COMPOSITIONS AND METHODS FOR DETECTION OF TRICHOMONAS VAGINALIS

Abstract

Methods for the rapid detection of the presence or absence of Trichomonas vaginalis (TV) in a biological or non-biological sample are described. The methods can include performing an amplifying step, a hybridizing step, and a detecting step. Furthermore, primers, probes targeting the target TV gene, along with kits are provided that are designed for the detection of TV.

Claims

1. A method of detecting Trichomonas vaginalis (TV) in a sample, the method comprising: performing an amplifying step comprising contacting the sample with a set of target TV gene primers to produce an amplification product if a target TV gene nucleic acid is present in the sample; performing a hybridizing step comprising contacting the amplification product with one or more detectable target TV gene probes; and detecting the presence or absence of the amplification product, wherein the presence of the amplification product is indicative of the presence of TV in the sample and wherein the absence of the amplification product is indicative of the absence of TV in the sample; wherein the set of target TV gene primers comprise a first primer comprising a first oligonucleotide sequence selected from the group consisting of SEQ ID NOs: 1-9, 19-28, 45-48, 55-64, and 80-89 or a complement thereof, and a second primer comprising a second oligonucleotide sequence selected from the group consisting of SEQ ID NOs: 10-13, 29-38, 49-52, 65-74, and 90-99, or a complement thereof; and wherein the one or more detectable target TV gene probes comprises a third oligonucleotide sequence selected from the group consisting of SEQ ID NOs: 14-18, 39-44, 53-54, 75-79, and 100-105, or the complement thereof.

2. The method of claim 1, wherein: the hybridizing step comprises contacting the amplification product with the detectable target TV gene probe that is labeled with a donor fluorescent moiety and a corresponding acceptor moiety; and the detecting step comprises detecting the presence or absence of fluorescence resonance energy transfer (FRET) between the donor fluorescent moiety and the acceptor moiety of the probe, wherein the presence or absence of fluorescence is indicative of the presence or absence of TV in the sample.

3. The method of claim 2, wherein said amplifying step employs a polymerase enzyme having 5′ to 3′ nuclease activity.

4. The method of claim 2, wherein the donor fluorescent moiety and the corresponding acceptor moiety are within no more than 8-20 nucleotides of each other on the probe.

5. The method of claim 2, wherein the acceptor moiety is a quencher.

6. A kit for detecting a nucleic acid of Trichomonas vaginalis (TV) comprising: a first primer comprising a first oligonucleotide sequence selected from the group consisting of SEQ ID NOs: 1-9, 19-28, 45-48, 55-64, and 80-89, or a complement thereof; a second primer comprising a second oligonucleotide sequence selected from the group consisting of SEQ ID NOs: 10-13, 29-38, 49-52, 65-74, and 90-99, or a complement thereof; and a fluorescently detectably labeled probe comprising a third oligonucleotide sequence selected from the group consisting of SEQ ID NOs: 14-18, 39-44, 53-54, 75-79, and 100-105, or a complement thereof, the detectably labeled probe configured to hybridize to an amplicon generated by the first primer and the second primer.

7. The kit of claim 6, wherein the third detectably labeled oligonucleotide sequence comprises a donor fluorescent moiety and a corresponding acceptor moiety.

8. The kit of claim 7, wherein the acceptor moiety is a quencher.

9. The kit of claim 6, further comprising at least one of nucleoside triphosphates, nucleic acid polymerase, and buffers necessary for the function of the nucleic acid polymerase.

10. The kit of claim 6, wherein at least one of the first, second, and third oligonucleotides comprises at least one modified nucleotide.

11. The kit of claim 6, wherein the first, second, and third oligonucleotides have 40 or fewer nucleotides.

Description

BRIEF DESCRIPTION OF THE FIGURES

[0025] FIG. 1 shows the location of the 5.8s ribosomal RNA gene, the inter-transcribed sequence 2 (ITS2) and neighboring ribosomal genes in the T. vaginalis genome.

[0026] FIG. 2 shows PCR growth curves of a real-time PCR experiment in the presence of various concentrations of genomic T. vaginalis DNA template (present in 1000 [black], 100 [light grey] and 10 [grey] genomic equivalent concentrations per PCR reaction).

[0027] FIG. 3 shows PCR growth curves of a real-time PCR experiment with concentrations of genomic T. vaginalis DNA template present in 100, 10, 5 and 1 genomic equivalent concentrations per PCR reaction (ge/PCR), in a co-amplification with internal control standard and Mycoplasma genitalium DNA template at 10 ge/PCR .

[0028] FIG. 4 shows PCR growth curves of the same real-time PCR experiment as shown on FIG. 3 with the amplification of the internal control standard and Mycoplasma genitalium DNA template at 10 ge/PCR .

DETAILED DESCRIPTION OF THE INVENTION

[0029] Diagnosis of TV infection by nucleic acid amplification provides a method for rapidly and accurately detecting the protozoan infection. A real-time assay for detecting TV in a sample is described herein. Primers and probes for detecting TV are provided, as are articles of manufacture or kits containing such primers and probes. The increased sensitivity of real-time PCR for detection of TV compared to other methods, as well as the improved features of real-time PCR including sample containment and real-time detection of the amplified product, make feasible the implementation of this technology for routine diagnosis of TV infections in the clinical laboratory.

[0030] The present disclosure includes oligonucleotide primers and fluorescent labeled hydrolysis probes that hybridize to a specific gene locus of the TV genome in order to specifically identify TV using TaqMan® amplification and detection technology. Target selection for TV required a comprehensive search of the public sequence database, as well as literature search for TV targets with a potential to discriminate against the nearest neighbors, Trichomonas tenax and Pentatrichomonas hominis. Multiple targets from the public sequence database were analyzed in the target selection process but many showed cross reactivity with T. tenax and P. hominis. Furthermore, sequences in the public database are complicated by “bulk” sequence data from multicopy targets.

[0031] As a result of the analysis, possible target TV genes include the 5.8s ribosomal RNA gene (GenBank accession number U86613), the 18s ribosomal RNA gene (GenBank accession number NW001533462), the DNA mismatch repair homolog, post-meiotic segregation increased-1 (PMS1) gene (GenBank accession number NW001581675), the MutL homolog la (Mlh1a) gene (GenBank accession number)34001320341) and the coronin (CRN) gene (GenBank accession number XM001581132). In certain aspects, the target TV gene is the 5.8s ribosomal RNA gene as this gene is present in over 200 copies per genome and will hence benefit sensitivity of the assay. Further, the 5.8s ribosomal RNA gene is present in metronidazole resistant and metronidazole sensitive TV and hence allows for the combined detection of both TV types.

[0032] The disclosed methods may include performing at least one cycling step that includes amplifying one or more portions of the nucleic acid molecule gene target from a sample using one or more pairs of primers. “Primer(s)” as used herein refer to oligonucleotide primers that specifically anneal to the target gene in TV, and initiate DNA synthesis therefrom under appropriate conditions producing the respective amplification products. Each of the discussed primers anneals to a target within or adjacent to the respective target nucleic acid molecule such that at least a portion of each amplification product contains nucleic acid sequence corresponding to the target. The one or more amplification products are produced provided that one or more of the target TV gene nucleic acid is present in the sample, thus the presence of the one or more of target TV gene amplification products is indicative of the presence of TV in the sample. The amplification product should contain the nucleic acid sequences that are complementary to one or more detectable probes for target TV gene. “Probe(s)” as used herein refer to oligonucleotide probes that specifically anneal to nucleic acid sequence encoding the target TV gene. Each cycling step includes an amplification step, a hybridization step, and a detection step, in which the sample is contacted with the one or more detectable probes for detection of the presence or absence of TV in the sample.

