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    • 专利摘要:
    TEST FOR GARDNERELLA VAGINALIS The present invention relates to nucleic acid amplification assays for the detection of Gardnerella Vaginalis nucleic acid sequences. The present invention provides oligonucleotides that are complementary to or annular to the nucleic acid sequences of the GV vly gene. The present invention also provides the internal amplification controls (IAC) that can be used in nucleic acid amplification reactions.
    公开号:BR112013010856B1
    申请号:R112013010856-8
    申请日:2011-10-28
    公开日:2020-12-22
    发明作者:Jason P. Stevens
    申请人:Becton, Dickinson And Company；
    IPC主号:
    专利说明:

    Cross-references to related orders
    [001] This application claims the benefit of the filing date of United States Provisional Patent Application No. 61 / 408,840, filed on November 1, 2010, and its disclosure is incorporated herein by reference. Sequence Listing
    [002] The present application contains a Sequence Listing that was presented in ASCII format through EFS-Web and is hereby incorporated by reference in its entirety. Said ASCII copy, created on October 19, 2011, is called the Sequence Listing for Gardnerella vaginalis_ST25.txt and is 15.6 kilobytes in size. Field of the Invention
    The present invention relates to nucleic acid amplification methods for the detection and / or quantification of Gardnerella vaginalis nucleic acid sequences (also referred to herein as GV). The present invention provides oligonucleotides that are complementary or that anneal to the nucleic acid sequences of Gardnerella vaginalis, for amplification and / or detection. The present invention provides a tape displacement amplification assay (SDA), or a PCR assay for the amplification and / or detection of Gardnerella vaginalis nucleic acid sequences. The SDA assay can optionally be a diplex SDA that includes internal amplification controls (IAC). Background of the Invention
    [004] Gardnerella vaginalis (GV) is a gram-variable coccobacillus that has been discussed to be the only causative agent of nonspecific vaginitis. Kretzschmar U, et al. “Purification and Characterization of Gardnerella vaginalis Hemolysin Curr. Microbiol. 23 (1): 713 (1991). The diagnosis and detection of this organism is often based on clinical or pathological findings and can be confirmed by isolation and staining techniques. For example, in Kretzschmar et al., The basis for the detection and characterization of GV was the extracellular hemolysin produced by the organism. Gelber S., et al. “Functional and Phylogenetic Characterization of Vaginolisin, the Human Specific Cytolysin from Gardnerella vaginalis” J. Bacteriol. 190 (11): 3896 3903 (2008) identified another of the extracellular hemolysins produced by GV as vaginolysin. Rottini, G., et al. “Identification and Partial Characterization of a Cytolytic Toxin Produced by Gardnerella vaginalis” Infect. and Immun. 58 (11): 3751 3758 (1990) identifies the hemolysin produced by GV as cytolysin The difficulties in isolating these toxins produced by GV are described Cuaci S, et al. “Pore forming and haemolytic properties of the Gardnerella vaginalis cytolisin,” Mole. Microbe. 9 (6): 1143 1155 (1993).
    [005] Much has been written about the measurement and detection of toxins produced by GV to detect GV. However, a method for detecting GV based on the body itself, as opposed to the toxins it produces, remains in demand. Thus, there is a need for an assay that reduces the chances of false negative results.
    [006] The citation or discussion of a reference in this document should not be interpreted as an admission that this is prior art to the present invention. Summary of the Invention
    [007] A method for qualitatively and / or quantitatively detecting the presence or absence of Gardnerella vaginalis in a sample is described herein, said method comprising: (a) amplifying the target sequence using a first amplification primer having a sequence consisting essentially of the target binding sequence of any amplification primer disclosed herein and (b) detecting the amplified target sequence. In certain embodiments, the use of a second amplification primer which essentially consists of the target binding sequence of any amplification primer described herein is also described.
    [008] The oligonucleotides described here can be used to detect the presence of GV by selecting an amplified nucleic acid sequence found in the genes that produce the vaginolysin and cytolysin / hemolysin toxins. In this regard, the inventors have chosen to refer to this target as the vly gene. However, the literature also refers to the cytolysin gene and the GV hemolysin gene. Whether or not these are different genes or simply different names for the same gene is irrelevant to the invention described here. Although the target sequence is referred to here as the "vly gene" or the "Vly target" is the target itself (ie, a gene that produces one of the toxins mentioned above), and not the name of the target gene, which is the focus of the present invention. Although applicants do not wish to be bound by any particular theory, applicants believe that these toxins are produced by the same gene. However, the present invention should not be limited to the name of the GV gene in which the target sequence is located.
    [009] In one embodiment, a method for detecting a target sequence of Gardnerella vaginalis is described here. In this method, at least one oligonucleotide primer is provided that will amplify at least a part of the GV vly gene and, after amplification, the amplified target sequence is detected. Examples of the vly gene include GV SEQ ID NOs. 1, 2, 23, 24 and 25.
    [0010] Highly conserved regions of the vly gene have been identified. The highly conserved sequence is located in the vicinity of base pairs 328-523 in the vly gene (for strains 14018, 14019 and 49145, described here). In a preferred embodiment, the target sequence is the highly conserved region of the vly gene.
    The highly conserved vly target gene for strains 14018, 14019 and 49145 (corresponding to the respective Genbank Accession Nos. EU522486, EU522487 and EU522488) is SEQ ID. 1, 23 and 24. SEQ ID NOs. 2 and 25 are highly conserved vly target genes for two clones (T10 and T11, respectively). The clones have Genbank membership numbers EU697811 and EU697812. The location of the highly conserved region in clones is in the vicinity of the 331-526 base pairs. The vly gene is highly conserved among strains and clones, but there are variations between strains and clones.
    [0012] Contained in the vly gene are advantageous target regions that are highly conserved. Such a target region is illustrated in Figure 1 and is also identified as SEQ ID NO. 20. SEQ ID NO: 20 is base pair 325-524 of SEQ ID NO. 1. Among the three strains of vly, there is no variation in SEQ ID NO. 20. However, Figure 1 shows that there are minor sequential variations in this target region between GV strains and clones. Although the sequence is identical for all three strains, the sequence for each strain is illustrated (as 100, 110 and 120) in Figure 1. SEQ ID NO: 21 is the target region sequence for the two clones (T10 and T11 ) and is identical for each of the two clones. However, there is some minor difference between SEQ ID NO: 20 and SEQ ID NO. 21. These variations of SEQ ID NO. 21 (with respect to SEQ ID NO. 20) are shown in 130 and 140 of Figure 1. The variations are much smaller: 7 base pairs of the 196 base pairs in the advantageous target sequence. Also, the variations are in the same positions for all strings. One usually versed in the technique can design primers and probes that do not align with the positions in the target regions where the variations are found.
