Gardnerella vaginalis assay
The present invention relates to nucleic acid amplification assays for the detection of nucleic acid sequences of Gardnerella vaginalis. The present invention provides oligonucleotides that are complementary or that anneal to nucleic acid sequences of the vly gene of GV. The present invention also provides internal amplification controls (IACs) that can be used in nucleic acid amplification reactions.
1. A method for detecting a Gardnerella vaginalis (GV) target sequence if present in a sample comprising:
(a) providing at least one oligonucleotide primer that will anneal to at least some portion of a target region of the vly gene of GV selected from the group consisting of SEQ ID NO. 20 and SEQ ID NO. 21;
(b) combining the at least one oligonucleotide primer with a biological sample;
(c) subjecting the sample to conditions to cause amplification of a portion of the target sequence, if present, in the sample; and
(d) determining the presence or absence of the amplified target sequence.
2. The method of claim 1 wherein at least one oligonucleotide primer has a target binding sequence that is selected from one of SEQ ID NO. 3-13, complements of SEQ ID NO. 3-13 and sequences that share at least 70% sequence similarity with SEQ ID NO. 3-13 and complements thereof.
3. The method of claim 1 wherein at least one oligonucleotide primer has a target binding sequence that is selected from one of SEQ ID NO. 3-13, complements of SEQ ID NO. 3-13 and sequences that share at least 80% sequence similarity with SEQ ID NO. 3-13 and complements thereof.
4. The method of claim 1 wherein at least one oligonucleotide primer has a target binding sequence that is selected from one of SEQ ID NO. 3 to 13, complements of SEQ ID NO. 3-13 and sequences that share at least 90% sequence similarity with SEQ ID NO. 3 to 13 and complements thereof.
5. The method of claim 1 wherein the at least one oligonucleotide primer is a set of oligonucleotide primers wherein:
(a) the first amplification primer has a target binding sequence that consists essentially of SEQ ID NO: 3, 6, 8 or 11; and
(b) the second amplification primer has a target that consists essentially of binding sequence of SEQ ID NO: 4, 7, 9 or 12.
6. The method of claim 1 wherein said amplification is accomplished by an amplification reaction that is selected from the group consisting of a Strand Displacement Amplification (SDA) reaction and a Polymerase Chain Reaction (PCR).
7. The method of claim 1 wherein said amplification is accomplished by an amplification or detection reaction that is selected from the group consisting of direct detection, polymerase chain reaction (PCR), in situ hybridization, transcription mediated amplification (TMA), self sustained sequence replication (SSR) rolling circle amplification or nucleic acid sequence based amplification (NASBA).
8. The method of claim 1 wherein the amplification primer further comprises a hairpin, G-quartet, restriction site or a sequence which hybridizes to a reporter probe.
9. The method of claim 1 wherein the reporter probe further comprises a detectable label.
10. The method of claim 9 wherein the label is a fluorescent label.
11. The method of claim 1 wherein the amplification primer further comprises a restriction endonuclease recognition site or a RNA polymerase promoter.
12. The method of claim 1 further comprising amplifying an internal amplification control (IAC).
13. A method for detecting a Gardnerella vaginalis (GV) target sequence comprising:
(a) providing a biological sample;
(b) combining one or more amplification primers for a target region of the vly gene of GV, wherein the target region of the vly gene of GV has a sequence selected from the group consisting of SEQ ID NO. 20 and SEQ ID NO. 21 with the biological sample;
(c) subjecting the biological sample combined with the one or more amplification primers to conditions that cause the one or more amplification primers to hybridize to the target region of the vly gene of GV; and
(d) determining the presence or absence of the hybridized amplification primer in the biological sample.
14. The method of claim 13 wherein the one or more amplification primers have a target binding sequence of any one of SEQ ID NOS: 3 to 13 and complements thereof, and sequences that share at least 70% sequence similarity with SEQ ID NO. 3 to 13 and complements thereof.
15. The method of claim 13 wherein the one or more amplification primers have a target binding sequence of any one of SEQ ID NOS: 3 to 13 and complements thereof, and sequences that share at least 80% sequence similarity with SEQ ID NO. 3 to 13 and complements thereof.
16. The method of claim 15 wherein the one or more amplification primers have a target binding sequence of any one of SEQ ID NOS: 3 to 13 and complements thereof, and sequences that share at least 90% sequence similarity with SEQ ID NO. 3 to 13 and complements thereof.
17. The method of claim 13 wherein at least one amplification primer is a reporter probe that further comprises a detectable label.
18. The method of claim 17 wherein said detectable label is TAMRA, 6ROX, or 6FAM.