# Patent

## Title
HPV detection and quantification by real-time multiplex amplification

## Abstract

The present invention relates to amplification primers and detection probes, which are useful for the detection of human papillomaviruses (HPV), and more particularly of HPV, which can be oncogenic for the mucosal epithelia. The amplification and detection systems provided by the present invention are group-targeted systems, namely A5-, A6- A7-, and A9-targeted systems. The amplification and detection systems of the invention allow for an amplification of HPV in multiplex as well as for a real-time detection, whereby at least the thirteen HR HPV can be detected in a single-tube assay. The invention further allows for a reliable quantitation of HPV viral loads in real-time multiplex amplification.

## Background
This application is the U.S. nation phase of International Application No. PCT/EP2006/004314, filed Apr. 11, 2006, which designated the U.S. and the entire contents of which is hereby incorporated by reference.
FIELD
The present invention relates to the detection of human papillomaviruses (HPV), more particularly of HPV, which have a tropism for the mucosal epithelia (mucosal-type HPV), still more particularly of HPV, which can be oncogenic for the mucosal epithelia. The present invention provides amplification primers and detection probes, which are useful therefor, as well as reference template sequences suitable for designing and building such primers and probes.
BACKGROUND OF THE INVENTION
Human papillomavirus (HPV) contains a circular double-stranded DNA genome of about 7,900 bp, which is organized into three main regions, i.e.:

    
    
        an early coding region containing genes E1, E2, E4, E5, E6 and E7, which are involved in viral replication and in neoplastic transformation,
        a late coding region, containing genes L1 and L2, which code for viral capside proteins,
        a non-coding regulatory region, which is referred to as LRC (Long Control Region), which is located between the E genes and the L genes.
    
    


HPV constitute a group of viruses, which are associated with benign and malignant lesions of cutaneous or mucosal epithelia. To date, more than 100 different HPV types have been identified.
More than 40 HPV types belonging to the mucosal group have been detected in the anogenital mucosa.
HPV is the major risk factor in the development of squamous intraepithelial lesions (SILs), which are classified as low grade (LSIL) or high grade (HSIL) in severity.
HPV may induce cervical intraepithelial neoplasia (CIN), ranging from benign lesions (CIN1), such as condylomata acuminata, through pre-cancerous lesions (CIN2 to CIN3), up to in situ carcinoma and invasive cancer.
It is now established that HPV is directly involved in cervical carcinogenesis. Detecting HPV is essential to the prognosis of CIN and cervical cancer.
Early and precise detection of HPV is the key factor for recovery from cervical cancer.
It has also been shown that an increased HPV viral load within a cervical smear to specimen is associated with an increased risk of CIN3 and of cervical carcinomas.
A number of oncogenic HPV genotypes that infect the anogenital tract have been classified as potentially high risk HPV genotypes (HR HPV), based on their occurrence or prevalence in cervical carcinomas. The presence, persistence and/or re-occurrence of HR HPV is a bad prognostic indicator. So far, thirteen HPV types are said to be HR HPV, namely HPV 56, 51, 58, 33, 52, 35, 31, 16, 68, 39, 59, 45 and 18. Those HR HPV, which have the highest prevalence, are HPV types 33, 31, 16, 45 and 18.
Other oncogenic HPV are considered to be Low Risk HPV (LR HPV), e.g., HPV2, HPV3, HPV6, HPV11, HPV13, HPV32, HPV40, HPV42, HPV43, HPV44, HPV57.
The clinical classification of HPV types into either the HR or the LR group might evolve, or slightly diverge from one author to another, as the classification of a given HPV into the LR group only stands for as long as this HPV type is not found to be associated with a cervical carcinoma.
For example, it is now contemplated that HPV53 and HPV66 probably are HR HPV (van Ham et al. 2005, J. Clin. Microbiol. Vol. 43, n°6, p. 2662-2667). Hence, the initial group of thirteen HR HPV might further increase to a number of at least 15 HPV types.
Other HPV have been described as oncogenic HPV, but without any definitive settlement on the issue of their HR or LR status, such as is the case for HPV67, HPV82, HPV85. Appropriate detection means are required to analyze their oncogenicity.
New, or yet unidentified, mucosal oncogenic HPV types may further arise.
Furthermore, HPV multi-infection, involving several types of HPV, is a common situation: multi-infection is thought to account for about 20% of the HPV infection cases. An HPV multi-infection case may involve HPV types, which all are oncogenic HPV, or which comprise at least one oncogenic HPV and at least one non-oncogenic HPV. An HPV multi-infection case may involve HPV types, which all are mucosal HPV types, or may involve at least one mucosal type and at least one cutaneous type.
Also, co-infection may also occur, which involves at least one HPV and at least one virus other than HPV, e.g., a co-infection with at least one HPV, and at least one HIV.
Such multi- and/or co-infection situations render accurate HPV detection much more difficult.
HPV primers and probes, which are suitable for the detection of mucosal oncogenic HPV, have been disclosed in prior art.
The first techniques that were developed involved type-specific probes, which were designed to detect oncogenic HPV by direct hybridization of a type-specific probe to a non-amplified HPV genome, e.g., by Southern blotting or dot blotting.
Signal-amplified tests have then been developed, such as the Hybrid Capture test (HC2®) of Digene Corporation, Gaithersburg, Md., USA. The HC2® test has been approved by the FDA, and is at present time the reference test for clinical diagnosis.
The HC2® system is a liquid phase microplate system using DNA/RNA hybridization assay, which does not comprise any target amplification: viral DNA hybridizes in liquid phase to a RNA probe which targets the 13 HR HPV, the hybrids thus formed being detected by anti-DNA/RNA antibodies and visualized by chemoluminescence.
The HC2® test is a sensitive assay. It however is only of qualitative value. Viral loads assessed by the HC2® test does not increase with increasing grade of SIL, and are not sufficiently reliable in case of multiple HPV infections. Hence, the HC2® test is not a quantitative assay.
As the HC2® test does not reflect the viral load initially contained in the analyzed sample, it is recommended to combine it with classic cytology, to distinguish the cases with high grade lesions from those without high grade lesions.
Amplification methods have then been developed, wherein HPV target(s) is(are) amplified by at least one primer pair, the amplicon thus produced being detected either by this (labelled) primer pair or by a probe.
Such prior art primers have first been designed as general consensus primers, which are intended for amplifying several HPV, usually several of the thirteen HR HPV, as well as other HPV (oncogenic LR, and sometimes also non-oncogenic HPV).
Such consensus primers are also referred to as “universal” primers. These consensus primers target conserved regions in the HPV L1 gene (e.g., the MY09/MY11/HMB01 primers, the GP5+/GP6+ primers, the PGMY09/PGMY11 primers, and the SPF1/SPF2 or SPF10 primers), or the E1 ORF region (e.g., the CPIIG/CPI primers described in Tieben et al. 1993, J. Virol. Methods 42:265-279).
To render consensus PCR applicable to clinical diagnosis, HPV probes have been developed to detect and type HPV amplicons generated by consensus primer sets. Detection of the HPV amplicons generated by consensus primers is usually performed by a reverse hybridization line blot assay, or by calorimetric microtiter plate-based enzyme immunoassay.
Illustrative of such consensus PCR methods are the INNO-LiPA HPV test (Innogenetics, Gent, Belgium), and the Amplicor HPV test (Roche Molecular Systems, Branchburg, N.J., USA).
The INNO-LiPA HPV test is a reverse hybridization line probe assay, the prototype research version of which has been described in Kleter et al., 1999 (Journal of Clinical Microbiology, vol. 37, n°8, p. 2508-2517), and Kleter et al. 1998 (American Journal of Pathology, vol. 153, n°6, p. 1731-1739),
Briefly, a PCR primer set is used to generate a short PCR fragment (SPF PCR) of 65-bp from the L1 open reading frame. The prototype research INNO-LiPA primer set consists of 10 biotinylated primers (referred to as the SPF10 primer set), namely the six primers of the SPF1/2 system (described in Kleter et al. 1998), and four additional primers (MY09/11 and GP5+/6+).
The SPF10 amplimers are denatured, and incubated under hybridization conditions with poly(dT)-tailed type-specific oligonucleotide probes, which are immobilized as parallel lines on nitrocellulose membrane strips. The probe strips are then washed out for detection of the retained hybrids.
The INNO-LiPA HPV test allows the detection of at least 25 HPV genotypes (the 13 HR HPV, i.e., HPV 56, 51, 58, 33, 52, 35, 31, 16, 68, 39, 59, 45, 18, as well as other HPV, e.g., HPV 6, 11, 34, 40, 42, 43, 44, 53, 66, 70, and 74). It is a genotyping line probe assay, and is of qualitative value. The INNO-LiPA HPV test is not a quantitative assay.
The Amplicor HPV test uses amplification of target HPV DNA by PCR followed by nucleic acid hybridization for the detection of the thirteen HR HPV. The Amplicor HPV test amplifies a sequence of about 165 bp within the L1 region. The primer sets consist of 12 primers, which have been designed as general consensus primers, to amplify the initial group of 13 HR HPV. After amplification and denaturation, the amplified HPV sequences are distributed in a microwell plate, and incubated with L1 capture probes, the hybrids being detected and visualized by colorimetric enzyme immunoassay (avidin-horseradish peroxidase conjugate).
The Amplicor HPV test has been reported as being of higher analytical specificity, compared to the HC2® test (less false negative results, see Poljak et al. 2005, Acta Dermatoven APA, vol. 14, n°4, p. 147-152).
The Amplicor HPV test is sensitive, but its HPV spectrum is restricted to those 13 HPV, which have been initially considered as being the HR HPV. For example, the Amplicor HPV test does not detect HPV66 and HPV53, which are now thought to be HR HPV. In other words, the Amplicor test is not designed to be adaptive to any change or evolution in HPV classification or knowledge.
Furthermore, the Amplicor HPV test is not a quantitative assay.
These line blot or microwell-based prior art techniques use consensus HPV primers, i.e., primers which result from sequence alignment of a pre-determined set of selected oncogenic HPV, and from the determination of those consensus sequences, which have a sufficient similarity or identity score with all of the selected HPV, to hybridize to all of them. Consensus primers are thus designed to amplify a predetermined sub-set of oncogenic HPV, and may not succeed in amplifying other oncogenic HPV (such as HR new corners, or non-HR oncogenic HPV).
Such a consensus approach is restricted by the possibility of determining primer sequences, which would still sufficiently hybridize to the ever increasing and ever evolving desired targets.
If one or several new oncogenic HPV strain(s) appear, such prior art consensus primers might give false negative results.
Also, none of the prior art line blot or microwell-based techniques is of a quantitative nature, whereas recent findings show that the HPV copy number accounts for the phase and/or severity of the disease, and/or have a diagnostic and/or prognostic value in the field of oncogeny.
Absence of quantitative performance limits the spectrum of clinical applicability, as such tests cannot give information on the actual cancer risk level, or on the actual cancer grade.
Moreover, according to these prior art consensus line blot or microwell-based techniques, the detection step is an additional and tedious step, which has to be performed as a separated step after amplification has occurred.
Real-time PCR amplification techniques have recently been developed for the detection of HPV16 or HPV18 (Hesselink et al. 2005, Journal of Clinical Microbiology, vol. 43, n°9, p. 4868-4871; Gravitt et al. 2003, Cancer Epidemiology, Biomarkers & Prevention, vol. 12, p. 477-484).
These real-time PCR either are based on FRET (LightCycler), or use TaqMan probes (Applied Biosystems).
Compared to prior art line blot or microwell-based techniques, such real-time PCR have the advantage of combining amplification and detection in one single step, and of opening the way to quantification.
For example, van Duin et al. 2002 (Int. J. Cancer, vol. 98, n°4, p. 590-595) describes a quantitative real-time PCR assay for the detection of HPV16.
Prior art real-time PCR protocols however are type-specific PCR protocols, which are limited to the detection of only one HPV per amplification run, and more particularly to the sole detection of HPV16 or HPV18. They thus represent valuable research tool, but have a very limited clinical applicability.
Attempts have been made to develop multiplex real-time PCR amplification of HPV. These attempts are however limited to duplex or triplex real-time PCR for the detection of HPV16, HPV18, HPV45. For example, Szuhai et al. 2001 (American Journal of Pathology, 159(5): 1651-1660) disclose seven type-specific to molecular beacons, which are said to be type-specific molecular beacons, namely five HR HPV molecular beacons (HPV16, 18, 31, 33, 45) and two LR HPV molecular beacons (HPV6, 11); see table 1 of Szuhai et al. These molecular beacons are described as being useful for the detection of amplicons generated by the CPI/CPIIG “universal” primers. Multiplex attempts are disclosed in Szuhai et al., but are limited to duplex or triplex assays (HPV16, HPV18, HPV45). The authors explicitly indicate that “although the multiplexing capacity of molecular beacon PCR is higher than three, it is unlikely that it will approach the number of different HPV genotypes” (see page 1656, right-hand column, second paragraph). For this reason, the authors came to the conclusion that type-specific molecular beacons cannot by their own solve the problem of HPV clinical diagnosis, and that they shall be used in combination with a general pre-screening HPV detection method, to arrive at a two-step HPV detection and genotyping strategy (see e.g., FIG. 6 of Szuhai et al.), wherein type-specific HPV molecular beacon PCR is disclosed to be used in combination with a SybrGreen general primer PCR pre-screening.
Hence, to the best of the inventors' knowledge, prior art does neither describe nor suggest any real-time amplification technique that could be worked in multiplex, whilst retaining the required HPV detection specificity, which would allow to cover at least the 13 HR HPV in a single step (amplification+detection) run. Furthermore, to the best of the inventors' knowledge, prior art does not describe any quantitative real-time HPV amplification technique, which would allow to cover at least the five most common HR HPV (namely, HPV16, 18, 45, 31 and 33), preferably at least the 13 HR HPV, more preferably at least the 13 HR HPV as well as five other oncogenic HPV, in a single step (amplification+detection) run, and which would be quantitative, even when implemented in multiplex.
ABSTRACT OF THE INVENTION
The present invention relates to the detection of HPV by amplification, more particularly of mucosal-type HPV, still more particularly of HPV, which can be oncogenic for the mucosal epithelia.
The present invention allows the detection of at least the five most common HR HPV (HPV16, 18, 45, 31, 33), preferably at least 7 HR HPV, still preferably the five most common HR HPV as well as at least two other HR HPV, advantageously at least two other HR HPV belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18), more preferably at least the 13 HR HPV (HPV 56, 51, 58, 33, 52, 35, 31, 16, 68, 39, 59, 45, 18), most preferably at least the 13 HR HPV and five other oncogenic HPV (HPV66, 53, 82, 67, 85).
The present invention relates to amplification primer systems, and to detection probe systems, as well as to the amplification-detection systems (i.e. real-time amplification systems), which result from the combination of at least one amplification primer system of the invention and at least one detection probe system of the invention.
The present invention also relates to reference template HPV sequences, which are suitable for the production of amplification primers and detection probes of the invention, as well as to amplicons obtainable by amplification of an HPV nucleic acid with at least one amplification primer system of the invention, and optionally by detection with at least one detection probe system of the invention.
The present invention further relates to the biological and pharmaceutical applications thereof, more particularly to the diagnostic and prognostic applications thereof, notably in the field of CIN and cervical cancer.
The HPV amplification method of the invention is based on an approach of HPV tropism and oncogenicity, which is completely different from, and completely innovative compared to prior art approaches: contrary to the global consensus approaches, or to the type-specific approaches, which prior art methods have up to now followed, the present inventors have designed and built an approach, which is an HPV group-based approach (see the phylogenetic tree shown in FIG. 1, which has been built by the present inventors). According to the inventors' HPV group-based approach, amplification primer systems and detection probe systems are provided for each HPV group that comprises at least one HPV type capable of being oncogenic for the mucosal epithelia, namely at least for each of groups A6, A5, A9 and A7.
Indeed, the present inventors have selected appropriate targets within each of said HPV groups, which are suitable for the production of primers and probes covering
at least the five most common HR HPV (namely, HPV16, 18, 45, 31 and 33),
preferably at least 7 HR HPV, still preferably the five most common HR HPV as well as at least two other HR HPV, advantageously at least two other HR HPV belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18), more preferably at least the 13 HR HPV, most preferably at least the 13 HR HPV and five other oncogenic HPV (HPV66, 53, 82, 67, 85), in a single step (amplification+detection) run.
The selected targets of the present invention are reference template sequences, which allow designing and building primers (hybridizing to one end of said selected targets, or to the complementary sequence thereof), as well as amplicon-annealing probes, which allow to cover said HPV in a single step (amplification+detection) run.
The amplification primer systems of the present invention are targeted to the HPV of group A6 or A5 or A9 or A7, and are intended to amplify as many HPV types belonging to one of these groups as possible.
The detection probe systems of the present invention allow the detection of one or several of the amplicon(s) obtainable by amplification of a given HPV by an amplification system of the present invention. They are targeted to group(s) A6 and/or A5 and/or A9 and/or A7, and are especially adapted to implementation in real-time with said amplification primer systems.
The detection probe systems of the invention comprise probes, which allow for the general detection of at least one HPV that belongs to the HPV set formed by groups A6 and A5 and A9 and A7, as well as more precise detections, such as:

    
    
        the detection of at least one HPV that belongs to group A6 or A5 or A9 or A7, or
        the detection of at least one HPV that belongs to a sub-set of group A6 HPV, or of group A5 HPV, or of group A9 HPV, or of group A7 HPV, or
        the detection of at least one particular HPV type.
    
