected from the group consisting of SEQ ID NO:23, SEQ ID NO:56, SEQ ID NO:61, SEQ ID NO:66, SEQ ID NO:72, SEQ ID NO:81 and combinations thereof.
27. The method of claim 20 , wherein the at least one promoter based oligomer member of step a) comprises a nucleobase sequence selected from the group consisting of SEQ ID NO:73, 78, 81.