[0033] As used herein, the term “amplifying” refers to the process of synthesizing nucleic acid molecules that are complementary to one or both strands of a template nucleic acid molecule. Amplifying a nucleic acid molecule typically includes denaturing the template nucleic acid, annealing primers to the template nucleic acid at a temperature that is below the melting temperatures of the primers, and enzymatically elongating from the primers to generate an amplification product. Amplification typically requires the presence of deoxyribonucleoside triphosphates, a DNA polymerase enzyme (e.g., Platinum® Taq) and an appropriate buffer and/or co-factors for optimal activity of the polymerase enzyme (e.g., MgCl.sub.2 and/or KCl).

[0034] The term “primer” as used herein is known to those skilled in the art and refers to oligomeric compounds, primarily to oligonucleotides but also to modified oligonucleotides that are able to “prime” DNA synthesis by a template-dependent DNA polymerase, i.e., the 3′-end of the, e.g., oligonucleotide provides a free 3′-OH group whereto further “nucleotides” may be attached by a template-dependent DNA polymerase establishing 3′ to 5′ phosphodiester linkage whereby deoxynucleoside triphosphates are used and whereby pyrophosphate is released. Therefore, there is—except possibly for the intended function—no fundamental difference between a “primer”, an “oligonucleotide”, or a “probe”.

[0035] The term “hybridizing” refers to the annealing of one or more probes to an amplification product. Hybridization conditions typically include a temperature that is below the melting temperature of the probes but that avoids non-specific hybridization of the probes.

[0036] The term “5′ to 3′ nuclease activity” refers to an activity of a nucleic acid polymerase, typically associated with the nucleic acid strand synthesis, whereby nucleotides are removed from the 5′ end of nucleic acid strand.

[0037] The term “thermostable polymerase” refers to a polymerase enzyme that is heat stable, i.e., the enzyme catalyzes the formation of primer extension products complementary to a template and does not irreversibly denature when subjected to the elevated temperatures for the time necessary to effect denaturation of double-stranded template nucleic acids. Generally, the synthesis is initiated at the 3′ end of each primer and proceeds in the 5′ to 3′ direction along the template strand. Thermostable polymerases have been isolated from Thermus flavus, T. ruber, T. thermophilus, T. aquaticus, T. lacteus, T. rubens, Bacillus stearothermophilus, and Methanothermus fervidus. Nonetheless, polymerases that are not thermostable also can be employed in PCR assays provided the enzyme is replenished.

[0038] The term “complement thereof” refers to nucleic acid that is both the same length as, and exactly complementary to, a given nucleic acid.

[0039] The term “extension” or “elongation” when used with respect to nucleic acids refers to when additional nucleotides (or other analogous molecules) are incorporated into the nucleic acids. For example, a nucleic acid is optionally extended by a nucleotide incorporating biocatalyst, such as a polymerase that typically adds nucleotides at the 3′ terminal end of a nucleic acid.

[0040] The terms “identical” or percent “identity” in the context of two or more nucleic acid sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of nucleotides that are the same, when compared and aligned for maximum correspondence, e.g., as measured using one of the sequence comparison algorithms available to persons of skill or by visual inspection. Exemplary algorithms that are suitable for determining percent sequence identity and sequence similarity are the BLAST programs, which are described in, e.g., Altschul et al. (1990) “Basic local alignment search tool” J. Mol. Biol. 215:403-410, Gish et al. (1993) “Identification of protein coding regions by database similarity search” Nature Genet. 3:266-272, Madden et al. (1996) “Applications of network BLAST server” Meth. Enzymol. 266:131-141, Altschul et al. (1997) “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs” Nucleic Acids Res. 25:3389-3402, and Zhang et al. (1997) “PowerBLAST: A new network BLAST application for interactive or automated sequence analysis and annotation” Genome Res. 7:649-656, which are each incorporated herein by reference.

[0041] A “modified nucleotide” in the context of an oligonucleotide refers to an alteration in which at least one nucleotide of the oligonucleotide sequence is replaced by a different nucleotide that provides a desired property to the oligonucleotide. Exemplary modified nucleotides that can be substituted in the oligonucleotides described herein include, e.g., a C5-methyl-dC, a C5-ethyl-dC, a C5-methyl-dU, a C5-ethyl-dU, a 2,6-diaminopurine, a C5-propynyl-dC, a C5-propynyl-dU, a C7-propynyl-dA, a C7-propynyl-dG, a C5-propargylamino-dC, a C5-propargylamino-dU, a C7-propargylamino-dA, a C7-propargylamino-dG, a 7-deaza-2-deoxyxanthosine, a pyrazolopyrimidine analog, a pseudo-dU, a nitro pyrrole, a nitro indole, 2′-0-methyl Ribo-U, 2′-0-methyl Ribo-C, an N4-ethyl-dC, an N6-methyl-dA, and the like. Many other modified nucleotides that can be substituted in the oligonucleotides are referred to herein or are otherwise known in the art. In certain embodiments, modified nucleotide substitutions modify melting temperatures (Tm) of the oligonucleotides relative to the melting temperatures of corresponding unmodified oligonucleotides. To further illustrate, certain modified nucleotide substitutions can reduce non-specific nucleic acid amplification (e.g., minimize primer dimer formation or the like), increase the yield of an intended target amplicon, and/or the like in some embodiments. Examples of these types of nucleic acid modifications are described in, e.g., U.S. Pat. No. 6,001,611, which is incorporated herein by reference.

Detection of TV

[0042] The present disclosure provides methods to detect TV by amplifying, for example, a portion of the target TV gene nucleic acid sequence. Nucleic acid sequences of the 5.8s gene, the 18s gene, the PMS1 gene, the Mlhla gene and the CRN gene are publicly available (e.g., GenBank). Specifically, primers and probes to amplify and detect specific TV nucleic acid molecule targets are provided by the embodiments in the present disclosure.

[0043] For detection of TV, primers and probes to amplify the target TV gene are provided. Nucleic acids other than those exemplified herein can also be used to detect TV in a sample. For example, functional variants can be evaluated for specificity and/or sensitivity by those of skill in the art using routine methods. Representative functional variants can include, e.g., one or more deletions, insertions, and/or substitutions in the target TV gene nucleic acids disclosed herein.

[0044] More specifically, embodiments of the oligonucleotides each include a nucleic acid with a sequence selected from SEQ ID NOs: 1-105, a substantially identical variant thereof in which the variant has at least, e.g., 80%, 90%, or 95% sequence identity to one of SEQ ID NOs: 1-105, or a complement of SEQ ID NOs: 1-105 and the variant.

TABLE-US-00001 TABLE I 5.8s Forward Primers Forward Primers Oligo Name SEQ ID NO: Sequence Modifications KMTV5.8s110FBBC 1 CCAAGTCTCTAAGCAATGGATGT<t_ t-butylbenzyldC BB_dC> KMTV5.8s117FBBC 2 AAGCAATGGATGTCTTGGCT<t_BB_ t-butylbenzyldC dC> KMTV5.8s169FBBC 3 TGTTAAGTAACCGGAGTTGCAAA<t_ t-butylbenzyldC BB_dC> KMTV170FBBC 4 TTAAGTAACCGGAGTTGCAAA<t_BB_ t-butylbenzyldC dC> KMTV195FBBC 5 CAAATTGCGCTAAACTCGATCT<t_BB_ t-butylbenzyldC dC> KMTV203FBBA 6 CTAAACTCGATCTCGGTCG<t_BB_ t-butylbenzyldA dA> KMTV201FBBC 7 CGCTAAACTCGATCTCGGT<t_BB_ t-butylbenzyldC dC> KMTV196FBBC 8 AAATTGCGCTAAACTCGATCT<t_BB_ t-butylbenzyldC dC> KMTV194FBBC 9 GCAAATTGCGCTAAACTCGAT<t_BB_ t-butylbenzyldC dC>

TABLE-US-00002 TABLE II 5.8s Reverse Primers Reverse Primers Oligo Name SEQ ID NO: Sequence Modifications KMTV5.8s220RBBA 10 TCACACCCATGCTTCTCG<t_BB_dA> t-butylbenzyldA KMTV5.8s212RBBC 11 CATGCTTCTCGACCGAGAT<t_BB_ t-butylbenzyldC dC> KMTV5.8s268RBBA 12 TGTTTGTCTTATATATTATTTACTTA t-butylbenzyldA TTCGCTTAGA<t_BB_dA> KMTV270RBBA 13 TTTGTCTTATATATTATTTACTTATT t-butylbenzyldA CGCTTAGA<t_BB_dA>

