Compositions and methods for detecting or quantifying Hepatitis B virus
This disclosure provides oligomers, compositions, and kits for detecting and quantifying Hepatitis B virus (HBV), including different genotypes and variants thereof, and related methods and uses. In some embodiments, oligomers target the P and/or S open reading frames of HBV and are configured to provide substantially equivalent quantification of different genotypes and variants of HBV.
1. A method of detecting Hepatitis B virus in a sample, comprising:
contacting the sample with at least first, second, third, and fourth amplification oligomers, thereby forming a composition,
performing a nucleic acid amplification reaction in the composition which produces at least first and second amplicons in the presence of a Hepatitis B virus nucleic acid, and quantifying the first and second amplicons,
wherein:
the first amplicon is produced through extension of the first and second amplification oligomers in the presence of the Hepatitis B virus nucleic acid;
the second amplicon is produced through extension of the third and fourth amplification oligomers in the presence of the Hepatitis B virus nucleic acid;
the second amplification oligomer comprises a target-hybridizing sequence comprising at least 10 contiguous nucleotides of one of SEQ ID NOs: 20, 21, or 22;
the third amplification oligomer comprises a target-hybridizing sequence comprising at least 10 contiguous nucleotides of SEQ ID NO: 41; and
(a) the first amplification oligomer comprises the sequence of SEQ ID NO: 2 and the fourth amplification oligomer comprises a target-hybridizing sequence comprising at least 14 contiguous nucleotides of Hepatitis B virus sequence, the at least 14 contiguous nucleotides of Hepatitis B virus sequence comprising at least 10 contiguous nucleotides of one of SEQ ID NOs: 34 or 35; or
(b) the first amplification oligomer comprises a target-hybridizing sequence comprising at least 10 contiguous nucleotides of one of SEQ ID NOs: 2 or 3 and the fourth amplification oligomer comprises at least 14 contiguous nucleotides of Hepatitis B virus sequence, the at least 14 contiguous nucleotides of Hepatitis B virus sequence comprising at least 10 contiguous nucleotides of SEQ ID NO: 35, wherein one of the at least 10 contiguous nucleotides of SEQ ID NO: 35 is the inosine at position 30 of SEQ ID NO: 35; or
(c) the first amplification oligomer comprises a target-hybridizing sequence comprising at least 10 contiguous nucleotides of one of SEQ ID NOs: 2 or 3, the fourth amplification oligomer comprises a target-hybridizing sequence comprising at least 14 contiguous nucleotides of Hepatitis B virus sequence, the at least 14 contiguous nucleotides of Hepatitis B virus sequence comprising at least 10 contiguous nucleotides of one of SEQ ID NOs: 34 or 35, and the method further comprises contacting the sample or composition with a probe oligomer comprising the sequence of SEQ ID NO: 29, wherein the sequence of SEQ ID NO: 29 includes a c9 linker between nucleotides 33 and 34 of SEQ ID NO: 29.
2. The method of claim 1 , wherein the first amplification oligomer comprises the sequence of SEQ ID NO: 2.
3. The method of claim 1 , wherein the fourth amplification oligomer comprises at least 10 contiguous nucleotides of SEQ ID NO: 35, wherein one of the at least 10 contiguous nucleotides of SEQ ID NO: 35 is the inosine at position 30 of SEQ ID NO: 35.
4. The method of claim 3 , wherein the fourth amplification oligomer comprises at least 14 contiguous nucleotides of SEQ ID NO: 35 including the inosine at position 30 of SEQ ID NO: 35.
5. The method of claim 3 , wherein the fourth amplification oligomer comprises at least 18 contiguous nucleotides of SEQ ID NO: 35 including the inosine at position 30 of SEQ ID NO: 35.
6. The method of claim 3 , wherein the fourth amplification oligomer comprises the sequence of SEQ ID NO: 35.
7. The method of claim 1 , further comprising contacting the sample or composition with a probe oligomer comprising the sequence of SEQ ID NO: 29, wherein the sequence of SEQ ID NO: 29 includes a c9 linker between nucleotides 33 and 34 of SEQ ID NO: 29.
8. The method of claim 7 , wherein the probe oligomer further comprises a non-nucleotide detectable label.
9. The method of claim 7 , wherein the probe oligomer further comprises a fluorescent label.
10. The method of claim 9 , wherein the probe oligomer further comprises a quencher, wherein the quencher absorbs fluorescence to a greater extent when the probe is free than when the probe is annealed to a target nucleic acid.
11. The method of claim 10 , wherein the fluorescent label is attached to the 5′-terminus of the probe oligomer and the quencher is attached to the 3′-terminus of the probe oligomer, or the fluorescent label is attached to the 3′-terminus of the probe oligomer and the quencher is attached to the 5′-terminus of the probe oligomer.
12. The method of claim 1 , wherein the nucleic acid amplification reaction is isothermal.
13. The method of claim 1 , wherein the nucleic acid amplification reaction is transcription-mediated amplification.
14. The method of claim 1 , further comprising performing a linear amplification reaction wherein at least one amplification oligomer is extended before performing the nucleic acid amplification that produces at least first and second amplicons in the presence of a Hepatitis B virus nucleic acid.
15. The method of claim 14 , wherein the nucleic acid amplification that produces at least first and second amplicons in the presence of a Hepatitis B virus nucleic acid is an exponential amplification reaction.
16. The method of claim 1 , wherein the second amplification oligomer comprises the sequence of SEQ ID NO: 20.
17. The method of claim 1 , wherein the second amplification oligomer comprises the sequence of SEQ ID NO: 21.
18. The method of claim 1 , wherein the second amplification oligomer comprises the sequence of SEQ ID NO: 22.
19. The method of claim 1 , wherein the third amplification oligomer comprises the sequence of SEQ ID NO: 41.
20. The method of claim 1 , further comprising contacting the sample or composition with a probe oligomer, wherein the probe oligomer comprises a non-nucleotide detectable label, a first self-complementary region at its 5′ end, and a second self-complementary region at its 3′ end.