    [0013] As seen from Figure 1, the highly conserved target region of the vly gene is substantially identical for several strains and clones identified above. Only the sense tape of the target region is illustrated in Figure 1. Since the antisense tape is the complement of the felt tape, the antisense tape, although not specifically illustrated in Figure 1, is known from the sequence listed in Figure 1. The sequences in Figure 1 are four nucleotides larger than SEQ ID NOS: 20 and 21, but are otherwise identical. Additional nucleotides are provided in Figure 1 to more clearly illustrate the relationship between the primers and the target at the ends of the target sequence.
    [0014] Oligonucleotide probe sets are described here which are selected for this highly conserved region and provide a mechanism for detection. The design of the probe set is based on a number of factors, the main of which is the assay in which the probe set is used. Assays for detecting DNA or RNA sequences are well known in the art. These assays typically use some kind of amplification or some kind of image to confirm the presence of the target DNA. Examples of amplification reactions include PCR (Polymerase Chain Reaction - Polymerase Chain Reaction), SDA (Strand Displacement Amplification), TMA (Transcription Mediated Amplification - Transcription Mediated Amplification) and LCR (Ligase Chain Reaction - Ligase Chain Reaction).
    [0015] In one embodiment, the amplification mechanism selected for detection is the SDA. SDA is an isothermal amplification mechanism and, therefore, does not involve performing thermal cycles. As such, SDA probe assemblies are designed for a target melting temperature (Tm), within a predetermined narrow range. The target melting temperature (Tm) is the temperature at which at least fifty percent of the oligonucleotide is annealed to its perfect complement. One usually skilled in the art is aware that the Tm of an oligonucleotide sequence is determined by the number of base pairs in the sequence as well as the type of the bases in the sequence. These guidelines for the design of oligonucleotides are well known to a person skilled in the art and are not presented in detail here.
    [0016] In one embodiment of the present invention, portions of the primers and probes for the SDA assay are complementary to the target region of the vly gene, represented by SEQ ID NO: 20. The target is first denatured. The probe sets are configured in such a way that the forward initiators and the probe connect to (that is, they are complementary) to the denatured target's antisense tape and the reverse primers connect to the same sense tape as the denatured target. The portions of the primers and probes that bind to the target for an embodiment of an SDA probe set are listed in Table 1 below, along with their positioning in the highly conserved portion of the vly gene. Since the highly conserved region of the vly gene is practically identical for the various GV strains, the highly conserved region of the vly gene for each strain or clone is not listed separately.
    [0017] The primer / probe sets of the SDA oligonucleotide described herein are sufficiently complementary to these portions of the gene to selectively bind to those portions.

    * GenBank Accession Number EU522486
    [0018] For the SDA modality described here, the oligonucleotide probe set has protective primers ('bumpers') for left and right, amplification primers for left and right and a probe. As indicated above, the left and forward or forward primers and probes bind to the vly gene antisense strand and the right or reverse primers bind to the sense strands. Thus, the portions of the vly gene to which these primers and probes bind are sufficiently complementary to the target ligand sequences SEQ ID NOS: 3-7 to facilitate hybridization of the primers and probes to them.
    [0019] Primers and probes may have additional nucleotides or sequences attached to them. The probe also has additional image portions attached to it. These fractions facilitate the direction of the target DNA sequence. Using such an oligonucleotide probe set, an SDA assay can be performed on a sample in order to determine the presence or absence of most GV strains. In an illustrative embodiment, a 144 base pair region of the vly gene is amplified between a section of the vly gene near base pair 343 to about base pair 486 of the vly gene.
    Other embodiments of the invention use different oligonucleotide sequences that bind to the region of the vly gene described above. Primer / probe sets are configured to not only selectively bind in that region of the vly gene, but to amplify some portion of the vly gene sequence for detection. The oligonucleotides described here have a sequence that is sufficiently complementary to either the sense tape or the antisense tape to make them capable of binding to the target. The oligonucleotides described herein can be further used, either individually or in combination, to facilitate detection by amplifying the nucleic acid sequence of the vly gene. In one embodiment, the probes are designed to perform a real-time Taqman® PCR assay on the target portion of the gene. Examples of two probe sets used for Taqman® real-time PCR assays, described in terms of their oligonucleotide sequences, are: Table 2: Primer / Probe Sets for Quantitative Real-Time PCR
    * Accession No. EU522486
    [0021] In PCR assays, forward primers and probes are sufficiently complementary to hybridize to the target nucleic acid antisense strand (under appropriate conditions) and reverse primers are sufficiently complementary to hybridize to the sense nucleic acid strand target (under appropriate conditions). Figure 2 illustrates the binding position of the primers and probes described in Table 2 in relation to the sense strand of the target sequence (the boxed portion of the sequence indicates the location of the specific primer / probe associated with the box).
    [0022] In yet another embodiment, oligonucleotides can be used in a method for detecting the presence or absence of GV in the sample. In another embodiment, the method includes treating a sample, using one or more oligonucleotides specific for the target sequence, in a nucleic acid amplification reaction and detecting the presence or absence of the amplified nucleic acid product.
    [0023] In an illustrative mode, the SDA is selected as the amplification reaction. In the context of this modality, the oligonucleotides described herein as suitable for use in the SDA assay are used in combination, as amplification primers, protective primers and a detector in that assay.
    [0024] In another mode, a kit for the detection of GV is provided. The kit includes one or more of the oligonucleotides described here, which selectively bind to the GV vly gene and are capable of amplifying a target sequence that can be used for the detection of that organism. The kit is supplied with one or more of the oligonucleotides and buffer reagents to perform amplification tests.
    [0025] In one aspect of the kit, oligonucleotides and reagents for SDA purposes can be provided. In this regard, two oligonucleotides are provided as amplification primers, two oligonucleotides are provided as protective primers, and one oligonucleotide can be provided for use as a detector.
    [0026] In yet another aspect of the kit, oligonucleotides for SDA purposes can be provided in dry or liquid form. In the dry format, the composition can be applied to an appropriate container where the sample and suitable SDA buffers can be added to perform the assay.
    [0027] In yet another aspect of the kit, oligonucleotides and reagents for the purposes of the Taqman PCR assay can be provided. In this regard, three oligonucleotides are provided. Two of the three are amplification primers and the third oligonucleotide is configured as a detector.
    [0028] In representative embodiments, the kit for an amplification or detection reaction has an oligonucleotide having a target-binding sequence, which is any of SEQ ID NOs: 3 and 13 and their complements, and sequences that share at least 70 % sequence similarity with SEQ. 3 and 13 and their complements. In other embodiments, the kit has an oligonucleotide having a target-binding sequence, which is any of SEQ ID NOs: 3 and 13 and their complements, and sequences that share at least 80% sequence similarity with SEQ. 3 and 13 and their complements. In other embodiments, the kit has an oligonucleotide having a target-binding sequence, which is any of SEQ ID NOs: 3 and 13 and their complements, and sequences that share at least 90% sequence similarity with SEQ ID NOs. 3 and 13 and their complements. In other embodiments, the kit has an oligonucleotide having a target-binding sequence, which is any of SEQ ID NOs: 3 and 13 and their complements.