    


The present invention thereby provides a great flexibility of precision levels for the detection of HPV. Such flexibility has, to the best of the inventors' knowledge, never has been previously attained.
The present invention further provides A6- and/or A5- and/or A9- and/or A7-targeted systems, resulting from the combination of at least one amplification primer system of the invention and at least one detection probe system of the invention.
The present invention more particularly provides A6- or A5- or A9- or A7-targeted systems, which comprise at least one amplification primer system of the invention and at least one detection probe system of the invention, wherein said at least one amplification primer system and said at least one detection probe system are targeted to the same group, i.e., A6 or A5 or A9 or A7.
Most of the amplification primer and/or detection probe systems of the present invention comprise more than two primers and/or more than one probe. Hence, most of the amplification primer and/or detection probe systems of the invention, and notably the A9-targeted systems, and the A7-targeted systems, already are by themselves multiplex systems.
According to a very advantageous feature of the present invention, the group-targeted systems of the present invention are suitable for use together in a single-tube amplification, i.e., the present invention allows for implementation of at least one A6-targeted system, and at least one A5-targeted system, and at least one A9-targeted system, and at least one A7-targeted system, together in a single-tube assay, thereby resulting in what could be called a multi-multiplex, i.e., a “megaplex” amplification and/or detection: see e.g., in the examples below, illustrative “megaplex” involving 17 primers and 12 probes, which are capable of amplifying and detecting seventeen oncogenic mucosal-type HPV in a single-tube assay, without any significant loss in specificity, and without any significant loss in sensitivity.
Hence, the amplification primer systems and detection probe systems are specifically adapted to real-time multiplex amplification.
To the best of the inventors' knowledge, there is no prior art method, which would allow for a real-time multiplex amplification of at least the five most common HR HPV, preferably at least 7 HR HPV, still preferably the five most common HR HPV as well as at least two other HR HPV, advantageously at least two other HR HPV belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18), more preferably at least the 13 HR HPV.
Advantageously, the present invention allows for the detection of at least 18 oncogenic mucosal-type HPV in a single-tube assay, namely the 13 HR HPV, as well as five other oncogenic HPV (HPV66, 53, 82, 67, 85).
A further advantageous aspect of the present invention is that it is especially adapted to HPV viral load quantification. The HPV method of the invention is able to remain specific and quantitative, even when implemented in a single-tube multiplex.
The amplification primer systems and detection probe systems are specifically adapted to real-time quantitative multiplex amplification, and retain this capacity even when implemented in a “megaplex” mode comprising at least one A6-targeted system, and at least one A5-targeted system, and at least one A9-targeted system, and at least one A7-targeted system, together in a single-tube assay.
To the best of the inventors' knowledge, there is no prior art method, which would allow for a real-time quantitative multiplex amplification of said at least five most common HR HPV, preferably at least 7 HR HPV, still preferably the five most common HR HPV as well as at least two other HR HPV, advantageously at least two other HR HPV belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18), more preferably at least the 13 HR HPV, more preferably at least the 13 HR HPV and five other oncogenic HPV (HPV66, 53, 82, 67, 85).
The amplification primer systems and the detection probe systems of the invention all share the special technical feature of being designed and built according to a group-based approach of HPV oncogenicity, and of being suitable for implementation together in a the same assay tube.
More particularly, they enable a real-time “megaplex” implementation covering at least the five most common HR HPV types, preferably at least 7 HR HPV (e.g., HPV 56, 51, 33, 31, 16, 45, 18), still preferably the five most common HR HPV as well as at least two other HR HPV, advantageously at least two other HR HPV belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18), more preferably at least the 13 HR HPV, more preferably at least 18 oncogenic mucosal-type HPV (i.e., at least the 13 HR HPV, and five other oncogenic HPV, e.g., HPV66, 53, 82, 67, 85), in a single-tube assay, without any significant loss in the qualitative accuracy of the HPV detection.
The amplification primer systems and the detection probe systems of the invention further show levels of specificity, Ct and sensitivity, which are sufficiently homogeneous to allow for a real-time “megaplex” amplification, which is of quantitative value.
The group-based approach of the present invention further provides flexibility to the amplification and/or detection systems, as their intrinsic design is likely to make them suitable for detection of any oncogenic HPV “new corner” that may arise by mutagenesis.
The group-based approach of the present invention also confers flexibility in the use for clinical diagnosis: depending on the choice of probe system(s) that is made by the user, the precision level in HPV detection can range from a general response indicating the detection of at least one HPV belonging to the set formed by groups A6 and A5 and A9 and A7, to the very precise response indicating the detection of at least one particular HPV type. To the best of the inventors' knowledge, such flexibility has up to now never been attained.
The group-based approach of the present invention further is suitable for providing accuracy in case of multi- and/or co-infections.
It is believed that such an achievement represents a technological breakthrough, compared to prior art HPV detection systems.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1: phylogenic tree of the present invention;
FIGS. 2A and 2B: schematic presentation of the amplification targets for HPV groups A6 (HPV56) and A5 (HPV51) (FIG. 2A), and for groups A9 (HPV16) and A7 (HPV18) (FIG. 2B);
FIG. 3: reprint of NCBI—001594.1, sequence of HPV56 (reference HPV for group A6); SEQ ID NO:420;
FIG. 4: reprint of NCBI—001533.1, sequence of HPV51 (reference HPV for group A5); SEQ ID NO:421;
FIG. 5: reprint of NCBI—001526.1, sequence of HPV16 (reference HPV for group A9); SEQ ID NO:422;
FIG. 6: reprint of NCBI—001357.1, sequence of HPV18 (reference HPV for group A7); SEQ ID NO:423;
FIG. 7: convention for positions, which is followed in present application.



All sequences, including reverse primers, are listed in their 5′ to 3′ orientation. Start and stop positions on a reference HPV sequences are given in increasing value order. Hence:

    
    
        concerning primers: start and stop positions are either the start and stop positions of the reference HPV fragment, to which the sequence of the primer corresponds (case of forward primer), or the start and stop positions of the reference HPV target fragment, to which the primer anneals (case of the reverse primers);
        with regards to the probes: as a probe and its complementary sequence are, at least in simplex amplification, products, which have equivalent functions, the start and stop positions are either those of the reference HPV fragment, to which the sequence of the probe corresponds, or those of the reference HPV target fragment, to which the probe anneals.
    
    


DETAILED DESCRIPTION
The present invention is based on an approach, which is completely different from, and truly innovative, compared to prior art techniques. The invention overcomes the drawbacks of prior art techniques, and has numerous advantages, notably in terms of clinical applicability, performance, reliance and flexibility.
As mentioned in “the above background” section, prior art primers are designed either as type-specific primers, or as general consensus primers by classic alignment of as many mucosal HPV sequence as required, or desired, or as possible (e.g., by direct alignment of the 13 HR HPV).
On the contrary, the primers of the invention have been designed by HPV groups (=HPV genera).
Indeed, the present inventors analyzed the phylogeny of HPV, and have constructed the resulting phylogenic tree, which is shown in FIG. 1.
The present inventors selected one HPV sub-family, which is involved in carcinogenesis of the mucosal epithelia, namely sub-family A. They further selected a set of HPV types, which is representative of HPV sub-family A. This representative set consists in 35 different HPV types, among which 18 types are mucosal HPV, which are at least potentially oncogenic HPV (i.e., the 13 HPV known as the 13 HR; two potentially HR HPV -HPV53 and HPV66-; and three other HPV, which are believed to have an oncogenic potential -HPV82, HPV67 and HPV85-), the remaining 17 other HPV types being up to now known as being non-oncogenic HPV (see FIG. 1).
The inventors thus came to the conclusion that those HPV, which have a tropism for the mucosal epithelia, and which are at least potentially oncogenic HPV, are distributed among groups A6, A5, A9 and A7 (see FIG. 1). More precisely, said mucosal oncogenic HPV are distributed among:

    
    
        group A6, for HPV66, HPV56, HPV53;
        group A5, for HPV51, HPV82;
        group A9, for HPV58, HPV33, HPV67, HPV52, HPV35, HPV31, HPV16;
        group A7, for HPV68, HPV39, HPV85, HPV59, HPV45, HPV18.
    
    


By “HPV, which is at least potentially oncogenic”, it is meant that said HPV is either known to be oncogenic (such as those 13 HPV, which are usually referred to as the 13 HR HPV, as well as other oncogenic HPV, such as HPV66, HPV53, and HPV82), or which have been described at least by some authors as potentially oncogenic (such as HPV85), or which would be in the future described as associated to a tumorous mucosa.
The design by group is a special feature shared by all the products of the invention.
In addition to covering at least the five most common HR HPV types, preferably at least 7 HR HPV, still preferably the five most common HR HPV as well as at least two other HR HPV, advantageously at least two other HR HPV belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18), more preferably at least the thirteen HR HPV types, in a single-tube experiment, the means offered by the present invention is likely to detect any particular variant that a patient may have. Hence, the method of the invention is much safer than any prior art method.
In case of multiple HPV infections, several HPV types are present in the collected sample. A competitive effect may then be observed, wherein one HPV type takes prevalence over another one for the same consensus primer. Detection of the competed HPV may then be hampered, although the primer has initially been designed to hybridize to both HPV.
The present invention further has the advantage of enabling the analysis of multi- and/or co-infection cases, without any loss in specificity and sensitivity.
The present invention thus relates to amplification primer systems, to detection probes system, and to pharmaceutical compositions, biological compositions, and detection kits comprising at least one of said amplification and detection systems.
The present invention also relates to a method of HPV detection, which comprises the amplification of at least one HPV nucleic acid fragment, by at least one amplification primer system of the invention, and which optionally comprises the detection of the amplicon(s) thereby produced, by at least one detection probe system of the invention.
The HPV detection method of the invention is notably useful for the diagnosis of an HPV-related disease or condition, for the prognosis or risk assessment of such an HPV-related disease or condition, for monitoring of the evolution of an HPV-related disease or condition, for monitoring the efficiency of an anti-HPV drug or treatment, such as e.g., an anti-HPV vaccine or an anti-HPV vaccine candidate (e.g., an anti-HPV16 and/or anti-HPV18 and/or anti-HPV45 vaccine, or vaccine candidate).
Said HPV-related disease or condition is any disease or condition involving HPV, and more particularly an HPV-related neoplasia (e.g., cervical intraepithelial neoplasia) or cancer, such as a cervical cancer.
The present invention thus provides amplification primer systems and detection probe systems, which are targeted to the oncogenic HPV of group A6, and/or to the oncogenic HPV of A5, and/or to the oncogenic HPV of A9, and/or to the oncogenic HPV of A7.
Most of the amplification and/or detection systems of the present invention are multiplex systems, which comprises more than two primers and/or more than one probe. It is notably the case of the A9-targeted systems and of the A7-targeted systems.
Each amplification primer system can be implemented with an amplification primer system of another group in a single-tube amplification assay, without any significant loss in specificity. Hence, at least one A6-targeted amplification primer system of the present invention and at least one A5-targeted amplification primer system of the present invention and at least one A9-targeted amplification primer system of the present invention and at least one A7-targeted amplification primer system of the present invention, can be used together in a single-tube amplification assay, without any significant loss in specificity.
For each amplification primer system, the invention provides at least one detection probe system, thereby forming an amplification and detection system (i.e., a real-time amplification system).
Each detection probe system of the present invention can be implemented with its corresponding amplification primer system in a single-tube assay, without any significant loss in specificity, thereby allowing for a real-time HPV amplification and detection.
The present invention thus provides with group-targeted amplification and detection systems, namely:

    
    
        several A6-targeted amplification and detection systems,
        several A5-targeted amplification and detection systems,
        several A9-targeted amplification and detection systems,
        several A7-targeted amplification and detection systems.
    
    


Each amplification and detection system can be implemented with an amplification and detection system of another group in a single-tube amplification assay, without any significant loss in specificity, thereby allowing for a single-tube multi-multiplex (or “megaplex”) real-time amplification and detection of those HPV, which have a tropism for the mucosal epithelia, and which are at least potentially oncogenic HPV.
Hence, at least one A6-targeted amplification and detection system of the present invention, and at least one A5-targeted amplification and detection system of the present invention, and at least one A9-targeted amplification and detection system of the present invention, and at least one A7-targeted amplification and detection system of the present invention, can be used together in a single-tube amplification assay, without any significant loss in specificity.
Whilst the invention provides systems, which are especially adapted to multiplex or multi-multiplex implementation, the implementation of a system of the invention in simplex mode is of course also encompassed by the present invention.
The amplification and detection systems of the present invention further have levels of Ct and sensitivity, which are sufficiently homogeneous to allow for a quantitative HPV amplification and detection. The present invention thereby allows for the identification of the presence of one or several mucosal HPV in a single-tube assay, as well as for the determination of the viral HPV load(s). The quantitative property of the present invention is retained, even when it is implemented in a “megaplex” mode.
The invention thus relates to group-targeted amplification and/or detection systems, and to their use for the detection of mucosal HPV, said group-targeted amplification and/or detection systems sharing the special technical feature of being suitable for multiplex (in fact, multi-multiplex, i.e., “megaplex”) amplification and for real-time detection thereof, whereby these systems allow for the detection in a single-tube assay of at least the five most common HR HPV (i.e., HPV16, 18, 45, 31, 33),
preferably at least 7 HR HPV,
still preferably the five most common HR HPV as well as at least two other HR HPV, advantageously at least two other HR HPV belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18),
even still preferably at least the thirteen HPV known as HR HPV (HPV types 56, 51, 58, 33, 52, 35, 31, 16, 68, 39, 59, 45 and 18),
more preferably, at least the thirteen HPV as well as at least one among HPV types 66, 82, 67, 85, and 53
still more preferably, at least the thirteen HPV as well as at least two among HPV types 66, 82, 67, 85, and 53
even still more preferably, at least the thirteen HPV as well as at least three among HPV types 66, 82, 67, 85, and 53
most preferably, at least the thirteen. HPV as well as at least four among HPV types 66, 82, 67, 85, and 53, notably of least the seventeen mucosal HPV, consisting of said 13 HR HPV and HPV types 66, 82, 67, 85,
still most preferably, at least the thirteen HPV as well as at least the five HPV types 66, 82, 67, 85, and 53.
The group-targeted amplification and/or detection systems of the present invention further share the special technical feature of allowing such a real-time “megaplex” amplification to be quantitative.
As above-mentioned, the amplification and detection systems of the present invention are based on a truly innovative group-based approach.
Indeed, according to prior art general consensus techniques, the design of the primers (also referred to as “universal” primers) is made by alignment of all HPV sequences to be amplified, e.g., the 13 HR HPV, and determination of consensus sequences, which targets as many of the 13 HPV as possible. Hence, such consensus sequences are found in a conserved gene or region, such as a gene of late coding region (e.g., gene L1), and the same conserved gene or region is selected for the whole set of HPV to be amplified.
On the contrary, the present inventors made a design per HPV group, i.e., they selected appropriate targets for each HPV group. More particularly, they selected to genes of the early coding region, more particularly genes E1, E2, E6, E7. The present inventors have designed particular targets for each the desired HPV groups.
For example, the primers, which have been designed for group A5, have their target within genes E7, E1; the primers, which have been designed for group A6, have their target within genes E6, E7; the primers, which have been designed for group A7, have their target within gene E1; and the primers, which have been designed for group A9, have their target within genes E1, E2. Illustrative targets of the invention are shown in FIGS. 2A (groups A5 and A6) and 2B (groups A7 and A9).
Hence, the present inventors selected reference template sequences for each of groups A5, A6, A7 and A9, wherein the A5 reference template sequences are within the region consisting of genes E7 and E1, the A6 reference template sequences are within the region consisting of genes E6 and E7, the A7 reference template sequences are within gene E1, and the A9 reference template sequences are within the region consisting of genes E1 and E2.
The primers are designed and built to hybridize to one end of said targets (or to the complementary sequence thereof), whereby a primer pair anneals to each end of said target (or to the complementary sequence thereof).
The probes are designed and built to anneal to one of said reference template sequences, whereby each probe anneals to at least one of the amplicons generated by a primer system of the invention.
An amplification primer system of the invention comprises at least two primers.
A detection probe system of the invention comprises at least one probe.
The amplification primer systems of the invention preferentially amplify HPV that belong to group A6 or A5 or A9 or A7, i.e., oncogenic HPV.
The present inventors further succeeded in producing amplification primer systems, which are specific of the HPV set formed by groups A5 and A6 and A7 and A9. These amplification primer systems of the invention do not amplify any HPV that would belong to a group other than A5, A6, A7, A9. Indeed, most primer systems of the invention are specific of the HPV set formed by groups A6 and A5 and A9 and A7.
Moreover, most of amplification primer systems of the invention are specific of the group to which they are targeted, i.e., most primer systems of the invention are specific of group A6 or A5 or A9 or A7: most primers of a given amplification system amplify one or several HPV of the same HPV group, without amplifying any HPV that would belong to another HPV group.
Those primer systems of the invention, which are not specific of the HPV set formed by groups A5 and A6 and A7 and A9, may amplify nucleic acids that are not from an HPV of said groups, e.g., a non-oncogenic HPV. In such a case, these primer systems of the invention do however show a much lower amplification efficiency for these non-target amplicons (e.g., they lead to a PCR efficiency that is much lower than the one obtained for HPV of groups A5 and/or A6 and/or A9 and/or A7, and are therefore not quantitative).
When a group-targeted primer system of the invention is combined with a probe system of the invention that is targeted to the same group, the group-targeted real-time amplification system that results therefrom is specific of the HPV set formed by groups A5 and A6 and A9 and A7: none of such real-time amplification systems detects an HPV that would not belong to group A5 or A6 or A9 or A7. Furthermore, most of these real-time amplification systems are specific of the group to which they targeted.
Only one real-time amplification system of the invention has a cross-group reactivity: the real-time amplification primer system designed for group A9, which is referred to in the examples below as system C, detects the seven HPV types of group A9, and also HPV53, which is an oncogenic HPV belonging to group A6 (HPV53 being a potentially HR HPV); this group A9 system C does however not detect any other HPV among the 42 HPV tested (no group A6 HPV other than HPV53; no group A5 HPV; no group A11 HPV; no group A7 HPV, no group A4 HPV; no group A3 HPV).
In any case, does a real-time amplification system of the present invention detect a nucleic acid that would be a human nucleic acid.
When it is desired to amplify any HPV, which belongs to group A6, A5, A9, or A7, most of the amplification primer systems of the present invention will in fact comprise more than two primers, i.e., at least three primers.
For example, the amplification primer systems, which are targeted to group A6 or A5, only require a primer pair to amplify HPV56 and optionally HPV66 (for group A6), or HPV51 and optionally HPV82 (for group A5). But, those amplification primer systems, which are targeted to group A9 or A7, have to amplify six or seven HPV types of group A9, or five or six HPV types of group A7, if a complete coverage of the HPV spectrum of the group is desired. Under such instances, an A9- or A7-targeted amplification system of the invention may comprise e.g., at least three or four forward primers, and two, three, four, five or more reverse primers. Such A9- or A7-targeted amplification primer systems therefore are already multiplex systems by themselves.
Of course, the skilled person, who would like to restrict the spectrum of amplified HPV, might select fewer forward and/or reverse primers, depending on which HPV types or strain he/she would like to amplify.
Similarly, when it is desired to detect any HPV, which belongs to group A6, A5, A9, or A7, most of the detection probe systems of the present invention will in fact comprise more than one probe, i.e. at least two probes.
For example, the detection probe systems, which are targeted to group A6 or A5, only require probe to detect HPV56 and optionally HPV66 (for group A6), or HPV51 and optionally HPV82 (for group A5). But, those detection probe systems, which are targeted to group A9 or A7, may comprise one probe per HPV type or strain to be detected, notably when a both a complete coverage of the HPV group spectrum, and a simultaneous HPV group or type discrimination are desired. An A9- or A7-targeted detection probe system may thus comprise at least four probes, for example four, five or six probes.
As above-mentioned, all detection probe systems of the present invention are adapted to real-time detection, and can thus be implemented with their corresponding amplification primer systems in the very same tube.
In the examples below, are described several A6-, A5-, A9 and A7-targeted amplification and/or detection systems of the invention.
In these examples, are shown table 12 to table 88:

    
    
        tables 12-35: these tables gives the SEQ ID NO: and positions of the reference amplicons (the sequences of these reference template amplicons are also listed after the last table, i.e., before the “claims” section), the forward primers, the reverse primers, the probes, the beacons probes of illustrative group-targeted systems of the invention;
        tables 35-50: these tables show the number of nucleotide mismatches shown by primers and probes of the invention (alignment of the sequences of 50 HPV types); an empty box indicates there is no coherent sequence alignment;
        tables 51-68: specificity of the detection systems of the invention;
        tables 69-82: system sensitivity;
        tables 83-88: “megaplex” specificity and sensitivity,
        table 89: list of HPV genome sequences.
    