TABLE-US-00003 TABLE III 5.8s Probes Probes Oligo Name SEQ ID NO: Sequence Modifications KMTV5.8s167FQ6 14 <F>AACATC<Q>ATGACAGGTTAAT P = phosphate, F = th-FAM, CTTTGAATGCAAATTG<P> Q = BHQ2 KMTV5.8s153FQ6 15 <F>TAACCG<Q>GAGTTGCAAACAT P = phosphate, F = th-FAM, CATGACAGG<P> Q = BHQ2 KMTV5.8s198FQ6 16 <F>ATTGCG<Q>CTAAACTCGATCTC P = phosphate, F = th-FAM, GGTCGA<P> Q = BHQ2 KMTV5.8s204FQ6 17 <F>CTAAAC<Q>TCGATCTCGGTCG P = phosphate, F = th-FAM, AGAAGCATGG<P> Q = BHQ2 KMTV5.8s220FQ6 18 <F>TCGAGA<Q>AGCATGGGTGTGA P = phosphate, F = th-FAM, CAGTACTACATCT<P> Q = BHQ2

TABLE-US-00004 TABLE IV 18s Forward Primers Forward Primers Oligo Name SEQ ID NO: Sequence Modifications 16S101BZ 19 CGTAGTTGGGATTGACGTTTGTAAT t-benzyldA C<t_BZ_dA> 16S101BU 20 CGTAGTTGGGATTGACGTTTGTAAT t-butylbenzyldA C<t_BB_dA> 16S103BZ 21 GGGAAACTTACCAGGACCAG<t_BZ_ t-benzyldA dA> 16S103BU 22 GGGAAACTTACCAGGACCAG<t_BB_ t-butylbenzyldA dA> 16S105BZ 23 GAAACTTACCAGGACCAGATGTTTT t-benzyldA TT<t_BZ_dA> 16S105BU 24 GAAACTTACCAGGACCAGATGTTTT t-butylbenzyldA TT<t_BB_dA> 16S107BZ 25 CTTGAAGGAATTGACGGAAGGGCA t-benzyldA C<t_BZ_dA> 16S107BU 26 CTTGAAGGAATTGACGGAAGGGCA t-butylbenzyldA C<t_BB_dA> 16S109BZ 27 GCCATTCGACTGAGTGACCTATC<t_ t-benzyldA BZ_dA> 16S109BU 28 GCCATTCGACTGAGTGACCTATC<t_ t-butylbenzyldA BB_dA>

TABLE-US-00005 TABLE V 18s Reverse Primers Reverse Primers Oligo Name SEQ ID NO: Sequence Modifications 16S102BZ 29 GACTTCTCCTTCCTCTAGATAACGT t-benzyldA G<t_BZ_dA> 16S102BU 30 GACTTCTCCTTCCTCTAGATAACGT t-butylbenzyldA G<t_BB_dA> 16S104BZ 31 TTGCTACCCTCTTCCACCTGCTAA<t_ t-benzyldA BZ_dA> 16S104BU 32 TTGCTACCCTCTTCCACCTGCTAA<t_ t-butylbenzyldA BB_dA> 16S106BZ 33 GCTACCCTCTTCCACCTGCTAAAAT t-benzyldC <t_BZ_dC> 16S106BU 34 GCTACCCTCTTCCACCTGCTAAAAT t-butylbenzyldC <t_BB_dC> 16S108BZ 35 TGAATCAACGCTAGACAGGTCAA<t_ t-benzyldC BZ_dC> 16S108BU 36 TGAATCAACGCTAGACAGGTCAA<t_ t-butylbenzyldC BB_dC> 16S110BZ 37 AAAAGGCACCAATGGAACTGGTCA t-benzyldA TT<t_BZ_dA> 16S110BU 38 AAAAGGCACCAATGGAACTGGTCA t-butylbenzyldA TT<t_BB_dA>

TABLE-US-00006 TABLE VI 18s Probes Probes Oligo Name SEQ ID NO: Sequence Modifications 165141FQ6 39 <F>AATCCC<Q>TTGTAAATGTGTGT P = phosphate, F = th-FAM, CAACAACGCA<P> Q = BHQ2 165142FQ6 40 <F>CCACCA<Q>AAAACAATATCCT P = phosphate, F = th-FAM, GAAAGACCCGAAG<P> Q = BHQ2 16S144FQ6 41 <F>CCAAAA<Q>ACAATATCCTGAA P = phosphate, F = th-FAM, AGACCCGAAGCCT<P> Q = BHQ2 16S146FQ6 42 <F>ACCAAA<Q>AACAATATCCTGA P = phosphate, F = th-FAM, AAGACCCGAAGCC<P> Q = BHQ2 16S148FQ6 43 <F>CTGCTA<Q>CCCGTGGATATAG P = phosphate, F = th-FAM, TCGCTATCTCTC<P> Q = BHQ2 16S143FQ6 44 <F>CTGAGA<Q>GATAGCGACTATA P = phosphate, F = th-FAM, TCCACGGGTAGC<P> Q = BHQ2

TABLE-US-00007 TABLE VII PMS1 Forward Primers Forward Primers Oligo Name SEQ ID NO: Sequence Modifications PMS103BZ 45 CCGAGAGATGATTGAGAACGTATT t-benzyldA TG<t_BZ_dA> PMS103BU 46 CCGAGAGATGATTGAGAACGTATT t-butylbenzyldA TG<t_BB_dA> PMS107BZ 47 CACTCCGAGAGATGATTGAGAACG t-benzyldA T<t_BZ_dA> PMS107BU 48 CACTCCGAGAGATGATTGAGAACG t-butylbenzyldA T<t_BB_dA>

TABLE-US-00008 TABLE VIII PMS1 Reverse Primers Reverse Primers Oligo Name SEQ ID NO: Sequence Modifications PMS104BZ 49 GCCACTTACATCTTTTCCAAATT<t_ t-benzyldC BZ_dC> PMS104BU 50 GCCACTTACATCTTTTCCAAATT<t_ t-butylbenzyldC BB_dC> PMS108BZ 51 GTGACACCTTCATCACAAATCATTGAA< t-benzyldA t_BZ_dA> PMS108BU 52 GTGACACCTTCATCACAAATCATTGAA< t-butylbenzyldA t_BB_dA>

TABLE-US-00009 TABLE IX PMS1 Probes Probes Oligo Name SEQ ID NO: Sequence Modifications PMA144FQ6 53 <F>CCACCA<Q>TTTCCAACTCGAAT P = phosphate, F = th-FAM, TGTCAAAAGT<P> Q = BHQ2 PMS146FQ6 54 <F>CCACCA<Q>TTTCCAACTCGAAT P = phosphate, F = th-FAM, TGTCAAAAGTGT<P> Q = BHQ2

TABLE-US-00010 TABLE X Mlh1a Forward Primers Forward Primers Oligo Name SEQ ID NO: Sequence Modifications MLH101BZ 55 CTCCTGTATCTATAAATGAAGAGA< t-benzyldA t_BZ_dA> MLH101BU 56 CTCCTGTATCTATAAATGAAGAGA< t-butylbenzyldA t_BB_dA> MLH103BZ 57 GATTTCTGATAATGGCTGTGGAATA t-benzyldA A<t_BZ_dA> MLH103BU 58 GATTTCTGATAATGGCTGTGGAATA t-butylbenzyldA A<t_BB_dA> MLH105BZ 59 GAATTATCTCCTGTATCTATAAATG t-benzyldA A<t_BZ_dA> MLH105BU 60 GAATTATCTCCTGTATCTATAAATG t-butylbenzyldA A<t_BB_dA> MLH107BZ 61 AGTAACAGCAAGTTCACTTTTGT<t_ t-benzyldC BZ_dC> MLH107BU 62 AGTAACAGCAAGTTCACTTTTGT<t_ t-butylbenzyldC BB_dC> MLH109BZ 63 CAGGTGATATCGCGAAGAACAC<t_ t-benzyldA BZ_dA> MLH109BU 64 CAGGTGATATCGCGAAGAACAC<t_ t-butylbenzyldA BB_dA>