    [0029] The present invention also provides a method for detecting a Gardnerella vaginalis target sequence, comprising: (a) hybridizing one or more amplification primers described herein with a target sequence in the target gene vly to GV and (b) detecting said hybridization amplifier primer. In the method, at least one amplification primer is a reporter probe which further comprises a detectable marker. Examples of detectable markers include TAMRA, 6ROX or 6FAM. Brief Description of the Figures Figure 1 illustrates the sense strand of the target region of the GV vly gene and the variations in the sense streak sequence for various GV strains and clones and the hybridization positions of the primer and probe modalities described here with respect to felt tape; Figure 2 illustrates both nt 328-523 sense and antisense tapes in the target region and the relative hybridization positions of two representative sets of PCR probes in the target region and with the hybridization positions of the primers and probes further illustrated by the sketch on the sense tape; Figure 3 illustrates both nt 328-523 sense and antisense tapes in the target region and the relative hybridization positions of a representative set of SDA primer / probe in the target region and with the hybridization positions of the primers and probe additionally. illustrated by the outline on the same sense tape as the target region; and Figure 4 illustrates both an IAC sense and antisense tapes for the method described here and the relative hybridization positions of a representative primer / probe SDA probe set in the target region and with the primers and probe hybridization positions. . Detailed Description of the Invention
    [0030] Any definitions are provided for the sake of clarity and should not be considered as limiting. Except where indicated, the technical and scientific terms used herein are intended to have the same meaning as usually understood by those usually versed in the technique to which the invention belongs.
    [0031] Nucleic acid amplification methods and assays for the detection and / or quantification of Gardnerella vaginalis (GV) nucleic acid sequences are described herein. The present invention provides one or more oligonucleotides that are complementary or that match the nucleic acid sequences of Gardnerella vaginalis, for the amplification and / or detection of said sequences. In an embodiment of the present invention, an internal amplification control (IAC) is provided. The ICA can be used in nucleic acid amplification assays of the invention to determine whether the conditions of the assay are permissive for the amplification and / or detection of a target sequence. Oligonucleotides can be used in all types of amplification reactions; such as, for example, tape displacement amplification (SDA), such as, for example, Strand Displacement Amplification (SDA), Polymerase Chain Reaction (PCR), Ligase Chain Reaction, Nucleic Acid Sequence Based Amplification ( NASBA), Rolling Circle Amplification (RCA), Transcription Mediated Amplification (TMA), and QB Replicase Mediated Amplification.
    [0032] The methods of the invention are particularly advantageous over the traditional methods used for the detection of Gardnerella vaginalis, in that they detect the organism properly, rather than the methods and kits of the existing technique that detect toxins (for example, vaginolysin ) that are produced by the organism instead of the organism itself.
    [0033] The sensitivity of an assay refers to the tolerance of false negatives. A test result is false negative if the test result is negative, but the sample actually contains the target sequence. The smaller the amount of target sequence that an assay can detect, the greater the sensitivity that the assay has.
    [0034] The specificity of an assay refers to the tolerance of false positives. A test result is false positive if the test result is positive, but in reality the sample does not contain the target sequence. Thus, the more specific an assay is, the lower the level of false positive results.
    [0035] According to an embodiment of the present invention, a test result to detect Gardnerella vaginalis in a sample using an IAC can be interpreted as described in Table 3. Table 3. Interpretation of an SDA Diplex Assay


    [0036] An IAC can be used instead of, and / or in conjunction with, a conventional amplification control (AC). It is understood by those usually skilled in the art that the AC reaction is carried out in a reaction mixture separately from the sample to be tested. A conventional AC reaction comprises amplification reagents and target DNA. If the amplification and / or detection of the target DNA in the AC reaction is suppressed, an indication that the target sequence is missing from a test sample can be attributed to inhibitory signals in the reaction. Although this type of control reaction is effective, it is not the most desirable. Since the AC reaction is carried out separately, it may not exactly reflect the conditions of the reactions containing the test sample. The methods of the invention are particularly useful in that they have an IAC and the control reaction is performed under identical spatial and temporal conditions as those of amplification and / or detection of the target sequence, thus minimizing human error.
    [0037] Amplification primers, which bind to a target sequence (i.e., a Gardnerella vaginalis sequence) are described herein. In these modalities where an IAC is used, amplification initiators are provided that annul the IAC. In some embodiments of the invention, a protective primer or its respective target binding sequence described in Table 1 or Figures 1, 3 and 4, can be used as an amplification primer. In some embodiments of the invention, an amplification primer is chosen from among the amplification primers described in Tables 1 and 2 or Figures 1 to 4, as disclosed herein. In another embodiment of the invention, an amplification primer is chosen from the target binding sequences of the amplification primers described in Figures 1 to 4, as disclosed herein. Amplification methods
    [0038] The oligonucleotides described herein can be used in any method of amplifying nucleic acids known in the art.
    [0039] Suitable amplification methods include, but are not limited to, Polymerase Chain Reaction ("PCR"; see US Patent Nos. 4,683,195; 4,683,202; 4,800,159; and 4,965,188), Strand Displacement Amplification ("SDA"; see Walker et al., Proc. Nat'l Acad. Sci. USA 89: 392 (1992); Walker et al., Nucl. Acids Res. 20: 1691 (1992); and US Patent No. 5,270,184, the disclosure of which is hereby incorporated by reference in its entirety), thermophilic Strand Displacement Amplification (“tSDA”; see EP 0 684 315), Self-Sustained Sequence Replication (“3SR”; see Guatelli et al., Proc. Nat'l Acad. Sci. USA 87: 1874-78 (1990)), Nucleic Acid Sequence-Based Amplification (“NASBA”; see US Patent No. 5,130,238), Qβ replicase system (see Lizardi et al. , BioTechnology 6: 1197 (1988)); Ligase Chain Reaction ("LCR"; see U.S. Patent No. 5,427,930); Rolling Circle Amplification (see Lizardi et al., Nat Genet 19: 225-232 (1998)) and transcription based amplification (see Kwoh et al., Proc. Nat'l Acad. Sci. USA 86: 1173-77 (1989) ). The amplification primers of the present invention can be used to perform PCR, SDA or tSDA.
    [0040] Nucleic acid amplification techniques are traditionally classified according to the temperature needs of the amplification process. Isothermal amplifications are conducted at a constant temperature, in contrast to amplifications that require cycling between high and low temperatures. Examples of isothermal amplification techniques are: SDA; 3SR, the Qβ replicase system; and the techniques disclosed in WO 90/10064 and WO 91/03573. Examples of techniques that require temperature cycling are: PCR, LCR, transcription-based amplification, and restriction amplification (U.S. Patent No. 5,102,784.).