    


A reference genome has been elected for each HPV group, namely:

    
    
        for group A5: the reference genome is the genome sequence of HPV51 available under accession number NC—001533.1,
        for group A6: the reference genome is the genome sequence of HPV56 available under accession number NC—001594.1,
        for group A7: the reference genome is the genome sequence of HPV18 available under accession number NC—001357.1,
        for group A9: the reference genome is the genome sequence of HPV16 available under accession number NC—001526.1,
    
    


In the following tables, the term <<address>> means a nucleotide position in the reference genome. More precisely:

    
    
        a forward primer having an address X is an isolated oligonucleotide, which has a sequence which is the sequence of a fragment of the reference genome starting at position X in said reference genome, or a variant of such a fragment sequence (see the mismatch count tables below),
        a reverse primer having an address X is an isolated oligonucleotide, which has a sequence which is complementary to the sequence of a fragment of the reference genome ending at position X in said reference genome, or a variant of such a fragment sequence (see the mismatch count tables below),
        a probe having an address X is an isolated oligonucleotide, the sequence of which is the sequence of a fragment of the reference genome starting at position X in said reference genome, or which is the complementary sequence of such a fragment sequence (over the entire length of this fragment sequence), or a variant of such a fragment sequence or of such a complementary fragment sequence (see the mismatch count tables below).
    
    


As a consequence, when a primer pair, which is selected from a given system, to consist of a forward primer having the address Xf, and of a reverse primer having the address Xr, is implemented on its reference HPV genome under conditions favorable to nucleic acid amplification, this primer pair then amplifies from said HPV reference genome an amplicon, which consists of the sequence that extends from position Xf to position Xr in said reference HPV genome (start and stop positions included).
When this primer pair is, under conditions favorable to nucleic acid amplification, implemented on a given HPV genome, which is not its reference HPV genome, but which belongs to the same group as this reference HPV genome, this primer pair then amplifies from said given HPV genome an amplicon, which consists in the sequence of the fragment of said given HPV genome, which corresponds by sequence alignment to the fragment that extends from position Xf to position Xr in said reference HPV genome.
A fragment. A, which is a fragment of a given HPV genome and, which corresponds by sequence alignment to a fragment B of a HPV reference genome, means that said fragment A has the same length as said fragment B, and that the start and stop positions of said fragment A within said given HPV genome are such that, among those fragments of said given HPV genome, which have the same length as said fragment B, said fragment A is the fragment, which gives the best identity score when compared to the nucleotide sequence of said fragment B, as determined by global alignment to the nucleotide sequence of fragment B.
It will also be understood that:

    
    
        a forward primer having an address Xf and a length Lf is an isolated oligonucleotide, which has a sequence which is the sequence of a fragment of the reference genome starting at position Xf in said reference genome, and ending at position Xf+Lf−1 in said reference genome, or a variant of such a fragment sequence (see the alignments shown below),
        a reverse primer having an address Xr and a length Lr is an isolated oligonucleotide, which has a sequence which is complementary to the sequence of a fragment of the reference genome starting at position Xr−Lr−1, and ending at position Xr in said reference genome, or a variant of such a fragment sequence (see the alignments shown below),
        a probe having an address Xp and a length Lp is an isolated oligonucleotide, the sequence of which is the sequence of a fragment of the reference genome starting at position Xp and ending at position Xp+Lp−1 in said reference genome, or which is complementary to such a fragment sequence, or a variant of such a fragment sequence or of such a complementary fragment sequence (see the alignments shown below).
    
    


The present invention thus relates to a process for the nucleic acid amplification of at least one HPV target, wherein said HPV is an HPV, which has a tropism for the mucosal epithelia, and which is at least potentially oncogenic, preferably at least one oncogenic anogenital HPV target, most preferably at least one oncogenic cervical HPV. The amplification process of the invention comprises the step of producing from said at least one HPV target at least one amplicon by means of at least two primers.
According to an advantageous embodiment of the present invention, the amplification process of the present invention can be a real-time multiplex amplification process, involving at least one probe that can anneal to the amplicon(s) generated by said t least two primers.
The present invention relates to a process for the detection of at least one HPV, which has a tropism for the mucosal epithelia, and which is an at least potentially oncogenic HPV, preferably at least one oncogenic anogenital HPV, most preferably at least one oncogenic cervical HPV, in a sample. The detection process of the present invention comprises the detection of at least one nucleic acid HPV target which has been amplified by the process of nucleic acid amplification of the invention.
The present invention relates to a process for the detection of at least one HPV, which has a tropism for the mucosal epithelia, and which is an at least potentially oncogenic HPV, preferably at least one oncogenic anogenital HPV, most preferably at least one oncogenic cervical HPV, in a sample, by determination of whether at least one amplicon has been, or is produced from said sample, or from nucleic acid material thereof, by amplification by means of at least two amplification primers of the invention, and/or at least one amplification primer system of the invention.
The production of at least one amplicon indicates that at least one HPV, which has a tropism for the mucosal epithelia, and which is at least potentially oncogenic, preferably at least one oncogenic anogenital HPV, most preferably at least one oncogenic cervical HPV, is present in said sample.
According to an advantageous embodiment of the present invention, the determination of whether at least one amplicon is produced can be carried out in real-time multiplex amplification, preferably with at least one probe of the invention and/or at least one probe system of the invention.
The present invention thus relates to a process for the detection of at least one HPV, which has a tropism for the mucosal epithelia, and which is at least potentially oncogenic, preferably at least one oncogenic anogenital HPV, most preferably at least one oncogenic cervical HPV, in a sample, which comprises:

    
    
        contacting said sample, or nucleic acid material thereof, with at least two amplification primers of the invention and/or at least one primer system of the invention, under conditions suitable to the production of at least one amplicon by said primers (i.e., under conditions, which would be suitable to the production by said primers of at least one amplicon from said at least one HPV to be detected, if this HPV were present in said sample),
        determining whether at least one amplicon has been produced, or is produced by said primers (e.g., by means of at least one detection probe, preferably in real-time amplification involving at least one probe of the invention and/or at least one detection probe system of the invention).
    
    


The production of at least one amplicon indicates that at least one HPV, which has a tropism for the mucosal epithelia, and which is an at least potentially oncogenic HPV, preferably at least one oncogenic anogenital HPV, most preferably at least one oncogenic cervical HPV, is present in said sample.
By “sample containing nucleic acid material”, it is meant any sample, which contains at least one nucleic acid, e.g., a biological sample, such as a sample which has been collected from a cell culture, or from an animal or a human being, e.g., from a female human being, preferably a sample which has been collected from a uterine cervix.
Said sample may optionally have been further treated and/or purified according to any technique known by the skilled person, to improve the amplification efficiency and/or qualitative accuracy and/or quantitative accuracy. The sample may thus exclusively, or essentially, consist of nucleic acid(s), whether obtained by purification, isolation, or by chemical synthesis. Means are available to the skilled person, who would like to isolate or purify nucleic acids, such as DNA, from a biological sample, for example to isolate or purify DNA from cervical scrapes (e.g., QIAamp-DNA Mini-Kit; Qiagen, Hilden, Germany).
Hence, the detection method of the present invention enables the real-time multiplex detection, preferably the real-time quantitative multiplex detection of: at least the five most common HR HPV (i.e., HPV16, 18, 45, 31, 33),
preferably at least 7 HR HPV,
still preferably the five most common HR HPV as well as at least two other HR HPV, advantageously at least two other HR HPV belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18),
even still preferably at least the thirteen HPV known as HR HPV (HPV types 56, 51, 58, 33, 52, 35, 31, 16, 68, 39, 59, 45 and 18),
more preferably, at least the thirteen HPV as well as at least one among HPV types 66, 82, 67, 85, and 53
still more preferably, at least the thirteen HPV as well as at least two among HPV types 66, 82, 67, 85, and 53
even still more preferably, at least the thirteen HPV as well as at least three among HPV types 66, 82, 67, 85, and 53
most preferably, at least the thirteen HPV as well as at least four among HPV types 66, 82, 67, 85, and 53, notably of least the seventeen mucosal HPV, consisting of said 13 HR HPV and HPV types 66, 82, 67, 85,
still most preferably, at least the thirteen HPV as well as at least the five HPV types 66, 82, 67, 85, and 53,
in a single-tube assay.
The present invention also relates to all the medical, biological, pharmaceutical applications of the detection method of the invention, and/or of the primers and/or probes of the invention.
The present invention thus relates to a process for the diagnosis or prognosis of cervical neoplasia or cancer, which comprises determining the presence, re-occurrence, persistence, or cellular spread of at least one HPV by the detection method of the invention, e.g., by implementing it on a sample, which may have been collected from a patient, whereby a positive determination indicates that there is a cervical neoplasia or cancer, or that there is a prevalent risk of such a condition or disease.
The present invention also relates to a process for monitoring the efficiency of an anti-HPV treatment or drug, or an anti-HPV candidate treatment or drug, such as an anti-HPV16 and/or 18 and/or 45 treatment, drug, candidate treatment or candidate drug, which comprises determining said treatment, drug, candidate treatment or candidate drug induces the non-reoccurrence, non-persistence, disappearance, or a decrease in cellular spread of at least one HPV by the detection method of the invention, whereby a positive determination indicates that said treatment, drug, candidate treatment or candidate drug is an efficient anti-HPV drug.
The present invention also relates to a method to produce an anti-HPV drug, which comprises:

    
    
        providing at least one anti-HPV candidate drug,
        administering said at least one candidate anti-HPV drug to a cell culture or to a non-human animal, wherein said cell culture or animal is or comprises at least one cervical neoplasia or cancer, and
        determining by the HPV detection method of the invention whether said candidate anti-HPV drug induces the regression or disappearance of said at least one neoplasia or cancer,

whereby a positive determination indicates that said candidate drug is an efficient anti-HPV drug.

    
    


As above-mentioned, the present invention thus provides HPV amplification and detection means, which can be implemented in real-time and in multiplex, i.e., which combine target amplification and detection in one single operative step, and which enables the detection of mucosal HPV in one single operative step, without any significant loss in specificity.
Furthermore, the amplification and detection systems of the invention have Ct and sensitivity levels, which are sufficiently homogeneous to allow for a real-time quantitative multiplex HPV detection.
According to the present invention, said amplification primers may comprise:

    
    
        at least two primers, which are intended for targeting oncogenic HPV of group A6, wherein said at least two A6-targeted primers are oligonucleotides, which consist of 14-30 nucleotides, preferably of 15-29, more preferably of 16-28, most preferably of 17-25 nucleotides, the sequences of which are suitable for use as forward and reverse primers, respectively, in the amplification of at least one nucleic acid of 90-390 nucleotides, preferably of 95-385 nucleotides, more preferably of 100-379 nucleotides, from the A6-target region consisting of the E6 and E7 genes of HPV56, and/or
        at least two primers, which are intended for targeting oncogenic HPV of group A5, wherein said at least two A5-targeted primers are oligonucleotides, which consist of 14-30 nucleotides, preferably of 15-29, more preferably of 16-28, most preferably of 17-25 nucleotides, the sequences of which are suitable for use as forward and reverse primers, respectively, in the amplification of at least one nucleic acid of at least 90-240 nucleotides, preferably of 100-230 nucleotides, more preferably of 106-225 nucleotides, from the A5-target region consisting of the E7 and E1 genes of HPV51, and/or
        at least two primers, which are intended for targeting oncogenic HPV of group A9, wherein said at least two A9-targeted primers are oligonucleotides, which consist of 14-30 nucleotides, preferably of 15-29, more preferably of 16-28, most preferably of 17-25 nucleotides, the sequences of which are suitable for use as forward and reverse primers, respectively, in the amplification of at least one nucleic acid of at least 80-260 nucleotides, preferably of 85-250 nucleotides, more preferably of 88-241 nucleotides, from the A9-target region consisting of the E1 and E2 genes of each of the following group A9 HPV: HPV58, HPV33, HPV52, HPV35, HPV31 and HPV16, preferably from the E2 gene of each of said group A9 HPV, and/or
        at least two primers, which are intended for targeting oncogenic HPV of group A7, wherein said at least two A7-targeted primers are oligonucleotides, which consist of 14-30 nucleotides, preferably of 15-29, more preferably of 16-28, most preferably of 17-25 nucleotides, the sequences of which are suitable for use as forward and reverse primers, respectively, in the amplification of at least one nucleic acid of at least 100-220 nucleotides, preferably of 120-215 nucleotides, more preferably of 125-209 nucleotides, from the A7-target region consisting of the E1 gene of each of the following group A7 HPV: HPV68, HPV39, HPV59, HPV45, and HPV18.
    
    