TABLE-US-00011 TABLE XI Mlh1a Reverse Primers Reverse Primers Oligo Name SEQ ID NO: Sequence Modifications MLH102BZ 65 GGAATATTTGATTTTGGAATTTCAG<t_ t-benzyldA BZ_dA> MLH102BU 66 GGAATATTTGATTTTGGAATTTCAG<t_ t-butylbenzyldA BB_dA> MLH104BZ 67 CCAAATGAACTTTCTTCTGTTTTAG<t_ t-benzyldA BZ_dA> MLH104BU 68 CCAAATGAACTTTCTTCTGTTTTAG<t_ t-butylbenzyldA BB_dA> MLH106BZ 69 ATTTGATTTTGGAATTTCAGAGTTTT<t_ t-benzyldC BZ_dC> MLH106BU 70 ATTTGATTTTGGAATTTCAGAGTTTT<t_ t-butylbenzyldC BB_dC> MLH108BZ 71 CTGAAGACTTGGAATAGATGTACTG<t_ t-benzyldC BZ_dC> MLH108BU 72 CTGAAGACTTGGAATAGATGTACTG<t_ t-butylbenzyldC BB_dC> MLH110BZ 73 GGCATCCTTAATAAAACAAAAGCAA<t_ t-benzyldA BZ_dA> MLH110BU 74 GGCATCCTTAATAAAACAAAAGCAA<t_ t-butylbenzyldA BB_dA>

TABLE-US-00012 TABLE XII Mlh1a Probes Probes Oligo Name SEQ ID NO: Sequence Modifications MLH141FQ6 75 <F>AAAATC<Q>CAAGAAAAAGAGC P = phosphate, F = th-FAM, AAGAAGAAATCCT<P> Q = BHQ2 MLH142FQ6 76 <F>CACCTC<Q>TGAATCCAAATGTA P = phosphate, F = th-FAM, GTTACGTTCCTT<P> Q = BHQ2 MLH144FQ6 77 <F>CTTGCT<Q>CTTTTTCTTGGATT P = phosphate, F = th-FAM, TTCTGTATCTGA<P> Q = BHQ2 MLH146FQ6 78 <F>TTCAAA<Q>CCAATCAAACCAA P = phosphate, F = th-FAM, CAAAAGAATGAGC<P> Q = BHQ2 MLH148FQ6 79 <F>AAAACC<Q>GCTGATTCTTTGA P = phosphate, F = th-FAM, GTTGTTTTTTGGC<P> Q = BHQ2

TABLE-US-00013 TABLE XIII CRN Forward Primers Forward Primers Oligo Name SEQ ID NO: Sequence Modifications CRN101BZ 80 GCAATCTGGGATCTCAACAAGGAA<t_ t-benzyldA BZ_dA> CRN101BU 81 GCAATCTGGGATCTCAACAAGGAA<t_ t-butylbenzyldA BB_dA> CRN103BZ 82 TTTCATCGGACAGGGCAATC<t_BZ_ t-benzyldC dC> CRN103BU 83 TTTCATCGGACAGGGCAATC<t_BB_ t-butylbenzyldC dC> CRN105BZ 84 GAGGGACCACAAGAAGAAGTCGTT t-benzyldA C<t_BZ_dA> CRN105BU 85 GAGGGACCACAAGAAGAAGTCGTT t-butylbenzyldA C<t_BB_dA> CRN107BZ 86 GACGAGGGACCACAAGAAGAAGT<t_ t-benzyldC BZ_dC> CRN107BU 87 GACGAGGGACCACAAGAAGAAGT<t_ t-butylbenzyldC BB dC> CRN109BZ 88 CAGAGATCATCCAGCCAGAT<t_BZ_ t-benzyldC dC> CRN109BU 89 CAGAGATCATCCAGCCAGAT<t_BB_ t-butylbenzyldC dC>

TABLE-US-00014 TABLE XIV CRN Reverse Primers Reverse Primers Oligo Name SEQ ID NO: Sequence Modifications CRN102BZ 90 GGTTGTAATCTGGAAGGTCGAGA<t_ t-benzyldA BZ_dA> CRN102BU 91 GGTTGTAATCTGGAAGGTCGAGA<t t-butylbenzyldA BB_dA> CRN104BZ 92 AACGTCAGGAACATCCCAAAGG<t_ t-benzyldC BZ_dC> CRN104BU 93 AACGTCAGGAACATCCCAAAGG<t_ t-butylbenzyldC BB_dC> CRN106BZ 94 GCGAGTTGGCTTATCAAGGTTCATG t-benzyldA A<t_BZ_dA> CRN106BU 95 GCGAGTTGGCTTATCAAGGTTCATGA<t_ t-butylbenzyldA BB_dA> CRN108BZ 96 GTTGATTGGATAGCGAGTTGG<t_BZ t-benzyldC dC> CRN108BU 97 GTTGATTGGATAGCGAGTTGG<t_BB t-butylbenzyldC dC> CRN110BZ 98 CTCGTCGACAACTTCCTCCT<t_BZ_ t-benzyldC dC> CRN110BU 99 CTCGTCGACAACTTCCTCCT<t_BZ_ t-butylbenzyldC dC>

TABLE-US-00015 TABLE XV CRN Probes Probes Oligo Name SEQ ID NO: Sequence Modifications CRN141FQ6 100 <F> CCAAGA<Q>CTCAACATTCAAC P = phosphate, F = th-FAM, TCATTATCTAACG<P> Q = BHQ2 CRN143FQ6 101 <F>ACATCA<Q>CATACTCACCACAT P = phosphate, F = th-FAM, AATCCAAATCT<P> Q = BHQ2 CRN142FQ6 102 <F>ACAATG<Q>CCAACTGGAAGAT P = phosphate, F = th-FAM, AAGTAAAGTAGT<P> Q = BHQ2 CRN144FQ6 103 <F>ACAATG<Q>CCAACTGGAAGAT P = phosphate, F = th-FAM, AAGTAAAGTAGTT<P> Q = BHQ2 CRN146FQ6 104 <F>TTGGAA<Q>GATGGGATTTGTC P = phosphate, F = th-FAM, AACTGTCAATCTG<P> Q = BHQ2 CRN148FQ6 105 <F>TTGGAA<Q>GATGGGATTTGTC P = phosphate, F = th-FAM, AACTGTCAATCT<P> Q = BHQ2

[0045] In one embodiment, the above described sets of primers and probes are used in order to provide for detection of TV in a biological sample suspected of containing TV. The sets of primers and probes may comprise or consist of the primers and probes specific for the nucleic acid sequences of the 5.8s gene, 18s gene, PMS1 gene, Mlh1a gene and CRN gene comprising or consisting of the nucleic acid sequences of SEQ ID NOs: 1-105. In another embodiment, the primers and probes for the target TV genes comprise or consist of a functionally active variant of any of the primers and probes of SEQ ID NOs: 1-105.

[0046] A functionally active variant of any of the primers and/or probes of SEQ ID NOs: 1-105 may be identified by using the primers and/or probes in the disclosed methods. A functionally active variant of a primer and/or probe of any of the SEQ ID NOs: 1-105 pertains to a primer and/or probe which provides a similar or higher specificity and sensitivity in the described method or kit as compared to the respective sequence of SEQ ID NOs: 1-105.

