# Patent

## Title
Methods and compositions for detecting BK virus

## Abstract

The invention provides methods and compositions for rapid, sensitive, and highly specific nucleic acid-based (e.g., DNA based) detection of a BK virus in a sample. In general, the methods involve detecting a target nucleic acid having a target sequence of a conserved region of BK viral genomes. The invention also features compositions, including primers, probes, and kits, for use in the methods of the invention.

## Background
CROSS-REFERENCE
This application is a continuation of U.S. Utility application Ser. No. 11/246,904, filed Oct. 6, 2005, which claims the benefit of U.S. Provisional Application No. 60/705,217, filed Aug. 2, 2005; the entire contents of each are incorporated by reference herein.


FIELD OF THE INVENTION
The invention relates to detection of BK viruses.
BACKGROUND OF THE INVENTION
Human polyomavirus type BK (BK virus) is a non-enveloped virus with a circular, double-stranded-DNA genome of about 5,300 bp. BK virus was first recognized as a member of the polyomavirus family in 1971, after isolation from the urine of a renal-transplant recipient. Subsequent studies documented a worldwide rate of seroprevalence in adults of more than 80 percent. Typically, primary infection with the BK virus occurs during childhood by the respiratory route, followed by latency of the virus in the urogenital tract. Asymptomatic reactivation and intermittent shedding of virus in the urine occur spontaneously in immunocompetent persons but are more frequent among those with altered cellular immunity, such as pregnant women, patients with cancer who are receiving chemotherapy, HIV-1 infected individuals and recipients of renal or other allografts. Overt clinical disease from BK virus infection is rare and is clearly linked to the degree of immunosuppression.
BK-virus associated nephropathy has become an increasingly recognized cause of renal dysfunction in renal transplant patients. According to retrospective studies, BK virus nephropathy develops in 1 to 5 percent of renal-transplant recipients, with loss of allograft function occurring in as many as 45 percent of the affected patients. Although BK virus-specific antiviral therapy is not available, in some cases, BK virus replication may be controlled by reducing the level of maintenance immunosuppression. Recent evidence suggests that detection of BK virus DNA closely follows the course of BK virus nephropathy and may serve as a noninvasive tool for diagnosis and monitoring. Therefore, quantification of BK virus load in renal transplant patients would be useful both for diagnosing BK virus nephropathy and for monitoring the response to therapy, i.e., reduction in immunosuppression. In addition, BK virus has been implicated in other diseases, such as prostate cancer.
Accordingly, there remains a need for the development of reliable diagnostic tests to detect BK virus with a sensitivity that allows detection of low titers of virus, as well as for detection of different BK virus genotypes. In addition, there remains a need for a reliable diagnostic test to distinguish between BK virus and other polyoma viruses, such as JC virus. Such assays are critical to prevent transmission of the virus through blood and plasma derivatives or by close personal contact. The present invention addresses these needs.
LITERATURE
Literature of interest includes:
U.S. Pat. Nos. 5,213,796; 6,605,602; WO 92/19774; Watzinger et al., Journal of Clinical Microbiology, 42(11):5189-5198 (2004); Anna Marta Degener, et al., J Medical Virology 58:413 (1999); and Stoner et al., American J of Kidney Diseases. 33:1102 (2002).
SUMMARY OF THE INVENTION
The invention provides methods and compositions for rapid, sensitive; and highly specific nucleic acid-based (e.g., DNA based) detection of a BK virus in a sample. In general, the methods involve detecting a target nucleic acid having a target sequence of conserved regions of BK viral genome. The invention also features compositions, including primers, probes, and kits, for use in the methods of the invention.
An advantage of the invention is that it provides for detection of BK virus while avoiding detection of viruses that are closely related genetically. Thus, the invention decreases the incidence of false positives.
Another advantage of the invention is that it decreases the incidence of false negative results that can result from failure to detect genetic variants of the BK virus (e.g., BK viruses of different genotype or strain).
Still another advantage is that the invention encompasses embodiments that require detection of only a relatively short target sequence. This can be particularly advantageous where the assay uses amplification-based technology, such as real-time PCR.
The present invention can be developed into assays or manufactured into kits to be use in reference laboratories or hospitals for the diagnostics of BK virus. The assay can also be utilized in the development and clinical trials of therapeutic drugs for treating diseases caused by BKV infection.
These and other advantages will be readily apparent to the ordinarily skilled artisan upon reading the present specification.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1A-FIG. 1AAA shows the alignment of the nucleic acid sequences of the 32 BK virus genotypes. The target nucleic acid regions for detection of BK virus (BKV) according to the invention, which regions are designated as BK1, BK2, BK3, BK4, and BK5 (also referred to herein as Target Regions I, II, III, IV and V, respectively) as denoted in underline typeface and start and end arrows.
The numbering system on the right side of the figure represents the sequence numbering for each of the genotypes according to the respective GenBank Accession Numbers for each genotype or the numbering for a sequenced genome. All references to sequences numbering herein are based on the sequence numbering for GenBank Accession No. AY628224, unless stated otherwise. Exemplary primers and probes within the Target Regions I-V suitable for use in the methods of the invention are indicated by bold typeface. Probes suitable for use in the invention include any sequence positioned within the sequence of an amplification product that would be produced using two selected primers.
FIG. 2 is a graph showing the standard curves for the Taqman real-time assay for each of BK1, BK2. BK3, BK4, and BK5. Template concentrations ranged from 50 copies per reaction to 50,000 per reaction. All assays were performed in duplicate. For the BK1 assay: slope=−3.58, intercept=43.428, and R2=0.997. For the BK2 assay: slope=−3.48, intercept=44.053, R2=0.999. For the BK3 assay: slope=−3.49, intercept=44.819, R2=0.999. For the BK4 assay: slope=−3.21, intercept=41.466, R2=0.999. For the BK5 assay: slope=−3.61, intercept=47.324, R2=0.994.