The nucleic acid which is amplified from said A6 or A5 or A9 or A7 target region corresponds in said HPV to the nucleic acid sequence of the A6 or A5 or A9 or A7 reference template, respectively. Hence, these amplified nucleic acids usually have a high degree of identity with their respective reference template sequences, e.g., an identity of at least 80%, preferably of at least 85%, more preferably of at least 90%, most preferably of at least 95%, over the entire length of said respective reference template sequence.
By nucleic acid, it herein preferably meant DNA.
Preferably, the at least two primers, which are intended for targeting one HPV group, are different from the at least two primers, which are intended for targeting the three other groups.
Said at least two A6-targeted primers may target a sequence, which is entirely within the E6 gene of each of said group A6 HPV (namely, HPV56), or which is entirely within the E7 gene of each of said group A6 HPV, or which overlap the E6 and E7 genes, for example with a forward primer targeting E6 and the reverse primer targeting E7, or conversely. Preferably, said at least two A6-targeted primers target a sequence, which overlap the E6 and E7 genes, for example with a forward primer targeting E6 and the reverse primer targeting E7, or conversely.
Said at least two A5-targeted primers may target a sequence, which is entirely within the E7 gene of each of said group A5 HPV (namely, HPV51), or which is entirely within the E1 gene of each of said group A5 HPV, or which overlap the E7 and E1 genes, for example with a forward primer targeting E7 and the reverse primer targeting E1, or conversely.
Said at least two A9-targeted primers may target a sequence, which is entirely within the E1 gene of each of said group A9 HPV (namely, of at least each of HPV58, HPV33, HPV52, HPV35, HPV31 and HPV16), or which is entirely within the E2 gene of each of said group A9 HPV, or which overlap the E1 and E2 genes, for example with a forward primer targeting E1 and the reverse primer targeting E2, or conversely. In the examples given below, all A9 amplification systems target the E2 gene, except system C, which has a target that overlaps the E1 and E2 genes.
Said at least two A7-targeted primers may target a sequence, which is entirely within the E1 gene of each of said group A7 HPV (namely, within the E1 gene of at least each of HPV68, HPV39, HPV59, HPV45, HPV18).
In accordance with the present invention, said at least two A6-, A5-, A9- and A7-targeted primers notably share the specific technical feature of being suitable for use in a real-time (quantitative) multiplex detection of HPV, which can be oncogenic for the mucosal epithelia.
By “consisting of 14-30 nucleotides”, it is meant “consisting of 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 nucleotides”.
The same applies mutatis mutandis to any range, which is recited in the present application.
The nucleotide lengths of the primers can be chosen independently from each other.
By oligonucleotide or primer, “the sequence of which is suitable for use in the amplification of” at least one HPV, or nucleic acid or sequence, it is meant that the sequence of the oligonucleotide or primer is such that they can hybridize to this HPV or nucleic acid or sequence, under conditions of moderate, but preferably high or very high stringency.
A primer of the invention may consist of a 1430 nt oligonucleotide (preferably a 17-25 nt oligonucleotide), the sequence of which has an identity of at least 80%, preferably of at least 85%, more preferably of at least 90%, most preferably of at least 92%, with a sequence of the same length contained in its group reference template sequence, most preferably with a sequence of the same length contained at the very 3′ end or at the very 5′ end of said group reference template sequence.
According to an advantageous embodiment of the present invention, said determination of whether at least one amplicon is produced can be carried out by using in real-time amplification at least one probe, preferably at least one A6-targeted probe and/or at least one at least one A5-targeted probe and/or at least one A9-targeted probe and/or at least one A7-targeted probe.
Preferably, said at least two A6-targeted primers are suitable for use in the amplification of more than one oncogenic HPV of group A6, namely at least HPV56 and at least one other oncogenic HPV of group A6 (e.g., HPV66, HPV53). According to the present invention, said at least two A6-targeted primers anneal to each of the group A6 HPV they target, in their E6 and/or E7 genes. Hence, according to an advantageous embodiment of the present invention, said at least two A6-targeted primers are oligonucleotides, the respective sequences of which are suitable for use as forward and reverse primers in the amplification of at least one nucleic acid from the region consisting of the E6 and E7 genes of each of the following group A6 HPV: HPV56 and HPV66. HPV66 is at present time not listed within the 13 HR HPV; some authors however consider that HPV66 could be a HR HPV.
Preferably, said at least two A5-targeted primers are suitable for use in the amplification of more than one oncogenic HPV of group A5, namely at least HPV51 and at least one other oncogenic HPV of group A5 (e.g., HPV82). According to the present invention, said at least two A5-targeted primers anneal to each of the group A5 HPV they target, in their E7 and/or E1 genes. Hence, according to an advantageous embodiment of the present invention, said at least two A5-targeted primers are oligonucleotides, the respective sequences of which are suitable for use as forward and reverse primers in the amplification of at least one nucleic acid from the region consisting of the E7 and E1 genes of each of the following group A5 HPV: HPV51 and HPV82.
Preferably, said at least two A9-targeted primers are suitable for use in the amplification of more than the six above-mentioned oncogenic HPV of group A9, namely at least HPV58, HPV33, HPV52, HPV35, HPV31 and HPV16, and at least one other oncogenic HPV of group A9 (e.g., HPV67). According to the present invention, said at least two A9-targeted primers anneal to each of the group A9 HPV they target, in their E1 and/or E2 genes. Hence, according to an advantageous embodiment of the present invention, said at least two A9-targeted primers are oligonucleotides, the respective sequences of which are suitable for use as forward and reverse primers in the amplification of at least one nucleic acid from the region consisting of the E1 and the E2 genes of each of the following group A9 HPV: HPV58, HPV33, HPV67, HPV52, HPV35, HPV31 and HPV16.
A group-targeted primer of the present invention may further target a HPV, which does not belong to the same group (as long as it does not target any group other than A6, A5, A7 or A9), i.e., an A9-targeted primer pair may target an HPV belonging to group A6 (such as HPV53), in addition to targeting the above-mentioned HPV of group A9. Hence, the respective sequences of said at least two A9-targeted primers may further be suitable for use as forward and reverse primers in the amplification of at least one nucleic acid of HPV53.
Preferably, said at least two A7-targeted primers are suitable for use in the amplification of more than the five above-mentioned oncogenic HPV of group A7, namely at least HPV68, HPV39, HPV59, HPV45, and HPV18, and at least one other oncogenic HPV of group A7 (e.g., HPV85). According to the present invention, said at least two A7-targeted primers anneal to each of the group A7 HPV they target, in their E1 gene. Hence, according to an advantageous embodiment of the present invention, said at least two A7-targeted primers are oligonucleotides, the respective sequences of which are suitable for use as forward and reverse primers in the amplification of at least one nucleic acid from the E1 gene of each of the following group A7 HPV: HPV68, HPV39, HPV85, HPV59, HPV45, and HPV18.
To the best of the inventors' knowledge, there is no prior art multiplex process, which would allow the detection of a mucosal oncogenic HPV other than HPV56, HPV51, HPV58, HPV33, HPV52, HPV35, HPV31 and HPV16, HPV68, HPV39, HPV59, HPV45, and HPV18. Until recently, these thirteen HPV were considered to be the 13 HR HPV (i.e., the 13 high risk HPV, i.e., the HPV which have the highest tumor prevalence). However, other HPV are now thought to belong to the HR HPV group, e.g., HPV66 and HPV53 (group A6). As prior art techniques, such as the HPV Amplicor test, are based on a global consensus design, additional HPV cannot be encompassed. On the contrary, the present invention is based on a design by group, and cover more than the 13 basic HR HPV, which is much safer for the patient, and which has the special advantage of being evolutive, in the sense that any oncogenic A6, A5, A9 and A7 new corner are likely to be taken into account.
Hence, to the best of the inventors' knowledge, the present invention has a mucosal oncogenic HPV spectrum, which is broadest than any other prior art technique, and has a bigger potential of adaptability to any evolution of HPV spectrum to be detected. The present invention therefore is safer than any other prior art technique.
The amplification primer systems of the invention preferentially amplify HPV that belong to group A6 or A5 or A9 or A7, i.e., oncogenic HPV.
As above-mentioned, most of amplification primer systems of the invention are specific of the HPV set formed by groups A5 and A6 and A7 and A9, and more particularly are specific of the group to which they are targeted, i.e., most primer systems of the invention are specific of group A6 or A5 or A9 or A7 (and do not amplify any HPV of groups A11 or A4 or A3).
Hence, said at least two primers can advantageously be specific of the HPV set formed by groups A5 and A6 and A7 and A9, and more particularly of group A6, or group A5, or group A9, or group A7, preferably of the oncogenic HPV of group A6, or group A5, or group A9, or group A7.
Hence, according to a preferred embodiment of the present invention, said at least two primers can have such sequences that they are not suitable for use as forward and reverse primers in the amplification of any nucleic acid from an HPV, which would not belong to group A6, A5, A9 or A7. According to a more preferred embodiment of the present invention, the respective sequences of said at least two primers therefore are not suitable for use as forward and reverse primers in the amplification of a nucleic acid from an HPV, which is not oncogenic, preferably which is not oncogenic for the mucosal epithelia, more preferably which is not an anogenital HPV, most preferably which is not a cervical HPV.
In other words, said at least two primers preferably are specific of oncogenic HPV, compared to non-oncogenic HPV.
The present invention can be implemented in simplex, multi-tube simplex, in multiplex, as well as in multi-multiplex (“megaplex”). According to an advantageous embodiment of the present invention, said amplification can be a single-tube multiplex amplification, or a single-tube multi-multiplex amplification (“megaplex”).
By “single-tube multiplex amplification” or “multiplex amplification”, it is herein meant any amplification reaction aiming at the amplification, and optionally the detection, of more than one target in the same tube. For instance, multiplex amplification include duplex amplification (two targets), triplex amplification (three targets), as well as higher multiplex amplification. Multiplex amplification includes amplification reactions with more than one primer pair, for instance two primer pairs. In this case, there might be four different primers, but it is also possible for the two primer pairs to have one primer in common, e.g., the forward primer, and to have two distinct reverse primers. Multiplex amplification and detection also includes amplification reactions with a unique primer pair, but with more than one probe.
Hence, according to the multiplex embodiment of the present invention, more than one primer pair is present in the amplification reaction mixture. As a very advantageous embodiment of the present invention, at least four, preferably at least six, more preferably at least eight primer pairs can be present in the amplification reaction mixture. Indeed, the primers of the invention allow for a multiplex amplification, without any significant specificity loss. Hence, all reagents can be placed in the same tube to carry out the amplification assay on the sample to be tested, whereby whatever mucosal oncogenic HPV is present in this sample, it will be detected in a single-step procedure.
Preferably, said amplification primers comprise said at least two A6-targeted primers, and at least two primers selected from:

    
    
        said at least two A5-targeted primers,
        said at least two A9-targeted primers, and
        said at least two A7-targeted primers.
    
    


Preferably, said amplification primers comprise said at least two A5-targeted primers, and at least two primers selected from:

    
    
        said at least two A6-targeted primers, and/or
        said at least two A9-targeted primers, and/or
        said at least two A7-targeted primers.
    
    


Preferably, said amplification primers comprise said at least two A9-targeted primers, and at least two primers selected from:

    
    
        said at least two A5-targeted primers, and/or
        said at least two A6-targeted primers, and/or
        said at least two A7-targeted primers.
    
    


Preferably, said amplification primers comprise said at least two A7-targeted primers, and at least two primers selected from:

    
    
        said at least two A5-targeted primers, and/or
        said at least two A9-targeted primers, and/or
        said at least two A6-targeted primers.
    
    


Most preferably, said amplification primers comprise:

    
    
        said at least two A6-targeted primers, and
        said at least two A5-targeted primers, and
        said at least two A9-targeted primers, and
        said at least two A7-targeted primers.
    
    


According to an advantageous embodiment of the present invention, said determination of whether at least one amplicon is produced, is carried out by means of at least one probe, which is intended to anneal to said at least one amplicon, i.e., the sequence of the probe is sufficiently complementary to said at least one amplicon (or to the complementary sequence thereof) that the probe can anneal to said at least one amplicon, preferably under conditions of moderate, high or very high stringency.
The probe(s) of the invention can be implemented in any appropriate format.
Preferably, the probe(s) of the invention is(are) not immobilized onto a solid support.
Most preferably, the probe(s) of the invention is(are) used in real-time amplification.
Hence, according to an advantageous embodiment of the present invention, said amplification can be a real-time amplification.
According to an advantageous embodiment of the present invention, said at least one probe is used in real-time amplification, i.e., said at least two primers and said at least two probes can be both present in the amplification reaction mixture, whereby said at least one probe anneal to the amplicon(s) produced by said at least two primers in real-time. In other words, the amplification and the detection can be carried out in a single step, namely in real-time amplification.
By real-time amplification, we hereby understand any amplification-based process allowing for monitoring of fluorescence emitted during the reaction as an indicator of amplicon production during each amplification cycle as opposed to the endpoint detection by conventional amplification process.
The present invention provides probes, which are intended to target the amplicon(s) obtainable by amplification of a mucosal oncogenic HPV nucleic acid by at least two A6- and/or A5- and/or A9- and/or A7-targeted primers.
These probes share the specific technical features of being suitable for use in a real-time multiplex amplification.
Some probes of the present invention allow to detect all the HPV of one group (i.e., they anneal to every amplicon that is obtainable by means of a group-targeted primer pair of the invention). Other probes of the present invention detect one or only some HPV of one group. Hence, the present invention further provides different levels of detection: the response can be a global detection of the presence or absence of at least one mucosal oncogenic HPV, or a more precise response, such as presence or absence of at least one mucosal oncogenic HPV of group A6 and/or A5 and/or A9 and/or A7, or an even more precise response such as presence or absence of at least one mucosal oncogenic HPV type(s).
Preferably, said determination of whether at least one amplicon is produced, is carried out by using in real-time amplification at least one A6- and/or A5- and/or A9- and/or A7-targeted probe, the sequence of which is suitable for use as a probe for the detection of at least one amplicon produced by said at least two A6- and/or A5- and/or A9- and/or A7-targeted primers, respectively.
According to an advantageous embodiment of the present invention, said amplification can be a real-time multiplex amplification.
According to a very advantageous embodiment of the present invention, said amplification can be carried out as a real-time multiplex amplification. Hence, the amplification reaction mixture can comprise more than two primers, and also at least one probe, without any significant loss of specificity in the detection of HPV. To the best of the inventors' knowledge, the present technique is the first to allow a real-time multiplex amplification. It is very advantageous, in the sense that any mucosal oncogenic HPV can be screened in a single tube assay, wherein all reactants (primers and probe(s)) have been poured. More particularly, the present invention provides A6-, A5, A9- and A7-targeted primers and probes, which can all be placed in the same reaction mixture, without any significant loss in specificity.
The present invention therefore is much easier-to-handle and much quicker than any prior art technique. It further limits the possibility of any experimental error or contamination in the sample analysis.
To the best of the inventors' knowledge, the present technique is the first to enable a real-time multiplex amplification, which allows to cover at least the five most common HR HP V (HPV16, 18, 45, 31, 33), preferably at least 7 HR HPV, still preferably the five most common HR HPV as well as at least two other HR HPV, advantageously at least two other HR HPV belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18), more preferably at least the 13 HR HPV, and as above-mentioned, most preferably at least 18 oncogenic HPV (namely, at least the 13 HR and five other oncogenic HPV, i.e., HPV 66, 53, 82, 67, 85).
According to an advantageous embodiment of the present invention, said amplification can be a quantitative real-time multiplex amplification.
According to an even more advantageous embodiment of the present invention, said amplification can be carried out as a quantitative real-time multiplex amplification. Indeed, the primers and probes of the present invention have such a sequence that there is no loss in specificity and no loss in quantitative accuracy, even when they are implemented in real-time multiplex amplification.
To the best of the inventors' knowledge, the present technique is the first to enable a quantitative real-time multiplex amplification, which allows to cover at least the five most common HR HPV (HPV16, 18, 45, 31, 33), preferably at least 7 HR HPV, still preferably the five most common HR HPV as well as at least two other HR HPV, advantageously at least two other HR HPV belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18), more preferably at least the 13 HR HPV, and as above-mentioned, most preferably at least 18 oncogenic HPV (namely, at least the 13 HR and five other oncogenic HPV, i.e., HPV 66, 53, 82, 67, 85).
The invention thereby finds applications not only in the field of diagnostic, but also in the field of therapy evaluation, such as to monitor the efficiency of an anti-HPV treatment, or to evaluate the efficiency of an anti-HPV drug. To the best of the inventors' knowledge, such therapy-related applications were previously unattainable by any of the prior art process.
The present invention thus represents a technological breakthrough in the field of HPV monitoring.
Hence, said amplification can be a quantitative real-time multiplex amplification, which allows for the detection of one or several of HPV, which can be oncogenic for the mucosal epithelia, in a single-tube amplification run.
The present invention thereby allows for the real-time multiplex detection, preferably the real-time quantitative multiplex detection of: at least the five most common HPV (HPV16, 18, 45, 31, 33)
preferably at least 7 HR HPV,
still preferably the five most common HR HPV as well as at least two other HR HPV, advantageously at least two other HR HPV belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18),
even still preferably at least the thirteen HPV known as HR HPV (HPV types 56, 51, 58, 33, 52, 35, 31, 16, 68, 39, 59, 45 and 18),
more preferably, at least the thirteen HPV as well as at least one among HPV types 66, 82, 67, 85, and 53
still more preferably, at least the thirteen HPV as well as at least two among HPV types 66, 82, 67, 85, and 53
even still more preferably, at least the thirteen HPV as well as at least three among HPV types 66, 82, 67, 85, and 53
most preferably, at least the thirteen HPV as well as at least four among HPV types 66, 82, 67, 85, and 53, notably of least the seventeen mucosal HPV, consisting of said 13 HR HPV and HPV types 66, 82, 67, 85,
still most preferably, at least the thirteen HPV as well as at least the five HPV types 66, 82, 67, 85, and 53,
in a single-tube assay.
Preferably, the respective sequences of said at least two A6-targeted primers are suitable for use in the amplification of at least one reference template sequence, wherein said at least one reference template sequence is a fragment consisting of positions 413-791 (SEQ ID NO:337) of the HPV56 sequence of SEQ ID NO:420 (accession NC—001594.1); or a conservative sub-fragment thereof, which has retained the property of being a suitable reference template sequence, to construct and produce A6-targeted primers, which allow for a real-time multiplex detection of those HPV, which can be oncogenic for the mucosal epithelia, preferably of at least the five most common HPV (HPV16, 18, 45, 31, 33), still preferably at least 7 HR HPV, even still preferably the five most common HR HPV as well as at least two other HR HPV, advantageously at least two other HR HPV belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18), more preferably at least the 13 HR HPV, most preferably at least the 13 HR HPV and at least one, at least two, at least three, at least four, or the five of HPV66, 53, 82, 67, 85; or a sequence which is fully complementary to said fragment or sub-fragment over the entire length of said fragment or sub-fragment.
More preferably, the respective sequences of said at least two A6-targeted primers are suitable for use in the specific amplification of at least one reference template sequence, which consists of one of SEQ ID NO:25-29 and NO:334-338, as shown in Table 18 (A6 reference templates); or a sequence which is fully complementary thereto over the entire length of said SEQ ID NO sequence.
Said reference template sequences notably share the specific technical feature of being suitable references to construct and produce A6-targeted primers, which allow for a real-time multiplex detection of HPV, which can be oncogenic for the mucosal epithelia, preferably of at least the five most common HPV (HPV16, 18, 45, 31, 33), still preferably at least 7 HR HPV, even still preferably the five most common HR HPV as well as at least two other HR HPV, advantageously at least two other HR HPV belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18), more preferably at least the 13 HR HPV, most preferably at least the 13 HR HPV and at least one, at least two, at least three, at least four, or the five of HPV66, 53, 82, 67, 85, and preferably for a real-time quantitative multiplex detection of such HPV.
As the reference template sequence is defined as consisting of one of the above-mentioned SEQ ID NOs (and not as comprising one of the above-mentioned SEQ ID NOs), the primers do not flank these reference template sequences, but fall within the reference template sequence, in such a way that the amplicon consists of one of the listed SEQ ID NOs. Unless otherwise stated, it applies to any reference template sequence that is herein defined as consisting of a SEQ ID NO. Said at least two A6-targeted primers can, for example, be at least one of SEQ ID NO: 30-34 (forward primer) and at least one of SEQ ID NO: 35-37 (reverse primer).
As illustrated by the examples below (see e.g., Table 23), preferred combinations of forward and reverse primers are as follows:







TABLE 1







(A6 primer systems):












SEQ ID NO:
35
36
37







30
X

X



31
X

X



32
X
X
X



33
X

X



34


X










wherein X indicates that the primers can be combined with each other as a pair.