[0047] The variant may, e.g., vary from the sequence of SEQ ID NOs: 1-105 by one or more nucleotide additions, deletions or substitutions such as one or more nucleotide additions, deletions or substitutions at the 5′ end and/or the 3′ end of the respective sequence of SEQ ID NOs: 1-105. As detailed above, a primer (and/or probe) may be chemically modified, i.e., a primer and/or probe may comprise a modified nucleotide or a non-nucleotide compound. A probe (or a primer) is then a modified oligonucleotide. “Modified nucleotides” (or “nucleotide analogs”) differ from a natural “nucleotide” by some modification but still consist of a base or base-like compound, a pentofuranosyl sugar or a pentofuranosyl sugar-like compound, a phosphate portion or phosphate-like portion, or combinations thereof. For example, a “label” may be attached to the base portion of a “nucleotide” whereby a “modified nucleotide” is obtained. A natural base in a “nucleotide” may also be replaced by, e.g., a 7-deazapurine whereby a “modified nucleotide” is obtained as well. The terms “modified nucleotide” or “nucleotide analog” are used interchangeably in the present application. A “modified nucleoside” (or “nucleoside analog”) differs from a natural nucleoside by some modification in the manner as outlined above for a “modified nucleotide” (or a “nucleotide analog”).

[0048] Oligonucleotides including modified oligonucleotides and oligonucleotide analogs that amplify a nucleic acid molecule encoding the target TV gene, e.g. the 5.8s gene, can be designed using, for example, a computer program such as OLIGO (Molecular Biology Insights Inc., Cascade, Colo.). Important features when designing oligonucleotides to be used as amplification primers include, but are not limited to, an appropriate size amplification product to facilitate detection (e.g., by electrophoresis), similar melting temperatures for the members of a pair of primers, and the length of each primer (i.e., the primers need to be long enough to anneal with sequence-specificity and to initiate synthesis but not so long that fidelity is reduced during oligonucleotide synthesis). Typically, oligonucleotide primers are 8 to 50 nucleotides in length (e.g., 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, or 50 nucleotides in length). In some embodiments oligonucleotide primers are 40 or fewer nucleotides in length.

[0049] In addition to a set of primers, the methods may use one or more probes in order to detect the presence or absence of TV. The term “probe” refers to synthetically or biologically produced nucleic acids (DNA or RNA), which by design or selection, contain specific nucleotide sequences that allow them to hybridize under defined predetermined stringencies specifically (i.e., preferentially) to “target nucleic acids”, in the present case to an target TV gene nucleic acid. A “probe” can be referred to as a “detection probe” meaning that it detects the target nucleic acid.

[0050] In some embodiments, the described target TV gene probes can be labeled with at least one fluorescent label. In one embodiment, the target TV gene probes can be labeled with a donor fluorescent moiety, e.g., a fluorescent dye, and a corresponding acceptor moiety, e.g., a quencher. In one embodiment, the probe comprises or consists of a fluorescent moiety and the nucleic acid sequences comprise or consist of SEQ ID NOs: 14-18, 39-44, 53-54, 75-79, and 100-105.

[0051] Designing oligonucleotides to be used as probes can be performed in a manner similar to the design of primers. Embodiments may use a single probe or a pair of probes for detection of the amplification product. Depending on the embodiment, the probe(s) use may comprise at least one label and/or at least one quencher moiety. As with the primers, the probes usually have similar melting temperatures, and the length of each probe must be sufficient for sequence-specific hybridization to occur but not so long that fidelity is reduced during synthesis. Oligonucleotide probes are generally 15 to 40 (e.g., 16, 18, 20, 21, 22, 23, 24, or 25) nucleotides in length.

[0052] Constructs can include vectors each containing one of target TV gene primers and probes nucleic acid molecules. Constructs can be used, for example, as control template nucleic acid molecules. Vectors suitable for use are commercially available and/or produced by recombinant nucleic acid technology methods routine in the art. Target TV gene nucleic acid molecules can be obtained, for example, by chemical synthesis, direct cloning from TV, or by PCR amplification.

[0053] Constructs suitable for use in the methods typically include, in addition to the target TV gene nucleic acid molecules (e.g., a nucleic acid molecule that contains one or more sequences of SEQ ID NOs: 1-105), sequences encoding a selectable marker (e.g., an antibiotic resistance gene) for selecting desired constructs and/or transformants, and an origin of replication. The choice of vector systems usually depends upon several factors, including, but not limited to, the choice of host cells, replication efficiency, selectability, inducibility, and the ease of recovery.

[0054] Constructs containing target TV gene nucleic acid molecules can be propagated in a host cell. As used herein, the term host cell is meant to include prokaryotes and eukaryotes such as yeast, plant and animal cells. Prokaryotic hosts may include E. coli, Salmonella typhimurium, Serratia marcescens, and Bacillus subtilis. Eukaryotic hosts include yeasts such as S. cerevisiae, S. pombe, Pichia pastoris, mammalian cells such as COS cells or Chinese hamster ovary (CHO) cells, insect cells, and plant cells such as Arabidopsis thaliana and Nicotiana tabacum. A construct can be introduced into a host cell using any of the techniques commonly known to those of ordinary skill in the art. For example, calcium phosphate precipitation, electroporation, heat shock, lipofection, microinjection, and viral-mediated nucleic acid transfer are common methods for introducing nucleic acids into host cells. In addition, naked DNA can be delivered directly to cells (see, e.g., U.S. Pat. Nos. 5,580,859 and 5,589,466).

Polymerase Chain Reaction (PCR)

[0055] U.S. Pat. Nos. 4,683,202, 4,683,195, 4,800,159, and 4,965,188 disclose conventional PCR techniques. PCR typically employs two oligonucleotide primers that bind to a selected nucleic acid template (e.g., DNA or RNA). Primers useful in some embodiments include oligonucleotides capable of acting as points of initiation of nucleic acid synthesis within the described target TV gene nucleic acid sequences (e.g., SEQ ID NOs: 1-13, 19-38, 45-52, 55-74, and 80-99). A primer can be purified from a restriction digest by conventional methods, or it can be produced synthetically. The primer is preferably single-stranded for maximum efficiency in amplification, but the primer can be double-stranded. Double-stranded primers are first denatured, i.e., treated to separate the strands. One method of denaturing double stranded nucleic acids is by heating.

[0056] If the template nucleic acid is double-stranded, it is necessary to separate the two strands before it can be used as a template in PCR. Strand separation can be accomplished by any suitable denaturing method including physical, chemical or enzymatic means. One method of separating the nucleic acid strands involves heating the nucleic acid until it is predominately denatured (e.g., greater than 50%, 60%, 70%, 80%, 90% or 95% denatured). The heating conditions necessary for denaturing template nucleic acid will depend, e.g., on the buffer salt concentration and the length and nucleotide composition of the nucleic acids being denatured, but typically range from about 90° C. to about 105° C. for a time depending on features of the reaction such as temperature and the nucleic acid length. Denaturation is typically performed for about 30 sec to 4 min (e.g., 1 min to 2 min 30 sec, or 1.5 min).

[0057] If the double-stranded template nucleic acid is denatured by heat, the reaction mixture is allowed to cool to a temperature that promotes annealing of each primer to its target sequence on the described target TV gene nucleic acid molecules. The temperature for annealing is usually from about 35° C. to about 65° C. (e.g., about 40° C. to about 60° C.; about 45° C. to about 50° C.). Annealing times can be from about 10 sec to about 1 min (e.g., about 20 sec to about 50 sec; about 30 sec to about 40 sec). The reaction mixture is then adjusted to a temperature at which the activity of the polymerase is promoted or optimized, i.e., a temperature sufficient for extension to occur from the annealed primer to generate products complementary to the template nucleic acid. The temperature should be sufficient to synthesize an extension product from each primer that is annealed to a nucleic acid template, but should not be so high as to denature an extension product from its complementary template (e.g., the temperature for extension generally ranges from about 40° C. to about 80° C. (e.g., about 50° C. to about 70° C.; about 60° C.). Extension times can be from about 10 sec to about 5 min (e.g., about 30 sec to about 4 min; about 1 min to about 3 min; about 1 min 30 sec to about 2 min).

