Compositions, reaction mixtures and methods for detecting nucleic acids from type A1 and/or type C1 human papillomavirus

1. A kit containing at least two detection probes specific for a type A1 or type C1 HPV target region, wherein each of the detection probes individually has a contiguous base sequence that is 20 to 28 nucleotides in length and is at least 90% identical to a sequence selected from the group consisting of: SEQ ID NOs: 11, 13, 44-47, 49, 51, 52, and 54, complements, RNA equivalents, and RNA/DNA chimerics thereof,

wherein at least one detection probe is specific for a type A1 HPV nucleic acid and at least one detection probe is specific for a type C1 HPV nucleic acid, and

wherein the detection probe specific for a type A1 HPV nucleic acid is joined to an AE label that is different than an AE label to which the detection probe specific for a type C1 HPV nucleic acid is joined, in order to provide distinguishable signals.

2. The kit of claim 1 , wherein the kit further contains components for making a Probe Reagent, components for making a Selection Reagent, components for making a Detection Reagent, or combinations thereof.

3. The kit of claim 1 , wherein the kit further contains at least one amplification oligonucleotide selected from the group consisting of SEQ ID NOS:18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 38, 39 and 42.

4. A detection reaction mixture for detecting the presence of a type A1 HPV nucleic acid and/or a type C1 HPV nucleic acid in a sample, wherein the reaction mixture contains at least two detection probes specific for a type A1 or type C1 HPV target region, wherein each of the at least two detection probes individually has a contiguous base sequence that is 20 to 28 nucleotides in length and is at least 90% identical to a sequence selected from the group consisting of: SEQ ID NOs: 11, 13, 44-47, 49, 51, 52, and 54, complements, RNA equivalents, and RNA/DNA chimerics thereof,

wherein at least one detection probe is specific for a type A1 HPV nucleic acid and at least one detection probe is specific for a type C1 HPV nucleic acid, and

wherein the detection probe specific for a type A1 HPV nucleic acid is joined to an AE label that is different than an AE label to which the detection probe specific for a type C1 HPV nucleic acid is joined, in order to provide distinguishable signals.

5. A method for detecting the presence of a human papillomavirus (HPV) nucleic acid in a sample comprising the steps of:

(a) treating a biological sample suspected of containing a type A1 HPV nucleic acid and/or a type C1 HPV nucleic acid to release intracellular components;

(b) separating an HPV nucleic acid away from a component of the biological sample;

(c) contacting the separated HPV nucleic acid with at least two detection probes specific for a type A1 or type C1 HPV target region, wherein each of the at least two detection probes individually has a contiguous base sequence that is 20 to 28 nucleotides in length and is at least 90% identical to a sequence selected from the group consisting of: SEQ ID NOs: 11, 13, 44-47, 49, 51, 52, and 54, complements, RNA equivalents, and RNA/DNA chimerics thereof

wherein at least one detection probe is specific for a type A1 HPV nucleic acid and at least one detection probe is specific for a type C1 HPV nucleic acid, and

wherein the detection probe specific for a type A1 HPV nucleic acid is joined to an AE label that is different than an AE label to which the detection probe specific for a type C1 HPV nucleic acid is joined, in order to provide distinguishable signals; and

(d) detecting a signal that results from hybridization of at least one of the detection probes to an HPV target region to indicate the presence of a type A1 and/or type C1 HPV nucleic acid in the sample.

6. The kit of claim 1 , wherein each of the at least two detection probes individually has a contiguous base sequence selected from the group consisting of: SEQ ID NOs: 11, 13, 44-47, 49, 51, 52, and 54, complements, RNA equivalents, and RNA/DNA chimerics thereof.

7. The kit of claim 1 , wherein each of the at least two detection probes contains a 2′-methoxy backbone at one or more linkages in the nucleic acid backbone.

8. The detection reaction mixture of claim 4 , wherein each of the at least two detection probes individually has a contiguous base sequence selected from the group consisting of: SEQ ID NOs: 11, 13, 44-47, 49, 51, 52, and 54, complements, RNA equivalents, and RNA/DNA chimerics thereof.

9. The detection reaction mixture of claim 4 , wherein each of the at least two detection probes contains a 2′-methoxy backbone at one or more linkages in the nucleic acid backbone.

10. The method of claim 5 , wherein each of the at least two detection probes contains a 2′-methoxy backbone at one or more linkages in the nucleic acid backbone.

11. The method of claim 5 , wherein the separated HPV nucleic acid from step (b) is amplified in an in vitro amplification reaction that includes a combination of amplification oligonucleotides that amplify a HPV type A1 target sequence and a combination of amplification oligomers that amplify HPV type C1 target sequence in an E6/E7 target region sequence.

12. The method of claim 11 , wherein the combination of amplification oligonucleotides that amplify a HPV type A1 target sequence includes at least one amplification oligonucleotide selected from the group consisting of: SEQ ID NOS:18, 19, 20, 21, 22, 23, 38 and 42, complements, RNA equivalents, and RNA/DNA chimerics thereof.

13. The method of claim 11 , wherein the combination of amplification oligonucleotides that amplify a HPV type C1 target sequence includes at least one amplification oligonucleotide selected from the group consisting of: SEQ ID NOS:28, 29, 30, 31 and 39, complements, RNA equivalents, and RNA/DNA chimerics thereof.

14. The method of claim 11 , wherein each of the at least two detection probes individually has a contiguous base sequence selected from the group consisting of: SEQ ID NOs: 11, 13, 44-47, 49, 51, 52, and 54, complements, RNA equivalents, and RNA/DNA chimerics thereof.

15. The method of claim 14 , wherein (i) the combination of amplification oligonucleotides that amplify a HPV type A1 target sequence includes at least one amplification oligonucleotide that has a contiguous base sequence that is at least 90% identical to a sequence selected from the group consisting of SEQ ID NOS:18, 19, 20, 21, 22, 23, 38 and 42, complements, RNA equivalents, and RNA/DNA chimerics thereof, and wherein (ii) the combination of amplification oligonucleotides that amplify a HPV type C1 target sequence includes at least one amplification oligonucleotide that has a contiguous base sequence that is at least 90% identical to a sequence selected from the group consisting of: SEQ ID NOS:28, 29, 30, 31 and 39, complements, RNA equivalents, and RNA/DNA chimerics thereof.

16. The method of claim 11 , wherein the in vitro amplification reaction occurs before step (c).

17. The method of claim 5 , wherein the separating step (b) uses a capture oligonucleotide, wherein a capture oligonucleotide is selected from the group consisting of SEQ ID NO:1, SEQ ID NO:2 joined to a ligand moiety, SEQ ID NO:5, SEQ ID NO:6 joined to a ligand moiety, and combinations thereof.

18. The method of claim 5 , wherein the biological sample is treated to physically disrupt the sample and release intracellular components.

19. The method of claim 5 , wherein the biological sample is treated with an enzyme to release intracellular components.

20. The method of claim 5 , wherein the separating step (b) is a target capture step that uses a target capture reaction mixture containing, (i) a capture oligonucleotide selected from the group consisting of SEQ ID NO:1, SEQ ID NO:2 joined to a ligand moiety, SEQ ID NO:5, SEQ ID NO:6 joined to a ligand moiety, and combinations thereof, and (ii) at least one amplification oligonucleotide selected from the group consisting of SEQ ID NOS:18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 38, 39 and 42.