According to an advantageous embodiment of the present invention, said determination of whether at least one amplicon is produced by said at least one A6-targeted primer system, can be carried out by using in real-time amplification at least one probe, preferably at least one A6-targeted probe.
Advantageously, said determination of whether at least one amplicon is produced is carried out by using in real-time amplification at least one A6-targeted probe, which consists of one of SEQ ID NO:38-40, or of one of the complementary sequences thereof (i.e., sequences of the same length, which are fully complementary over the entire length of the sequence), and optionally at least one 5′ and/or 3′ detection label and/or at least one HPV-unrelated arm intended to carry a quencher or a reporter (e.g., a fluorophore), such as at least one beacon arm, or ScorpionTM arm, preferably at least one of such arms in 5′ and/or 3′, most preferably two of such arms, in 5′ and in 3′, respectively.
As illustrated by the examples below (see e.g., table 23), preferred combinations of primer pair and probe are as follows:







TABLE 2







(A6 primer and probe systems):











A6
Primer pair
At least one probe



amplification system
SEQ ID NO:
of SEQ ID NO:







A
30; 35
38



AE
30; 37
38 and/or 40



B
31; 35
38



BE
31; 37
38 and/or 40



C
32; 36
39



CA
32; 35
38 and/or 39



CE
32; 37
38 and/or 39 and/or 40



D
33; 35
38



DE
33; 37
38 and/or 40



E
34; 37
40










Advantageously, said at least one A6-targeted probe is a beacon probe, the sequence of which is one of SEQ ID NO:41-45, or of one of the complementary sequences thereof (i.e., sequences of the same length, which are fully complementary over the entire length of the sequence).
As illustrated by the examples below (see e.g., Table 23), most preferred combinations of primer pair and beacon probes are as follows:







TABLE 3







(A6 primer and beacon probe systems):









A6 amplification
Primer pair SEQ ID
At least one beacon probe


system
NO:
of SEQ ID NO:





A
30; 35
41


AE
30; 37
41 and/or 44 and/or 45


B
31; 35
41


BE
31; 37
41 and/or 44 and/or 45


C
32; 36
42 and/or 43


CA
32; 35
41 and/or 42 and/or 43


CE
32; 37
41 and/or 42 and/or 43 and/or 44




and/or 45


D
33; 35
41


DE
33; 37
41 and/or 44 and/or 45


E
34; 37
44 and/or 45









Preferably, the respective sequences of said at least two A5-targeted primers are suitable for use in the amplification of at least one reference template sequence, which is a fragment consisting of positions 678-902 (SEQ ID NO:326) of the HPV51 sequence of SEQ ID NO:421 (accession NC—001533.1), or a conservative sub-fragment thereof, which has retained the property of being a suitable reference template sequence, to construct and produce A5-targeted primers, which allow for a real-time multiplex detection of those HPV, which can be oncogenic for the mucosal epithelia, preferably of at least the five most common HPV (HPV16, 18, 45, 31, 33), still preferably at least 7 HR HPV, even still preferably the five most common HR HPV as well as at least two other HR HPV, advantageously at least two other HR HPV belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18), more preferably at least the 13 HR HPV, most preferably at least the 13 HR HPV and at least one, at least two, at least three, at least four, or the five of HPV66, 53, 82, 67, 85; or a sequence which is fully complementary to said fragment or sub-fragment over the entire length of said fragment or sub-fragment.
More preferably, the respective sequences of said at least two A5-targeted primers are suitable for use in the specific amplification of at least one reference template sequence, wherein said at least one reference template sequence consists of one of SEQ ID NO: 1-5 and NO: 320-333, as shown in Table 12; or a sequence which is fully complementary thereto over the entire length of said SEQ ID sequence.
Said reference template sequences share the specific technical feature of being suitable references to construct and produce A5-targeted primers, which allow for a real-time multiplex detection of HPV, which can be oncogenic for the mucosal epithelia, preferably of at least the five most common HPV (HPV16, 18, 45, 31, 33), still preferably at least 7 HR HPV, even still preferably the five most common HR HPV as well as at least two other HR HPV, advantageously at least two other HR HPV belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18), more preferably at least the 13 HR HPV, most preferably at least the 13 HR HPV and at least one, at least two, at least three, at least four, or the five of HPV66, 53, 82, 67, 85, and preferably for a real-time quantitative multiplex detection of such HPV.
Said at least two A5-targeted primers may, for example, be at least one of SEQ ID NO: 6-10 (forward primer) and at least one of SEQ ID NO: 11-15 (reverse primer).
As illustrated by the examples below (see e.g., Table 17), preferred combinations of forward and reverse primers are as follows:







TABLE 4







(A5 primer systems):














SEQ ID NO:
6
7
8
9
10







11
X
X
X
X
X



12
X
X
X
X
X



13


X



14
X
X
X
X
X



15


X
X
X










wherein X indicates that the primers can be combined with each other as a pair.

Advantageously, said determination of whether at least one amplicon is produced is carried out by using in real-time amplification at least one A5-targeted probe, which consists of one of SEQ ID NO:16-19, or of one of the complementary sequences thereof (i.e., sequences of the same length, which are fully complementary over the entire length of the sequence), and optionally at least one detection label and/or at least one HPV-unrelated arm intended to carry a quencher or a reporter (e.g., a fluorophore), such as at least one beacon arm, or ScorpionTM arm, preferably at least one of such arms in 5′ and/or 3′, most preferably two of such arms, in 5′ and in 3′, respectively.
As illustrated by the examples below (see e.g., Table 17), preferred combinations of primer pair and probe are as follows:







TABLE 5







(A5 primer and probe systems):











A5 amplification
Primer pair SEQ ID
At least one probe



system
NO:
of SEQ ID NO:







A
6; 11
16



AB
6; 12
16



AD
6; 14
16



B
7; 12
16; 17



BA
7; 11
16; 17



BD
7; 14
16; 17



C
8; 13
18



CA
8; 11
16; 17; 18; 19



CB
8; 12
16; 17; 18; 19



CD
8; 14
16; 17; 18; 19



CE
8; 15
18; 19



D
9; 14
16; 17; 19



DA
9; 11
16; 17; 19



DB
9; 12
16; 17; 19



DE
9; 15
19



E
10; 15 
19



EA
10; 11 
16; 17; 19



EB
10; 12 
16; 17; 19



ED
10; 14 
16; 17; 19










Advantageously, said at least one A5-targeted probe is a beacon probe, the sequence of which is one of SEQ ID NO: 20-24, or of one of the complementary sequences thereof (i.e., sequences of the same length, which are fully complementary over the entire length of the sequence).
As illustrated by the examples below (see e.g., Table 17), most preferred combinations of primer pair and probe are as follows:







TABLE 6







(A5 primer and beacon probe systems):









A5 amplification
Primer pair SEQ ID
At least one beacon probe


system
NO:
of SEQ ID NO:





A
6; 11
20; 21


AB
6; 12
20; 21


AD
6; 14
20; 21


B
7; 12
20; 21; 22


BA
7; 11
20; 21; 22


BD
7; 14
20; 21; 22


C
8; 13
23


CA
8; 11
20; 21; 22; 23; 24


CB
8; 12
20; 21; 22; 23; 24


CD
8; 14
20; 21; 22; 23; 24


CE
8; 15
23; 24


D
9; 14
20; 21; 22; 24


DA
9; 11
20; 21; 22; 24


DB
9; 12
20; 21; 22; 24


DE
9; 15
24


E
10; 15 
24


EA
10; 11 
20; 21; 22; 24


EB
10; 12 
20; 21; 22; 24


ED
10; 14 
20; 21; 22; 24









Preferably, the respective sequences of said at least two A9-targeted primers are suitable for use in the amplification of at least one reference template sequence, which is:

    
    
        a fragment consisting of positions 2707-2794 (SEQ ID NO:122) of the HPV16 sequence of SEQ ID NO:422 (accession NC—001526.1); or a conservative sub-fragment thereof, which has retained the property of being a suitable reference template sequence, to construct and produce A9-targeted primers, which allow for a real-time multiplex detection of those HPV, which can be oncogenic for the mucosal epithelia, preferably of at least the five most common HPV (HPV16, 18, 45, 31, 33), still preferably at least 7 HR HPV, even still preferably the five most common HR HPV as well as at least two other HR HPV, advantageously at least two other HR HPV belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18), more preferably at least the 13 HR HPV, most preferably at least the 13 HR HPV and at least one, at least two, at least three, at least four, or the five of HPV66, 53, 82, 67, 85; or a sequence which is fully complementary to said fragment or sub-fragment over the entire length of said fragment or sub-fragment or
        a fragment consisting of positions 3600-3840 (SEQ ID NO:377) of the HPV16 sequence of SEQ ID NO:422 (accession NC—001526.1); or a conservative sub-fragment thereof, which has retained the property of being a suitable reference template sequence, to construct and produce A9-targeted primers, which allow for a real-time multiplex detection of those HPV, which can be oncogenic for the mucosal epithelia, preferably of at least the five most common HPV (HPV16, 18, 45, 31, 33), still preferably at least 7 HR HPV, even still preferably the five most common HR HPV as well as at least two other HR HPV, advantageously at least two other HR HPV belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18), more preferably at least the 13 HR HPV, most preferably at least the 13 HR HPV and at least one, at least two, at least three, at least four, or the five of HPV66, 53, 82, 67, 85; or a sequence which is fully complementary to said fragment or sub-fragment over the entire length of said fragment or sub-fragment.
    
    


More preferably, the respective sequences of said at least two A9-targeted primers are suitable for use in the specific amplification of at least one reference template sequence, which consists of any one of SEQ ID NO: 122-210 and 359-419, as shown in Table 30; or a sequence which is fully complementary thereto over the entire length of said SEQ ID NO sequence.
Said reference template sequences notably share the specific technical feature of being suitable references to construct and produce A9-targeted primers, which allow for a real-time multiplex detection of HPV, which can be oncogenic for the mucosal epithelia, preferably of at least the five most common HPV (HPV16, 18, 45, 31, 33), still preferably at least 7 HR HPV, even still preferably the five most common HR HPV as well as at least two other HR HPV, advantageously at least two other HR HPV belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18), more preferably at least the 13 HR HPV, most preferably at least the 13 HR HPV and at least one, at least two, at least three, at least four, or the five of HPV66, 53, 82, 67, 85, and preferably for a real-time quantitative multiplex detection of such HPV.
Said at least two A9-targeted primers can, for example, be at least one of SEQ ID NO: 211-239 (forward primers) and at least one of SEQ ID NO: 240-265 (reverse primers).
As illustrated by the examples below (see e.g., Table 35), preferred combinations of forward and reverse primers are as follows:

    
    
        A9 amplification system C: at least one of SEQ ID NO:211-217 and at least one of SEQ ID NO:240-241; preferably, when amplification of all oncogenic HPV of group A9 is desired, at least three of SEQ ID NO: 211-217, e.g., 212, 214 and 216, and both of SEQ ID NO:240-241;
        A9 amplification system E1: at least one of SEQ ID NO:218-220 and at least one of SEQ ID NO:242-247; preferably, when amplification of all oncogenic HPV of group A9 is desired, at least the three of SEQ ID NO:218-220 and at least five of SEQ ID NO:242-247 (e.g., SEQ ID NO:242-243, 245-247);
        A9 amplification system E2: at least one of SEQ ID NO:221-223 and at least one of SEQ ID NO:242-247; preferably, when amplification of all oncogenic HPV of group A9 is desired, at least the three of SEQ ID NO:221-223 and at least five of SEQ ID NO:242-247 (e.g., SEQ ID NO:242-243, 245-247);
        A9 amplification system E3: at least one of SEQ ID NO:221-223 and at least one of SEQ ID NO:248-255; preferably, when amplification of all oncogenic HPV of group A9 is desired, at least the three of SEQ ID NO:221-223 and at least five of SEQ ID NO:248-255 (e.g., SEQ ID NO:248-252);
        A9 amplification system E4: at least one of SEQ ID NO:224-226 and at least one of SEQ ID NO:248-255; preferably, when amplification of all oncogenic HPV of group A9 is desired, at least the three: of SEQ ID NO:224-226 and at least five of SEQ ID NO:248-255 (e.g., SEQ ID NO:248-252);
        A9 amplification system E5: at least one of SEQ ID NO:224-226 and at least one of SEQ ID NO:242-247; preferably, when amplification of all oncogenic HPV of group A9 is desired, at least the three of SEQ ID NO:224-226 and at least five of SEQ ID NO:242-247 (e.g., SEQ ID NO:242-243, 245-247);
        A9 amplification system E6: at least one of SEQ ID NO:218-220 and at least one of SEQ ID NO:248-255; preferably, when amplification of all oncogenic HPV of group A9 is desired, at least the three of SEQ ID NO:218-220 and at least five of SEQ ID NO:248-255 (e.g., SEQ ID NO:248-252);
        A9 amplification system E1H Z7: at least one of SEQ ID NO:218-220 and at least one of SEQ ID NO:256-259; 261-265; preferably, when amplification of all oncogenic HPV of group A9 is desired, at least the three of SEQ ID NO:218-220 and at least four of SEQ ID NO: 256-259; 261-265 (e.g., SEQ ID NO:258; 261; 264; 265);
        A9 amplification system E1H Z8: at least one of SEQ ID NO: 218-220 and at least one of SEQ ID NO:256-259; 261-265; preferably, when amplification of all oncogenic HPV of group A9 is desired, at least the three of SEQ ID NO:218-220 and at least four of SEQ ID NO:256-259; 261-265 (e.g., SEQ ID NO:258; 261; 264; 265);
        A9 amplification system E2H Z7: at least one of SEQ ID NO:221-223 and at least one of SEQ ID NO:256-259; 261-265; preferably, when amplification of all oncogenic HPV of group A9 is desired, at least the three of SEQ ID NO:221-223 and at least four of SEQ ID NO:256-259; 261-265 (e.g., SEQ ID NO: 258; 261; 264; 265);
        A9 amplification system E2H Z8: identical to A9 amplification system E2H Z7, i.e., at least one of SEQ ID NO:221-223 and at least one of SEQ ID NO: 256-259; 261-265; preferably, when amplification of all oncogenic HPV of group A9 is desired, at least the three of SEQ ID NO:221-223 and at least four of SEQ ID NO:256-259; 261-265 (e.g., SEQ ID NO:258; 261; 264; 265);
        A9 amplification system E4H Z7: at least one of SEQ ID NO:224-226 and at least one of SEQ ID NO: 256-259; 261-265; preferably, when amplification of all oncogenic HPV of group A9 is desired, at least the three of SEQ ID NO:224-226 and at least four of SEQ ID NO:256-259; 261-265 (e.g., SEQ ID NO:258; 261; 264; 265);
        A9 amplification system E4H Z8: at least one of SEQ ID NO:224-226 and at least one of SEQ ID NO: 256-259; 261-265; preferably, when amplification of all oncogenic HPV of group A9 is desired, at least the three of SEQ ID NO:224-226 and at least four of SEQ ID NO:256-259; 261-265 (e.g., SEQ ID NO: 258; 261; 264; 265);
        A9 amplification system F: at least one of SEQ ID NO:227-230 and at least one of SEQ ID NO:248-255; preferably, when amplification of all oncogenic HPV of group A9 is desired, at least the four of SEQ ID NO:227-230 and at least five of SEQ ID NO:248-255 (e.g., SEQ ID NO:248-252);
        A9 amplification system FE: at least one of SEQ ID NO:227-230 and at least one of SEQ ID NO:242-247; preferably, when amplification of all oncogenic HPV of group A9 is desired, at least the four of SEQ ID NO:227-230 and at least five of SEQ ID NO:242-247 (e.g., SEQ ID NO:242-243; 245-247);
        A9 amplification system FH Z7: at least one of SEQ ID NO:227-230 and at least one of SEQ ID NO:256-259; 261-265; preferably, when amplification of all oncogenic HPV of group A9 is desired, at least the four of SEQ ID NO:227-230 and at least four of SEQ ID NO:256-259; 261-265 (e.g., SEQ ID NO:258; 261; 264; 265);
        A9 amplification system FHZ8: identical to A9 amplification system FH Z7, i.e., at least one of SEQ ID NO:227-230 and at least one of SEQ ID NO:256-259; 261-265; preferably, when amplification of all oncogenic HPV of group A9 is desired, at least the three of SEQ ID NO:227-230 and at least four of SEQ ID NO:256-259; 261-265 (e.g., SEQ ID NO:258; 261; 264; 265);
        A9 amplification system G Z7: at least one of SEQ ID NO:227-230 and at least one of SEQ ID NO:256-261; preferably, when amplification of all oncogenic HPV of group A9 is desired, at least the three of SEQ ID NO:227-230 and at least five of SEQ ID NO:256-261 (e.g., SEQ ID NO:257-261);
        A9 amplification system G Z8: identical to A9 amplification system G Z7, i.e., at least one of SEQ ID NO:227-230 and at least one of SEQ ID NO:256-261; preferably, when amplification of all oncogenic HPV of group A9 is desired, at least the three of SEQ ID NO:227-230 and at least five of SEQ ID NO:256-261 (e.g., SEQ ID NO:257-261);
        A9 amplification system H: at least one of SEQ ID NO:231-239 and at least one of SEQ ID NO: 256-259; 261-265; preferably, when amplification of all oncogenic HPV of group A9 is desired, at least three of SEQ ID NO:231-239 (e.g., SEQ ID NO:232; 234; 235) and at least four of SEQ ID NO: 256-259; 261-265 (e.g., SEQ ID NO:258; 261; 264; 265).
    