    [0041] SDA generally proceeds along the following route. First, the amplification primers bind to a target sequence or to a single displaced tape extension product that has been previously polymerized. Second, a deficient 5'-3 'exonuclease polymerase incorporates an α-thiodesoxynucleoside triphosphate ("α-thio dNTPs") in an extension product. If the α-thio dNTP is α-thio-dCTP, for example, it is incorporated in an extension product whenever there is a complementary G residue in the model. Incorporation of an α-thio dNTP into the extension product at an endonuclease recognition restriction site creates a hemimodified site; that is, modified only on the extension product ribbon. A restriction endonuclease then inserts into the hemimodified double-stranded restriction site. Then, the restriction endonuclease dissociates from the incision site. Finally, the polymerase that is deficient in the 5'-3 'exonuclease activity extends from the 3' end of the incision and displaces the DNA strand just ahead. The incision, ribbon extension and ribbon displacement occur at the same time and continuously because the extension from the incision regenerates another possible incision restriction site. When a pair of amplification primers is used in which each hybridizes to one of two strands of a double strand duplex comprising a target sequence, amplification is exponential because both the sense and antisense strands serve as models in each amplification cycle. When a single amplification primer is used, amplification is linear because only one ribbon serves as a template for the extension of the primer. Examples of restriction endonucleases that insert into their double-stranded recognition sites when an α-thio dNTP is incorporated and that are suitable for SDA include BsoB1, BsrI, BstNI, BsmAI, BstOI, BslI, AvaI, HincII and NciI. SDA is further described in U.S. Patent Nos. 5,270,184, No. 5,455,166 and No. 5,648,211, which are incorporated herein by reference in their entirety. An SDA assay can be, but is not limited to, a traditional (or conventional) SDA (as described in Walker et al., PNAS (1992) 89: 392-396, US Patent Nos. 5,962,273, 5,712 .124, and 5,744,311, each of which is incorporated herein by reference), a thermophilic SDA (+ SDA as described in Walker et al., Nuc. Acids Res. (1992) 20: 1691-1696, US Patents Nos. 5,648,211 and 5,744,311, each of which is incorporated herein by reference), and a real-time fluorescent thermophilic SDA (as described in U.S. Patent No. 6,379,888, which is hereby incorporated by reference).
    [0042] Cross contamination with amplification products resulting from previous amplification reactions in reagents, pipetting devices and laboratory surfaces, can be reduced by incorporating various residues in the extension products. For example, thymine may be substituted with 2'-deoxyuridine-5'-triphosphate (“dU”), as taught in patent EP 0 624 643. Excision of dU that is incorporated in amplification products is catalyzed by uracil DNA glycosylase (“UDG”), which makes amplification products containing dU incapable of further amplification. The UDG itself can be inactivated if it is necessary to continue amplification.
    [0043] In the case of tSDA, primers and their target sequences are preferably selected so that their GC content is less than 70% of the total nucleotide composition to minimize secondary structure and primer-primer interactions that can limit the target amplification efficiency. A suitable amplification primer for tSDA comprises, on the order of from the 3 'end of the probe to the 5' end, a target binding sequence, an endonuclease recognition restriction site, and a "tail". The target binding sequence hybridizes specifically to a complementary sequence of the target nucleic acid. The endonuclease recognition restriction site is recognized by a restriction endonuclease that punctures a duplex DNA strand when the recognition site is hemimodified, as described by Walker et al. Proc. Nat’l Acad. Sci. USA 89: 392 (1992) and Walker et al., Nucl. Acids. Res. 20: 1691 (1992). The tail 5 'serves as a reprinting site when the rest of the amplification primer is punctured and displaced during tSDA. The tail reprint function supports the tSDA reaction and allows the synthesis of multiple amplified fragments from a single target molecule. The length and sequence of the tail region can vary as long as the tail remains hybridized to the target after the incision and the tail does not contain sequences that will hybridize to the target binding sequence or other primers.
    [0044] Some amplification methods, such as tSDA, use a “protective initiator” or “external initiator” to move the extension products from the initiator. A "protective initiator" or "external initiator" is an initiator used to displace an amplification initiator and its extension product in an amplification reaction. A protective primer nests to a target sequence upstream of an amplification primer in such a way that the extension of the protective primer displaces the downstream amplification primer and its extension product. Initiator extension products can alternatively be moved by heating. Protective primers can hybridize to any target sequence which is upstream from the amplification primers and which is sufficiently close to the amplification primer binding site to displace the amplification primer extension product during the extension of the protective primer. Mismatches between the protective primer sequence and the target sequence generally do not influence the amplification efficiency, as long as the protective primer still hybridizes to the target sequence. In addition, the specificity of the SDA system for amplifying the target sequence preferably to other nucleic acids is not dependent on the specificity of the protective initiate (s) for hybridization to the target nucleic acid. The specificity of an SDA system with respect to the target sequence is derived from the fidelity of the hybridization of SDA primers and probes or oligonucleotides used for the detection of amplified products.
    [0045] When an amplification reaction used according to the invention is a tSDA reaction, the polymerases that can be used include, but are not limited to, exo- Vent (New England Biolabs), exo- Deep Vent (New England Biolabs), Bst (BioRad), exo- Pfu (Stratagene), BCA (Panvera) and Sequencing Grade Taq (Promega). Others can be routinely identified using the extension test already mentioned. The Tth (Boehringer), Tfi (Epicenter), REPLINASE (DuPont) and REPLITHERM (Epicenter) polymerases are able to dislodge a tape from an incision, but they also have a 5'-3 'exonuclease activity. Such polymerases are useful in the methods of the invention after removal of exonuclease activity, for example, by genetic engineering. As the thermostability of thermophilic restriction endonucleases is generally limited to less than 65 ° C, thermophilic polymerases with ideal activity around that temperature or lower temperature (for example, Bst and BCA) are more compatible with thermophilic restriction endonucleases in the reaction .
    [0046] The components of the present invention can be optimized to a way in which each component can be dried and rehydrated when necessary using any technique known in the art. (See Little et al, Clinical Chemistry 45 (6): 777-784 (1999), which is incorporated herein by reference). Sketch of the Initiator
    [0047] An "amplification primer" is an oligonucleotide for the amplification of a target sequence, by extending the oligonucleotide after hybridization to a target sequence, or by linking several adjacent oligonucleotides, when hybridized to the target sequence. At least a portion of the amplification primer hybridizes to the target sequence. That portion is referred to as the target binding sequence and determines the target specificity of the primer. It is to be understood that the targeting sequences exemplified in the present invention can also be used in a variety of other ways for the detection of GV. For example, the target-binding sequences described here can alternatively be used as hybridization probes for the direct detection of GV, with or without previous amplification or in a post-amplification assay. Such hybridization techniques are well known in the art and typically employ a detectable marker associated with or linked to the target binding sequence to facilitate detection of hybridization.
