Compositions and methods for detecting or quantifying parainfluenza virus
Compositions, methods, kits, and uses are provided for detecting or quantifying an Human Parainfluenza virus 1 (HPIV-1), HPIV-2, HPIV-3, and/or HPIV-4 nucleic acid, e.g., using nucleic acid amplification and hybridization assays. In some embodiments, the compositions, methods, kits, and uses target the HN gene of HPIV-1, HPIV-2, and/or HPIV-3 and/or the NP gene of HPIV-4.
1. A composition comprising first, second, third, and fourth amplification oligomers, wherein:
the first amplification oligomer and second amplification oligomer are configured to produce an HPIV-3 amplicon of at least about 50 nucleotides in length comprising at least one Human Parainfluenza Virus 3 (HPIV-3) position located in the range of positions 1350-1360, wherein the first oligomer comprises a target-hybridizing region consisting of the sequence of SEQ ID NO: 25 and the second oligomer comprises a target-hybridizing region consisting of the sequence of SEQ ID NO: 36;
the third amplification oligomer and fourth amplification oligomer are configured to produce an HPIV-4 amplicon, wherein the third oligomer comprises a target-hybridizing region consisting of the sequence of SEQ ID NO: 78 and the fourth oligomer comprises a target-hybridizing region consisting of the sequence of SEQ ID NO: 56;
the composition further comprises a fifth oligomer configured to hybridize to the HPIV-3 amplicon;
the composition further comprises a sixth oligomer configured to hybridize to the HPIV-4 amplicon, wherein the sixth oligomer is a detection probe; and
the sixth oligomer comprises a non-nucleotide detectable label.
2. A method of detecting HPIV-3 and HPIV-4 in a sample, comprising:
contacting the sample with the composition according to claim 1 ,
performing a nucleic acid amplification reaction to produce an HPIV-3 amplicon of at least about 50 nucleotides in length in the presence of an HPIV-3 nucleic acid and an HPIV-4 amplicon in the presence of an HPIV-4 nucleic acid, and
performing a detection reaction to detect the presence of at least one amplicon, if present, selected from the group consisting of the HPIV-3 amplicon and the HPIV-4 amplicon.
3. The composition of claim 1 , wherein the fifth oligomer competes for hybridization to an HPIV-3 nucleic acid under stringent conditions with an oligomer having a sequence consisting of the sequence of SEQ ID NO: 26.
4. The composition of claim 1 , wherein the fifth oligomer comprises the sequence of SEQ ID NO: 26.
5. The composition of claim 1 , wherein the fifth oligomer comprises a target-hybridizing region consisting of the sequence of SEQ ID NO: 26.
6. The composition of claim 1 , wherein the fifth oligomer consists of the sequence of SEQ ID NO: 26.
7. The composition of claim 1 , wherein the fifth oligomer consists of the sequence of SEQ ID NO: 26 and further comprises a detectable label.
8. The composition of claim 1 , wherein all or all but one or two of the C residues in one, two, or three of the first, second, and fifth oligomers are 5-methylated.
9. The composition of claim 1 , further comprising a first Human Parainfluenza Virus 1 (HPIV-1) amplification oligomer and a second HPIV-1 amplification oligomer, wherein:
the first HPIV-1 amplification oligomer and second HPIV-1 amplification oligomer are configured to amplify an HPIV-1 amplicon of at least about 50 nucleotides in length comprising at least one HPIV-1 position located within HPIV-1 positions 330-490 or 960-1100.
10. The composition of claim 1 , further comprising a first Human Parainfluenza Virus 2 (HPIV-2) amplification oligomer and a second HPIV-2 amplification oligomer, wherein:
the first HPIV-2 amplification oligomer and second HPIV-2 amplification oligomer are configured to amplify an HPIV-2 amplicon of at least about 50 nucleotides in length comprising at least one HPIV-2 position located within HPIV-2 positions 1600-1700.
11. The composition of claim 1 , wherein the fifth oligomer hybridizes to an HPIV nucleic acid at an antisense version of the site to which an oligomer having a sequence consisting of the sequence of SEQ ID NO: 26, 27, 29, or 30 hybridizes.
12. The composition of claim 1 , wherein at least one of the oligomers comprises a non-Watson Crick (NWC) position.
13. The composition of claim 1 , wherein at least one of the oligomers comprises at least one 5-methylcytosine.
14. The composition of claim 1 , wherein the sixth oligomer competes for hybridization to an HPIV-4 nucleic acid under stringent conditions with an oligomer having a sequence consisting of the sequence of SEQ ID NO: 71.
15. The composition of claim 1 , wherein the sixth oligomer comprises a target-hybridizing region consisting of the sequence of SEQ ID NO: 71.
16. The composition of claim 1 , wherein the sixth oligomer has a sequence consisting of the sequence of SEQ ID NO: 71.
17. The composition of claim 1 , wherein the composition is in a kit.