    


Advantageously, said determination of whether at least one amplicon is produced is carried out by using in real-time amplification at least one A9-targeted probe, which consists of one of SEQ ID NO: 266-282, or of one of the complementary sequences thereof (i.e., sequences of the same length, which are fully complementary over the entire length of the sequence), and optionally at least one detection label and/or at least one HPV-unrelated arm intended to carry a quencher or a reporter (e.g., a fluorophore), such as at least one beacon arm, or ScorpionTM arm, preferably at least one of such arms in 5′ and/or 3′, most preferably two of such arms, in 5′ and in 3′, respectively.
As illustrated by the examples below (see e.g., Table 35), preferred combinations of primer pair and probe are as follows:







TABLE 7







(A9 primer and probe systems):










A9 amplification




system
At least one probe of SEQ ID NO:







C
266-271



E1
272-276



E2
272-276



E3
272-276



E4
272-276



E5
272-276



E6
272-276



E1H Z7
272-276



E1H Z8
277-282



E2H Z7
272-276



E2H Z8
277-282



E4H Z7
272-276



E4H Z8
277-282



F
272-276



FE
272-276



FH Z7
272-276



FH Z8
277-282



G Z7
272-276



G Z8
277-282



H
277-282










Advantageously, said at least one A9-targeted probe is a beacon probe, the sequence of which is one of SEQ ID NO: 283-319, or of one of the complementary sequences thereof (i.e., sequences of the same length, which are fully complementary over the entire length of the sequence).
As illustrated by the examples below (see e.g., Table 35), most preferred combinations of primer pair and probe are as follows:







TABLE 8







(A9 primer and beacon probe systems):










A9 amplification




system
At least one beacon probe of SEQ ID NO:







C
283-295



E1
296-303



E2
296-303



E3
296-303



E4
296-303



E5
296-303



E6
296-303



E1H Z7
296-303



E1H Z8
304-319



E2H Z7
296-303



E2H Z8
304-319



E4H Z7
296-303



E4H Z8
304-319



F
296-303



FE
296-303



FH Z7
296-303



FH Z8
304-319



G Z7
296-303



G Z8
304-319



H
304-319










Some of the specificity results of the above-mentioned probes are shown in Tables 60-68 (Specificity A9).
In all tables, when the name of a probe differs from the name of another probe by only the last letter (e.g., A9E1S10 and A9E1S10a), these probes have the same hybridizing segment, and only differ in their beacon arms.
Gray boxes indicate that the tested probe detects the amplicon.
For example, probe A9E1S11 of SEQ ID NO: 285 detects HPV31 and HPV35, without detecting the other HPV.
For example, probe A9E1S10a of SEQ ID NO: 284 detects all oncogenic HPV of group A9 (HPV16, 31, 33, 35, 52, 58, 67) and one HPV of group A6 (HPV53), and probe A9E1S12a of SEQ ID NO: 288 detects HPV31 and HPV35, without detecting HPV53 (“ND”). Hence, a combination of A9E1S10a and of A9E1S12a allows the specific detection of HPV16, 31, 33, 35, 52, 58, 67, 53.
Any combination that the skilled person may find appropriate is herein specifically encompassed.
Preferably, the respective sequences of said at least two A7-targeted primers are suitable for use in the amplification of at least one reference template sequence, wherein said at least one reference template sequence is:

    
    
        a fragment consisting of positions 1895-2103 (SEQ ID NO:48) of the HPV18 sequence of SEQ ID NO:423 (accession NC—001357.1); or a conservative sub-fragment thereof, which has retained the property of being a suitable reference template sequence, to construct and produce A7-targeted primers, which allow for a real-time multiplex detection of those HPV, which can be oncogenic for the mucosal epithelia, preferably of at least the five most common HPV (HPV16, 18, 45, 31, 33), still preferably at least 7 HR HPV, even still preferably the five most common HR HPV as well as at least two other HR HPV, advantageously at least two other HR HPV belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18), more preferably at least the 13 HR HPV, most preferably at least the 13 HR HPV and at least one, at least two, at least three, at least four, or the five of HPV66, 53, 82, 67, 85; or a sequence which is fully complementary to said fragment or sub-fragment over the entire length of said fragment or sub-fragment, or
        a fragment consisting of positions 916-1044 (SEQ ID NO: 65) of the HPV18 sequence of SEQ ID NO:423 (accession NC—001357.1); or a conservative sub-fragment thereof, which has retained the property of being a suitable reference template sequence, to construct and produce A7-targeted primers, which allow for a real-time multiplex detection of those HPV, which can be oncogenic for the mucosal epithelia, preferably of at least the five most common HPV (HPV16, 18, 45, 31, 33), still preferably at least 7 HR HPV, even still preferably the five most common HR HPV as well as at least two other HR HPV, advantageously at least two other HR HPV belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18), more preferably at least the 13 HR HPV, most preferably at least the 13 HR HPV and at least one, at least two, at least three, at least four, or the five of HPV66, 53, 82, 67, 85; or a sequence which is fully complementary to said fragment or sub-fragment over the entire length of said fragment or sub-fragment.
    
    


More preferably, the respective sequences of said at least two A7-targeted primers are suitable for use in the specific amplification of at least one reference template sequence, which consists of one of SEQ ID NO:46-67; 339-358, as shown in Table 24; or a sequence which is fully complementary thereto over the entire length of said SEQ ID NO sequence.
Said reference template sequences notably share the specific technical feature of being suitable references to construct and produce A7-targeted primers, which allow for a real-time multiplex detection of HPV, which can be oncogenic for the mucosal epithelia, preferably of at least the five most common HPV (HPV16, 18, 45, 31, 33), still preferably at least 7 HR HPV, even still preferably the five most common HR HPV as well as at least two other HR HPV, advantageously at least two other HR HPV belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18), more preferably at least the 13 HR HPV, most preferably at least the 13 HR HPV and at least one, at least two, at least three, at least four, or the five of HPV66, 53, 82, 67, 85, and preferably for a real-time quantitative multiplex detection of such HPV.
Said at least two A7-targeted primers can, for example, be at least one of SEQ ID NO: 68-78 (forward primer) and at least one of SEQ ID NO: 79-87 (reverse primer).
As illustrated by the examples below (see e.g., Table 29), preferred combinations of forward and reverse primers are as follows:

    
    
        A7 amplification system A: at least one of SEQ ID NO:68-70 and at least one of SEQ ID NO:79-81; preferably, when amplification of all oncogenic HPV of group A7 is desired, all of them;
        A7 amplification system A1: identical to A7 amplification system A, i.e., at least one of SEQ ID NO:68-70 and at least one of SEQ ID NO:79-81; preferably, when amplification of all oncogenic HPV of group A7 is desired, all of them;
        A7 amplification system A2: identical to A7 amplification system A or A1, i.e., at least one of SEQ ID NO:68-70 and at least one of SEQ ID NO:79-81; preferably, when amplification of all oncogenic HPV of group A7 is desired, all of them;
        A7 amplification system AB: at least one of SEQ ID NO:68-70 and at least one of SEQ ID NO:82-83; preferably, when amplification of all oncogenic HPV of group A7 is desired, all of them;
        A7 amplification system AC1: at least one of SEQ ID NO:68-70 and at least one of SEQ ID NO:84-85; preferably, when amplification of all oncogenic HPV of group A7 is desired, all of them;
        A7 amplification system AC2: identical to A7 amplification system AC1, i.e., at least one of SEQ ID NO:68-70 and at least one of SEQ ID NO:84-85; preferably, when amplification of all oncogenic HPV of group A7 is desired, all of them;
        A7 amplification system AC3: identical to A7 amplification system AC1 or AC2, i.e., at least one of SEQ ID NO:68-70 and at least one of SEQ ID NO:84-85; preferably, when amplification of all oncogenic HPV of group A7 is desired, all of them;
        A7 amplification system B: at least one of SEQ ID NO:71-73 and at least one of SEQ ID NO:82-83; preferably, when amplification of all oncogenic HPV of group A7 is desired, all of them;
        A7 amplification system BA1: at least one of SEQ ID NO:71-73 and at least one of SEQ ID NO:79-81; preferably, when amplification of all oncogenic HPV of group A7 is desired, all of them;
        A7 amplification system BA2: identical to A7 amplification system BA1, i.e., at least one of SEQ ID NO:71-73 and at least one of SEQ ID NO:79-81; preferably, when amplification of all oncogenic HPV of group A7 is desired, all of them;
        A7 amplification system BA3: identical to A7 amplification system BA1 or BA2, i.e., at least one of SEQ ID NO:71-73 and at least one of SEQ ID NO:79-81; preferably, when amplification of all oncogenic HPV of group A7 is desired, all of them;
        A7 amplification system BC1: at least one of SEQ ID NO:71-73 and at least one of SEQ ID NO:84-85; preferably, when amplification of all oncogenic HPV of group A7 is desired, all of them;
        A7 amplification system BC2: identical to A7 amplification system BC1, i.e., at least one of SEQ ID NO:71-73 and at least one of SEQ ID NO:84-85; preferably, when amplification of all oncogenic HPV of group A7 is desired, all of them;
        A7 amplification system BC3: identical to A7 amplification system BC1 or BC2, i.e., at least one of SEQ ID NO:71-73 and at least one of SEQ ID NO:84-85; preferably, when amplification of all oncogenic HPV of group A7 is desired, all of them;
        A7 amplification system C: at least one of SEQ ID NO:74-76 and at least one of SEQ ID NO:84-85; preferably, when amplification of all oncogenic HPV of group A7 is desired, all of them;
        A7 amplification system C1: identical to A7 amplification system C, i.e., at least one of SEQ ID NO:74-76 and at least one of SEQ ID NO:84-85; preferably, when amplification of all oncogenic HPV of group A7 is desired, all of them;
        A7 amplification system CA1: identical to A7 amplification system C1, i.e., at least one of SEQ ID NO:74-76 and at least one of SEQ ID NO:79-81; preferably, when amplification of all oncogenic HPV of group A7 is desired, all of them;
        A7 amplification system CA2: identical to A7 amplification system C1 or CA1, i.e., at least one of SEQ ID NO:7476 and at least one of SEQ ID NO:79-81; preferably, when amplification of all oncogenic HPV of group A7 is desired, all of them;
        A7 amplification system D: at least one of SEQ ID NO:77-78 and at least one of SEQ ID NO:86-87; preferably, when amplification of all oncogenic HPV of group A7 is desired, all of them.
    
    


Advantageously, said determination of whether at least one amplicon is produced is carried out by using in real-time amplification at least one A7-targeted probe, which consists of one of SEQ ID NO:88-101, or of one of the complementary sequences thereof (i.e., sequences of the same length, which are fully complementary over the entire length of the sequence), and optionally at least one detection label and/or at least one HPV-unrelated arm intended to carry a quencher or a reporter (e.g., a fluorophore), such as at least one beacon arm, or ScorpionTM arm, preferably at least one of such arms in 5′ and/or 3′, most preferably two of such arms, in 5′ and in 3′, respectively.
As illustrated by the examples below (see e.g., Table 29), preferred combinations of primer pair and probe are as follows:







TABLE 10







(A7 primer and probe systems):










A7 amplification
At least one probe



system
of SEQ ID NO:







A
88-92



A1
92-95



A2
89-91; 96



AB
92-95



AC1
88-92



AC2
92-95



AC3
89-91; 96



B
92-95



BA1
88-92



BA2
92-95



BA3
89-91; 96



BC1
88-92



BC2
92-95



BC3
89-91; 96



C
89-91; 96



C1
88-91; 96



CA1
89-91; 96



CA2
88-91; 96



D
97-101










Advantageously, said at least one A7-targeted probe is a beacon probe, the sequence of which is one of SEQ ID NO:102-121, or of one of the complementary sequences thereof (i.e., sequences of the same length, which are fully complementary over the entire length of the sequence).
As illustrated by the examples below (see e.g., Table 29), most preferred combinations of primer pair and probe are as follows:







TABLE 11







(A7 primer and beacon probe systems):










A7 amplification
At least one beacon



system
probe of SEQ ID NO:







A
102-106



A1
106-110



A2
105; 111-114



AB
106-110



AC1
102-106



AC2
106-110



AC3
105; 111-114



B
106-110



BA1
102-106



BA2
106-110



BA3
105; 111-114



BC1
102-106



BC2
106-110



BC3
105; 111-114



C
105; 111-114



C1
102-105; 114



CA1
105; 111-114



CA2
102-105; 114



D
115-121










Said amplification can be any nucleic acid amplification, which is found appropriate to the skilled person, for example a PCR (Polymerase Chain Reaction), or an isothermal amplification technique, e.g., TMA (transcription mediated amplification), NASBA (nucleic acid sequence based amplification), 3SR (self sustained sequence replication) or strand displacement amplification. Said amplification preferably is a PCR.
In a preferred embodiment, the primers according to the invention are used in a final concentration range 100-200 nM. Typically, said primers can be used at a final concentration range 200-1500 nM, preferably 250-1000 nM, more preferably 500-1000 nM, even more preferably 600-1000 nM.
Probe concentration in a PCR reaction can be optimized, typically by varying the final concentration from 50 nM to 1000 nM. In a preferred embodiment, the probes according to the invention are used at a final concentration range 50-1000 nM, preferably 100-800 nM, more preferably 100-600 nM, even more preferably 200-600 nM.
Appropriate amplification conditions are known to those skilled in the art. They include temperature conditions, in particular thermal cycling conditions, e.g. temperature, duration, number, heating rate of the cycles. In a preferred embodiment, said temperature conditions include conditions suitable for a PCR. In another preferred embodiment, said conditions include conditions suitable for a Q-PCR.
Any megaplex, i.e., multi-multiplex comprising at least A6-targeted one real-time amplification system of the invention and at least one A5-targeted one real-time amplification system of the invention and at least one A9-targeted one real-time amplification system of the invention and at least one A7-targeted one real-time amplification system of the invention, which would be contemplated by the person of ordinary skill in the art is encompassed by the present application.
For example, the A5-targeted system E, and the A6-targeted system A, and the A7-targeted system A, and the A9-targeted system H, can be used together in a single-tube assay, thereby forming a megaplex (“megaplex EAAH”).
For example, the A5-targeted system E, and the A6-targeted system B, and the A7-targeted system A, and the A9-targeted system C, can be used together in a single-tube assay, thereby forming a megaplex (“megaplex EBAC”).
Illustrative specificity and sensitivity results of such megaplex are shown in tables 83-88 below.
From tables 84 and 87 (“megaplex EAAH”), it can be seen that such a megaplex enable to efficiently detect the oncogenic HPV, namely the 13 HR HPV and five other oncogenic HPV (HPV66, 53, 82, 67, 85), and that this megaplex has sufficiently homogeneous sensitivity and specificity (Ct) results to be quantitative for at least the 13 HR HPV and four other oncogenic HPV (HPV66, 53, 82, 85).
From tables 86 and 88 (“megaplex EBAC”), it can be seen that such a megaplex enable to efficiently detect the oncogenic HPV, namely at least the 13 HR HPV, and that this megaplex has sufficiently homogeneous sensitivity and specificity (Ct) results to be quantitative for at least the five most common HR HPV (HPV16, 18, 45, 31, 33).
Preferred megaplex notably comprise the above-mentioned EAAH and EBAC megaplex, as well as the following megaplex systems:

    
    
        the combination of A5-targeted system E, and the A6-targeted system B, and the A7-targeted system C, and the A9-targeted system C, can be used together in a single-tube assay, thereby forming a megaplex (“megaplex EBCC”);
        the combination of A5-targeted system E, and the A6-targeted system B, and the A7-targeted system B, and the A9-targeted system C, can be used together in a single-tube assay, thereby forming a megaplex (“megaplex EBBC”);
        the combination of A5-targeted system E, and the A6-targeted system B, and the A7-targeted system D, and the A9-targeted system C, can be used together in a single-tube assay, thereby forming a megaplex (“megaplex EBDC”);
        the combination of A5-targeted system E, and the A6-targeted system B, and the A7-targeted system A, and the A9-targeted system H, can be used together in a single-tube assay, thereby forming a megaplex (“megaplex EBAH”).
    
    


The present application also relates to any amplicon obtainable by implementation of the process according to any one claims 1-45 on a HPV-containing sample, which contains at least one HPV of group A6, A5, A9 or A7, for example, a sample which contains HPV66 and/or HPV53 and/or HPV82 and/or HPV58 and/or HPV33 and/or HPV67 and/or HPV52 and/or HPV35 and/or HPV31 and/or HPV68 and/or HPV39 and/or HPV85 and/or HPV59 and/or HPV45.
The invention is also directed to a polynucleotide suitable for use as a reference template sequence in the design of primers that can be used in multiplex to cover at least the five most common HR HPV (HPV16, 18, 45, 31, 33),
preferably at least 7 HR HPV, still preferably the five most common HR HPV as well as at least two other HR HPV, advantageously at least two other HR HPV belonging to groups A6 and/or A5 (e.g., HPV 56, 51, 33, 31, 16, 45, 18),
even still preferably at least the thirteen HPV known as HR HPV (HPV types 56, 51, 58, 33, 52, 35, 31, 16, 68, 39, 59, 45 and 18),
more preferably, at least the thirteen HPV as well as at least one among HPV types 66, 82, 67, 85, and 53
still more preferably, at least the thirteen HPV as well as at least two among HPV types 66, 82, 67, 85, and 53
even still more preferably, at least the thirteen HPV as well as at least three among HPV types 66, 82, 67, 85, and 53
most preferably, at least the thirteen HPV as well as at least four among HPV types 66, 82, 67, 85, and 53, notably of least the seventeen mucosal HPV, consisting of said 13 HR HPV and HPV types 66, 82, 67, 85,
still most preferably, at least the thirteen HPV as well as at least the five HPV types 66, 82, 67, 85, and 53,
in a single amplification run while still offering a real time quantitative amplification thereof.
Of course, the polynucleotides according to the present invention are also suitable for further protocols, including simplex protocols, multiplex protocols, end-point protocols, qualitative protocols, quantitative protocols, combinations thereof, and the like.
By polynucleotide, we hereby understand any polymer of nucleotides, wherein nucleotides can be ribonucleotides, deoxyribonucleotides, dideoxyribonucleotides, degenerated nucleotides, and the like. Said nucleotides are preferably single-stranded, but can also be double stranded. The length of said polynucleotides can vary, and is usually under 500 nucleotides (nt), preferably in the range of 50-400 nt, more preferably 100-300 nt, even more preferably 80-260 nt.
The present application also relates to any polynucleotide suitable for use as a reference template sequence in the design of primers that can be used in a single-tube multiplex to amplify those HPV of groups A6, A5, A9 and A7, and in the design of probes that can be used in said single-tube multiplex for real-time detection of said amplified HPV, said reference template polynucleotide being selected from:

    
    
        for group A6: a fragment consisting of positions 413-791 of the HPV56 sequence of SEQ ID NO:420 (accession NC—001594.1), or a conservative sub-fragment thereof, or a sequence which is fully complementary to said fragment or sub-fragment over the entire length of said fragment or sub-fragment;
        for group A5: a fragment consisting of positions 678-902 of the HPV51 sequence of SEQ ID NO:421 (accession NC—001533.1), or a conservative sub-fragment thereof, or a sequence which is fully complementary to said fragment or sub-fragment over the entire length of said fragment or sub-fragment;
        for group A9: a fragment consisting of positions 2707-2794 of the HPV16 sequence of SEQ ID NO:422 (accession NC—001526.1), or a conservative sub-fragment thereof, or a sequence which is fully complementary to said fragment or sub-fragment over the entire length of said fragment or sub-fragment; or a fragment consisting of positions 3600-3840 of the HPV16 sequence of SEQ ID NO:422 (accession NC—001526.1), or a conservative sub-fragment thereof, or a sequence which is fully complementary to said fragment or sub-fragment over the entire length of said fragment or sub-fragment;
        for group A7: a fragment consisting of positions 1895-2103 of the HPV18 sequence of SEQ ID NO:423 (accession NC—001357.1), or a conservative sub-fragment thereof, or a sequence which is fully complementary to said fragment or sub-fragment over the entire length of said fragment or sub-fragment; or a fragment consisting of positions 916-1044 of the HPV18 sequence of SEQ ID NO:423 (accession NC—001357.1), or a conservative sub-fragment thereof, or a sequence which is fully complementary to said fragment or sub-fragment over the entire length of said fragment or sub-fragment,

wherein said conservative fragment thereof have retained the property of being a suitable reference template sequence, to construct and produce group-targeted primers, which allow for a real-time multiplex detection of those HPV, which can be oncogenic for the mucosal epithelia.