    [0048] The scope of the amplification initiators can be optimized for each of the amplification methods. Since no special sequences or structures are required to conduct the amplification reaction, amplification primers for a Polymerase Chain Reaction (PCR) may consist of only linker sequences to the model. However, other amplification reactions that require specialized nucleotide sequences, in addition to the target-binding sequence, for the reaction to proceed. For example, an amplification primer for use in an SDA assay further comprises a 5 'endonuclease recognition restriction site for the target sequence (see U.S. Patent Nos. 5,455,166 and 5,270,184). The amplification primer can also comprise a 3'-OH group, which is extensible by DNA polymerase, when the amplifier primer template-binding sequence is annealed to the target sequence. Amplification primers for Self-Sustained Sequence Replication (3SR) and Sequence-Based Nucleic Acid Assay (NASBA), in contrast, comprise an RNA polymerase promoter near the 5 'end. (3SR assays are described in Guatelli et al., 1990, Proc. Natl. Acad. Sci. USA 87: 1874-1878). The promoter is attached to the target-binding sequence and serves to conduct the amplification reaction by directing the transcription of multiple RNA copies of the model. These sequences in addition to the target binding sequence that are necessary for a particular amplification reaction are well known in the art.
    [0049] In the design of the amplification primers and protective primers of the present invention, the general issues known in the art must be taken into account. For example, when a target sequence comprising a large number of GC and AT repeats is used to design a primer, care must be taken to minimize potential dimer interactions to prevent self-hybridization of the primers. Initiators who can form four or more consecutive bonds with themselves, or eight or more interrelated bonds with other initiators should generally be avoided. Primers that can form 3 'dimers should be especially avoided, because hybridization at the 3' ends of the primer, albeit transiently, will lead to the extension of the primer due to the action of the polymerase and the ruin of the primer. Certain computer software programs (for example, Oligo ™ National Biosciences, Inc., Plymouth, Minn) can be used in the design of the initiators to avoid problems. Combinations of initiators are also searched for ideal conditions.
    [0050] As is known in the art, the girdling or hybridization of complementary and partially complementary nucleic acid sequences can also be obtained by adjusting the reaction conditions to increase or decrease the stringency (for example, adjusting the temperature or the content buffer salt). Such modifications to the described sequences and any necessary adjustments to the conditions are covered by the present invention. Information regarding buffer conditions can be found in Experimental Design in Biotechnology by Dr. Perry Haaland (Marcell Dekker, NY, 1989), incorporated herein by reference in its entirety.
    [0051] In the modalities that implant an IAC, a diplex amplification reaction, an amplification primer is designed to be able to hybridize to both a GV target sequence and an IAC sequence and to amplify the sequence to which it is hybridized. This is achieved through a nucleic acid sequence shared between the target GV sequence and an IAC sequence to design an amplification primer. Other sequences, as required for the performance of a selected amplification reaction, can optionally be added to an amplification primer as disclosed herein.
    [0052] By way of example and not by way of limitation, amplification primers for use in an SDA assay generally comprise a 3 'template linker sequence, a possible endonuclease recognition restriction site of incision 5' to the linker sequence to model, and a tail sequence of about 10-25 nucleotides in length 5 'to the endonuclease recognition restriction site. Such an amplification primer may contain a BsoBI endonuclease recognition restriction site, which is inserted during the SDA reaction. It will be apparent to one skilled in the art that other possible restriction endonuclease recognition sites for incision may be substitutes for the BsoBI recognition site. The tail sequence should not contain the restriction site used for SDA and sequences that will ring or with their own binding sequence to the target or other primers (for example, protective primers).
    [0053] In some embodiments, a pair of amplification primers is used, each of which rings with one of two strands of a double stranded target sequence or an IAC sequence. In this case, the amplification is exponential because both the sense and antisense strips serve as models for the opposite primer in subsequent amplification cycles. When a single amplification primer is used, amplification is linear because only one ribbon serves as a template for the extension of the primer.
    [0054] In some embodiments, the methods of the present invention comprise an amplification primer comprising a nucleotide sequence consisting essentially of SEQ IDs NOs: 3 and 4, or their respective target binding sequences. In other embodiments, the methods of the present invention comprise at least two amplification primers, wherein a first amplification primer comprises a nucleotide sequence consisting essentially of SEQ ID NO: 3 or its respective target binding sequences, and a second primer The amplification sequence comprises a nucleotide sequence consisting essentially of SEQ ID NO: 4 or its respective target binding sequences.
    [0055] In some embodiments, the methods of the present invention comprise one or more protective primers. A protective primer is a primer used to displace an amplification primer and its extension product in an amplification reaction. A protective primer nests to a target sequence upstream of an amplification primer, such that the extension of the protective primer displaces the downstream amplification primer and its extension product. A protective primer can also function as an amplification primer. In some embodiments, the methods of the present invention comprise one or more protective primers. In certain embodiments, the protective primer comprises an oligonucleotide having the sequence comprising SEQ ID NO: 6 or 7. In one embodiment, a protective primer comprises an oligonucleotide having a complete or partial sequence of SEQ ID NO: 6 or 7. In another embodiment , the methods of the present invention encompass at least two protective primers, wherein a first primer comprises a nucleotide sequence consisting essentially of SEQ ID NO: 6 and a second primer comprises a nucleotide sequence consisting essentially of SEQ ID NO: 7.
    [0056] The primer / probes described here are described in terms of being 100% complementary to their target binding sequences. However, based on the design conditions of the primer described above, the primers and probes can bind to the target sequences despite being less than 100% complementary to these regions. The degree of complementarity required depends on a variety of factors including the severity of binding conditions. Depending on the stringent conditions employed, the primers and probes can be modified to include different bases in their sequence and still be sufficiently complementary to bind to the target region. As used here, sufficiently complementary includes a complementarity of 70% or more. In preferred embodiments, the complementarity of the primers / probes to their target sequences is at least 80% relative to the length of the linker portion of the primers / probes. Most preferably, the complementarity of the primers and probes with respect to the target sequences is 90% or more. Target strings
    [0057] "Target", or "target sequence" refers to a GV nucleic acid sequence to be amplified and / or detected. A target or target sequence includes the GV nucleic acid sequence to be amplified and any second complementary strand. In some embodiments, a target sequence may be single-stranded or double-stranded, in which case, one or both strands may bind to an amplification primer. A target or target sequence can also comprise a nucleotide sequence that is recognized by an adapter oligonucleotide (i.e., the adapter-linker sequence). The primers of the present invention are designed to ring with a region of the GV vly gene as identified in SEQ ID NOS: 1, 2 and 23-25. The target sequence is preferably the target regions identified in SEQ ID NOS. 20 and 21. Internal Amplification Control
    [0058] "Internal amplification control", "IAC" or "IAC sequence", refers to a nucleic acid sequence comprising a sequence that rings an amplification primer and a sequence that can be detected separately from the target sequence. Any detection method known in the art can be employed.