DEFINITIONS
The terms “BK virus” or “BKV” as used herein refer to a virus from the polyomavirus family that has been associated with nephropathy and renal dysfunction. BK virus is a small non-enveloped virus whose genome includes a circular, double-stranded-DNA molecule around 5,300 bp.
The terms “polynucleotide,” “oligonucleotide,” “nucleic acid” and “nucleic acid molecule” are used interchangeably herein to include a polymeric form of nucleotides, either ribonucleotides or deoxyribonucleotides. This term refers only to the primary structure of the molecule. Thus, the terms include triple-, double- and single-stranded DNA, as well as triple-, double- and single-stranded RNA. It also includes modifications, such as by methylation and/or by capping, and unmodified forms of the polynucleotide. More particularly, the terms “polynucleotide,” “oligonucleotide,” “nucleic acid” and “nucleic acid molecule” include polydeoxyribonucleotides (containing 2-deoxy-D-ribose), polyribonucleotides (containing D-ribose), any other type of polynucleotide which is an N- or C-glycoside of a purine or pyrimidine base, and other polymers containing normucleotidic backbones, for example, polyamide (e.g., peptide nucleic acids (PNAs)) and polymorpholino (commercially available from the Anti-Virals, Inc., Corvallis, Oreg., as Neugene) polymers, and other synthetic sequence-specific nucleic acid polymers providing that the polymers contain nucleobases in a configuration which allows for base pairing and base stacking, such as is found in DNA and RNA.
Unless specifically indicated otherwise, there is no intended distinction in length between the terms “polynucleotide,” “oligonucleotide,” “nucleic acid” and “nucleic acid molecule” and these terms will be used interchangeably. These terms refer only to the primary structure of the molecule. Thus, these terms include, for example, 3′-deoxy-2′,5′-DNA, oligodeoxyribonucleotide N3′ P5′ phosphoramidates, 2′-O-alkyl-substituted RNA, double- and single-stranded DNA, as well as double- and single-stranded RNA, DNA:RNA hybrids, and hybrids between PNAs and DNA or RNA, and also include known types of modifications, for example, labels which are known in the art, methylation, “caps,” substitution of one or more of the naturally occurring nucleotides with an analog, internucleotide modifications such as, for example, those with uncharged linkages (e.g., methyl phosphonates, phosphotriesters, phosphoramidates, carbamates, etc.), with negatively charged linkages (e.g., phosphorothioates, phosphorodithioates, etc.), and with positively charged linkages (e.g., aminoalklyphosphoramidates, aminoalkylphosphotriesters), those containing pendant moieties, such as, for example, proteins (including nucleases, toxins, antibodies, signal peptides, poly-L-lysine, etc.), those with intercalators (e.g., acridine, psoralen, etc.), those containing chelators (e.g., metals, radioactive metals, boron, oxidative metals, etc.), those containing alkylators, those with modified linkages (e.g., alpha anomeric nucleic acids, etc.), as well as unmodified forms of the polynucleotide or oligonucleotide. In particular, DNA is deoxyribonucleic acid.
Throughout the specification, abbreviations are used to refer to nucleotides (also referred to as bases), including abbreviations that refer to multiple nucleotides. As used herein, G=guanine, A=adenine, T=thymine, C=cytosine, and U=uracil. In addition, R=a purine nucleotide (A or G); Y=a pyrimidine nucleotide (A or T (U)); S=C or G; W=A or T (U); M=A or C; K=G or T (U); V=A, C or G; and N=any nucleotide (A, T (U), C, or G). Nucleotides can be referred to throughout using lower or upper case letters. It is also understood that nucleotides sequences provided for DNA in the specification also represent nucleotide sequences for RNA, where T is substituted by U.
The terms “deoxyribonucleic acid” and “DNA” as used herein mean a polymer composed of deoxyribonucleotides.
The terms “ribonucleic acid” and “RNA” as used herein refer to a polymer composed of ribonucleotides. Where sequences of a nucleic acid are provided using nucleotides of a DNA sequence, it is understood that such sequences encompass complementary DNA sequences and further also encompass RNA sequences based on the given DNA sequence or its complement, where uracil (U) replaces thymine (T) in the DNA sequence or its complement.
Two nucleotide sequences are “complementary” to one another when those molecules share base pair organization homology. “Complementary” nucleotide sequences will combine with specificity to form a stable duplex under appropriate hybridization conditions. For instance, two sequences are complementary when a section of a first sequence can bind to a section of a second sequence in an anti-parallel sense wherein the 3′-end of each sequence binds to the 5′-end of the other sequence and each A, T(U), G, and C of one sequence is then aligned with a T(U), A, C, and G, respectively, of the other sequence. RNA sequences can also include complementary G=U or U=G base pairs. Thus, two sequences need not have perfect homology to be “complementary” under the invention. Usually two sequences are sufficiently complementary when at least about 85% (preferably at least about 90%, and most preferably at least about 95%) of the nucleotides share base pair organization over a defined length of the molecule.
As used herein the term “isolated,” when used in the context of an isolated compound, refers to a compound of interest that is in an environment different from that in which the compound naturally occurs. “Isolated” is meant to include compounds that are within samples that are substantially enriched for the compound of interest and/or in which the compound of interest is partially or substantially purified. The term “isolated” encompasses instances in which the recited material is unaccompanied by at least some of the material with which it is normally associated in its natural state, preferably constituting at least about 0.5%, more preferably at least about 5% by weight of the total protein in a given sample. For example, the term “isolated” with respect to a polynucleotide generally refers to a nucleic acid molecule devoid, in whole or part, of sequences normally associated with it in nature; or a sequence, as it exists in nature, but having heterologous sequences in association therewith; or a molecule disassociated from the chromosome.
“Purified” as used herein means that the recited material comprises at least about 75% by weight of the total material, with at least about 80% being preferred, and at least about 90% being particularly preferred. As used herein, the term “substantially pure” refers to a compound that is removed from its natural environment and is at least 60% free, preferably 75% free, and most preferably 90% free from other components with which it is naturally associated.
A polynucleotide “derived from” or “specific for” a designated sequence, such as a target sequence of a target nucleic acid, refers to a polynucleotide sequence which comprises a contiguous sequence of approximately at least about 6 nucleotides, preferably at least about 8 nucleotides, more preferably at least about 10-12 nucleotides, and even more preferably at least about 15-20 nucleotides corresponding to, i.e., identical or complementary to, a region of the designated nucleotide sequence. The derived polynucleotide will not necessarily be derived physically from the nucleotide sequence of interest, but may be generated in any manner, including, but not limited to, chemical synthesis, replication, reverse transcription or transcription, which is based on the information provided by the sequence of bases in the region(s) from which the polynucleotide is derived or specific for. Polynucleotides that are derived from” or “specific for” a designated sequence include polynucleotides that are in a sense or an antisense orientations relative to the original polynucleotide.
“Homology” refers to the percent similarity between two polynucleotide or two polypeptide moieties. Two DNA, or two polypeptide sequences are “substantially homologous” to each other when the sequences exhibit at least about 50%, preferably at least about 75%, more preferably at least about 80%, at least about 85%, preferably at least about 90%, and most preferably at least about 95% or at least about 98% sequence similarity over a defined length of the molecules. As used herein, substantially homologous also refers to sequences showing complete Identity to the specified DNA or polypeptide sequence.
In general, “identity” refers to an exact nucleotide-to-nucleotide or amino acid-to-amino acid correspondence of two polynucleotides or polypeptide sequences, respectively. Percent identity can be determined by a direct comparison of the sequence information between two molecules by aligning the sequences, counting the exact number of matches between the two aligned sequences, dividing by the length of the shorter sequence, and multiplying the result by 100.
Readily available computer programs can be used to aid in the analysis of homology and identity, such as Lasergene from DNASTAR, Inc., and ALIGN, Dayhoff, M. O. in Atlas of Protein Sequence and Structure M. O. Dayhoff ed., 5 Suppl. 3:353-358, National biomedical Research Foundation, Washington, D.C., which adapts the local homology algorithm of Smith and Waterman Advances in Appl. Math. 2:482-489, 1981 for peptide analysis. Programs for determining nucleotide sequence homology are available in the Wisconsin Sequence Analysis Package, Version 8 (available from Genetics Computer Group, Madison, Wis.) for example, the BESTFIT, PASTA and GAP programs, which also rely on the Smith and Waterman algorithm. These programs are readily utilized with the default parameters recommended by the manufacturer and described in the Wisconsin Sequence Analysis Package referred to above. For example, percent homology of a particular nucleotide sequence to a reference sequence can be determined using the homology algorithm of Smith and Waterman with a default scoring table and a gap penalty of six nucleotide positions.
Another method of establishing percent homology in the context of the present invention is to use the MPSRCH package of programs copyrighted by the University of Edinburgh, developed by John F. Collins and Shane S. Sturrok, and distributed by IntelliGenetics. Inc. (Mountain View, Calif.). From this suite of packages the Smith-Waterman algorithm can be employed where default parameters are used for the scoring table (for example, gap open penalty of 12, gap extension penalty of one, and a gap of six). From the data generated the “Match” value reflects “sequence homology.” Other suitable programs for calculating the percent identity or similarity between sequences are generally known in the art, for example, another alignment program is BLAST, used with default parameters. For example, BLASTN and BLASTP can be used using the following default parameters: genetic code=standard; filter=none; strand=both; cutoff=60; expect=10; Matrix=BLOSUM62; Descriptions=50 sequences; sort by=HIGH SCORE; Databases=non-redundant, GenBank+EMBL+DDBJ+PDB+GenBank CDS translations+Swiss protein+Spupdate+PIR. Details of these programs can be found on the internet on a website sponsored by the National Center for Biotechnology Information (NCBI) and the National Library of Medicine (see the world wide website at ncbi.nlm.gov/cgi-bin/BLAST).
Alternatively, homology can be determined by hybridization of polynucleotides under conditions which form stable duplexes between homologous regions, followed by digestion with single-stranded-specific nuclease(s), and size determination of the digested fragments. DNA sequences that are substantially homologous can be identified in a Southern hybridization experiment under, for example, stringent conditions, as defined for that particular system. Defining appropriate hybridization conditions is within the skill of the art. See, e.g., Sambrook et al., supra; DNA Cloning, supra; Nucleic Acid Hybridization, supra.
“Recombinant” as used herein to describe a nucleic acid molecule refers to a polynucleotide of genomic, cDNA, mammalian, bacterial, viral, semisynthetic, synthetic or other origin which, by virtue of its origin, manipulation, or both is not associated with all or a portion of the polynucleotide with which it is associated in nature. The term “recombinant” as used with respect to a protein or polypeptide means a polypeptide produced by expression of a recombinant polynucleotide.
A “control element” refers to a polynucleotide sequence which aids in the transcription and/or translation of a nucleotide sequence to which it is linked. The term includes promoters, transcription termination sequences, upstream regulatory domains, polyadenylation signals, untranslated regions, including 5′-UTRs and 3′-UTRs and when appropriate, leader sequences and enhancers, which collectively provide for or facilitate the transcription and translation of a coding sequence in a host cell.
A “DNA-dependent DNA polymerase” is an enzyme that synthesizes a complementary DNA copy from a DNA template. Examples include DNA polymerase I from E. coli and bacteriophage T7 DNA polymerase. All known DNA-dependent DNA polymerases require a complementary primer to initiate synthesis. Under suitable conditions, a DNA-dependent DNA polymerase may synthesize a complementary DNA copy from an RNA template.
As used herein, the term “target nucleic acid region” or “target nucleic acid” or “target molecules” refers to a nucleic acid molecule with a “target sequence” to be detected (e.g., by amplification). The target nucleic acid may be either single-stranded or double-stranded and may or may not include other sequences besides the target sequence (e.g., the target nucleic acid may or may not include nucleic acid sequences upstream or 5′ flanking sequence, may or may not include downstream or 3′ flanking sequence, and in some embodiments may not include either upstream (5′) or downstream (3′) nucleic acid sequence relative to the target sequence. Where detection is by amplification, these other sequences in addition to the target sequence may or may not be amplified with the target sequence.
The term “target sequence” or “target nucleic acid sequence” refers to the particular nucleotide sequence of the target nucleic acid to be detected (e.g., through amplification). The target sequence may include a probe-hybridizing region contained within the target molecule with which a probe will form a stable hybrid under desired conditions. The “target sequence” may also include the complexing sequences to which the oligonucleotide primers complex and be extended using the target sequence as a template. Where the target nucleic acid is single-stranded, the term “target sequence” also refers to the sequence complementary to the “target sequence” as present in the target nucleic acid. If the “target nucleic acid” is originally double-stranded, the term “target sequence” refers to both the plus (+) and minus (−) strands. The invention also contemplates target regions having the full-length of the sequences provided herein, as well as fragments or subsequences of such target regions, and complementary sequences thereof. The terms “fragment” and “subsequence” are used interchangeably in this context. Moreover, where sequences of a “target sequence” are provided herein, it is understood that the sequence may be either DNA or RNA. Thus where a DNA sequence is provided, the RNA sequence is also contemplated and is readily provided by substituting “T” of the DNA sequence with “U” to provide the RNA sequence.
The term “primer” or “oligonucleotide primer” as used herein, refers to an oligonucleotide which acts to initiate synthesis of a complementary nucleic acid strand when placed under conditions in which synthesis of a primer extension product is induced, e.g., in the presence of nucleotides and a polymerization-inducing agent such as a DNA or RNA polymerase and at suitable temperature, pH, metal concentration, and salt concentration. Primers are generally of a length compatible with its use in synthesis of primer extension products, and are usually are in the range of between 8 to 100 nucleotides in length, such as 10 to 75, 15 to 60, 15 to 40, 18 to 30, 20 to 40, 21 to 50, 22 to 45, 25 to 40, and so on, more typically in the range of between 18-40, 20-35, 21-30 nucleotides long, and any length between the stated ranges. Typical primers can be in the range of between 10-50 nucleotides long, such as 15-45, 18-40, 20-30, 21-25 and so on, and any length between the stated ranges. In some embodiments, the primers are usually not more than about 10, 12, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 55, 60, 65, or 70 nucleotides in length.
Primers are usually single-stranded for maximum efficiency in amplification, but may alternatively be double-stranded. If double-stranded, the primer is usually first treated to separate its strands before being used to prepare extension products. This denaturation step is typically effected by heat, but may alternatively be carried out using alkali, followed by neutralization. Thus, a “primer” is complementary to a template, and complexes by hydrogen bonding or hybridization with the template to give a primer/template complex for initiation of synthesis by a polymerase, which is extended by the addition of covalently bonded bases linked at its 3′ end complementary to the template in the process of DNA synthesis.
A “primer pair” as used herein refers to first and second primers having nucleic acid sequence suitable for nucleic acid-based amplification of a target nucleic acid. Such primer pairs generally include a first primer having a sequence that is the same or similar to that of a first portion of a target nucleic acid, and a second primer having a sequence that is complementary to a second portion of a target nucleic acid to provide for amplification of the target nucleic acid or a fragment thereof. Reference to “first” and “second” primers herein is arbitrary, unless specifically indicated otherwise. For example, the first primer can be designed as a “forward primer” (which initiates nucleic acid synthesis from a 5′ end of the target nucleic acid) or as a “reverse primer” (which initiates nucleic acid synthesis from a 5′ end of the extension product produced from synthesis initiated from the forward primer). Likewise, the second primer can be designed as a forward primer or a reverse primer.
As used herein, the term “probe” or “oligonucleotide probe”, used interchangeable herein, refers to a structure comprised of a polynucleotide, as defined above, that contains a nucleic acid sequence complementary to a nucleic acid sequence present in the target nucleic acid analyte (e.g., a nucleic acid amplification product). The polynucleotide regions of probes may be composed of DNA, and/or RNA, and/or synthetic nucleotide analogs. Probes are generally of a length compatible with its use in specific detection of all or a portion of a target sequence of a target nucleic acid, and are usually are in the range of between 8 to 100 nucleotides in length, such as 8 to 75, 10 to 74, 12 to 72, 15 to 60, 15 to 40, 18 to 30, 20 to 40, 21 to 50, 22 to 45, 25 to 40, and so on, more typically in the range of between 18-40, 20-35, 21-30 nucleotides long, and any length between the stated ranges. The typical probe is in the range of between 10-50 nucleotides long, such as 15-45, 18-40, 20-30, 21-28, 22-25 and so on, and any length between the stated ranges. In some embodiments, the primers are usually not more than about 10, 12, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 55, 60, 65, or 70 nucleotides in length.
Probes contemplated herein include probes that include a detectable label. For example, when an “oligonucleotide probe” is to be used in a 5′ nuclease assay, such as the TaqManTM assay, the probe includes at least one fluorescer and at least one quencher which is digested by the 5′ endonuclease activity of a polymerase used in the reaction in order to detect any amplified target oligonucleotide sequences. In this context, the oligonucleotide probe will have a sufficient number of phosphodiester linkages adjacent to its 5′ end so that the 5′ to 3′ nuclease activity employed can efficiently degrade the bound probe to separate the fluorescers and quenchers. When an oligonucleotide probe is used in the TMA technique, it will be suitably labeled, as described below.
As used herein, the terms “label” and “detectable label” refer to a molecule capable of detection, including, but not limited to, radioactive isotopes, fluorescers, chemiluminescers, chromophores, enzymes, enzyme substrates, enzyme cofactors, enzyme inhibitors, chromophores, dyes, metal ions, metal sols, ligands (e.g., biotin, avidin, strepavidin or haptens) and the like. The term “fluorescer” refers to a substance or a portion thereof which is capable of exhibiting fluorescence in the detectable range.
The terms “hybridize” and “hybridization” refer to the formation of complexes between nucleotide sequences which are sufficiently complementary to form complexes via Watson-Crick base pairing. Where a primer “hybridizes” with target (template), such complexes (or hybrids) are sufficiently stable to serve the priming function required by, e.g., the DNA polymerase to initiate DNA synthesis.
The term “stringent conditions” refers to conditions under which a primer will hybridize preferentially to, or specifically bind to, its complementary binding partner, and to a lesser extent to, or not at all to, other sequences. Put another way, the term “stringent hybridization conditions” as used herein refers to conditions that are compatible to produce duplexes on an array surface between complementary binding members, e.g., between probes and complementary targets in a sample, e.g., duplexes of nucleic acid probes, such as DNA probes, and their corresponding nucleic acid targets that are present in the sample, e.g., their corresponding mRNA analytes present in the sample.
As used herein, the term “binding pair” refers to first and second molecules that specifically bind to each other, such as complementary polynucleotide pairs capable of forming nucleic acid duplexes. “Specific binding” of the first member of the binding pair to the second member of the binding pair in a sample is evidenced by the binding of the first member to the second member, or vice versa, with greater affinity and specificity than to other components in the sample. The binding between the members of the binding pair is typically noncovalent.
By “selectively bind” is meant that the molecule binds preferentially to the target of interest or binds with greater affinity to the target than to other molecules. For example, a DNA molecule will bind to a substantially complementary sequence and not to unrelated sequences.
A “stringent hybridization” and “stringent hybridization wash conditions” in the context of nucleic acid hybridization (e.g., as in array, Southern or Northern hybridizations) are sequence dependent, and are different under different environmental parameters. Stringent hybridization conditions that can be used to identify nucleic acids within the scope of the invention can include, e.g., hybridization in a buffer comprising 50% formamide, 5×SSC, and 1% SDS at 42° C., or hybridization in a buffer comprising 5×SSC and 1% SDS at 65° C., both with a wash of 0.2×SSC and 0.1% SDS at 65° C. Exemplary stringent hybridization conditions can also include a hybridization in a buffer of 40% formamide, 1 M NaCl, and 1% SDS at 37° C., and a wash in 1×SSC at 45° C. Alternatively, hybridization to filter-bound DNA in 0.5 M NaHPO4, 7% sodium dodecyl sulfate (SDS), 1 mnM EDTA at 65° C., and washing in 0.1×SSC/0.1% SDS at 68° C. can be employed. Yet additional stringent hybridization conditions include hybridization at 60° C. or higher and 3×SSC (450 mM sodium chloride/45 mM sodium citrate) or incubation at 42° C. in a solution containing 30% formamide, 1M NaCl, 0.5% sodium sarcosine, 50 mM MES, pH 6.5. Those of ordinary skill will readily recognize that alternative but comparable hybridization and wash conditions can be utilized to provide conditions of similar stringency.
In certain embodiments, the stringency of the wash conditions that set forth the conditions which determine whether a nucleic acid is specifically hybridized to a probe. Wash conditions used to identify nucleic acids may include, e.g.: a salt concentration of about 0.02 molar at pH 7 and a temperature of at least about 50. ° C. or about 55° C. to about 60° C.; or, a salt concentration of about 0.15 M NaCl at 72° C. for about 15 minutes; or, a salt concentration of about 0.2×SSC at a temperature of at least about 50° C. or about 55. ° C. to about 60° C. for about 15 to about 20 minutes; or, the hybridization complex is washed twice with a solution with a salt concentration of about 2×SSC containing 0.1% SDS at room temperature for 15 minutes and then washed twice by 0.1×SSC containing 0.1% SDS at 68° C. for 15 minutes; or, equivalent conditions. Stringent conditions for washing can also be, e.g., 0.2×SSC/0.1% SDS at 42° C. In instances wherein the nucleic acid molecules are deoxyoligonucleotides (“oligos”), stringent conditions can include washing in 6×SSC/0.05% sodium pyrophosphate at 37. ° C. (for 14-base oligos), 48. ° C. (for 17-base oligos), 55° C. (for 20-base oligos), and 60° C. (for 23-base oligos). See Sambrook Ausubel, or Tijssen (cited below) for detailed descriptions of equivalent hybridization and wash conditions and for reagents and buffers, e.g., SSC buffers and equivalent reagents and conditions.
Stringent hybridization conditions are hybridization conditions that are at least as stringent as the above representative conditions, where conditions are considered to be at least as stringent if they are at least about 80% as stringent, typically at least about 90% as stringent as the above specific stringent conditions. Other stringent hybridization conditions are known in the art and may also be employed, as appropriate.
The “melting temperature” or “Tm” of double-stranded DNA is defined as the temperature at which half of the helical structure of DNA is lost due to heating or other dissociation of the hydrogen bonding between base pairs, for example, by acid or alkali treatment, or the like. The Tm of a DNA molecule depends on its length and on its base composition. DNA molecules rich in GC base pairs have a higher Tm than those having an abundance of AT base pairs. Separated complementary strands of DNA spontaneously reassociate or anneal to form duplex DNA when the temperature is lowered below the Tm. The highest rate of nucleic acid hybridization occurs approximately 25.degree. C. below the Tm. The Tm may be estimated using the following relationship: Tm=69.3+0.41 (GC) % (Marmur et al. (1962) J. Mol. Biol. 5:109-118).
As used herein, a “biological sample” refers to a sample of tissue or fluid isolated from a subject, which in the context of the invention generally refers to samples suspected of containing nucleic acid and/or viral particles of BK virus, which samples, after optional processing, can be analyzed in an in vitro assay. Typical samples of interest include, but are not necessarily limited to, respiratory secretions (e.g., samples obtained from fluids or tissue of nasal passages, lung, and the like), blood, plasma, serum, blood cells, cerebrospinal fluid, fecal matter, urine, tears, saliva, milk, organs, biopsies, and secretions of the intestinal and respiratory tracts. Samples also include samples of in vitro cell culture constituents including but not limited to conditioned media resulting from the growth of cells and tissues in culture medium, e.g., recombinant cells, and cell components.
The term “assessing” includes any form of measurement, and includes determining if an element is present or not. The terms “determining”, “measuring”, “evaluating”, “assessing” and “assaying” are used interchangeably and includes quantitative and qualitative determinations. Assessing may be relative or absolute. “Assessing the presence of” includes determining the amount of something present, and/or determining whether it is present or absent. As used herein, the terms “determining.” “measuring,” and “assessing,” and “assaying” are used interchangeably and include both quantitative and qualitative determinations.
In the context of the methods involving nucleic acid-based amplification of a target sequence, the term “reference range” refers to a range of CT (threshold cycle) values from BK virus-negative specimens representative of results that are deemed to indicate that the sample (e.g., a patient specimen) is BK virus-negative.
In the context of the methods involving nucleic acid-based amplification of a target sequence, the term “reportable range” refers to a range of CT values generated by BK virus-positive specimens that are representative of results to be reported as BK virus-positive patient specimens.
“Analytical specificity” as used herein refers to the ability of a detection system to specifically detect the target virus and not detect other related viruses, or pathogenic or commensal flora found in the specimen types being validated. For example, “analytical specificity” in reference to assays using BK virus primers and a probe refers to the ability of this detection system to specifically amplify and detect the target virus and not detect other related viruses, or pathogenic or commensal flora found in the specimen types being validated.
“Analytical sensitivity” in the context of the methods involving nucleic acid-based amplification of a target sequence refers to the lowest measurable amount of BK virus target DNA that can be detected for each specimen type validated.
“Precision” refers to the ability of an assay to reproducibly generate the same or comparable result for a given sample.
“Accuracy” refers to the ability of an assay to correctly detect a target molecule in a blinded panel containing both positive and negative specimens.
It is further noted that the claims may be drafted to exclude any optional element. As such, this statement is intended to serve as antecedent basis for use of such exclusive terminology as “solely”, “only” and the like in connection with the recitation of claim elements, or the use of a “negative” limitation.
Before the present invention is further described, it is to be understood that this invention is not limited to particular embodiments described, as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting, since the scope of the present invention will be limited only by the appended claims.
Where a range of values is provided, it is understood that each intervening value, to the tenth of the unit of the lower limit unless the context clearly dictates otherwise, between the upper and lower limit of that range and any other stated or intervening value in that stated range, is encompassed within the invention. The upper and lower limits of these smaller ranges may independently be included in the smaller ranges, and are also encompassed within the invention, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding either or both of those included limits are also included in the invention.
Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although any methods and materials similar or equivalent to those described herein can also be used in the practice or testing of the present invention, the preferred methods and materials are now described. All publications mentioned herein are incorporated herein by reference to disclose and describe the methods and/or materials in connection with which the publications are cited.
It must be noted that as used herein and in the appended claims, the singular forms “a”, “and”, and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to a “oligonucleotide primer” includes a plurality of such primers and reference to “primer” includes reference to one or more the primers and equivalents thereof known to those skilled in the art, and so forth.
The publications discussed herein are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that the present invention is not entitled to antedate such publication by virtue of prior invention. Further, the dates of publication provided may be different from the actual publication dates which may need to be independently confirmed.
The practice of the present invention will employ, unless otherwise indicated, conventional methods of chemistry, biochemistry, recombinant DNA techniques and virology, within the skill of the art. Such techniques are explained fully in the literature. See, e.g., Fundamental Virology, 2nd Edition, vol. I & II (B. N. Fields and D. M. Knipe, eds.); A. L. Lehninger, Biochemistry (Worth Publishers, Inc., current addition); Sambrook, et al. Molecular Cloning: A Laboratory Manual (2nd Edition, 1989); Methods In Enzymology (S. Colowick and N. Kaplan eds., Academic Press, Inc.); Oligonucleotide Synthesis (N. Gait, ed. 1984); A Practical Guide to Molecular Cloning (1984).
The invention will now be described in more detail.
DETAILED DESCRIPTION OF THE INVENTION
The invention is based on the discovery of consensus target nucleic acid regions within the BK virus (BKV) genome that include target nucleic acid sequences (also referred to herein as target sequences) for detection of BKV in a sample, particularly a biological sample, with specificity and sensitivity. In particular the detection of one or more target nucleic acid sequence regions allows for detection of BKV in a sample, in general, while also being able to discriminate between, for example, BKV and JC virus (JCV) and/or BKV and SV40. The specificity and simplicity of these assays facilitate rapid, reliable and inexpensive assays for detection of BKV in general. The subject invention finds use in a variety of different applications, including research, medical, drug development and diagnostic applications.
In general, the subject methods provide for detection of BKV in a sample, such as a biological sample, by detection of a target nucleic acid region of the BKV genome. Five such target nucleic acid regions are described herein, termed as Target Regions I-V as designated in FIG. 1.
In some embodiments, the subject methods provide for detection of any BKV isolates, in a sample, such a biological sample. In such embodiments, the subject methods detect a target nucleic acid region, or fragment thereof, by using primers and probe that correspond to sequences within the target region. Exemplary primers within the Target Regions I-V suitable for use in the methods of the invention are provided in Table 1. Probes suitable for use in the invention include any sequence positioned within the sequence of an amplification product that would be produced using selected primers. A probe suitable for use with such an embodiment is selected such that it corresponds to a region that shares a nucleotide sequence between the different BKV isolates to be detected.
We note that the sequences provided herein, and particularly the consensus sequences are provided as DNA sequences. It is understood that the DNA sequences provided may be single stranded or double stranded, and as such the description of the DNA sequences below is intended to also provide the complementary sequence as well.
The compositions and methods of the invention will now be described in more detail.
Target Nucleic Acid Regions
Target nucleic acid sequence regions were identified by alignment of various BKV isolate genomes. The present invention provides for identification of BKV in a sample, such as a biological sample, by detecting one or more target nucleic acid region or a portion thereof. In general, detection is by nucleic acid amplification, which in some embodiments is followed by detection of the amplification product using a hybridization probe. The target nucleic acid regions are described in further detail below.
It will be appreciated that since BKV contains a double-stranded DNA genome from which RNA is generated during viral replication, the primers and probes described herein encompass those having the nucleic acid sequence described herein, as well as primers and probes having the complement of such nucleic acid sequences.
Furthermore, it will be understood that primer pairs useful in the invention include a first primer having a sequence that is the same or similar to that of the BKV sequence provided herein, and a second primer having a sequence that is complementary to the BKV sequence provided herein to provide for amplification of a BKV target nucleic acid region described herein or a fragment thereof (e.g., the first primer is a “forward” primer and the second primer is a “reverse” primer). It will be further understood that primer pairs useful in the invention also include a first primer having a sequence that is complementary to that of the BKV sequence provided herein, and a second primer having a sequence that is the same or similar to the BKV sequence provided herein to provide for amplification of an BKV target nucleic acid region described herein or a fragment thereof (e.g., the first primer is a “reverse” primer and the second primer is a “forward” primer).
It also will be understood that the nucleic acid sequence of probes described herein can be the same or similar to that of the BKV sequence provided or a complement thereof. In addition, primers described herein can also be used as probes, e.g., to detect an amplification product.
Target Region I (BK1)
In one embodiment, the invention provides for detection of BKV in a sample, such as a biological sample, by detection of target nucleic acid sequence region I (FIG. 1, Target Region I (also referred to as BK1), alignment position 435-585 based on numbering of GenBank Accession No. AY628224) as follows:







(SEQ ID NO: 01)


AACAAAAAAAAGAGCTCAGAGGATTTTTATTTTTATTTTAGAGCTTTTG


 


CTGGAATTTTGTAGAGGTGAAGACAGTGTAGACGGGAAAAACAAAGGTA


 


CCACTGCTTTACCTGCTGTAAAAGACTCTGTAAAAGACTCCTAGGTAAG


 


TAAT






or a complement thereof, or a fragment thereof, wherein the 5′ and 3′ end of the nucleic acid is contained within SEQ ID NO:01. This conserved sequence in BKV genome is shown in the alignment of in FIG. 1. In one embodiment of particular interest, the target region is a subsequence of Target Region I, such as








(SEQ ID NO: 55)


AACAAAAAAAAGAGCTCAGAGGATTTTTATTTTTATTTTAGAGCTTTTG


 


CTGGAATTTTGTAGAGGTGAAGACAGTGTAGACGGGAAAAACAAAAGTA


 


CCACTGCTTTACCTGCTGTAA 






or a complement thereof, or a fragment thereof.

Exemplary nucleic acid sequences suitable for design of primers for amplification of a Target Region I nucleic acid, and suitable for use in the methods of the invention, are indicated by underlined typeface in FIG. 1. Suitable sequences for primers for amplification of Target Region I nucleic acid correspond to nucleotides 1-26 and 94-119 of the nucleotide sequence of SEQ ID NO:01, or a complement thereof.
Probes suitable for use in the invention can be designed from any sequence positioned within the sequence of an amplification product that would be produced using two selected primers. Suitable sequences for use as a probe for detection of Target Region I nucleic acid correspond to nucleotides 57-90 of the nucleotide sequence of SEQ ID NO:01, or a complement thereof.
In one embodiment, detection of target region I nucleic acid involves production of an amplification product of at least 151, at least 145, at least 140, at least 135, at least 130, at least 125 at least 120, at least 115, at least 110, at least 105, at least 100, at least 95, at least 90, at least 85, at least 80, at least 75, at least 70, at least 65, at least 60, at least 55, at least 50, at least 45, at least 40, at least 35, at least 30, at least 28, at least 26, at least 24, at least 22, at least 20 consecutive nucleotides of SEQ ID NO:01.
The methods of the invention can involve detection of target region I nucleic acid either alone or in combination with detection of one or more of target regions II-V as described herein. For example, the methods of the invention can involve detection of target region I (BK1) and target region II (BK2); target region I (BK1) and target region III (BK3); target region I (BK1) and target region IV (BK4); target region I (BK1) and target region V (BK5); target region I (BK1), target region II (BK2), and target region III (BK3); target region I (BK1), target region IV (BK4), and target region V (BK5); target region I (BK1), target region III (BK3), and target region V (BK5) and the like. It will be understood that detection of all combination of target regions I-V are contemplates by the present methods.
Exemplary primers and probes are discussed in greater detail below.
Target Region II (BK2)
In one embodiment, the invention provides for detection of BKV in a sample, such as a biological sample, by detection of target nucleic acid sequence region I (FIG. 1, Target Region II (also referred to as BK2), alignment position 1418-1545 based on numbering of GenBank Accession No. AY628224) as follows:







(SEQ ID NO: 02)


TGTACATTCAGGAGAGTTTATAGAAAAAACTATTGCCCCAGGAGGTGCT


 


AATCAAAGAACTGCTCCTCAATGGATGTTGCCTTTACTTCTAGGCCTGT


 


ACGGGACTGTAACACCTGCTCTTGAAGCAT 






or a complement thereof, or a fragment thereof, wherein the 5′ and 3′ end of the nucleic acid is contained within SEQ ID NO:02. This conserved sequence as found in the BKV genome is illustrated in the alignment of FIG. 1. In one embodiment of particular interest, the target region is a subsequence of Target Region II, such as:








(SEQ ID NO: 56)


TTGCCCCAGGAGGTGCTAATCAAAGAACTGCTCCTCAATGGATGTTGCC


 


TTTACTTCTAGGCCTGTACGGGA 






or a complement thereof, or a fragment thereof.

