Compositions and reaction mixtures for the detection of nucleic acids from multiple types of human papillomavirus

• US 9,074,263 B2
• Filed: 08/04/2014
• Issued: 07/07/2015
• Est. Priority Date: 12/08/2004
• Status: Active Grant

• Current Assignee: Gen-Probe Incorporated (Hologic Incorporated)
• Original Assignee: Gen-Probe Incorporated (Hologic Incorporated)
• Inventors: Norman, Sylvia A., Bungo, Jennifer J., Hanna, William L., Rao, Neeraj P.
• Primary Examiner(s): Mummert, Stephanie K
• Assistant Examiner(s): PRIEST, AARON A
• Application Number:
  US14/451,263
• Publication Number:
  US 20140342351A1
• Time in Patent Office: 337 Days
• Field of Search: None
• US Class Current: 1/1
• CPC Class Codes: C07K 14/005 from viruses
• CPC Class Codes: C12N 2710/20022 New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
• CPC Class Codes: C12Q 1/708 for papilloma
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays

Abstract

Nucleic acid oligonucleotide sequences are disclosed which include amplification oligomers and probe oligomers which are useful for detecting multiple types of human papillomaviruses (HPV) associated with cervical cancer. Methods for detecting multiple HPV types in biological specimens by amplifying HPV nucleic acid sequences in vitro and detecting the amplified products are disclosed.

Claims

1. A combination of amplification oligomers for detecting human papillomavirus (HPV) of multiple HPV types, the combination comprising first amplification oligonucleotides, comprising a target binding region and a 5′

promoter sequence, and second amplification oligonucleotides, comprising a target binding region, wherein pairs of the first and second amplification oligonucleotides can hybridize to opposing strands of HPV nucleic acid for transcription mediated amplification of HPV nucleic acid between hybridized pairs of the first and second amplification oligonucleotides, wherein

(a) the target binding regions of the first amplification oligomers consist of SEQ ID Nos. 19, 21, 23, 25, 29, 31, 33, 35, and 37, respectively, and the target binding regions of the second amplification oligomers consist of SEQ ID Nos. 38, 39, 40, and 41, respectively;

or complements thereof;

RNA equivalents thereof;

or RNA equivalents of the complements thereof;

or

(b) the target binding regions of the first amplification oligomers consists of SEQ ID Nos. 21, 23, 25, 29, 31, 33, 35, 37, and 42, respectively, and the target binding regions of the second amplification oligomers consist of SEQ ID Nos. 38, 39, 40, and 41, respectively, or complements thereof;

RNA equivalents thereof;

or RNA equivalents of the complements thereof.

2. The combination of oligonucleotides of claim 1, wherein the first amplification oligonucleotides consist of SEQ ID Nos. 18, 20, 22, 24, 28, 30, 32, 34 and 36, respectively.

3. The combination of oligonucleotides of claim 1, in which one or more individual oligonucleotide sequences include a backbone that includes at least one 2′

-methoxy RNA group, at least one 2′

fluoro-substituted RNA group, at least one peptide nucleic acid linkage, at least one phosphorothioate linkage, at least one methylphosphonate linkage or any combination thereof.

4. The combination of oligonucleotides of claim 1, further comprising at least two probe oligonucleotides wherein each probe oligonucleotide comprises an oligonucleotide sequence selected from SEQ ID Nos. 11 to 17, 44 to 54, and 58, sequences that are completely complementary to SEQ ID Nos. 11 to 17, 44 to 54, and 58, RNA equivalents of SEQ ID Nos. 11 to 17, 44 to 54, and 58, or RNA equivalents of the sequences that are completely complementary to SEQ ID Nos. 11 to 17, 44 to 54, and 58, and wherein each probe oligonucleotide optionally includes a label joined directly or indirectly to the oligonucleotide.

5. The combination of oligonucleotides of claim 4, wherein the probe oligonucleotide sequences comprise at least one 2′

-methoxy RNA group.

6. The combination of oligonucleotides of claim 1, further comprising at least two oligonucleotides wherein each oligonucleotide sequence is selected from the group consisting of SEQ ID Nos. 1 to 10 and RNA equivalents of the sequences identified by SEQ ID Nos. 1 to 10, and wherein the oligonucleotide sequences consisting of SEQ ID Nos. 2, 4, 6, 8 and 10 optionally include a ligand moiety joined to the oligonucleotide sequence.

7. The combination of oligonucleotides of claim 6, wherein at least one of the oligonucleotide sequences identified by SEQ ID Nos. 1 to 10 comprises at least one 2′

-methoxy RNA group, at least one 2′

fluoro-substituted RNA group, at least one peptide nucleic acid linkage, at least one phosphorothioate linkage, or at least one methylphosphonate linkage.

8. An amplification reaction mixture containing amplification oligomers comprising sequences that consist of the sequences of claim 1.

9. An amplified product detection reaction mixture comprising the oligonucleotide combination of claim 4.