    [0059] According to the present invention, an IAC sequence is designed to share nucleic acid sequences with a GV target sequence, and thus, the same amplification primer (s) can amplify both an IAC sequence and a sequence target if present in a sample. An IAC sequence is also designed to have some nucleic acid sequences that differ from a GV target sequence, so that the detection of the IAC sequence and the target sequence can be differentiated. Since an IAC sequence is amplified and / or detected in the same reaction mixture as a target sequence, diplex assays have the advantage of detecting human error or an inhibitory reaction condition; for example, the presence of an inhibitor or the absence of a critical reagent. The presence of an IAC in the same reaction as the sample to be tested eliminates the need for separate amplification control reactions, as required by the current monoplex SDA assays.
    [0060] Although not intended to be limited by a particular mechanism of action, the presence of an IAC in the same reaction as a target sequence allows the amplification assay of the present invention to detect the presence of reaction inhibitors and / or conditions that may indicate a false negative result. As used herein, a false negative result refers to a result that indicates that there is no detection of a target sequence, however, this indication is not due to the absence of the target sequence in the sample, but due to human error or a condition reaction; for example, the lack of a critical reaction element, or the existence of a reaction inhibitor, or an error in performing the test.
    [0061] A detection method that is used whose method differentiates the amplification products of a target sequence from the amplification products of an IAC sequence. In one embodiment, the target sequence and IAC amplification products can be detected by different dye-labeled detection probes. In one example, fluorescein is used to detect amplification products of the target sequence and rhodamine fluorescence is used to detect IAC amplification products.
    [0062] In some embodiments, an IAC sequence is designed in such a way that one of its 3 'and 5' terminals contains a sequence in common with a GV DNA sequence. In some other embodiments, an IAC is designed in such a way that both 3 'and 5' positions contain sequences in common with a DNA sequence for an amplification primer to be linked.
    [0063] An IAC sequence has also been designed to include a nucleic acid sequence that is different from the GV target sequence to be amplified, such that the detection of the IAC amplification products and the target sequence can be differentiated.
    [0064] In some embodiments, the methods of the present invention use an IAC that comprises a nucleotide sequence consisting essentially of SEQ ID NO: 19. Note that SEQ ID NO: 19 is quite similar to SEQ ID NO. 20 and 21 (preferred target binding sequences) except for the region where the detector (GVvlyACD2b) binds to the IAC target. GVvlyACD2b is identified here as SEQ ID NO. 22. In addition to the detector, the protectors and initiators for the IAC target are the same protectors and initiators for the SDA. (SEQ ID NOs. 14-17).
    [0065] The primers described above are described in terms of being 100% complementary to their target binding sequences. As described below, primers and probes can bind to the target sequences despite being less than 100% complementary to those regions. The degree of complementarity required depends on a variety of factors including the severity of binding conditions. Depending on the stringency conditions employed, the primers and probes can be modified to include different bases in their sequences and still remain sufficiently complementary for binding to the target vly gene. Complementary enough includes a complementarity of 70% or more. In preferred embodiments, the complementarity of the primers / probes to their target sequences is at least 80% relative to the length of the linker portion of the primers / probes. Most preferably, the complementarity of the primers and probes with respect to the target sequences is 90% or more.
    [0066] Although the oligonucleotides described herein must be sufficiently complementary to bind to their respective portions of the target, it is recognized that at some point the sequence of the oligonucleotide becomes less complementary to the target sequence and can bind other nucleic acid sequences. Therefore, it is desirable that the oligonucleotide probes remain sufficiently complementary with their respective portions of the target, and do not lose selectivity to their respective binding sites to the target. Nucleic Acid Detection
    [0067] Amplification products generated using one or more primers of the invention can be detected by any method known in the art. As used herein, amplification products include both the amplified target sequences and the amplified IAC sequences. Amplification products can be detected by hybridization with a labeled probe using conventional techniques, for example, one that hybridizes to the amplified nucleic acids of a sequence that lies between the amplification primers. Alternatively, amplification products can be detected by their characteristic size, for example, by electrophoresis followed by staining with ethidium bromide to visualize nucleic acids. In another alternative, a marked amplification primer is used. In yet another alternative, a labeled internal primer / amplification probe is extended over the target sequence, as described by Walker et al. Proc. Nat’l. Acad. Sci. USA 89: 392 (1992), or Walker et al., Nucl. Acids Res. 20: 1691 (1992). In another embodiment, detection is performed directly by hybridizing and extending a labeled reporter probe, as described in U.S. Patent No. 5,928,869 and U.S. Patent No. 5,958,700. Detection methods also include a chemiluminescent method in which amplified products are detected using a biotinylated capture probe and an enzyme-conjugated detector probe, as described in U.S. Patent No. 5,470,723. After the hybridization of these two probes at different sites between the two binding sites of the amplification primer, the complex is captured in a microtiter plate coated with streptavidin, and the chemiluminescent signal is developed and read in a luminometer.
    [0068] In one embodiment of the present invention, the detection method must detect both the target amplification products and the IAC amplification products (if present), and differentiate between the detected amplification products. Any method known in the art capable of achieving this goal can be used. For example, the detection methods that are disclosed in Walker et al., Nucl. Acids., (1992) 20: 1691-1696, U.S. Patent Nos. 5,648,211, 5,962,273, 5,814,490, 5,928,869, 6, 316, 200, and in European Patent EP 0 678 582 (each of which is incorporated herein by reference), may be used in accordance with this invention. In another embodiment, universal probes and methods for detecting nucleic acids are used (see U.S. Patent No. 6,379,888, which is incorporated herein by reference).
    [0069] Many donor / extinguisher dye pairs known in the art are useful in the present invention. These include, but are not limited to, for example, fluorescein isothiocyanate (FITC) / tetramethyl rhodamine isothiocyanate (TRITC), FITC / Texas red. (Molecular Probes), FITC / rhodamine X, FITC / tetramethylrodamine (TAMRA), 6-Carboxyfluorescein (6 FAM) / TAMRA and others. The selection of a particular donor / extinguisher pair is not critical. For energy transfer inactivation mechanisms, it is only necessary that the emission wavelengths of the donor fluorophore overlap with the excitation wavelengths of the extinguisher; that is, there must be sufficient spectral overlap between the two dyes to allow for efficient energy transfer, charge transfer or fluorescence extinction. P- (dimethylaminophenylazo) benzoic acid (DABCYL) is a non-fluorescent extinguishing dye that effectively extinguishes the fluorescence of an adjacent fluorophore, for example, fluorescein or 5- (2'-aminoethyl) aminonaphthalene (EDANS). Any dye pair that produces fluorescence quenching in the detection probe of the invention can be used in the methods of the invention, regardless of the mechanism by which the quenching occurs. Internal and terminal marking methods are also known in the art and can be routinely used to link the donor and extinguishing dyes to their respective sites on the detection probe.