Exemplary nucleic acid sequences suitable for design of primers for amplification of a Target Region II nucleic acid, and suitable for use in the methods of the invention, are indicated by underlined typeface in FIG. 1. Suitable sequences for primers for amplification of Target Region II nucleic acid correspond to nucleotides 33-50 and 82-104 of the nucleotide sequence of SEQ ID NO:02, or a complement thereof.
Probes suitable for use in the invention can be designed from any sequence positioned within the sequence of an amplification product that would be produced using two selected primers. Suitable sequences for use as a probe for detection of Target Region II nucleic acid correspond to nucleotides 52-80 of the nucleotide sequence of SEQ ID NO:02, or a complement thereof.
In one embodiment, detection of target region II nucleic acid involves production of an amplification product of at least 128, at least 120, at least 110, at least 100, at least 90, at least 80, at least 75, at least 70, at least 65, at least 60, at least 55, at least 50, at least at least 45, 40, at least 35, at least 30, at least 28, at least 26, at least 24, at least 22, at least 20 consecutive nucleotides of SEQ ID NO:02.
The methods of the invention can involve detection of target region II nucleic acid either alone or in combination with detection of one or more of target regions I and III-V as described herein. For example, the methods of the invention can involve detection of target region II (BK2) and target region I (BK1); target region II (BK2) and target region III (BK3); target region II (BK2) and target region IV (BK4); target region II (BK2) and target region V (BK5); target region I (BK1), target region II (BK2), and target region III (BK3); target region II (BK2), target region IV (BK4), and target region V (BK5); or target region II (BK2), target region III (BK3), and target region V (BK5) and the like. It will be understood that detection of all combination of target regions I-V are contemplates by the present methods.
Exemplary primers and probes are discussed in greater detail below.
Target Region III (BK3)
In another embodiment, the invention provides for detection of BJKV in a sample, such as a biological sample, by detection of target nucleic acid sequence region III (FIG. 1, Target Region III (also referred to as BK3), alignment position 4097-4560 based on numbering of GenBank Accession No. AY628224) as follows:







(SEQ ID NO: 03)


AGTAAGTATTCCTTATTAACACCCTTACAAATTAAAAAACTAAAGGTAC


 


ACAGCTTTTGACAGAAATTATTAATTGCAGAAACTCTATGTCTATGTGG


 


AGTTAAAAAGAATATAATATTATGCCCAGCACACATGTGTCTACTAATG


 


AAAGTTACAGAATATTTTTCCATAAGTTTTTTATACAGAATTTGAGCTT


 


TTTCTTTAGTAGTATACACAGCAAAGCAGGCAAGGGTTCTATTACTAAA


 


TACAGCTTGACTAAGAAACTGGTGTAGATCAGAGGGAAAGTCTTTAGGG


 


TCTTCTACCTTTCTCTTTTTCTTGGGTGGTGTGGAGTGTTGAGAATCTG


 


CTGTTGCTTCTTCATCACTGGCAAACATATCTTCATGGCAAAATAAATC


 


TTCATCCCATTTTTCATTAAAGGAGCTCCACCAGGACTCCCACTCTTCT 


 


GTTCCATAGGTTGGCACCTATAA






or a complement thereof, or a fragment thereof, wherein the 5′ and 3′ end of the nucleic acid is contained within SEQ ID NO:03. This conserved sequence in the BKV genome is shown in the alignment of the three genomes in FIG. 1. In one embodiment of particular interest, the target region is a subsequence of Target Region III, such as:








(SEQ ID NO: 57)


GGAAAGTCTTTAGGGTCTTCTACCTTTCTCTTTTTCTTGGGTGGTGTGG


 


AGTGTTGAGAATCTGCTGTTGCTTCTTCATCACTGGCAAACATATCTTC


 


ATG






or a complement thereof, or a fragment thereof.

Exemplary nucleic acid sequences suitable for design of primers for amplification of a Target Region III nucleic acid, and suitable for use in the methods of the invention, are indicated by underlined typeface in FIG. 1. Suitable sequences for primers for amplification of Target Region III nucleic acid correspond to nucleotides 280-306 and 355-380 of the nucleotide sequence of SEQ ID NO:03, or a complement thereof.
Probes suitable for use in the invention can be designed from any sequence positioned within the sequence of an amplification product that would be produced using two selected primers. Suitable sequences for use as a probe for detection of Target Region III nucleic acid correspond to nucleotides 330-354 of the nucleotide sequence of SEQ ID NO:03, or a complement thereof.
In one embodiment, detection of target region III nucleic acid involves production of an amplification product of at least 464, at least 425, at least 400, at least 375, at least 350, at least 325, at least 300, at least 275, at least 250, at least 225, at least 200, at least 175, at least 150, at least 125, at least 120, at least 115, at least 110, at least 100, at least 95, at least 90, at least 85, at least 80, at least 75, at least 70, at least 65, at least 60, at least 55, at least 50, at least 45, at least 40, at least 35, at least 30, at least 28, at least 26, at least 24, at least 22, at least 20 consecutive nucleotides of SEQ ID NO:03.
The methods of the invention can involve detection of target region III nucleic acid either alone or in combination with detection of one or more of target regions I-II and IV-V as described herein. For example, the methods of the invention can involve detection of target region III (BK3) and target region IV (BK4); target region III (BK3) and target region V (BK5); target region III (BK3) and target region I (BK1); target region III (BK3) and target region II (BK); target region I (BK1), target region II (BK2), and target region III (BK3); target region III (BK3), target region IV (BK4), and target region V (BK5); or target region III (BK3), target region I (BK1), and target region V (BK5) and the like. It will be understood that detection of all combination of target regions I-V are contemplates by the present methods.
Exemplary primers and probes are discussed in greater detail below.
Target Region IV (BK4)
In another embodiment, the invention provides for detection of BKV in a sample, such as a biological sample, by detection of target nucleic acid sequence region IV (FIG. 1, Target Region IV (also referred to as BK4), alignment position 612-864 based on numbering of GenBank Accession No. AY628224) as follows:







(SEQ ID NO: 04)


ATGGGTGCTGCTCTAGCACTTTTGGGGGACCTAGTTGCCAGTGTATCTG


 


AGGCTGCTGCTGCCACAGGATTTTCAGTGGCTGAAATTGCTGCTGGGGA


 


GGCTGCTGCTGCTATAGAAGTTCAAATTGCATCCCTTGCTACTGTAGAG


 


GGCATAACAAGTACCTCAGAGGCTATAGCTGCCATAGGCCTAACTCCTC


 


AAACATATGCTGTAATTGCTGGTGCTCCTGGGGCTATTGCTGGGTTTGC


 


TGCTTTAA






or a complement thereof, or a fragment thereof, wherein the 5′ and 3′ end of the nucleic acid is contained within SEQ ID NO:04. This conserved sequence in the BKV genome is shown in the alignment of the three genomes in FIG. 1. In one embodiment of particular interest, the target region is a subsequence of Target Region IV, such as:








(SEQ ID NO: 58)


ATGGGTGCTGCTCTAGCACTTTTGGGGGACCTAGTTGCCAGTGTATCTGA


 


GGCTGCTGCTGCCACAGGATTTTCAGTGGCTGAAATTGCTGCTGG






or a complement thereof, or a fragment thereof.

Exemplary nucleic acid sequences suitable for design of primers for amplification of a Target Region IV nucleic acid, and suitable for use in the methods of the invention, are indicated by underlined typeface in FIG. 1. Suitable sequences for primers for amplification of Target Region IV nucleic acid correspond to nucleotides 1-19 and 76-95 of the nucleotide sequence of SEQ ID NO:04, or a complement thereof.
Probes suitable for use in the invention can be designed from any sequence positioned within the sequence of an amplification product that would be produced using two selected primers. Suitable sequences for use as a probe for detection of Target Region IV nucleic acid correspond to nucleotides 36-62 of the nucleotide sequence of SEQ ID NO:04, or a complement thereof.
In one embodiment, detection of target region IV nucleic acid involves production of an amplification product of at least 253, at least 250, at least 225, at least 200, at least 175, at least 150, at least 125, at least 120, at least 115, at least 100, at least 95, at least 90, at least 85, at least 80, at least 75, at least 70, at least 65, at least 60, at least 55, at least 50, at least 45, at least 40, at least 35, at least 30, at least 28, at least 26, at least 24, at least 22, at least 20 consecutive nucleotides of SEQ ID NO:04.
The methods of the invention can involve detection of target region IV nucleic acid either alone or in combination with detection of one or more of target regions I-III and V as described herein. For example, the methods of the invention can involve detection of target region IV (BK4) and target region I (BK1); target region TV (BK4) and target region II (BK2); target region IV (BK4) and target region III (BK3); target region IV (BK4) and target region IV (BK5); target region I (BK1), target region II (BK2), and target region IV (BK4); target region III (BK3), target region IV (BK4) and target region V (BK5); or target region I (BK1), target region TV (BK4) and target region V (BK5) and the like. It will be understood that detection of all combination of target regions I-V are contemplates by the present methods.
Exemplary primers and probes are discussed in greater detail below.
Target Region V
In another embodiment, the invention provides for detection of BKV in a sample, such as a biological sample, by detection of target nucleic acid sequence region V (FIG. 1, Target Region V (also refereed to as BK5), alignment position 2810-2895 based on numbering of GenBank Accession No. AY628224) as follows:







(SEQ 1D NO: 05)


GGGGCTGAAGTATCTGAGACTTGGGAAGAGCATTGTGATTGGGATTCAGT


 


GCTTGATCCATGTCCAGAGTCTTCAGTTTCTGAATC






or complement thereof, or a fragment thereof, wherein the 5′ and 3′ end of the nucleic acid is contained within SEQ ID NO:05. This conserved sequence in the BKV genome is shown in the alignment of the three genomes in FIG. 1. In one embodiment of particular interest, the target region is a subsequence of Target Region V, such as:








(SEQ ID NO: 59)


GGGCTGAAGTATCTGAGACTTGGGAAGAGCATTGTGATTGGGATTCAGTG


 


CTTGATCCATGTC






or complement thereof, or a fragment thereof.

Exemplary nucleic acid sequences suitable for design of primers for amplification of a Target Region V nucleic acid, and suitable for use in the methods of the invention, are indicated by underlined typeface in FIG. 1. Suitable sequences for primers for amplification of Target Region V nucleic acid correspond to nucleotides 2-18 and 47-64 of the nucleotide sequence of SEQ ID NO:05, or a complement thereof.
Probes suitable for use in the invention can be designed from any sequence positioned within the sequence of an amplification product that would be produced using two selected primers. Suitable sequences for use as a probe for detection of Target Region V nucleic acid correspond to nucleotides 19-41 of the nucleotide sequence of SEQ ID NO:05, or a complement thereof.
In one embodiment, detection of target region V nucleic acid involves production of an amplification product of at least 86, at least 80, at least 75, at least 70, at least 65, at least 60, at least 55, at least 50, at least 45, at least 40, at least 35, at least 30, at least 28, at least 26, at least 24, at least 22, at least 20 consecutive nucleotides of SEQ ID NO:05.
The methods of the invention can involve detection of target region V nucleic acid either alone or in combination with detection of one or more of target regions I-IV as described herein. For example, the methods of the invention can involve detection of target region V (BK5) and target region I (BK1); target region V (BK5) and target region II (BK2); target region V (BK5) and target region III (BK3); target region IV (BK4) and target region V (BKV); target region V (BK5), target region II (BK2), and target region III (BK3); target region III (BK3), target region IV (BK4), and target region V (BK5); or target region I (BK1), target region III (BK3), and target region V (BK5) and the like. It will be understood that detection of all combination of target regions I-V are contemplates by the present methods.
Exemplary primers and probes are discussed in greater detail below.
Primers and Probes
As described above, the target nucleic acid sequence regions I-V are conserved nucleic acid regions in different BKV genotypes. Primers and probes for use in these assays are preferably derived from the target nucleic acid sequence regions I-V as described above. In one embodiment of particular interest, primers and probes for use with the present assays are designed from the highly conserved nucleotide sequences of the target nucleic acid sequence regions I-V.
In general, the primers provide for amplification of target nucleic acid to produce as target nucleic acid amplification product (also referred to as an “amplicon”). Primers may be, and preferably are, used in connection with a probe. 5′ primers generally bind to a region to provide for amplification of the target nucleic, and preferably bind to a 5′ portion of the target sequence, as exemplified in FIG. 1. 3′ primers generally bind to a sequence that is complementary to a 3′ portion of the nucleic acid generated by extension from the 5′ primer, as exemplified in FIG. 1. The 5′ and 3′ primers may be separated by about 10, 20, 30, or 40 contiguous nucleotides, usually about 30 contiguous nucleotides. In certain embodiments, primers are designed so as to have a sequence complementary to one or more variant nucleotides within a target region sequence and/or to have a 3′ end adjacent a variant nucleotide of a sequence of a target region. Probes are generally designed so as to have a sequence complementary to one or more variant nucleotides within a target region sequence. In some embodiments involving amplification-based detection, probes are designed so as to have a sequence complementary to a sequence flanked by the sequence(s) complementary to one or more primers used for amplification.
Primers and probes for use in the assays herein are designed based on the sequence disclosed herein and are readily synthesized by standard techniques, e.g., solid phase synthesis via phosphoramidite chemistry, as disclosed in U.S. Pat. Nos. 4,458,066 and 4,415,732, incorporated herein by reference; Beaucage et al. (1992) Tetrahedron 48:2223-2311; and Applied Biosystems User Bulletin No. 13 (1 Apr. 1987). Other chemical synthesis methods include, for example, the phosphotriester method described by Narang et al., Meth. Enzymol. (1979) 68:90 and the phosphodiester method disclosed by Brown et al., Meth. Enzymol. (1979) 68:109. Poly(A) or poly(C), or other non-complementary nucleotide extensions may be incorporated into probes using these same methods. Hexaethylene oxide extensions may be coupled to probes by methods known in the art. Cload et al. (1991) J. Am. Chem. Soc. 113:6324-6326; U.S. Pat. No. 4,914,210 to Levenson et al.; Durand et al. (1990) Nucleic Acids Res. 18:6353-6359; and Horn et al. (1986) Tet. Lett. 27:4705-4708.
Typically, the primer sequences are in the range of between 10-75 nucleotides in length, such as 10 to 70, 12 to 65, 15 to 60, 20 to 55, 25 to 50, 30 to 45, and the like. More typically, primers are in the range of between 18 to 40, 19 to 35, 20 to 30, 21 to 29, 22 to 28, 23 to 27, 24-25 nucleotides lone, and any length between the stated ranges. Primers of about 20 to 22 nucleotides in length are of particular interest.
The typical probe is in the range of between 10-50 nucleotides long, such as such as 10 to 50, 12 to 45, 15 to 40, 20 to 35, 25 to 30 and the like. More typically, probes are in the range of between 18 to 40, 19 to 35, 20 to 30, 21 to 29, 22 to 28, 23 to 27, 24-25 nucleotides long, and any length between the stated ranges. Probes of about 20 to 22 nucleotides in length are of particular interest.
In some embodiments, the subject methods provide for detection of any BKV genotype in a sample, such a biological sample. In such embodiments, the subject methods detect a target nucleic acid region, or fragment thereof, by using primers and probe that correspond to sequences within the target region. Exemplary primers within the Target Regions I-V suitable for use in the methods of the invention are indicated by bold typeface in FIG. 1. Probes suitable for use in the invention can be designed from any sequence positioned within the sequence of an amplification product that would be produced using two selected primers. A probe suitable for use with such an embodiment is selected such that it corresponds to a region that shares a nucleotide sequence between the different BKV genotypes to be detected.
In other embodiments, the subject methods provide for detection and discrimination between different genotypes in a sample, such a biological sample. In such embodiments, the subject methods detect a target nucleic acid region, or fragment thereof, by using primers and probe that correspond to sequences within the target region. Exemplary primers within the Target Regions I-V suitable for use in the methods of the invention are indicated by bold typeface in FIG. 1. Probes suitable for use in the invention can be designed from any sequence positioned within the sequence of an amplification product that would be produced using two selected primers. In such embodiments the sequence of the probe is selected such that it corresponds to a region that differs in sequence by one or more nucleotides between the different BKV genotypes to be detected.
Exemplary nucleic acid sequences of the BKV genotypes that are suitable for use are primers and probes in the assays of the present invention are described in Table 1. The sequence numbering presented in Table 1 is the numbering of GenBank Accession No. AY628224 in FIG. 1.