    
    


The present application more particularly relates to any reference template polynucleotide, which consists of one of SEQ ID NO:25-29 and NO:334-338 (group A6-targeted reference template polynucleotides), or a sequence which is fully complementary thereto over the entire length of said SEQ ID NO sequence.
The present application more particularly relates to any reference template polynucleotide, which consists of one of SEQ ID NO: 1-5 and NO:320-333 (group A5-targeted reference template sequences), or a sequence which is fully complementary thereto over the entire length of said SEQ ID NO sequence.
The present application more particularly relates to any reference template polynucleotide, which consists of one of SEQ ID NO: SEQ ID NO:122-210 and 359-419 (group A9-targeted reference template sequences), or a sequence which is fully complementary thereto over the entire length of said SEQ ID NO sequence.
The present application more particularly relates to any reference template polynucleotide, which consists of one of SEQ ID NO: 46-67; 339-358 (group A7-targeted reference template sequences), or a sequence which is fully complementary thereto over the entire length of said SEQ ID NO sequence.
Conservative variants of the reference template polynucleotide of the invention are also encompassed by the present application. Conservative variants of a given parent reference template polynucleotide notably include any polynucleotide, which derives from said parent reference template polynucleotide, or the sequence which is fully complementary thereto, by deletion and/or substitution and/or addition of at least one nucleotide, but which has retained the capacity of being a reference template polynucleotide for designing and building an A5- and/or A6- and/or A7- and/or A9-targeted primer pair enabling the amplification of at least one HPV, which can be oncogenic for the mucosal epithelia. Illustrative conservative variants usually comprise those polynucleotides, which have a sequence identity of at least 80%, preferably of at least 85%, more preferably of at least 90%, most preferably of at least 95%, with said parent reference template polynucleotide or with the sequence which is fully complementary thereto (said identity score being computed over the entire length of said parent reference template polynucleotide, or fully complementary sequence). Illustrative conservative variants comprise those which do not differ from plus or minus 5 nucleotides in length from the parent sequence.
The present application also relates to the primers and probes of the present invention, as such, i.e., as individual oligonucleotide products.
Conservative variants of the primers of the invention are also encompassed by the present application. Conservative variants of a given parent primer notably include any oligonucleotide, which derives from said parent primer by deletion and/or substitution and/or addition of at least one nucleotide, but which has retained the capacity of being a forward or reverse A5- and/or A6- and/or A7- and/or A9-targeted primer for the amplification of at least one HPV, which can be oncogenic for the mucosal epithelia. Illustrative conservative variants usually comprise those oligonucleotides, which have a sequence identity of at least 80%, preferably of at least 81%, more preferably of at least 83%, most preferably of least 85%, with said parent primer (said identity score being computed over the entire length of said parent primer). Illustrative conservative variants comprise those which do not differ from plus or minus 5 nucleotides in length from the parent sequence.
Conservative variants of the probes of the invention are also encompassed by the present application. Conservative variants of a given parent probe notably include any oligonucleotide, which derives from said parent probe, or the sequence which is fully complementary thereto, by deletion and/or substitution and/or addition of at least one nucleotide, but which has retained the capacity of being an A5- and/or A6- and/or A7- and/or A9-targeted probe for the detection of at least one HPV, which can be oncogenic for the mucosal epithelia. Illustrative conservative variants usually comprise those oligonucleotides, which have a sequence identity of at least 90%, preferably of at least 91%, more preferably of at least 93%, most preferably of at least 95%, with said parent probe or with the sequence which is fully complementary thereto (said identity score being computed over the entire length of said parent probe). Illustrative conservative variants comprise those which do not differ from plus or minus 5 nucleotides in length from the parent sequence.
The present application more particularly relates to primers, which are suitable for HPV amplification, and which are especially adapted to the real-time multiplex amplification of HPV groups A6 and A5 and A9 and A7.
Said primer can e.g., be:

    
    
        an A6-targeted primer, consisting of any one of SEQ ID NO: 30-34 and SEQ ID NO: 35-37; or
        an A5-targeted primer, consisting of any one of SEQ ID NO: 6-10 and SEQ ID NO: 11-15; or
        an A9-targeted primer, consisting of any one of SEQ ID NO: 211-239 and SEQ ID NO: 240-265; or
        an A7-targeted primer, consisting of any one of SEQ ID NO: 68-78 and SEQ ID NO: 79-87.
    
    


The present application more particularly relates to primer systems suitable for HPV amplification, which are especially adapted to the real-time multiplex amplification of HPV groups A6 and A5 and A9 and A7.
Said primer system may e.g., be:

    
    
        at least one A6-targeted primer consisting of one of SEQ ID NO: 30-34, and at least one A6-targeted primer consisting of one of SEQ ID NO: 35-37; and/or
        at least one A5-targeted primer consisting of one of SEQ ID NO: 6-10, and at least one A5-targeted primer consisting of one of SEQ ID NO: 11-15; and/or
        at least one A9-targeted primer consisting of one of SEQ ID NO: 211-239, and at least one A9-targeted primer consisting of one of SEQ ID NO: 240-265; and/or
        at least one A7-targeted primer consisting of one of SEQ ID NO: 68-78, and at least one A7-targeted primer consisting of one of SEQ ID NO: 79-87.
    
    


The present application more particularly relates to probes, which are suitable for HPV detection, and which are especially adapted to the real-time multiplex amplification of HPV groups A6 and A5 and A9 and A7.
Said probe may e.g., be:

    
    
        an A6-targeted probe, consisting of any one of SEQ ID NO:38-40, or a sequence which is fully complementary thereto over the entire length of said SEQ ID NO sequence; or
    
    


an A5-targeted probe, consisting of any one of SEQ ID NO:16-19, or a sequence which is fully complementary thereto over the entire length of said SEQ ID NO sequence; or

    
    
        an A9-targeted probe, consisting of any one of SEQ ID NO: 266-282, or a sequence which is fully complementary thereto over the entire length of said SEQ ID NO sequence; or
        an A7-targeted probe, consisting of any one of SEQ ID NO:88-101, or a sequence which is fully complementary thereto over the entire length of said SEQ ID NO sequence.
    
    


Said probes can be produced in various format, e.g., including TaqmanTM probes (hydrolysis probes), molecular BeaconsTM (beacon probes or molecular beacon probes), and ScorpionTM probes. One of preferred formats is the beacon format.
Hence, the present application more particularly relates to beacon probes, which are suitable for HPV detection, and which are especially adapted to the real-time multiplex amplification of HPV groups A6 and A5 and A9 and A7.
Said beacon probe may e.g., be:

    
    
        an A6-targeted probe, consisting of any one of SEQ ID NO:41-45, or a sequence which is fully complementary thereto over the entire length of said SEQ ID NO sequence; or
        an A5-targeted probe, consisting of any one of SEQ ID NO:20-24, or a sequence which is fully complementary thereto over the entire length of said SEQ ID NO sequence; or
        an A9-targeted probe, consisting of any one of SEQ ID NO: 283-319, or a sequence which is fully complementary thereto over the entire length of said SEQ ID NO sequence; or
        an A7-targeted probe, consisting of any one of SEQ ID NO:102-121, or a sequence which is fully complementary thereto over the entire length of said SEQ ID NO sequence.
    
    


Beacon probe may further comprise a quencher and a reporter (e.g., a fluorophore).
Preferably, each probe has its own reporter, whereby each probe has a reporter that is different from the ones displayed by the other probes, whereby each probe can be easily distinguished from the other probes.
The present application more particularly relates to primer and probe systems, which are suitable for HPV amplification, and which are especially adapted to the real-time multiplex amplification of HPV groups A6 and A5 and A9 and A7.
Said primer and probe system comprises at least one primer system according to the invention, and at least one probe according to the invention.
The present application further relates to any amplicon obtainable by amplification of at least one nucleic acid from an HPV of group A6, A5, A9 or A7, by means of at least one primer system according to claim 53, for example, HPV66 and/or HPV53 and/or HPV82 and/or HPV58 and/or HPV33 and/or HPV67 and/or HPV52 and/or HPV35 and/or HPV31 and/or HPV68 and/or HPV39 and/or HPV85 and/or HPV59 and/or HPV45.
An amplification composition comprising such an amplicon is also encompassed by the present invention.
The present invention also relates to an amplification composition, a pharmaceutical composition, a biological composition, comprising at least one primer or probe of the invention.
The present invention also relates to a kit for the diagnostic or prognostic of a cervical neoplasia or cancer, comprising:

    
    
        at least one primer system according to the invention, and/or
        at least one probe according to the invention,
        optionally, instructions for the use thereof and/or nucleotides.
    
    