    [0070] The present invention provides detection probes which are single-stranded oligonucleotides comprising SEQ ID NOS: 5, 10 or 13 and a label. In certain embodiments, the label comprises at least one fluorescent donor / extinguisher pair attached to the oligonucleotide, where the fluorescent fraction is TAMRA or 6-FAM. For the IAC the fluorescent fraction is ROX.
    [0071] In some embodiments, the present invention provides a homogeneous real-time fluoride thermophilic SDA (tSDA). The homogeneous real-time fluoride thermophilic SDA is a tSDA that detects target nucleic acid sequences through fluorescence extinction mechanisms (see, for example, US Patent No. 6,379,888, which is incorporated herein by reference in its entirety) . For example, in one embodiment, a detection probe can comprise a donor / recipient pair such that the fluorescence extinction occurs in the absence of a target sequence. Although not intending to be limited by a particular mechanism of action, in the absence of hybridization of the detection probe to a second oligonucleotide (which is produced by amplifying a target sequence), the probe adopts a conformation that places the donor and the extinguisher in close contact spatial proximity and results in the extinction of donor fluorescence. The probe can bend into an orderly secondary structure (for example, a G-quartet, winding or triple helix), a random spiral, or another conformation that places the donor and extinguisher in close enough proximity to produce the fluorescence extinction . However, when the detection probe hybridizes to a second oligonucleotide, the secondary intramolecular paired structure of the detection probe is unfolded or linearized, which increases the distance between the donor and the extinguisher and thus reduces or eliminates the reduction in fluorescence. . Alternatively, the detection probe can be designed as a linear detection probe (i.e., it does not fold into a secondary structure), in which the distance between the donor and the extinguishing agent is short enough to produce the fluorescence extinguishing. In this case (and, optionally, in the case where a non-linear detection probe described herein is used), the detection probe also contains an endonuclease recognition restriction site (RERS) between the fluorescent donor / extinguisher pair. The pairing of intermolecular bases between the detection probe and a second oligonucleotide produces the double-stranded RERS and thus allows cleavage or incision by a restriction endonuclease. Although not intended to be limited by a particular mechanism of action, cleavage or incision by the restriction endonuclease separates the donor and recipient in the form of separate nucleic acid fragments, which lead to a decrease in extinction.
    [0072] An associated change in a fluorescence parameter (for example, an increase in donor fluorescence intensity, a decrease in fluorescence intensity, or a ratio of donor and / or recipient fluorescence intensities) can be monitored accordingly with the methods of the invention to detect and / or monitor the presence of the target sequence. Monitoring a change in donor fluorescence intensity is generally preferred, as this change is typically greater than the change in the recipient's fluorescence intensity. Other fluorescence parameters, such as a change in fluorescence lifetime can also be monitored according to the invention. Kits
    [0073] The present invention also provides kits for the amplification and / or detection of GV nucleic acids comprising one or more amplification primers consisting essentially of SEQ ID NOS: 8-18 or the respective target binding sequences and at least one container that contains such initiators. The kit can optionally include one or more of the following: an IAC, adapter oligonucleotides, or detection probes. The kit can also include other components and reagents to perform an amplification or hybridization reaction, such as Southern hybridization, dot blot hybridization, PCR or SDA. For hybridization detection, a suitable solution to perform hybridization can be included, for example, 0.3 M NaCl, 0.03 M sodium citrate, 0.1% SDS. Components for detection methods can also be included in the kit, for example, a second probe, a radioactive marker, an enzyme substrate, an antibody, etc. Reagents suitable for use with a nucleic acid amplification method can also be included. The kit components are packaged together in a common container, which typically includes instructions for carrying out specific modalities selected from the methods described here. EXAMPLES Example 1: SDA Starter Set Design
    [0074] A portion of the vly gene for GV has been sequenced and characterized for targeting by amplification assays. For the purpose of this assay, a portion of the GV genome (ie, the vly gene), which had not previously been targeted for amplification assays, was selected. This sub-region of the GV genome was analyzed in the current GenBank database for GV specificity. The vly gene for GV is represented by SEQ ID NOs. 1, 2 and 23-25.
    [0075] Amplification primers were designed to amplify the GV target sequences as described in Table 1. The positions of the regions of the GV vly gene to which the selected amplification primers (protectors, primers, and adapter oligonucleotides) ring are illustrated in Figures 1, 3 and 4. Example of a set of SDA primers and probes is described in Table 4 below. The underlined portions of the primer / probe sequences represent the target ligand sequences. The local endonuclease recognition restriction (RERS) sites are in bold. Table 4. Primary SDA oligonucleotides Assays for GV amplification and / or detection

    * Accession No. EU522486 Example 2: Sensitivity test with three strains of GV
    [0076] The sensitivity of the VV GV assay was determined by conducting a limit detection (LOD) experiment. Genomic DNA, isolated from three strains of GV, was tested and an LOD calculated for each strain. Twenty-four repetitions were performed for each target level and the data was analyzed using the Lect calculator from Becton Dickinson & Co. The data shows that the assay is sensitive and specific for GV.
    [0077] The DNA of all three strains was diluted in 10 mM Tris, 1 mM EDTA, pH 8.0 and boiled for five minutes and allowed to cool or 10 minutes. The DNA was diluted to the appropriate working dilution in the eluate described in Table 5 below. The target levels tested were 100, 50, 20, 5, 1 and 0 copies / reaction (w / rxn). The sample (159 μL) was added to the appropriate priming microwells. Table 5: Eluate

    [0078] The microwell plates were transferred to a heat block at 72 ° C. The corresponding microwell amplification plates were placed in a heating block at 54 ° C. The microwells were then incubated for 10 minutes. Aliquots (100 μL) of the microwell contents of the priming reaction were transferred to the amplification microwells.
    [0079] The contents of the amplification microwells were mixed 3 x 50 μL. The amplification microwells were sealed and the microwell plates were transferred to a BD ProbeTec ™ ET instrument supplied by Becton Dickinson & Co. of Franklin Lakes, New Jersey. The final reaction conditions were: Table 6: The final SDA reaction conditions


    [0080] The calculated levels of detection (LOD) for each strain in a clean non-extracted system, without foreign human DNA, were: Table 7: LOD
    Note: CI is the 95% confidence interval
    [0081] The sensitivity of the VV GV assay is given in Table 7. This assay is capable of detecting the three GV strains tested. The data indicate that the SDA assay described in the present invention can detect at least 58 genomic copies of Gardnerella vaginalis per reaction, where a 95% LOD can be 55 genomic copies per reaction. Example 3: Cross Reactivity Test
    [0082] A cross-reactivity survey was carried out. Nucleic acids from 34 organisms were extracted and tested on the Viper XTR instrument. A negative result was obtained for each one.