TABLE 1







Exemplary Primer and Probe Sequences for Detection of Target


Regions I-V of BKV Nucleic Acid (Sequence Provided Based on


BKV Genome Sequence; Sequence Numbering Based on Numbering


of GenBank Accession No. AY628224 of FIG. 1)











SEQ ID NO.:
Start
End
Length
Sequence 5′ to 3′










Target Region I (BK1)


(corresponding to nucleotides 435-585 of AY628224)











SEQ ID NO: 06 F
 435
 460
26
AACAAAAAAAAGAGCTCAGAGGATTT


 


SEQ ID NO: 07 R
 527
 552
26
AAGTACCACTGCTTTACCTGCTGTAA


 


SEQ ID NO: 08 P
 490
 524
34
TTTGTAGAGGTGAAGACAGTGTAGACG






GGAAAAA


 







Target Region II (BK2)


(corresponding to nucleotides 1418-1545 of AY628224)











SEQ ID NO: 09 F
1450
1467
18
TTGCCCCAGGAGGTGCTA


 


SEQ ID NO: 10 R
1498
1520
23
TTTACTTCTAGGCCTGTACGGGA


 


SEQ ID NO: 11 P
1469
1497
29
TCAAAGAACTGCTCCTCAATGGATGTT






GC


 







Target Region III (BK3)


(corresponding to nucleotides 4097-4560 of AY628224)











SEQ ID NO: 12 F
4375
4404
27
GGAAAGTCTTTAGGGTCTTCTACCTTT


 


SEQ ID NO: 13 R
4452
4478
26
TCATCACTGGCAAACATATCTTCATG


 


SEQ ID NO: 14 P
4426
4450
25
GTGTTGAGAATCTGCTGTTGCTTCT


 







Target Region IV (BK4)


(corresponding to nucleotides 612-864 of AY628224)











SEQ ID NO: 15 F
 612
 620
19
ATGGGTGCTGCTCTAGCAC


 


SEQ ID NO: 16 R
 677
 696
20
GTGGCTGAAATTGCTGCTGG


 


SEQ ID NO: 17 P
 646
 663
27
TGCCAGTGTATCTGAGGCTGCTGCTGC


 







Target Region V (BK5)


(corresponding to nucleotides 2810-2895 of AY628224)











SEQ ID NO: 18 F
2811
2827
17
GGGCTGAAGTATCTGAG


 


SEQ ID NO: 19 R
2856
2873
18
CAGTGCTTGATCCATGTC


 


SEQ ID NO: 20 P
2828
2950
23
CTTGGGAAGAGCATTGTGATTGG





“F” refers to forward primer, “R” refers to reverse primer, and “P” refers to probe.