[0058] PCR assays can employ nucleic acid such as RNA or DNA (cDNA). The template nucleic acid need not be purified; it may be a minor fraction of a complex mixture, such as nucleic acid contained in human cells. Nucleic acid molecules may be extracted from a biological sample by routine techniques such as those described in Diagnostic Molecular Microbiology: Principles and Applications (Persing et al. (eds), 1993, American Society for Microbiology, Washington D.C.). Nucleic acids can be obtained from any number of sources, such as plasmids, or natural sources including bacteria, yeast, protozoa viruses, organelles, or higher organisms such as plants or animals.

[0059] The oligonucleotide primers are combined with PCR reagents under reaction conditions that induce primer extension. For example, chain extension reactions generally include 50 mM KCl, 10 mM Tris-HCl (pH 8.3), 15 mM MgCl.sub.2, 0.001% (w/v) gelatin, 0.5-1.0 μgprotodenatured template DNA, 50 pmoles of each oligonucleotide primer, 2.5 U of Taq polymerase, and 10% DMSO). The reactions usually contain 150 to 320 μM each of dATP, dCTP, dTTP, dGTP, or one or more analogs thereof.

[0060] The newly synthesized strands form a double-stranded molecule that can be used in the succeeding steps of the reaction. The steps of strand separation, annealing, and elongation can be repeated as often as needed to produce the desired quantity of amplification products corresponding to the target nucleic acid molecules. The limiting factors in the reaction are the amounts of primers, thermostable enzyme, and nucleoside triphosphates present in the reaction. The cycling steps (i.e., denaturation, annealing, and extension) are preferably repeated at least once. For use in detection, the number of cycling steps will depend, e.g., on the nature of the sample. If the sample is a complex mixture of nucleic acids, more cycling steps will be required to amplify the target sequence sufficient for detection. Generally, the cycling steps are repeated at least about 20 times, but may be repeated as many as 40, 60, or even 100 times.

Fluorescence Resonance Energy Transfer (FRET)

[0061] FRET technology (see, for example, U.S. Pat. Nos. 4,996,143, 5,565,322, 5,849,489, and 6,162,603) is based on a concept that when a donor fluorescent moiety and a corresponding acceptor fluorescent moiety are positioned within a certain distance of each other, energy transfer takes place between the two fluorescent moieties that can be visualized or otherwise detected and/or quantitated. The donor typically transfers the energy to the acceptor when the donor is excited by light radiation with a suitable wavelength. The acceptor typically re-emits the transferred energy in the form of light radiation with a different wavelength. In certain systems, non-fluorescent energy can be transferred between donor and acceptor moieties, by way of biomolecules that include substantially non-fluorescent donor moieties (see, for example, U.S. Pat. No. 7,741,467).

[0062] In one example, a oligonucleotide probe can contain a donor fluorescent moiety and a corresponding quencher, which may or not be fluorescent, and which dissipates the transferred energy in a form other than light. When the probe is intact, energy transfer typically occurs between the donor and acceptor moieties such that fluorescent emission from the donor fluorescent moiety is quenched the acceptor moiety. During an extension step of a polymerase chain reaction, a probe bound to an amplification product is cleaved by the 5′ to 3′ nuclease activity of, e.g., a Taq Polymerase such that the fluorescent emission of the donor fluorescent moiety is no longer quenched. Exemplary probes for this purpose are described in, e.g., U.S. Pat. Nos. 5,210,015, 5,994,056, and 6,171,785. Commonly used donor-acceptor pairs include the FAM-TAMRA pair. Commonly used quenchers are DABCYL and TAMRA. Commonly used dark quenchers include BlackHole Quenchers™ (BHQ), (Biosearch Technologies, Inc., Novato, Cal.), Iowa Black™, (Integrated DNA Tech., Inc., Coralville, Iowa), BlackBerry™ Quencher 650 (BBQ-650), (Berry & Assoc., Dexter, Mich.).

[0063] In another example, two oligonucleotide probes, each containing a fluorescent moiety, can hybridize to an amplification product at particular positions determined by the complementarity of the oligonucleotide probes to the target nucleic acid sequence. Upon hybridization of the oligonucleotide probes to the amplification product nucleic acid at the appropriate positions, a FRET signal is generated. Hybridization temperatures can range from about 35° C. to about 65° C. for about 10 sec to about 1 min.

[0064] Fluorescent analysis can be carried out using, for example, a photon counting epifluorescent microscope system (containing the appropriate dichroic mirror and filters for monitoring fluorescent emission at the particular range), a photon counting photomultiplier system, or a fluorimeter. Excitation to initiate energy transfer, or to allow direct detection of a fluorophore, can be carried out with an argon ion laser, a high intensity mercury (Hg) arc lamp, a fiber optic light source, or other high intensity light source appropriately filtered for excitation in the desired range.

[0065] As used herein with respect to donor and corresponding acceptor moieties “corresponding” refers to an acceptor fluorescent moiety or a dark quencher having an absorbance spectrum that overlaps the emission spectrum of the donor fluorescent moiety. The wavelength maximum of the emission spectrum of the acceptor fluorescent moiety should be at least 100 nm greater than the wavelength maximum of the excitation spectrum of the donor fluorescent moiety. Accordingly, efficient non-radiative energy transfer can be produced there between.

[0066] Fluorescent donor and corresponding acceptor moieties are generally chosen for (a) high efficiency Forster energy transfer; (b) a large final Stokes shift (>100 nm); (c) shift of the emission as far as possible into the red portion of the visible spectrum (>600 nm); and (d) shift of the emission to a higher wavelength than the Raman water fluorescent emission produced by excitation at the donor excitation wavelength. For example, a donor fluorescent moiety can be chosen that has its excitation maximum near a laser line (for example, Helium-Cadmium 442 nm or Argon 488 nm), a high extinction coefficient, a high quantum yield, and a good overlap of its fluorescent emission with the excitation spectrum of the corresponding acceptor fluorescent moiety. A corresponding acceptor fluorescent moiety can be chosen that has a high extinction coefficient, a high quantum yield, a good overlap of its excitation with the emission of the donor fluorescent moiety, and emission in the red part of the visible spectrum (>600 nm).

[0067] Representative donor fluorescent moieties that can be used with various acceptor fluorescent moieties in FRET technology include fluorescein, Lucifer Yellow, B-phycoerythrin, 9-acridineisothiocyanate, Lucifer Yellow VS, 4-acetamido-4′-isothio-cyanatostilbene-2,2′-disulfonic acid, 7-diethylamino-3-(4′-isothiocyanatophenyl)-4-methylcoumarin, succinimdyl 1-pyrenebutyrate, and 4-acetamido-4′-isothiocyanatostilbene-2,2′-disulfonic acid derivatives. Representative acceptor fluorescent moieties, depending upon the donor fluorescent moiety used, include LC Red 640, LC Red 705, Cy5, Cy5.5, Lissamine rhodamine B sulfonyl chloride, tetramethyl rhodamine isothiocyanate, rhodamine x isothiocyanate, erythrosine isothiocyanate, fluorescein, diethylenetriamine pentaacetate, or other chelates of Lanthanide ions (e.g., Europium, or Terbium). Donor and acceptor fluorescent moieties can be obtained, for example, from Molecular Probes (Junction City, Oreg.) or Sigma Chemical Co. (St. Louis, Mo.).

[0068] The donor and acceptor fluorescent moieties can be attached to the appropriate probe oligonucleotide via a linker arm. The length of each linker arm is important, as the linker arms will affect the distance between the donor and acceptor fluorescent moieties. The length of a linker arm can be the distance in Angstroms (Å) from the nucleotide base to the fluorescent moiety. In general, a linker arm is from about 10 Å to about 25 Å. The linker arm may be of the kind described in WO 84/03285. WO 84/03285 also discloses methods for attaching linker arms to a particular nucleotide base, and also for attaching fluorescent moieties to a linker arm.