    [0083] The organisms were grown in culture syrup up to 1 McFarland and quantified by direct counting on the plate. Cell pellets were prepared by centrifuging aliquots of the culture syrup to harvest cells. After discarding the supernatant, the cell pellets were stored at -70 ° C. For this experiment, the cell pellets were resuspended in 1 ml of sample diluent. After processing on the Viper XTR instrument, each sample was tested at approximately 2x10-7 CFU / reaction. The organisms listed in Table 9 were tested at that concentration, with two exceptions. T. vaginalis was grown in culture syrup, quantified by direct counting and tested in 2x10-5 cells / reaction. C. trachomatis, was grown in BGMK cells, collected by sonication and differential centrifugation and quantified by immunocytochemistry. C. trachomatis, was tested at 5x10-6 EB / reaction. Positive control samples were prepared by diluting GV genomic DNA to a concentration of 1000 copies / mL, for use as a positive control. Non-enriched sample diluent (Table 8) was used as a negative control. Table 8: Sample Diluent


    [0084] The sample holders were preheated to 114 ° C for 15 minutes and then cooled to room temperature for 15 minutes. The prepared samples were transferred to the XTR Viper ™ instrument from Becton Dickinson & Co., Franklin Lakes, New Jersey, for extraction and analysis. In the XTR Viper system, nucleic acids are extracted from the samples using magnetic particles. The separation of the magnetic particles removes non-nucleic acid constituents from the sample. The nucleic acid is then eluted from the magnetic particles using the solution described in Table 5. The eluate was then tested using SDA, with sets of probes described in Table 4 above.
    [0085] The cross-reactivity panel included the organisms in Table 9. The results demonstrate that the only organisms detected were positive GV controls. No other organisms were detected, which demonstrated that the set of SDA primer probes described above in Table 4 had very low cross-reactivity with other organisms. Table 9: Results of the Cross Reactivity Tests


    Example 4: Additional Cross-Reactivity Tests Against Six Candida Species
    [0086] In a clinical setting, it is important for the clinician to be able to differentiate between bacterial vaginosis and vaginal candidiasis. To demonstrate the usefulness of the GVS SDA assay to do this, the assay was evaluated with the genomic DNA of six clinically relevant Candida species. The SDA GV assay did not cross-react with any of the tested Candida species. Specifically, the genomic DNA of six Candida species was tested in the VV Gly assay described in Example 1 above. Six repetitions for each target were performed. The species of organisms used are listed in Table 10 below: Table 10: Organism species Organism ID


    [0087] The DNA was diluted in 10 mM Tris, 1 mM EDTA, pH 8.0 and boiled for five minutes. The solution was allowed to cool for 10 minutes. The DNA was then diluted with the fluid described in Table 5. Sample (159 μL) was added to the appropriate priming microwells. The microwell plates were transferred to a heat block at 72 ° C. The corresponding microwell amplification plates were placed in a heating block at 54 ° C. The microwells were then incubated for 10 minutes. Aliquots (100 μL) of the microwell contents of the priming reaction were transferred to the amplification microwells. The amplification microwells were sealed and the microwell plates were transferred to a BD ProbeTec ™ ET instrument supplied by Becton Dickinson & Co. of Franklin Lakes, New Jersey. References and Equivalents Mentioned
    [0088] All references mentioned herein are incorporated by reference in their entirety for all purposes to the same extent as if each publication or patent or patent application was specifically and individually indicated to be incorporated by reference in its entirety for all purposes.
    [0089] Many modifications and variations with respect to this invention can be made without departing from the spirit and scope, as will be evident to those usually skilled in the art. The specific modalities described herein are offered by way of example only, and the invention is limited only by the terms of the appended claims together with the full scope of the equivalents to which such claims are intended.
    权利要求:
    Claims (9)
    [0001]
    1. Method for detecting whether a target sequence of Gardnerella vaginalis (GV) is present in a sample, CHARACTERIZED by the fact that it comprises: (a) providing at least one oligonucleotide primer that has a target binding sequence that is selected at from one of SEQ ID NO: 3 to 13 that will ring with at least a portion of a target region of the GV vly gene selected from the group consisting of SEQ ID NO: 20 and SEQ ID NO: 21; (b) combining at least one oligonucleotide primer with a biological sample; (c) amplify the target sequence, if present, in the sample; and (d) determining the presence or absence of the amplified target sequence.
    [0002]
    2. Method according to claim 1, CHARACTERIZED by the fact that the at least one oligonucleotide primer is a set of oligonucleotide primers in which: (a) the first amplification primer has a target binding sequence that consists of SEQ ID NO: 3, 6, 8 or 11; and (b) the second amplification primer has a target binding sequence which consists of the binding sequence of SEQ ID NO: 4, 7, 9 or 12.
    [0003]
    3. Method, according to claim 1, CHARACTERIZED by the fact that said amplification is performed by an amplification reaction that is selected from the group consisting of a Tape Shift Amplification reaction (SDA) and a Reaction Polymerase Chain (PCR).
    [0004]
    4. Method, according to claim 1, CHARACTERIZED by the fact that said amplification is carried out by an amplification or detection reaction that is selected from the group consisting of direct detection, polymerase chain reaction (PCR) , in situ hybridization, self-sustained sequence replication (SSR) or rolling circle amplification.
    [0005]
    5. Method according to claim 1, CHARACTERIZED by the fact that the amplification primer comprises a reporter probe that comprises a detectable marker.
    [0006]
    6. Method, according to claim 5, CHARACTERIZED by the fact that the marker is a fluorescent marker.
    [0007]
    7. Method according to claim 1, CHARACTERIZED by the fact that the amplification primer further comprises a restriction endonuclease recognition site or an RNA polymerase promoter.
    [0008]
    8. Method, according to claim 1, CHARACTERIZED by the fact that it also includes the amplification of an internal amplification control (IAC).
    [0009]
    9. Gardnerella vaginalis amplification or detection reaction kit, CHARACTERIZED by the fact that it comprises at least two oligonucleotides, each having a target binding sequence, in which the target binding sequences are selected from a from the groups of SEQ ID NO: 3 and SEQ ID NO: 4, SEQ ID NO: 8 and SEQ ID NO: 9, and SEQ ID NO: 11 and SEQ ID NO: 12.
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    法律状态:
    2018-04-03| B06F| Objections, documents and/or translations needed after an examination request according art. 34 industrial property law|
    2019-06-04| B06T| Formal requirements before examination|
    2019-10-22| B07A| Technical examination (opinion): publication of technical examination (opinion)|
    2020-10-06| B09A| Decision: intention to grant|
    2020-12-22| B16A| Patent or certificate of addition of invention granted|Free format text: PRAZO DE VALIDADE: 20 (VINTE) ANOS CONTADOS A PARTIR DE 28/10/2011, OBSERVADAS AS CONDICOES LEGAIS. |
    优先权:
    申请号 | 申请日 | 专利标题
    US40884010P| true| 2010-11-01|2010-11-01|
    US61/408,840|2010-11-01|
    PCT/US2011/058255|WO2012061225A2|2010-11-01|2011-10-28|Gardnerella vaginalis assay|
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