The probes may be coupled to labels for detection. There are several methods and compositions known for derivatizing oligonucleotides with reactive functionalities which permit the addition of a label. For example, several approaches are available for biotinylating probes so that radioactive, fluorescent, chemiluminescent, enzymatic, or electron dense labels can be attached via avidin. See, e.g., Broken et al., Nucl. Acids Res. (1978) 5:363-384 which discloses the use of ferritin-avidin-biotin labels; and Chollet et al. Nucl. Acids Res. (1985) 13:1529-1541 which discloses biotinylation of the 5′ termini of oligonucleotides via an aminoalkylphosphoramide linker arm. Several methods are also available for synthesizing amino-derivatized oligonucleotides which are readily labeled by fluorescent or other types of compounds derivatized by amino-reactive groups, such as isothiocyanate, N-hydroxysuccinimide, or the like, see, e.g., Connolly (1987) Nucl. Acids Res. 15:3131-3139, Gibson et al. (1987) Nucl. Acids Res. 15:6455-6467 and U.S. Pat. No. 4,605,735 to Miyoshi et al. Methods are also available for synthesizing sulfhydryl-derivatized oligonucleotides which can be reacted with thiol-specific labels, see, e.g., U.S. Pat. No. 4,757,141 to Fung et al., Connolly et al. (1985) Nuc. Acids Res. 13:4485-4502 and Spoat et al. (1987) Nucl. Acids Res. 15:4837-4848. A comprehensive review of methodologies for labeling DNA fragments is provided in Matthews et al., Anal. Biochem. (1988) 169:1-25.
For example, probes may be fluorescently labeled by linking a fluorescent molecule to the non-ligating terminus of the probe. Guidance for selecting appropriate fluorescent labels can be found in Smith et al., Meth. Enzymol. (1987) 155:260-301; Karger et al., Nucl. Acids Res. (1991) 19:4955-4962; Haugland (1989) Handbook of Fluorescent Probes and Research Chemicals (Molecular Probes, Inc., Eugene, Oreg.). Preferred fluorescent labels include fluorescein and derivatives thereof, such as disclosed in U.S. Pat. No. 4,318,846 and Lee et al., Cytometry (1989) 10:151-164, and 6-FAM, JOE, TAMRA, ROX, HEX-1, HEX-2, ZOE, TET-1 or NAN-2, and the like.
Additionally, probes can be labeled with an acridinium ester (AE). Current technologies allow the AE label to be placed at any location within the probe. See, e.g., Nelson et al. (1995) “Detection of Acridinium Esters by Chemiluminescence” in Nonisotopic Probing, Blotting and Sequencing, Kricka L. J. (ed) Academic Press, San Diego, Calif.; Nelson et al. (1994) “Application of the Hybridization Protection Assay (HPA) to PCR” in The Polymerase Chain Reaction, Mullis et al. (eds.) Birkhauser, Boston, Mass.; Weeks et al., Clin. Chem. (1983) 29:1474-1479; Berry et al., Clin. Chem. (1988) 34:2087-2090. An AE molecule can be directly attached to the probe using non-nucleotide-based linker arm chemistry that allows placement of the label at any location within the probe. See, e.g., U.S. Pat. Nos. 5,585,481 and 5,185,439.
If a solid support is used in the assay (e.g., to capture amplicons of target nucleic acid using a probe), the oligonucleotide probe may be attached to the solid support in a variety of manners. For example, the probe may be attached to the solid support by attachment of the 3′ or 5′ terminal nucleotide of the probe to the solid support. More preferably, the probe is attached to the solid support by a linker which serves to distance the probe from the solid support. The linker is usually at least 15-30 atoms in length, more preferably at least 15-50 atoms in length. The required length of the linker will depend on the particular solid support used. For example, a six atom linker is generally sufficient when high cross-linked polystyrene is used as the solid support.
A wide variety of linkers are known in the art which may be used to attach the oligonucleotide probe to the solid support. The linker may be formed of any compound which does not significantly interfere with the hybridization of the target sequence to the probe attached to the solid support. The linker may be formed of a homopolymeric oligonucleotide which can be readily added on to the linker by automated synthesis. Alternatively, polymers such as functionalized polyethylene glycol can be used as the linker. Such polymers are preferred over homopolymeric oligonucleotides because they do not significantly interfere with the hybridization of probe to the target oligonucleotide. Polyethylene glycol is particularly preferred.
The linkages between the solid support, the linker and the probe are normally not cleaved during removal of base protecting groups under basic conditions at high temperature. Examples of preferred linkages include carbamate and amide linkages.
Examples of preferred types of solid supports for immobilization of the oligonucleotide probe include controlled pore glass, glass plates, polystyrene, avidin-coated polystyrene beads, cellulose, nylon, acrylamide gel and activated dextran.
In certain embodiments, an internal control (IC) or an internal standard is added to serve as a control to show that any negative result is not due to failure of the assay. The use of the IC permits the control of the separation process, the amplification process, and the detection system, and permits the monitoring of assay performance and quantification for the sample(s). The IC can be included at any suitable point, for example, in the lysis buffer. In one embodiment, the IC comprises phage nucleic acid. Where a solid support is used in the assay, the solid support may additionally include probes specific to the internal standard (IC probe), thereby facilitating capture when using the IC probe. The IC probe can optionally be coupled with a detectable label that is different from the detectable label for the target sequence. In embodiments where the detectable label is a fluorophore, the IC can be quantified spectrophotometrically and by limit of detection studies.
Detection of BKV in a Sample
In one aspect, the assay detects the presence of BKV in a sample. In such an aspect, the assay is an amplification-based assay using degenerate primers and probes, where the primers and probes are designed to provide for amplification of a target nucleic acid sequence region of the BKV genome.
As discussed above, the assay detects the presence of one or more target nucleic acid regions (e.g., Target Regions I-V), or a portion thereof. The target nucleic acid sequence regions I-V are conserved nucleic acid regions in different BKV genotypes. Primers and probes for use in these assays are preferably derived from the target nucleic acid sequence regions I-V as described above. Particularly preferred primers and probes for use with the present assays are designed from the highly conserved nucleotide sequences of the target nucleic acid sequence regions I-V.
As discussed above, in one embodiment, the primers and/or probes are designed for nucleic acid-based detection, particularly an amplification method, of a target nucleic acid having a target nucleic acid sequence described above, e.g., target nucleic acid sequence region I-V. That is, in such an embodiment, the primers are designed to amplify a target sequence having the nucleic acid sequence of a nucleic acid sequence described above, e.g., target nucleic acid sequence region I-V.
In another embodiment, the primers and/or probes are designed for nucleic acid-based detection, particularly an amplification method, of a target nucleic acid having a nucleic acid sequence that is a fragment of a target nucleic acid sequence described above, e.g., target nucleic acid sequence region I-V. That is, in such an embodiment, the primers are designed to amplify a target sequence having the nucleic acid sequence of a portion smaller than the entire nucleic acid sequence described above, e.g., target nucleic acid sequence region I-V.
Specific detection of BKV nucleic acid in a sample is generally accomplished by detection of one or more of the target sequence regions I-V, or a fragment thereof. In one embodiment, BKV target nucleic acid is detected by use of primers and probes designed upon the sequences of target sequence region V.
In an embodiment of particular interest, the target sequence is detected using primers having the sequence ATGGGTGCTGCTCTAGCAC (5′ primer) (SEQ ID NO:15), GTGGCTGAAATTGCTGCTGG (3′ primer) (SEQ ID NO:16), and a probe having the sequence TGCCAGTGTATCTGAGGCTGCTGCTGC (SEQ ID NO:17) is of particular interest.
In another embodiment of particular interest, the target sequence is detected using primers having the sequence GGGCTGAAGTATCTGAG (5′ primer) (SEQ ID NO:18), CAGTGCTTGATCCATGTC (3′ primer) (SEQ ID NO:19), and a probe having the sequence CTTGGGAAGAGCATTGTGATTGG (SEQ ID NO:20) is of particular interest.
Of particular interest is the use of these primers and probes in a real-time RT PCR method for detection of BKV in a sample, with use of a dual-labeled TaqMan Probe.
Methods of Detection
The invention provides DNA-based assay for detecting BKV in a sample. Detection may be done using a wide variety of methods, including direct sequencing, hybridization with sequence-specific oligomers, gel electrophoresis and mass spectrometry. These methods can use heterogeneous or homogeneous formats, isotopic or nonisotopic labels, as well as no labels at all.
Preferably, the methods involve amplifying nucleic acids from a sample. If a diagnostic nucleic acid is obtained, the presence of BKV in a sample is indicated. In general, the methods involve amplifying a nucleic acid from a sample using a detection primer and at least one other primer, as described above, and assessing the amplified nucleic acids. The methods are highly sensitive, and may detect as few as 5 copies of BKV per reaction, which is equivalent to 200 copies of DNA per mL of specimen, although detection may be limited by the limit of linear range detection. Thus, the invention generally provides for detection of BKV in a sample, where the BKV is present in at least 200 copies of DNA per mL of specimen.
As is known in the art, an amplified nucleic acid may be assessed by a number of methods, including, for example, determining the presence or absence of the nucleic acid, determining the size of the nucleic acid or determining the abundance of a nucleic acid in relation to another amplified nucleic acid. In most embodiments, an amplified nucleic acid is assessed using gel electrophoresis, nucleic acid hybridization, sequencing, and/or detection of a signal from a label bound to the amplified nucleic acid. Methods of amplifying (e.g., by polymerase chain reaction) nucleic acid, methods of performing primers extension, and methods of assessing nucleic acids are generally well known in the art (e.g., see Ausubel, et al, Short Protocols in Molecular Biology, 3rd ed., Wiley & Sons, 1995 and Sambrook, et al, Molecular Cloning: A Laboratory Manual, Third Edition, (2001) Cold Spring Harbor, N.Y.) and need not be described in any great detail.
For example, primers and probes described above may be used in polymerase chain reaction (PCR)-based techniques to detect BKV in biological samples. PCR is a technique for amplifying a desired target nucleic acid sequence contained in a nucleic acid molecule or mixture of molecules. In PCR, a pair of primers is employed in excess to hybridize to the complementary strands of the target nucleic acid. The primers are each extended by a polymerase using the target nucleic acid as a template. The extension products become target sequences themselves after dissociation from the original target strand. New primers are then hybridized and extended by a polymerase, and the cycle is repeated to geometrically increase the number of target sequence molecules. The PCR method for amplifying target nucleic acid sequences in a sample is well known in the art and has been described in, e.g., Innis et al. (eds.) PCR Protocols (Academic Press, NY 1990); Taylor (1991) Polymerase chain reaction: basic principles and automation, in PCR: A Practical Approach, McPherson et al. (eds.) IRL Press, Oxford; Saiki et al. (1986) Nature 324:163; as well as in U.S. Pat. Nos. 4,683,195, 4,683,202 and 4,889,818, all incorporated herein by reference in their entireties.
In particular, PCR uses relatively short oligonucleotide primers which flank the target nucleotide sequence to be amplified, oriented such that their 3′ ends face each other, each primer extending toward the other. The polynucleotide sample is extracted and denatured, preferably by heat, and hybridized with first and second primers which are present in molar excess. Polymerization is catalyzed in the presence of the four deoxyribonucleotide triphosphates (dNTPs—dATP, dGTP, dCTP and dTTP) using a primer- and template-dependent polynucleotide polymerizing agent, such as any enzyme capable of producing primer extension products, for example, E. coli DNA polymerase I, Klenow fragment of DNA polymerase I, T4 DNA polymerase, thermostable DNA polymerases isolated from Thermus aquaticus (Taq), available from a variety of sources (for example, Perkin Elmer). Thermus thermophilus (United States Biochemicals), Bacillus stereothermophilus (Bio-Rad), or Thermococcus litoralis (“Vent” polymerase, New England Biolabs). This results in two “long products” which contain the respective primers at their 5′ ends covalently linked to the newly synthesized complements of the original strands.
The reaction mixture is then returned to polymerizing conditions, e.g., by lowering the temperature, inactivating a denaturing agent, or adding more polymerase, and a second cycle is initiated. The second cycle provides the two original strands, the two long products from the first cycle, two new long products replicated from the original strands, and two “short products” replicated from the long products. The short products have the sequence of the target sequence with a primer at each end. On each additional cycle, an additional two long products are produced, and a number of short products equal to the number of long and short products remaining at the end of the previous cycle. Thus, the number of short products containing the target sequence grow exponentially with each cycle. Preferably, PCR is carried out with a commercially available thermal cycler, e.g., Perkin Elmer.
The fluorogenic 5′ nuclease assay, known as the TAQMANTM assay (Perkin-Elmer), is a powerful and versatile PCR-based detection system for nucleic acid targets. For a detailed description of the TAQMANTM assay, reagents and conditions for use therein, see, e.g., Holland et al., Proc. Natl. Acad. Sci, U.S.A. (1991) 88:7276-7280; U.S. Pat. Nos. 5,538,848, 5,723,591, and 5,876,930, all incorporated herein by reference in their entireties. Hence, primers and probes derived from regions of the BKV genome described herein can be used in TAQMANTM analyses to detect the presence of infection in a biological sample. Analysis is performed in conjunction with thermal cycling by monitoring the generation of fluorescence signals. The assay system dispenses with the need for gel electrophoretic analysis, and has the capability to generate quantitative data allowing the determination of target copy numbers.
The fluorogenic 5′ nuclease assay is conveniently performed using, for example, AMPLITAQ GOLDTM DNA polymerase, which has endogenous 5′ nuclease activity, to digest an internal oligonucleotide probe labeled with both a fluorescent reporter dye and a quencher (see, Holland et al., Proc. Natl. Acad. Sci. USA (1991) 88:7276-7280; and Lee et al., Nucl. Acids Res. (1993) 21:3761-3766). Assay results are detected by measuring changes in fluorescence that occur during the amplification cycle as the fluorescent probe is digested, uncoupling the dye and quencher labels and causing an increase in the fluorescent signal that is proportional to the amplification of target nucleic acid.
The amplification products can be detected in solution or using solid supports. In this method, the TAQMANTM probe is designed to hybridize to a target sequence within the desired PCR product. The 5′ end of the TAQMANTM probe contains a fluorescent reporter dye. The 3′ end of the probe is blocked to prevent probe extension and contains a dye that will quench the fluorescence of the 5′ fluorophore. During subsequent amplification, the 5′ fluorescent label is cleaved off if a polymerase with 5′ exonuclease activity is present in the reaction. Excision of the 5′ fluorophore results in an increase in fluorescence which can be detected.
In particular, the oligonucleotide probe is constructed such that the probe exists in at least one single-stranded conformation when unhybridized where the quencher molecule is near enough to the reporter molecule to quench the fluorescence of the reporter molecule. The oligonucleotide probe also exists in at least one conformation when hybridized to a target polynucleotide such that the quencher molecule is not positioned close enough to the reporter molecule to quench the fluorescence of the reporter molecule. By adopting these hybridized and unhybridized conformations, the reporter molecule and quencher molecule on the probe exhibit different fluorescence signal intensities when the probe is hybridized and unhybridized. As a result, it is possible to determine whether the probe is hybridized or unhybridized based on a change in the fluorescence intensity of the reporter molecule, the quencher molecule, or a combination thereof. In addition, because the probe can be designed such that the quencher molecule quenches the reporter molecule when the probe is not hybridized, the probe can be designed such that the reporter molecule exhibits limited fluorescence unless the probe is either hybridized or digested.
Accordingly, the present invention relates to methods for amplifying a target BKV nucleotide sequence using a nucleic acid polymerase having 5′ to 3′ nuclease activity, one or more primers capable of hybridizing to the target BKV sequence or its extension product, and an oligonucleotide probe capable of hybridizing to the target BKV sequence 3′ relative to the primer. During amplification, the polymerase digests the oligonucleotide probe when it is hybridized to the target sequence, thereby separating the reporter molecule from the quencher molecule. As the amplification is conducted, the fluorescence of the reporter molecule is monitored, with fluorescence corresponding to the occurrence of nucleic acid amplification. The reporter molecule is preferably a fluorescein dye and the quencher molecule is preferably a rhodamine dye.
Another method of detection involves use of target sequence-specific oligonucleotide probes, which contain a region of complementarity to the target sequence described above. The probes may be used in hybridization protection assays (HPA). In this embodiment, the probes are conveniently labeled with acridinium ester (AE), a highly chemiluminescent molecule. See, e.g., Nelson et al. (1995) “Detection of Acridinium Esters by Chemiluminescence” in Nonisotopic Probing, Blotting and Sequencing, Kricka L. J. (ed) Academic Press, San Diego, Calif.; Nelson et al. (1994) “Application of the Hybridization Protection Assay (HPA) to PCR” in The Polymerase Chain Reaction, Mullis et al. (eds.) Birkhauser, Boston, Mass.; Weeks et al., Clin. Chem. (1983) 29:1474-1479; Berry et al., Clin. Chem. (1988) 34:2087-2090. One AE molecule is directly attached to the probe using a non-nucleotide-based linker arm chemistry that allows placement of the label at any location within the probe. See, e.g., U.S. Pat. Nos. 5,585,481 and 5,185,439. Chemiluminescence is triggered by reaction with alkaline hydrogen peroxide which yields an excited N-methyl acridone that subsequently collapses to ground state with the emission of a photon. Additionally, AE causes ester hydrolysis which yields the nonchemiluminescent-methyl acridinium carboxylic acid.
When the AE molecule is covalently attached to a nucleic acid probe, hydrolysis is rapid under mildly alkaline conditions. When the AE-labeled probe is exactly complementary to the target nucleic acid, the rate of AE hydrolysis is greatly reduced. Thus, hybridized and unhybridized AE-labeled probe can be detected directly in solution, without the need for physical separation.
HPA generally consists of the following steps: (a) the AE-labeled probe is hybridized with the target nucleic acid in solution for about 15 to about 30 minutes. A mild alkaline solution is then added and AE coupled to the unhybridized probe is hydrolyzed. This reaction takes approximately 5 to 10 minutes. The remaining hybrid-associated AE is detected as a measure of the amount of target present. This step takes approximately 2 to 5 seconds. Preferably, the differential hydrolysis step is conducted at the same temperature as the hybridization step, typically at 50 to 70 degrees Celsius. Alternatively, a second differential hydrolysis step may be conducted at room temperature. This allows elevated pHs to be used, for example in the range of 10-11, which yields larger differences in the rate of hydrolysis between hybridized and unhybridized AE-labeled probe. HPA is described in detail in, e.g., U.S. Pat. Nos. 6,004,745; 5,948,899; and 5,283,174, the disclosures of which are incorporated by reference herein in their entireties.
The oligonucleotide molecules of the present invention may also be used in nucleic acid sequence-based amplification (NASBA). This method is a promoter-directed, enzymatic process that induces in vitro continuous, homogeneous and isothermal amplification of a specific nucleic acid to provide RNA copies of the nucleic acid. The reagents for conducting NASBA include a first DNA primer with a 5′ tail comprising a promoter, a second DNA primer, reverse transcriptase, RNAse-H. T7 RNA polymerase, NTP's and dNTP's. Using NASBA, large amounts of single-stranded RNA are generated from either single-stranded RNA or DNA, or double-stranded DNA. When RNA is to be amplified, the ssRNA serves as a template for the synthesis of a first DNA strand by elongation of a first primer containing an RNA polymerase recognition site. This DNA strand in turn serves as the template for the synthesis of a second, complementary, DNA strand by elongation of a second primer, resulting in a double-stranded active RNA-polymerase promoter site, and the second DNA strand serves as a template for the synthesis of large amounts of the first template, the ssRNA, with the aid of a RNA polymerase. The NASBA technique is known in the art and described in, e.g., European Patent 329,822, International Patent Application No. WO 91/02814, and U.S. Pat. Nos. 6,063,603, 5,554,517 and 5,409,818, all of which are incorporated herein in their entireties.
The BKV sequences described herein are also useful in nucleic acid hybridization and amplification techniques that utilize branched DNA molecules. In a basic nucleic acid hybridization assay, single-stranded analyte nucleic acid is hybridized to a labeled single-stranded nucleic acid probe and resulting labeled duplexes are detected. Variations of this basic scheme have been developed to facilitate separation of the duplexes to be detected from extraneous materials and/or to amplify the signal that is detected. One method for amplifying the signal uses amplification multimers that are polynucleotides with a first segment that hybridizes specifically to the analyte nucleic acid or a strand of nucleic acid bound to the analyte and iterations of a second segment that hybridizes specifically to a labeled probe. The amplification is theoretically proportional to the number of iterations of the second segment. The multimers may be either linear or branched. Two general types of branched multimers are useful in these techniques: forked and combed. Methods for making and using branched nucleic acid molecules are known in the art and described in, e.g., U.S. Pat. No. 5,849,481, incorporated herein by reference in its entirety.
As is readily apparent, design of the assays described herein are subject to a great deal of variation, and many formats are known in the art. The above descriptions are merely provided as guidance and one of skill in the art can readily modify the described protocols, using techniques well known in the art.
Kits
Kits for use in connection with the subject invention are also provided. The above-described assay reagents, including the primers, probes, solid support with bound probes, as well as other detection reagents, can be provided in kits, with suitable instructions and other necessary reagents, in order to conduct the assays as described above. The kit will normally contain in separate containers the combination of primers and probes (either already bound to a solid matrix or separate with reagents for binding them to the matrix), control formulations (positive and/or negative), labeled reagents when the assay format requires same and signal generating reagents (e.g., enzyme substrate) if the label does not generate a signal directly. Instructions (e.g., written, tape, VCR, CD-ROM, etc.) for carrying out the assay usually will be included in the kit. The kit can also contain, depending on the particular assay used, other packaged reagents and materials (i.e. wash buffers and the like). Standard assays, such as those described above, can be conducted using these kits.
The instructions are generally recorded on a suitable recording medium. For example, the instructions may be printed on a substrate, such as paper or plastic, etc. As such, the instructions may be present in the kits as a package insert, in the labeling of the container of the kit or components thereof (e.g., associated with the packaging or subpackaging), etc. In other embodiments, the instructions are present as an electronic storage data file present on a suitable computer readable storage medium, e.g., CD-ROM, diskette, etc, including the same medium on which the program is presented.
In yet other embodiments, the instructions are not themselves present in the kit, but means for obtaining the instructions from a remote source, e.g. via the Internet, are provided. An example of this embodiment is a kit that includes a web address where the instructions can be viewed from or from where the instructions can be downloaded.
Still further, the kit may be one in which the instructions are obtained are downloaded from a remote source, as in the Internet or world wide web. Some form of access security or identification protocol may be used to limit access to those entitled to use the subject invention. As with the instructions, the means for obtaining the instructions and/or programming is generally recorded on a suitable recording medium.
In general, kits of the invention include at least one primer, usually at least two primers (a 5′ and a 3′ primer), usually at least two primers and a probe, as described above. Kits may also contain instructions for using the kit to detect BKV in a sample using the methods described above, including the above discussed PCR methods. Also included in the subject kits may be buffers, dNTPs, and controls, (e.g., positive and negative control nucleic acids) for performing the subject methods. Primers in the subject kits may be detectably labeled or unlabeled).
EXAMPLES
The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how to make and use the present invention, and are not intended to limit the scope of what the inventors regard as their invention nor are they intended to represent that the experiments below are all or the only experiments performed. Efforts have been made to ensure accuracy with respect to numbers used (e.g. amounts, temperature, etc.) but some experimental errors and deviations should be accounted for. Unless indicated otherwise, parts are parts by weight, molecular weight is weight average molecular weight, temperature is in degrees Centigrade, and pressure is at or near atmospheric.
Materials and Methods
The following method and material were used in the Example(s) below.
Specimen Types and Handing.
Samples for use in detection of BKV according to the invention can be any suitable biological sample, such as serum, plasma, amniotic fluid, and tissue specimen. Tissue specimens should be stored frozen at −20±10° C. in saline or phosphate buffered saline (PBS). Serum, plasma, and amniotic fluid should be stored frozen at −20±10° C. All of the above specimen types, as needed, can be shipped on dry ice via overnight express,
Primers and Probes.
Oligonucleotide primers and probes were designed and analyzed for their suitability for PCR and hybridization by computer analysis using standard program (Primer Express, Applied Biosystems). Oligonucleotide primers and fluorogenic probes were synthesized by qualified vendors. Oligonucleotide primers were desalted and lyophilized. Oligonucleotide primer pair sets for detection of BKV were as follows:












SEQ ID NO.:

Sequence 5′ to 3′















Target Region I (BK1)









SEQ ID NO: 06
F
AACAAAAAAAAGAGCTCAGAGGATTT


 


SEQ ID NO: 07
R
AAGTACCACTGCTTTACCTGCTGTAA


 


SEQ ID NO: 08
P
TTTGTAGAGGTGAAGACAGTGTAGACGGGAAAAA


 







Target Region II (BK2)









SEQ ID NO: 09
F
TTGCCCCAGGAGGTGCTA


 


SEQ ID NO: 10
R
TTTACTTCTAGGCCTGTACGGGA


 


SEQ ID NO: 11
P
TCAAAGAACTGCTCCTCAATGGATGTTGC


 







Target Region III (BK3)









SEQ ID NO: 12
F
GGAAAGTCTTTAGGGTCTTCTACCTTT


 


SEQ ID NO: 13
R
TCATCACTGGCAAACATATCTTCATG


 


SEQ ID NO: 14
P
GTGTTGAGAATCTGCTGTTGCTTCT


 







Target Region IV (BK4)









SEQ ID NO: 15
F
ATGGGTGCTGCTCTAGCAC


 


SEQ ID NO: 16
R
GTGGCTGAAATTGCTGCTGG


 


SEQ ID NO: 17
P
TGCCAGTGTATCTGAGGCTGCTGCTGC


 







Target Region V (BK5)









SEQ ID NO: 18
F
GGGCTGAAGTATCTGAG


 


SEQ ID NO: 19
R
CAGTGCTTGATCCATGTC


 


SEQ ID NO: 20
P
CTTGGGAAGAGCATTGTGATTGG









“F” refers to the forward primer “R” to the reverse primer, and “P” refers to probe. Probes are frozen at a 100 μM concentration. The working concentration of the probes is 5 μM and are diluted 1:10 with 10 mM Tris-HCl, pH 8.0, and distributed into 100 μl aliquots. Probes can be stored at −20° C. or lower and protected from light.

Enzymes.
The following enzymes are used: 2× TaqMan® Universal PCR Master Mix Applied Biosystems Cat. #4304437 or 4318157, which includes the AmpliTaq Gold DNA Polymerase of Applied Biosystems
Reagents and Buffers.
The following were used in the assays: QIAamp DNA Blood Mini Kit (QIAGEN Cat. No. 51106);
Equipment.
Equipment used included the ABI PRISM® Sequence Detection System 7500
Amplification.
DNA amplification was achieved by widely used PCR method described above (see, for example, Persing et al, 1993, Diagnostic Molecular Microbiology: Principles and Amplifications, American Society for Microbiology, Washington D.C.). Amplified DNA sequence was detected by hybridization and cleavage of dual labeled oligonucleotide probe by the Taqman method. Briefly, the amplification and detection protocols were as follows: extracted DNA from clinical specimens were amplified in 25 μl PCR reaction mixture (PCR Master Mix, Applied Biosystems) containing 500 nM of each primers, 100 nM of dual labeled probed (Taqman probe), 200 uM of each of the four dNTPs. The AmpliTaq Gold polymerase was used in the mix, which is a heat activation (hot start) enzyme to enhance the specificity and sensitivity of the amplification. The PCR reaction was subjected to thermal cycling (10 min at 95 C, followed by 40 cycles of 30 second at 95 C, 30 second at 60 C) by using ABI7500 Real Time PCR System. The amplification and detection was monitored at real time, and was analyzed after completion of PCR cycling by using ABI's Sequence Detection Software (v1.2.2).
Specificity.
The specificity of oligonucleotide primers and probes, derived from the sequenced DNA and the sequences available in GenBank, were tested on a panel of clinical BKV positive and negative samples. The primers and probes were also tested on JCV positive and negative samples, as well as a number of controls. The results were compared with the result by PCR assay currently used in clinical laboratories. Some of the amplified nucleic acids were sequenced in order to validate the specificity of the assay. The sequencing of the amplified nucleic acids confirmed that all PCR fragments were indeed BKV sequences. None of these sequences fragments correlated to JCV sequences or sequences from any other species.
Sensitivity.
The sensitivity of the assays was analyzed by titration of known concentration series of BKV DNA and converting the concentrations into standard curves. Since there are several primer/probe sets targeting different regions, the sensitivity varied slightly. Overall, the analytical sensitivity reached 5 copy or lower per reaction tube. Based on the sample preparation procedure and volume adjustment protocol, this analytical sensitivity was equivalent to about 200 copies per ml for clinical specimen (e.g., serum, urine, or other form of liquid specimen).
Example 1
Complete Sequencing of BKV Whole Genome
In order to understand the genomic diversity of BKV and to identify candidate sequences for its diagnostic applications, whole viral genome sequencing was performed. Urine samples were collected from 13 BKV positive patients. To avoid close clinical relationship, these patients were chosen from, geographically diversified resources and were otherwise randomly selected. Samples were extracted for viral DNA by regular method. The extracted DNA was then amplified for its whole 5.1 kb genome by long PCR protocol (Stratagene). The amplified viral DNA was sequenced by four-color, dideoxy termination method with a set of pre-designed sequencing primers, and separated on ABI377 sequencer system. The sequence pieces were assembled into complete 5.1-5.2 kb contigs by Lasergene 6 software for each BKV genome for analysis.
Thirteen assembled BKV contigs were aligned against each other and also aligned against all published BKV sequences. Published sequence information was acquired from public databases (GenBank, EMBL and Swiss-Port). 32 complete BKV genome sequences were compared, including the 13 newly sequenced BKV sequences and the 19 published BKV sequences (GenBank Accession Nos.: AY628224, AY628225, AY628226, AY628227, AY628228, AY628229, AY628230, AY628231, AY628232, AY628233, AY628234, AY628235, AY628236, AY628237, AY628238, M23122, NC001538, V01108, and V01109).
First, all the sequences from the BKV strains were compared to one another. Then, the BKV sequences were then compared to genomes of other closely related species. Of all the species that were screened, of particular interest were the human polyomavirus JC viruses (JCV), another member in the polyomavirus family.
Complete sequence alignment within BKV genome allowed for the selection of several candidate sequence regions for diagnostic detection. These regions share consensus across all 32 BKV genomes, and have minimal variations in their sequences. Sequences outside these regions are either not consensus or are highly polymorphic, which make them very difficult to be used for ubiquity detection in diagnostic applications. A comparative analysis was further performed against sequences from all other species in public databases. Notably, JCV shares a high homology with BKV. Despite the homology, comparison of selected regions of BKV with JCV showed some sequence differences. These sequence differences, though limited, are critical for differential detection of BKV from JCV.
Of the 5100+ base pairs from the complete whole genome, there are a total of 142 previously unpublished nucleotide variations that were identified. Of these nucleotide variations, 105 were nucleotide substitutions (single or multiple base pairs) and 37 were deletions or insertions (multiple base pairs). The newly identified variations distributed throughout the entire BKV genome. A fine map of genetic diversity of BKV was created by combining the newly identified sequence variations with variations from public databases. As shown in FIG. 1, this map illustrates regions which are highly polymorphic and regions which are relatively conservative. Analysis of this fine map allows for selection of candidate sequence regions for diagnostic applications.
Example 2
Identification of Target Region I (“BK1”)
As shown in FIG. 1, the comparison of sequences across all newly completed nucleic acid sequences and published nucleic acid sequences allowed the selection of more than one sequence regions that are conserved and will provide for specific and sensitive nucleic acid based detection of the presence or absence of BKV in a biological sample. The BK1 region comprising of nucleotides 435 to 585 of GenBank Accession No. AY628224 was selected for PCR primer design. The nucleic acid sequence of the BK I target sequence is:







(SEQ ID NO: 01)


AACAAAAAAAAGAGCTCAGAGGATTTTTATTTTTATTTTAGAGCTTTTGC


 


TGGAATTTTGTAGAGGTGAAGACAGTGTAGACGGGAAAAACAAAGGTACC


 


ACTGCTTTACCTGCTGTAAAAGACTCTGTAAAAGACTCCTAGGTAAGTAA


 


T






The strategy used to design the nucleic acid based amplification primers was based on the analysis of multiple sequences alignment of all BKV genomic sequences and sequences of closely related viruses. This analysis was designed to include all variants of BKV. This analysis was also designed to exclude any closely related, but non BKV sequences, such as sequence of JCV. A careful analysis of these alignments allowed the selection of oligonucleotide sequences which cover sequences of all BKV variants but discriminate sequences from any other closely related genera, thereby permitting the genus-specific amplification and ubiquitous detection and identification of BKV. The sequences of the primers and probe for the BK1 target region are as follows:












SEQ ID NO.:

Sequence 5′ to 3′















Target Region I (BK1)









SEQ ID NO: 06
F
AACAAAAAAAAGAGCTCAGAGGATTT


 


SEQ ID NO: 07
R
AAGTACCACTGCTTTACCTGCTGTAA


 


SEQ ID NO: 08
P
TTTGTAGAGGTGAAGACAGTGTAGACGGGAAAAA









For confirmation of specific detection of BKV, PCR amplification products from BKV specimens were sequenced and analyzed. The amplification product sequences were aligned well with the sequence of BKV, and none of the amplification product sequences were identified as sequence of JCV or of any other genera. The results of the assay are shown in FIG. 2. Template concentrations ranged from 50 copies per reaction to 50,000 per reaction, and the assay were performed in duplicate. BK1 assay: slope=−3.58, intercept=43.428, and R2=0.997.
Example 3
Identification of Target Region II (“BK2”)
The comparison of nucleic acid sequences across all newly completed BKV nucleic acid sequences and published BKV nucleic acid sequences allowed the selection of the BK2 target region. The BK2 target region comprises nucleotides 1418 to 1545 of GenBank Accession No. AY628224. The nucleic acid sequence of the BK2 target sequence is:







(SEQ ID NO: 02)


TGTACATTCAGGAGAGTTTATAGAAAAAACTATTGCCCCAGGAGGTGCTA


 


ATCAAAGAACTGCTCCTCAATGGATGTTGCCTTTACTTCTAGGCCTGTAC


 


GGGACTGTAACACCTGCTCTTGAAGCAT






The strategy used to design the nucleic acid based amplification primers and probes was based on the analysis of multiple sequences alignment of all BKV sequences and sequences of closely related viruses. This analysis was designed to include all variants of BKV. This analysis was also designed to exclude any closely related, but non BK sequences, such as sequence of JCV. A careful analysis of these alignments allowed the selection of oligonucleotide sequences which cover sequences of all BKV variants but discriminate sequences from any other closely related genera, thereby permitting the genus-specific amplification and ubiquitous detection and identification of BKV. The sequences of the primers and probe for the BK2 target region are as follows:















SEQ ID NO.:

Sequence 5′ to 3′
















Target Region II (BK2)











SEQ ID NO: 09
F
TTGCCCCAGGAGGTGCTA



 



SEQ ID NO: 10
R
TTTACTTCTAGGCCTGTACGGGA



 



SEQ ID NO: 11
P
TCAAAGAACTGCTCCTCAATGGATGTTGC










For confirmation of specific detection of BKV, PCR amplification products from BKV specimens were sequenced and analyzed. The amplification product sequences were aligned well with the sequence of BKV, and none of the amplification product sequences were identified as sequence of JCV or of any other genera. The results of the assay are shown in FIG. 2. Template concentrations ranged from 50 copies per reaction to 50,000 per reaction, and the assay were performed in duplicate. For the BK2 assay: slope=−3.48, intercept=44.053, R2=0.999.
Example 4
Identification of Target Region III (“BK3”)
The comparison of nucleic acid sequences across all newly completed BKV nucleic acid sequences and published BKV nucleic acid sequences allowed the selection of the BK2 target region. The BK3 target region comprises nucleotides 4097 to 4560 of GenBank Accession No. AY628224. The nucleic acid sequence of the BK3 target sequence is:







(SEQ ID NO: 03)


AGTAAGTATTCCTTATTAACACCCTTACAAATTAAAAAACTAAAGGTACA


 


CAGCTTTTGACAGAAATTATTAATTGCAGAAACTCTATGTCTATGTGGAG


 


TTAAAAAGAATATAATATTATGCCCAGCACACATGTGTCTACTAATGAAA


 


GTTACAGAATATTTTTCCATAAGTTTTTTATACAGAATTTGAGCTTTTTC


 


TTAGTAGTATACACAGCAAAGCAGGCAAGGGTTCTATTACTAAATACAGC


 


TTGACTAAGAAACTGGTGTAGATCAGAGGGAAAGTCTTTAGGGTCTTCTA


 


CCTTTCTCTTTTTCTTGGGTGGTGTGGAGTGTTGAGAATCTGCTGTTGCT


 


TCTTCATCACTGGCAAACATATCTTCATGGCAAAATAAATCTTCATCCCA


 


TTTTTCATTAAAGGAGCTCCACCAGGACTCCCACTCTTCTGTTCCATAGG


 


TTGGCACCTATAA






The strategy used to design the nucleic acid based amplification primers and probes was based on the analysis of multiple sequences alignment of all BKV sequences and sequences of closely related viruses. This analysis was designed to include all variants of BKV. This analysis was also designed to exclude any closely related, but non BK sequences, such as sequence of JCV. A careful analysis of these alignments allowed the selection of oligonucleotide sequences which cover sequences of all BKV variants but discriminate sequences from any other closely related genera, thereby permitting the genus-specific amplification and ubiquitous detection and identification of BKV. The sequences of the primers and probe for the BK3 target region are as follows:















SEQ ID NO.:

Sequence 5′ to 3′
















Target Region III (BK3)











SEQ ID NO: 12
F
GGAAAGTCTTTAGGGTCTTCTACCTTT



 



SEQ ID NO: 13
R
TCATCACTGGCAAACATATCTTCATG



 



SEQ ID NO: 14
P
GTGTTGAGAATCTGCTGTTGCTTCT










For confirmation of specific detection of BKV, PCR amplification products from BKV specimens were sequenced and analyzed. The amplification product sequences were aligned well with the sequence of BKV, and none of amplification product sequences were identified as sequence of JCV or of any other genera. The results of the assay are shown in FIG. 2. Template concentrations ranged from 50 copies per reaction to 50,000 per reaction, and the assay were performed in duplicate. For the BK3 assay: slope=−3.49, intercept=44.819. R2=0.999.
Example 5
Identification of Target Region IV (“BK4”)
The comparison of nucleic acid sequences across all newly completed BKV nucleic acid sequences and published BKV nucleic acid sequences allowed the selection of the BK4 target region. The BK4 target region comprises nucleotides 612 to 864 of GenBank Accession No. AY628224. The nucleic acid sequence of the BK4 target sequence is:







(SEQ ID NO: 04)


ATGGGTGCTGCTCTAGCACTTTTGGGGGACCTAGTTGCCAGTGTATCTGA


 


GGCTGCTGCTGCCACAGGATTTTCAGTGGCTGAAATTGCTGCTGGGGAGG


 


CTGCTGCTGCTATAGAAGTTCAAATTGCATCCCTTGCTACTGTAGAGGGC


 


ATAACAAGTACCTCAGAGGCTATAGCTGCCATAGGCCTAACTCCTCAAAC


 


ATATGCTGTAATTGCTGGTGCTCCTGGGGCTATTGCTGGGTTTGCTGCTT


 


TAA






The strategy used to design the nucleic acid based amplification primers and probes was based on the analysis of multiple sequences alignment of all BKV sequences and sequences of closely related viruses. This analysis was designed to include all variants of BKV. This analysis was also designed to exclude any closely related, but non BK sequences, such as sequence of JCV. A careful analysis of these alignments allowed the selection of oligonucleotide sequences which cover sequences of all BKV variants but discriminate sequences from any other closely related genera, thereby permitting the genus-specific amplification and ubiquitous detection and identification of BKV. The sequences of the primers and probe for the BK4 target region are as follows:















SEQ ID NO.:

Sequence 5′ to 3′
















Target Region IV (BK4)











SEQ ID NO: 15
F
ATGGGTGCTGCTCTAGCAC



 



SEQ ID NO: 16
R
GTGGCTGAAATTGCTGCTGG



 



SEQ ID NO: 17
P
TGCCAGTGTATCTGAGGCTGCTGCTGC










For confirmation of specific detection of BKV, PCR amplification products from BKV specimens were sequenced and analyzed. The amplification product sequences were aligned well with the sequence of BKV, and none of amplification product sequences were identified as sequence of JCV or of any other genera. The results of the assay are shown in FIG. 2. Template concentrations ranged from 50 copies per reaction to 50,000 per reaction, and the assay were performed in duplicate. For the BK4 assay: slope=−3.21, intercept=41.466, R2=0.999.
The analytical sensitivity of the oligonucleotide primer and probe was tested by titration of known concentration series of DNA and calculated by using standard curve analysis. It was demonstrated that the analytical sensitivity of the assay reached 5 copy or lower per reaction tube. Adjusted from the sample preparation procedure and volume adjustment protocol, this analytical sensitivity is equivalent to about 200 copies per ml of liquid clinical specimens.
The primer/probe set was tested on a panel of total 333 previously tested clinical samples. The panel included 47 of known BKV positive (detected), and 286 of known BKV negative (non detected) samples. The oligonucleotide primer/probe set detected all 47 positive samples. Furthermore, out of the 284 negative samples, it detected 34 as BKV positive. To validate those “missed” positive result, 28 were sequenced. All of the 28 sequenced amplification products were identified as BKV. The remaining 6 samples could not be sequenced due to insufficient sample volume. Overall, at least 10% of clinically negative samples was detected as BKV positive by the new primer/probe strategy and were validated by sequencing as true positive. The failure of detecting such percentage of true positive could be caused by primer/probe mismatch on variation sites or poor PCR efficiency or both.
Example 6
Identification of Target Region V (“BK5”)
The comparison of nucleic acid sequences across all newly completed BKV nucleic acid sequences and published BKV nucleic acid sequences allowed the selection of the BK4 target region. The BK4 target region comprises nucleotides 2810 to 2895 of GenBank Accession No. AY628224. The nucleic acid sequence of the BK5 target sequence is:







(SEQ ID NO: 05)


GGGGCTGAAGTATCTGAGACTTGGGAAGAGCATTGTGATTGGGATTCAGT


 


GCTTGATCCATGTCCAGAGTCTTCAGTTTCTGAATC






The strategy used to design the nucleic acid based amplification primers and probes was based on the analysis of multiple sequences alignment of all BKV sequences and sequences of closely related viruses. This analysis was designed to include all variants of BKV. This analysis was also designed to exclude any closely related, but non BK sequences, such as sequence of JCV. A careful analysis of these alignments allowed the selection of oligonucleotide sequences which cover sequences of all BKV variants but discriminate sequences from any other closely related genera, thereby permitting the genus-specific amplification and ubiquitous detection and identification of BKV. The sequences of the primers and probe for the BK5 target region are as follows:















SEQ ID NO.:

Sequence 5′ to 3′
















Target Region V (BK5)











SEQ ID NO: 18
F
GGGCTGAAGTATCTGAG



 



SEQ ID NO: 19
R
CAGTGCTTGATCCATGTC



 



SEQ ID NO: 20
P
CTTGGGAAGAGCATTGTGATTGG










For confirmation of specific detection of BKV, PCR amplification products from BKV specimens were sequenced and analyzed. The amplification product sequences were aligned well with the sequence of BKV, and none of amplification product sequences were identified as sequence of JCV or of any other genera. The results of the assay are shown in FIG. 2. Template concentrations ranged from 50 copies per reaction to 50,000 per reaction, and the assay were performed in duplicate. For the BK5 assay: slope=−3.61, intercept=47.324, R2=0.994.
It is evident from the above results and discussion that the subject invention provides an important new means for the detection of BK virus as well as differentiating between different BK virus genotypes or strains. As such, the subject methods and systems find use in a variety of different applications, including research, medical, therapeutic, diagnostic, military and other applications. Accordingly, the present invention represents a significant contribution to the art.
While the present invention has been described with reference to the specific embodiments thereof, it should be understood by those skilled in the art that various changes may be made and equivalents may be substituted without departing from the true spirit and scope of the invention. In addition, many modifications may be made to adapt a particular situation, material, composition of matter, process, process step or steps, to the objective, spirit and scope of the present invention. All such modifications are intended to be within the scope of the claims appended hereto.

## Claims

1. A method of detecting the presence or absence of BK virus (BKV) nucleic acid in a sample, the method comprising contacting said sample with a primer pair that hybridizes to SEQ ID NO: 2 or a complement thereof but not to JC virus nucleic acid under conditions that discriminate between BKV and JCV nucleic acid and detecting if the hybridization of the primer pair to SEQ ID NO: 2 or a complement thereof has occurred, wherein said hybridization detects the presence or absence of BKV nucleic acid.

2. The method of claim 1, wherein said step of detecting if hybridization has occurred comprises nucleic acid-based amplification.

3. The method of claim 2, wherein said amplification generates a product about 30 nucleotides or less in length.

4. The method of claim 1, further comprising detecting the presence or absence of a second BKV nucleic acid in the sample, wherein said detecting a second BKV nucleic acid is achieved by contacting said sample with one or more oligonucleotides designed to hybridize to SEQ ID NO: 5 or a complement thereof but not to JC virus nucleic acid under conditions which discriminate between BKV and JCV nucleic acid and detecting if the hybridization of said one or more oligonucleotides to SEQ ID NO: 5 or a complement thereof has occurred, wherein said hybridization detects the presence or absence of BKV nucleic acid.

5. The method of claim 1, wherein one primer of said primer pair comprises nucleotides 52-80 of SEQ ID NO: 2 or a complement thereof.

6. The method of claim 2, wherein said nucleic acid amplification is achieved by amplifying a portion of SEQ ID NO: 2 using a primer pair consisting of SEQ ID NO: 9 and SEQ ID NO: 10 or a complement thereof.

7. The method of claim 1, wherein at least one primer of said primer pair is a degenerate oligonucleotide.

8. The method of claim 1, wherein at least one primer of said primer pair comprises a detectable label.

9. The method of claim 8, wherein said detectable label s a fluorophore.

10. The method of claim 9, wherein at least one primer of said primer pair comprises a quencher molecule.

11. The method of claim 10, wherein the fluorophore and quencher molecule are attached to same primer.

12. The method of claim 1, wherein said step of detecting if hybridization has occurred comprises nucleic acid sequencing.

13. The method of claim 4, wherein said detecting a second BKV nucleic acid is achieved by amplifying a portion of SEQ ID NO: 5 or complement thereof.

14. The method of claim 4, wherein at least one of said oligonucleotides designed to hybridize to SEQ ID NO: 5 or a complement thereof is a degenerate oligonucleotide.

15. The method of claim 4, wherein at least one of said oligonucleotides designed to hybridize to SEQ ID NO: 5 or a complement thereof comprises a detectable label.

16. The method of claim 15, wherein said detectable label is a fluorophore.

17. The method of claim 16, wherein at least one or more of said oligonucleotides designed to hybridize to SEQ ID NO: 5 or a complement thereof comprises a quencher molecule.

18. The method of claim 17, wherein the fluorophore and quencher molecule are attached to same oligonucleotide.

19. The method of claim 4, wherein said step detecting it hybridization has occurred comprises nucleic acid sequencing.

20. A method of detecting the presence or absence of BK virus (BKV) nucleic acid in a sample, the method comprising contacting said sample with one or more oligonucleotides designed to hybridize to SEQ ID NO: 5 or a complement thereof but not to JC virus nucleic acid under conditions which discriminate between BKV and JCV nucleic acid and detecting if the hybridization of said one or more oligonucleotides to SEQ ID NO: 5 or a complement thereof has occurred, wherein said hybridization detects the presence or absence of BKV nucleic acid.

21. The method of claim 20, wherein said step of detecting if hybridization has occurred comprises nucleic acid-based amplification.

22. The method of claim 21, wherein said amplification generates a product about 30 nucleotides or less in length.

23. The method of claim 20, wherein one of said oligonucleotides designed to hybridize to SEQ ID NO: 5 or a complement thereof comprises nucleotides 19.41 of SEQ ID NO: 5.

24. The method of claim 20, wherein at least one of said oligonucleotides designed to hybridize to SEQ ID NO: 5 or a complement thereof is a degenerate oligonucleotide.

25. The method of claim 20, wherein at least one of said oligonucleotides designed to hybridize to SEQ ID NO: 5 or a complement thereof comprises a detectable label.

26. The method of claim 25, wherein said detectable label is a fluorophore.

27. The method of claim 26, wherein at least one or more of said oligonucleotides designed to hybridize to SEQ ID NO: 5 or a complement thereof comprises a quencher molecule.

28. The method of claim 27, wherein the fluorophore and quencher molecule are attached to same oligonucleotide.

29. The method of claim 20, wherein said step of detecting if hybridization has occurred comprises nucleic acid sequencing.

30. The method of claim 21, wherein said nucleic acid amplification is achieved by amplifying a portion of SEQ ID NO: 5 or a complement thereof using primer pairs of SEQ ID NO: 18 and SEQ ID NO: 19.