[0069] An acceptor fluorescent moiety, such as an LC Red 640, can be combined with an oligonucleotide which contains an amino linker (e.g., C6-amino phosphoramidites available from ABI (Foster City, Calif.) or Glen Research (Sterling, Va.)) to produce, for example, LC Red 640-labeled oligonucleotide. Frequently used linkers to couple a donor fluorescent moiety such as fluorescein to an oligonucleotide include thiourea linkers (FITC-derived, for example, fluorescein-CPG's from Glen Research or ChemGene (Ashland, Mass.)), amide-linkers (fluorescein-NHS-ester-derived, such as CX-fluorescein-CPG from BioGenex (San Ramon, Calif.)), or 3′-amino-CPGs that require coupling of a fluorescein-NHS-ester after oligonucleotide synthesis.

Detection of TV

[0070] The present disclosure provides methods for detecting the presence or absence of TV in a biological or non-biological sample. Methods provided avoid problems of sample contamination, false negatives, and false positives. The methods include performing at least one cycling step that includes amplifying a portion of target nucleic acid molecules from a sample using one or more pairs of primers, and a FRET detecting step. Multiple cycling steps are performed, preferably in a thermocycler. Methods can be performed using the primers and probes to detect the presence of TV, and the detection of the target TV gene indicates the presence of TV in the sample.

[0071] As described herein, amplification products can be detected using labeled hybridization probes that take advantage of FRET technology. One FRET format utilizes TaqMan® technology to detect the presence or absence of an amplification product, and hence, the presence or absence of TV. TaqMan® technology utilizes one single-stranded hybridization probe labeled with, e.g., one fluorescent dye and one quencher, which may or may not be fluorescent. When a first fluorescent moiety is excited with light of a suitable wavelength, the absorbed energy is transferred to a second fluorescent moiety or a dark quencher according to the principles of FRET. The second moiety is generally a quencher molecule. During the annealing step of the PCR reaction, the labeled hybridization probe binds to the target DNA (i.e., the amplification product) and is degraded by the 5′ to 3′ nuclease activity of, e.g., the Taq Polymerase during the subsequent elongation phase. As a result, the fluorescent moiety and the quencher moiety become spatially separated from one another. As a consequence, upon excitation of the first fluorescent moiety in the absence of the quencher, the fluorescence emission from the first fluorescent moiety can be detected. By way of example, an ABI PRISM® 7700 Sequence Detection System (Applied Biosystems) uses TaqMan® technology, and is suitable for performing the methods described herein for detecting the presence or absence of TV in the sample.

[0072] Molecular beacons in conjunction with FRET can also be used to detect the presence of an amplification product using the real-time PCR methods. Molecular beacon technology uses a hybridization probe labeled with a first fluorescent moiety and a second fluorescent moiety. The second fluorescent moiety is generally a quencher, and the fluorescent labels are typically located at each end of the probe. Molecular beacon technology uses a probe oligonucleotide having sequences that permit secondary structure formation (e.g., a hairpin). As a result of secondary structure formation within the probe, both fluorescent moieties are in spatial proximity when the probe is in solution. After hybridization to the target nucleic acids (i.e., amplification products), the secondary structure of the probe is disrupted and the fluorescent moieties become separated from one another such that after excitation with light of a suitable wavelength, the emission of the first fluorescent moiety can be detected.

[0073] Another common format of FRET technology utilizes two hybridization probes. Each probe can be labeled with a different fluorescent moiety and are generally designed to hybridize in close proximity to each other in a target DNA molecule (e.g., an amplification product). A donor fluorescent moiety, for example, fluorescein, is excited at 470 nm by the light source of the LightCycler® Instrument. During FRET, the fluorescein transfers its energy to an acceptor fluorescent moiety such as LightCycler®-Red 640 (LC Red 640) or LightCycler®-Red 705 (LC Red 705). The acceptor fluorescent moiety then emits light of a longer wavelength, which is detected by the optical detection system of the LightCycler® instrument. Efficient FRET can only take place when the fluorescent moieties are in direct local proximity and when the emission spectrum of the donor fluorescent moiety overlaps with the absorption spectrum of the acceptor fluorescent moiety. The intensity of the emitted signal can be correlated with the number of original target DNA molecules (e.g., the number of TV genomes). If amplification of target nucleic acid occurs and an amplification product is produced, the step of hybridizing results in a detectable signal based upon FRET between the members of the pair of probes.

[0074] Generally, the presence of FRET indicates the presence of TV in the sample, and the absence of FRET indicates the absence of TV in the sample. Inadequate specimen collection, transportation delays, inappropriate transportation conditions, or use of certain collection swabs (calcium alginate or aluminum shaft) are all conditions that can affect the success and/or accuracy of a test result, however. Using the methods disclosed herein, detection of FRET within, e.g., 45 cycling steps is indicative of a TV infection.

[0075] Representative biological samples that can be used in practicing the methods include, but are not limited to respiratory specimens, fecal specimens, blood specimens, dermal swabs, nasal swabs, wound swabs, blood cultures, skin, and soft tissue infections. Collection and storage methods of biological samples are known to those of skill in the art. Biological samples can be processed (e.g., by nucleic acid extraction methods and/or kits known in the art) to release TV nucleic acid or in some cases, the biological sample can be contacted directly with the PCR reaction components and the appropriate oligonucleotides.

[0076] Melting curve analysis is an additional step that can be included in a cycling profile. Melting curve analysis is based on the fact that DNA melts at a characteristic temperature called the melting temperature (Tm), which is defined as the temperature at which half of the DNA duplexes have separated into single strands. The melting temperature of a DNA depends primarily upon its nucleotide composition. Thus, DNA molecules rich in G and C nucleotides have a higher Tm than those having an abundance of A and T nucleotides. By detecting the temperature at which signal is lost, the melting temperature of probes can be determined. Similarly, by detecting the temperature at which signal is generated, the annealing temperature of probes can be determined. The melting temperature(s) of the probes from the amplification products can confirm the presence or absence of TV in the sample.

[0077] Within each thermocycler run, control samples can be cycled as well. Positive control samples can amplify target nucleic acid control template (other than described amplification products of target genes) using, for example, control primers and control probes. Positive control samples can also amplify, for example, a plasmid construct containing the target nucleic acid molecules. Such a plasmid control can be amplified internally (e.g., within the sample) or in a separate sample run side-by-side with the patients' samples using the same primers and probe as used for detection of the intended target. Such controls are indicators of the success or failure of the amplification, hybridization, and/or FRET reaction. Each thermocycler run can also include a negative control that, for example, lacks target template DNA. Negative control can measure contamination. This ensures that the system and reagents would not give rise to a false positive signal. Therefore, control reactions can readily determine, for example, the ability of primers to anneal with sequence-specificity and to initiate elongation, as well as the ability of probes to hybridize with sequence-specificity and for FRET to occur.

[0078] In an embodiment, the methods include steps to avoid contamination. For example, an enzymatic method utilizing uracil-DNA glycosylase is described in U.S. Pat. Nos. 5,035,996, 5,683,896 and 5,945,313 to reduce or eliminate contamination between one thermocycler run and the next.

[0079] Conventional PCR methods in conjunction with FRET technology can be used to practice the methods. In one embodiment, a LightCycler® instrument is used. The following patent applications describe real-time PCR as used in the LightCycler® technology: WO 97/46707, WO 97/46714, and WO 97/46712.

[0080] The LightCycler® can be operated using a PC workstation and can utilize a Windows NT operating system. Signals from the samples are obtained as the machine positions the capillaries sequentially over the optical unit. The software can display the fluorescence signals in real-time immediately after each measurement. Fluorescent acquisition time is 10-100 milliseconds (msec). After each cycling step, a quantitative display of fluorescence vs. cycle number can be continually updated for all samples. The data generated can be stored for further analysis.

[0081] As an alternative to FRET, an amplification product can be detected using a double-stranded DNA binding dye such as a fluorescent DNA binding dye (e.g., SYBR® Green or SYBR® Gold (Molecular Probes)). Upon interaction with the double-stranded nucleic acid, such fluorescent DNA binding dyes emit a fluorescence signal after excitation with light at a suitable wavelength. A double-stranded DNA binding dye such as a nucleic acid intercalating dye also can be used. When double-stranded DNA binding dyes are used, a melting curve analysis is usually performed for confirmation of the presence of the amplification product.

[0082] It is understood that the embodiments of the present disclosure are not limited by the configuration of one or more commercially available instruments.

Articles of Manufacture/Kits

[0083] Embodiments of the present disclosure further provide for articles of manufacture, compositions or kits to detect TV. An article of manufacture can include primers and probes used to detect the target TV gene, together with suitable packaging materials. Compositions can include primers used to amplify the target TV gene. In certain embodiments compositions can also comprise probes for detecting the target TV gene. Representative primers and probes for detection of TV are capable of hybridizing to target nucleic acid molecules. In addition, the kits may also include suitably packaged reagents and materials needed for DNA immobilization, hybridization, and detection, such solid supports, buffers, enzymes, and DNA standards. Methods of designing primers and probes are disclosed herein, and representative examples of primers and probes that amplify and hybridize to target nucleic acid molecules are provided.

[0084] Articles of manufacture can also include one or more fluorescent moieties for labeling the probes or, alternatively, the probes supplied with the kit can be labeled. For example, an article of manufacture may include a donor and/or an acceptor fluorescent moiety for labeling the probes. Examples of suitable FRET donor fluorescent moieties and corresponding acceptor fluorescent moieties are provided above.

[0085] Articles of manufacture can also contain a package insert or package label having instructions thereon for using the primers and probes to detect TV in a sample. Articles of manufacture and compositions may additionally include reagents for carrying out the methods disclosed herein (e.g., buffers, polymerase enzymes, co-factors, or agents to prevent contamination). Such reagents may be specific for one of the commercially available instruments described herein.

[0086] Embodiments of the present disclosure will be further described in the following examples, which do not limit the scope of the invention described in the claims.

EXAMPLES

[0087] The following examples, tables and figures are provided to aid the understanding of the subject matter, the true scope of which is set forth in the appended claims. It is understood that modifications can be made in the procedures set forth without departing from the spirit of the invention.

Example I

[0088] Target selection for TV was the result of a comprehensive search of the public sequence database, as well as a literature search for TV targets with a potential to discriminate against the nearest neighbors, Trichomonas tenax and Pentatrichomonas hominis. Multiple targets from the public sequence database were analyzed in the target selection process of the design phase, but all showed cross reactivity with T. tenax and P. hominis. The sequences in the public database are complicated by “bulk” sequence data from multicopy targets. BLAST analysis of the chosen oligonucleotides indicated that the only significant cross reactivity will be with Trichomonas tenax.

[0089] Real-time PCR detection of TV were performed using either the cobas® 4800 system or the cobas® 6800/8800 systems platforms (Roche Molecular Systems, Inc., Pleasanton, CA). The final concentrations of the amplification reagents are shown below:

TABLE-US-00016 TABLE XVI PCR Amplification Reagents Master Mix Component Final Conc (50 uL) DMSO 0-5.4 % NaN3 0.027-0.030 % Potassium acetate 120.0 mM Glycerol 3.0 % Tween 20 0.02 % EDTA 0-43.9 uM Tricine 60.0 mM Aptamer 0.18-0.22 uM UNG Enzyme 5.0-10.0 U Z05-SP-PZ Polymerase 30.0-45.0 U dATP 400.0-521.70 uM dCTP 400.0-521.70 uM dGTP 400.0-521.70 uM dUTP 800.0-1043.40 uM Forward primer oligonucleotides 0.15-0.50 μM Reverse primer oligonucleotides 0.15-0.50 μM Probe oligonucleotides 0.10 μM Manganese Acetate 3.30-3.80 mM

[0090] The following table shows the typical thermoprofile used for PCR amplification reaction:

TABLE-US-00017 TABLE XVII PCR Thermoprofile Program Name Target (° C.) Acquisition Mode Hold (hh:mm:ss) Ramp Rate (° C./s) Cycles Analysis Mode Pre-PCR 50 None 00:02:00 4.4 1 None 94 None 00:00:05 4.4 55 None 00:02:00 2.2 60 None 00:06:00 4.4 65 None 00:04:00 4.4 1st Measurement 95 None 00:00:05 4.4 5 Quantification 55 Single 00:00:30 2.2 2nd Measurment 91 None 00:00:05 4.4 45 Quantification 58 Single 00:00:25 2.2 Cooling 40 None 00:02:00 2.2 1 None

[0091] The Pre-PCR program comprised initial denaturing and incubation at 55° C., 60° C. and 65° C. for reverse transcription of RNA templates. Incubating at three temperatures combines the advantageous effects that at lower temperatures slightly mismatched target sequences (such as genetic variants of an organism) are also transcribed, while at higher temperatures the formation of RNA secondary structures is suppressed, thus leading to a more efficient transcription. PCR cycling was divided into two measurements, wherein both measurements apply a one-step setup (combining annealing and extension). The first 5 cycles at 55° C. allow for an increased inclusivity by pre-amplifying slightly mismatched target sequences, whereas the 45 cycles of the second measurement provide for an increased specificity by using an annealing/extension temperature of 58° C. FIG. 2 depicts a typical amplification experiment where PCR growth curves are shown in various concentrations of genomic TV template DNA.

[0092] The amplification and detection of the target TV genes, 5.8s rRNA, 18s rRNA, PMS1, Mlh1a and CRN were performed using the conditions described above. The results of the experiments using several selected oligonucleotide primers and probes against genomic TV DNA present at a concentration of either 10 genomic equivalent/PCR (5.8s rRNA) or 1000 genomic equivalent/PCR (18s rRNA, PMS1, Mlh1a, CRN) are shown below as Ct values (threshold cycle) for the amplification reactions.

TABLE-US-00018 TABLE XVIII Amplification and Detection of target TV genes Forward Reverse Target primer primer Probe Ct values TV Gene SEQ ID NO SEQ ID NO SEQ ID NO 10 ge/PCR of TV 5.8s rRNA 3 12 16 27.3 3 12 17 30.1 3 12 18 27.5 6 12 18 28.5 7 12 18 28.1 9 12 18 28.0 18s rRNA 21 31 40 24.9 22 32 40 25.4 PMS1 45 49 54 31.6 46 50 54 32.0 47 51 54 32.3 48 52 54 32.2 Mlh1a 57 67 76 32.7 58 68 76 33.4 63 73 79 32.5 64 74 79 32.9 CRN 80 90 100 34.6 81 91 100 35.0 82 92 101 33.5 83 93 101 33.5

Example 2

[0093] The amplification and detection of the TV 5.8s rRNA gene was performed as described in Example 1 with the exception that genomic template DNA for Mycoplasma genitalium (MG) was included in the PCR assay together with primers and probes that can amplify and detect MG. In this experiment, primers and probes, disclosed in U.S. Provisional Application No. 62/342,519, that hybridize to the conserved region A of the mgpB gene (mgpB) and to the variable region EF of the mgpB gene (MgPar) were used.

[0094] TV Limit of Detection (LOD) was tested at 100, 10, 5 and 1 genomic equivalent concentrations per PCR reaction (ge/PCR), in a co-amplification with internal control standard and MG at 10 ge/PCR . The results are shown on FIGS. 3 and 4. All levels of TV were detected with no dropouts, and TV LOD is determined to be <1 ge/PCR.

[0095] While the foregoing invention has been described in some detail for purposes of clarity and understanding, it will be clear to one skilled in the art from a reading of this disclosure that various changes in form and detail can be made without departing from the true scope of the invention. For example, all the techniques and apparatus described above can be used in various combinations. All publications, patents, patent applications, and/or other documents cited in this application are incorporated by reference in their entirety for all purposes to the same extent as if each individual publication, patent, patent application, and/or other document were individually indicated to be incorporated by reference for all purposes.