Preferably, said kit comprises at least two primer systems according to the invention, more preferably at least three primer systems according to the invention, most preferably at least four primer systems according to the invention.
Said kit comprises more than one probe, e.g. at least two, at least three, at least four, at least five different probes, notably when the kit is intended to discriminate between different HPV types.
In the kit according to the invention, the oligonucleotides (primers, probes) can be either kept separately, or partially mixed, or totally mixed.
Said oligonucleotides can be provided under dry form, or solubilized in a suitable solvent, as judged by the skilled person. Suitable solvents include TE, PCR-grade water, and the like.
In a preferred embodiment, the kit according to the invention can also contain further reagents suitable for a PCR step.
Such reagents are known to those skilled in the art, and include water, like nuclease-free water, RNase free water, DNAse-free water, PCR-grade water; salts, like magnesium, potassium; buffers such as Tris; enzymes, including polymerases, such as Taq, Vent, Pfu (all of them Trade-Marks), activable polymerase, and the like; nucleotides like deoxynucleotides, dideoxynucleotides, dNTPs, dATP, dTTP, dCTP, dGTP, dUTP; other reagents, like DTT and/or RNase inhibitors; and polynucleotides like polyT, polydT, and other oligonucleotides, e.g., primers.
In another preferred embodiment, the kit according to the invention comprises PCR controls. Such controls are known in the art, and include qualitative controls, positive controls, negative controls, internal controls, quantitative controls, internal quantitative controls, as well as calibration ranges. The internal control for said PCR step can be a template which is unrelated to the target template in the PCR step. Such controls also may comprise control primers and/or control probes. For example, in the case of HPV detection, it is possible to use as an internal control, a polynucleotide chosen within a gene whose presence is excluded in a sample originating from a human body (for example, from a plant gene), and whose size and GC content is equivalent to those from the target sequence.
In a preferred embodiment, the kit according to the invention contains means for extracting and/or purifying nucleic acid from a biological sample, e.g. from blood, serum, plasma. Such means are well known to those skilled in the art.
In a preferred embodiment, the kit according to the invention contains instructions for the use thereof. Said instructions can advantageously be a leaflet, a card, or the like. Said instructions can also be present under two forms: a detailed one, gathering exhaustive information about the kit and the use thereof, possibly also including literature data; and a quick-guide form or a memo, e.g., in the shape of a card, gathering the essential information needed for the use thereof.
In a preferred embodiment, said kit is a diagnostics kit, especially an in vitro diagnostics kit, i.e., an HPV diagnostics kit.
The present invention also relates to the field of diagnostics, prognosis and drug/treatment efficiency monitoring, as above-described.
The oligonucleotides according to the present invention can be used for the diagnostic of HPV group, types, subtypes or strains. In particular, the primers and probes according to the invention can be used for in vitro typing, sub-typing, and quantification of HPV nucleic acids present in an in vitro sample, for instance, in a patient's cervical sample, or in a cell culture supernatant.
The term “comprising”, which is synonymous with “including” or “containing”, is open-ended, and does not exclude additional, unrecited element(s), ingredient(s) or method step(s), whereas the term “consisting of” is a closed term, which excludes any additional element, step, or ingredient which is not explicitly recited. The term essentially consisting of is a partially open terms which does not exclude additional, unrecited element(s), step(s), or ingredient(s), as long as these additional element(s), step(s) or ingredient(s) do not materially affect the basic and novel properties of the invention.
The term “comprising” (or “comprise(s)”) hence includes the term “consisting of” (“consist(s) of”), as well as the term “essentially consisting of” (“essentially consist(s) of”). Accordingly, the term “comprising” (or “comprise(s)”) is, in the present application, meant as more particularly encompassing the term “consisting of” (“consist(s) of”), and the term “essentially consisting of” (“essentially consist(s) of”).
In the present application, the term “at least x” relating to a set or group of n elements (wherein x is different from zero, and n is a number that is higher than x), explicitly encompasses each value, which is comprises between x and n. For example, the term “at least one” relating to a group or set of six elements explicitly encompasses one, two, three, four, five and six of said elements, as well as at least two, at least three, at least four, at least five of said elements.
Each of the relevant disclosures of all references cited herein is specifically incorporated by reference. The following examples are offered by way of illustration, and not by way of limitation.
DEFINITIONS
The terms and names used in the present application have their ordinary meaning in the field of HPV detection in general, and of molecular biology in particular.
By <<amplification>>, it is meant any technique of nucleic acid amplification, such as the PCR (Polymerase Chain Reaction), or the isothermal amplification techniques, e.g., TMA (transcription mediated amplification), NASBA (nucleic acid sequence based amplification), 3SR (self sustained sequence replication) or strand displacement amplification.
Amplification methods, especially PCR-based methods, are known in the art (Molecular Cloning: A Laboratory Manual, Maniatis, Fritsch, and Sambrook, CSHL Press; Molecular Biology of the Cell, Alberts et al.; PCR Primer: A Laboratory Manual, Dieffenbach and Dveksler, CSHL Press; The Polymerase Chain Reaction, Mullis, Ferré, and Gibbs, Birkhauser Boston Press; Gene quantification, Ferré, Birkhauser Boston Press).
By PCR or PCR reaction, we hereby understand any PCR-based method. This includes standard PCR, qualitative, quantitative and semi-quantitative PCR, real-time PCR, reverse-transcriptase PCR (RT-PCR), simplex and multiplex PCR, and the like.
By real-time PCR, we hereby understand any PCR-based method allowing for monitoring of a signal, such as fluorescence, emitted during the reaction as an indicator of amplicon production during each PCR cycle as opposed to the endpoint detection by conventional PCR methods.
By quantitative PCR, we hereby understand any PCR-based method allowing for the estimation of the initial amount of a given PCR target in a given sample.
By multiplex PCR, we hereby understand any PCR reaction aiming at the amplification of more than one target. For instance, multiplex PCR include duplex PCR (two targets), triplex PCR (three targets), and higher multiplex PCR. Multiplex PCR includes PCR reactions with more than one primer pair, for instance two primer pairs. In this case, there might be four different primers, but it is also possible for the two primer pairs to have one primer in common, e.g. the forward primer, and to have two distinct reverse primers. Multiplex PCR also includes PCR reactions with a unique primer pair, but with more than one probe.
The term “megaplex” is herein sometimes used: it basically has the same meaning as “multiplex”, but is used to distinguish multi-multiplex, which involves at least two different group-targeted systems (e.g., an A5- and an A6- and an A7- and an A9-targeted systems), from the “multiplex”, which involve one group-targeted system (e.g., an A7- or an A9-targeted system).
By nucleic acid, we hereby understand any nucleic acid: it can be synthetic or not, recombinant or naturally occurring, linear or circular. This includes DNA and RNA. The nucleic acid can be either single stranded or double stranded or even triple stranded. It can stem from various biological sources, such as micro organisms (bacteria, yeasts, and the like), or higher organisms, like mammal cells. Said nucleic acid can also be of viral nature, e.g., the HPV nucleic acids. The nucleic acid can also comprise total DNA, total RNA, genomic DNA, mitochondrial DNA, plasmidic DNA, BAC DNA, and mixtures thereof. Moreover, the nucleic acid can assume various states of purity.
By oligonucleotide, we hereby understand any short polymer of nucleotides, wherein nucleotides can be ribonucleotides, deoxyribonucleotides, dideoxyribonucleotides, degenerated nucleotides, and the like. Said oligonucleotides are preferably single-stranded. The length of said oligonucleotides can vary, and is usually under 150 nucleotides (nt), preferably in the range of 10-100 nt, more preferably 13-60 nt, even more preferably 13-50 nt. Said oligonucleotides can bear chemical modifications, such as tagging or marking, for instance radioactive, fluorescent, biotinylated, dig labelling. An oligonucleotide according to the invention can be either forward (sense) or reverse (antisense). In addition, it should be stressed, that although preferred functions may be mentioned in relation to some oligonucleotides according to the present invention, it is obvious that a given oligonucleotide may assume several functions, and may be used in different ways according to the present invention. For example, an oligonucleotide can be used either as a primer, or as a probe. Also, when an oligonucleotide is described as being useful as an amplicon-targeting probe, the skilled person understands that the complementary sequence of this oligonucleotide is equally useful as a probe to target the same amplicon. Moreover, it is also obvious, that any primer suitable for a multiplex assay, can also, within the meaning of the present invention, be used in a simplex protocol. The same applies to a primer suitable for a real-time protocol, which can also be used in the framework of an end-point assay within the meaning of the present invention.
Oligonucleotides according to the invention especially include PCR primers and probes. Unless otherwise stated, nucleic acid sequences are given in the 5′ to 3′ direction. Said oligonucleotides can be under many forms, e.g. under dry state, in solution/suspension with the desired solvent and the desired concentration. The skilled person would know, which solvents, concentrations, storage conditions are suitable for the oligonucleotides of the invention. In particular, the skilled person would know how to prepare said oligonucleotides as stock solutions. The oligonucleotides according to the invention can also assume various degrees of purity, as can be judged by those skilled in the art, e.g., by HPLC chromatography.
By set or systems of oligonucleotides, we hereby understand any combination comprising at least one oligonucleotide, preferably at least two, e.g. 2-10 oligonucleotides. Said set can thus comprise one PCR primer, or a pair of PCR primers, or a probe, or a probe and a pair of primers. Said oligonucleotides can be separately kept, or partially mixed, or entirely mixed.
The notion of primer or PCR primer is known to those skilled in the art. For example, it includes any oligonucleotide able to anneal to a target template under suitable stringency conditions, and allowing for polymerase strand elongation. The typical length of said primer is 13-30 nt, preferably 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26 or 27 nt.
The terms “primer”, “amplification primer” or “nucleic acid primer” are used interchangeably herein. A “primer” refers to a short polynucleotide, whether occurring naturally as in a purified restriction digest or produced synthetically, which is capable of acting as a point of initiation of synthesis when placed under conditions in which synthesis of a primer extension product, which is complementary to a nucleic acid strand, is induced, i.e., in the presence of nucleotides and an inducing agent such as a polymerase and at a suitable temperature and pH. The primer must be sufficiently long to prime the synthesis of the desired extension product. The exact length of the primer will depend upon experimental factors, and notably upon temperature, source of primer and use of the process.
A primer pair consists of a forward primer and a reverse primer, wherein the forward primer is sufficiently complementary to one HPV strand to hybridize thereto, and the reverse primer is sufficiently complementary to the other HPV strand to hybridize thereto.
Stringency refers to hybridization conditions chosen to optimize binding of polynucleotide sequences with different degrees of complementarity. Stringency is affected by factors such as temperature, salt conditions, the presence of organic solvents in the hybridization mixtures, and the lengths and base compositions of the sequences to be hybridized and the extent of base mismatching, and the combination of parameters is more important than the absolute measure of any one factor.
Very High Stringency: Very high stringency conditions refers to hybridization to filter-bound DNA in. 5×SSC, 2% sodium dodecyl sulfate (SDS), 100 microgrammes/ml single stranded DNA at 55-65° C. for 8 hours, and washing in 0.1×SSC and 0.1% SDS at 60-65° C. for thirty minutes.
High Stringency High stringency conditions refers to hybridization to filter-bound DNA in 5×SSC, 2% sodium dodecyl sulfate (SDS), 100 microgrammes/ml single stranded DNA at 55-65° C. for 8 hours, and washing in 0.2×SSC and 0.2% SDS at 60-65° C. for thirty minutes.
Moderate Stringency Moderate stringency conditions refers to hybridization to filter-bound DNA in 5×SSC, 2% sodium dodecyl sulfate (SDS), 100 microgrammes/ml single stranded DNA at 55-65° C. for 8 hours, and washing in 0.2×SSC and 0.2% SDS at 50-55° C. for thirty minutes.
The notion of probe is also known to those skilled in the art. For example, it includes any oligonucleotide able to anneal to a target template under the desired hybridization conditions. The typical length of said probe is 15-60 nt, preferably 16-50 nt, more preferably 17-40 nt, more preferably 17-35 nt, more preferably 20-30 nt. Preferably, said probe is fluorescently labelled. However, it is clear to those skilled in the art that under certain conditions, one may use a primer as a probe and vice-versa. Moreover, it is herein stressed that the products according to the present invention, especially, inter alia, oligonucleotides, are not limited to the intended use herein mentioned, but rather are to be broadly construed, irrespective of the indicated destination. For instance, a claim to a product (oligonucleotide) for a particular use should be construed as meaning a product (oligonucleotide) which is in fact suitable for the stated use. Thus, an oligonucleotide suitable for use as a primer in a multiplex protocol is also clearly adapted to a simplex protocol within the meaning of the present invention.
A probe may entirely consist of a hybridizing segment. By “hybridizing segment” or “annealing segment” of a probe, it is meant the nucleotide sequence, which is intended to anneal to the HPV target(s).
Alternatively, a probe may comprise at least one detection component, e.g. at least one detection label (such as a radioactive element, or a fluorophore). This detection label can be linked to the hybridizing segment of the probe via short HPV-unrelated oligonucleotide arms, which are known to the skilled person as beacon arm, or ScorpionTM arm. A probe, which comprises at least one 5′ and/or 3′ detection label, or at least one 5′ and/or 3′ beacon arm, consists of a hybridizing segment and of at least one 5′ and/or 3′ label or beacon arm.
Various formats (types) of probes, including TaqmanTM probes (hydrolysis probes), molecular BeaconsTM (beacon probes or molecular beacon probes), and ScorpionTM probes are known in the art.
In a preferred embodiment, the probes according to the invention can all be synthesized and used in the molecular beacon format.
The structure of molecular beacons is as follows. A short nucleotide sequence (so-called beacon arm) which is unrelated to the target sequence is thus covalently linked to both ends of the probe. A short unrelated arm is thus linked in 5′ of the probe, and is labelled with a fluorescent moiety (i.e. fluorescent dye or fluorescent marker). Another but still unrelated arm is linked to the 3′ end of probe and is labelled with a fluorescence quenching moiety. Thus, molecular beacons have a fluorophore and a quencher at opposite ends. The 5′ short arm is totally complementary to the one in 3′ so that they can anneal together, and thus can assume a hairpin structure when unhybridized to the target in solution. In this hairpin conformation, the quencher and the fluorescent dye are close enough to each other to allow efficient quenching of the fluorophore. However, when the probe encounters a target molecule, annealing is favoured with respect to the hairpin conformation when values of beacon arm Tm and probe Tm are suitably chosen (theoretically: probe Tm>beacon arm Tm>primer Tm, wherein Tm is the melting temperature of interest). The fluorophore and quencher move away from each other and the fluorophore can then fluoresce when illuminated by suitable light excitation. As PCR proceeds, amplification product accumulates, and the amount of fluorescence at any given cycle depends on the amount of amplification product present at that time. (See e.g., Sanjay Tyagi and Fred Russell Kramer, Nature Biotechnology 1996, volume 14, pages 303-308; Nature Biotechnology 1998, volume 16, pages 49-53).
(Remark: It is also possible to link the fluorophore at the 3′ end, while attaching the quencher at the 5′ end.)
Schematically, said probe can have the following formulae (molecular beacon format):
5′Fluorophore-(arm1)-probe-(arm2)-Quencher 3′
5′ Quencher-(arm1)-probe-(arm2)-Fluorophore 3′
wherein arm1 and arm2 can be any short nucleotide sequences, e.g. in the range of 3-10 nucleotides, preferably 5, 6, 7 nucleotides, allowing for the hair pin structure formation under suitable stringency conditions, i.e. arm1 and arm2 are totally complementary to anneal under the desired stringency conditions (standard PCR stringency conditions include, for example, an annealing temperature of 55 to 65° C. and an Mg concentration of 4 to 8 mM). However, arm1 and arm2 are unrelated to the target sequence of the probe, i.e. the hairpin conformation resulting from the annealing between arm1 and arm2 is essentially the only possible secondary structure for the probe when unhybridized. The skilled person would know how to choose such arms for a given probe.
Illustrative beacon formats include:










TGCGC-(probe sequence)-GCGCA




 



GCGCA-(probe sequence)-TGCGC



 



AGCGC-(probe sequence)-GCGCT



 



GCGCT-(probe sequence)-AGCGC



 



CGCGA-(probe sequence)-TCGCG



 



CGCGC-(probe sequence)-GCGCG.






By fluorophore, it is herein understood any fluorescent marker/dye known in the art. Examples of such suitable fluorescent markers include Fam, Hex, Tet, Joe, Rox, Tamra, Max, Edans, Cy dyes such as Cy5, Fluorescein, Coumarin, Eosine, Rhodamine, Bodipy, Alexa, Cascade Blue, Yakima Yellow, Lucifer Yellow and Texas Red (all of them are Trade-Marks), the family of ATTO dyes.
By quencher, we herein understand any quencher known in the art. Examples of such quenchers include Dabcyl, Dark Quencher, Eclipse Dark Quencher, ElleQuencher, Tamra, BHQ and QSY (all of them are Trade-Marks).
The skilled person would know which combinations of dye/quencher are suitable when designing a probe.
In a preferred embodiment according to the invention, spectral properties of said probes can be chosen as to not interfere with each other. In particular, when probes are used in multiplex, each single probe can have its own fluorophore being spectrally significantly different from each other, i.e. the absorption/emission spectra are essentially non-overlapping. This advantageously allows for low-noise multiplex detection for all single probes, making sure that individual signals do not interfere with each other in detection. Examples of dyes which can be used together in multiplex include Fam with Tamra, Fam with Tamra with Texas Red.
The choice of appropriate dyes to be used together may also be dependent of the filter contained in the amplification apparatus.
According to the invention, all the provided oligonucleotides can be either kept separately, or partially mixed, or totally mixed.
Said oligonucleotides can be provided under dry form, or solubilized in a suitable solvent, as judged by the skilled person. Suitable solvents include TE, PCR-grade water, and the like.
The term “significantly” is herein used in its usual meaning in the field of statistics (e.g., t test, z test, chi squared value, or F ratio, etc.), i.e., for comparing a value to another one, and determining whether these values differ from each other. The term “significantly” hence encompasses the fact that the skilled person may take into account the standard deviation (if any), which measures the amount of spread of data in a frequency distribution. The desired p value is usually set at an alpha level of 5%, or at the more stringent alpha level of 1%.
In the examples below, are described several A6-, A5-, A9 and A7-targeted amplification and/or detection systems of the invention.
Tables 12-35:
these tables give the SEQ ID NO: and positions of the reference amplicons, the forward primers, the reverse primers, the probes, the beacons probes of illustrative group-targeted systems of the invention.
Table 12: Reference amplicons of A5-targeted systems (from HPV51 genome)
Table 13: Forward primers of A5-targeted systems
Table 14: Reverse primers of A5-targeted systems
Table 15: Probes of A5-targeted systems
Table 16: Beacon probes of A5-targeted systems
Table 17: A5-targeted systems
Table 18: Reference amplicons of A6-targeted systems (from HPV56 genome)
Table 19: Forward primers of A6-targeted systems
Table 20: Reverse primers of A6-targeted systems
Table 21: Probes of A6-targeted systems
Table 22: Beacon probes of A6-targeted systems
Table 23: A6-targeted systems
Table 24: Reference amplicons of A7-targeted systems (from HPV18 genome)
Table 25: Forward primers of A7-targeted systems
Table 26: Reverse primers of A7-targeted systems
Table 27: Probes of A7-targeted systems
Table 28: Beacon probes of A7-targeted systems
Table 29: A7-targeted systems
Table 30: Reference amplicons of A9-targeted systems (from HPV16 genome)
Table 31: Forward primers of A9-targeted systems
Table 32: Reverse primers of A9-targeted systems
Table 33: Probes of A9-targeted systems
Table 34: Beacon probes of A9-targeted systems
Table 35: A9-targeted systems
Tables 36-50:
these tables show the number of nucleotide mismatches shown by primers and probes of the invention (alignment of the sequences of 50 HPV types); an empty box indicates there is no coherent sequence alignment; a gray box indicates that the number of mismatch(es) is of 0, 1, 2 or 3.
Table 36: mismatch numbers shown by primers and probes of A5-targeted systems of the invention (systems A to C)
Table 37: mismatch numbers shown by primers and probes of A5-targeted systems of the invention (systems D to E)
Table 38: mismatch numbers shown by primers and probes of A6-targeted systems of the invention (systems A to C)
Table 39: mismatch numbers shown by primers and probes of A6-targeted systems of the invention (systems D to E)
Table 40: mismatch numbers shown by primers and probes of A7-targeted systems of the invention (systems A to B)
Table 41: mismatch numbers shown by primers and probes of A7-targeted systems of the invention (systems C to D)
Table 42: mismatch numbers shown by primers and probes of A9-targeted systems of the invention (system C)
Table 43: mismatch numbers shown by primers and probes of A9-targeted systems of the invention (system E1)
Table 44: mismatch numbers shown by primers and probes of A9-targeted systems of the invention (system E2)
Table 45: mismatch numbers shown by primers and probes of A9-targeted systems of the invention (system E3)
Table 46: mismatch numbers shown by primers and probes of A9-targeted systems of the invention (system E4)
Table 47: mismatch numbers shown by primers and probes of A9-targeted systems of the invention (system F)
Table 48: mismatch numbers shown by primers and probes of A9-targeted systems of the invention (system GZ7)
Table 49: mismatch numbers shown by primers and probes of A9-targeted systems of the invention (system GZ8)
Table 50: mismatch numbers shown by primers and probes of A9-targeted systems of the invention (system H)
Tables 51-68: Specificity of the Detection Systems of the Invention
The amplification systems described in tables 36-50 have been used to test the specificity of the probes of the invention.
Table 51: illustrative list of HPV plasmids, which can be used to test the HPV specificity of the detection systems of the invention; the whole list of plasmids have been used for the specificity results, which are herein described
Table 52: illustrative PCR material and method conditions, which can be used to test the specificity of the A5- and A6-targeted detection systems of the invention
Table 53: specificity results of A5-targeted probes (box “other HPV”=all the other HPV of the list given in Table 51)
Table 54: specificity results of A6-targeted probes (box “other HPV”=all the other HPV of the list given in Table 51)
Table 55: illustrative PCR material and method conditions, which can be used to test the specificity of the A7-targeted detection systems of the invention
Tables 56-59: specificity results of A7-targeted probes (box “other HPV”=all the other HPV of the list given in Table 51)

    
    
        Table 56: A7-targeted amplification system A, and probes of A7-targeted amplification system A (one probe per PCR)
        Table 57: A7-targeted amplification system B, and probes of A7-targeted amplification system B (one probe per PCR)
        Table 58: A7-targeted amplification system C, and probes of A7-targeted amplification system C (one probe per PCR)
        Table 59: A7-targeted amplification system D, and probes of A7-targeted amplification system D (one probe per PCR)
    
    


Table 60: illustrative PCR material and method conditions, which can be used to test the specificity of the A9-targeted detection systems of the invention
Tables 61-68: specificity results of A9-targeted probes (box “other HPV”=all the other HPV of the list given in Table 51)

    
    
        Table 61: A9-targeted amplification system C, and probes of A9-targeted amplification system C (one probe per PCR)
        Table 62: A9-targeted amplification system E2, and probes of A9-targeted amplification system E2 (one probe per PCR)
        Table 63: A9-targeted amplification system E3, and probes of A9-targeted amplification system E3 (one probe per PCR)
        Table 64: A9-targeted amplification system E4, and probes of A9-targeted amplification system E4 (one probe per PCR)
        Table 65: A9-targeted amplification system F, and probes of A9-targeted amplification system F (one probe per PCR)
        Table 66: A9-targeted amplification system GZ7, and probes of A9-targeted amplification system GZ7 (one probe per PCR)
        Table 67: A9-targeted amplification system GZ8, and probes of A9-targeted amplification system GZ8 (one probe per PCR)
        Table 68: A9-targeted amplification system H, and probes of A9-targeted amplification system H (one probe per PCR)
    
    


The amplification and detection systems, which were used for the specificity tests, are those shown in Table 17 (A5-targeted systems); Table 23 (A6-targeted systems); Table 29 (A7-targeted systems); Table 35 (A9-targeted systems).
For the A9-targeted systems, those primers, which are shown between brackets in Table 35 were not used, as they would have been redundant: indeed, those primers, which are not between brackets, are sufficient to amplify all group A9 HPV. Hence, in table 35, those A9-targeted primers which are shown between brackets are optional and/or equivalent and/or alternative primers, if it is wished to amplify all group A9 HPV.
Tables 69-82: System Sensitivity
The sensitivity of systems of the invention has been tested under the same experimental conditions, as for the specificity tests (see Tables 52, 55, 60).
Table 69: sensitivity of A5-targeted systems (systems A, B, C, D and E)
Table 70: sensitivity of A6-targeted systems (systems A, B, C, D and E)
Tables 71-74: Sensitivity of A7-Targeted Systems

    
    
        Table 71: sensitivity of A7-targeted system A
        Table 72: sensitivity of A7-targeted system B
        Table 73: sensitivity of A7-targeted system C
        Table 74: sensitivity of A7-targeted system D

Tables 75-82: Sensitivity of A9-Targeted Systems

        Table 75: sensitivity of A9-targeted system C
        Table 76: sensitivity of A9-targeted system E2
        Table 77: sensitivity of A9-targeted system E3
        Table 78: sensitivity of A9-targeted system E4
        Table 79: sensitivity of A9-targeted system F
        Table 80: sensitivity of A9-targeted system GZ7
        Table 81: sensitivity of A9-targeted system GZ8
        Table 82: sensitivity of A9-targeted system H

Tables 83-88: “Megaplex” Specificity and Sensitivity

    
    


PCR runs have been conducted with one A5-targeted system, one A6-targeted system, one A7-targeted system, one A9-targeted system, in a single-tube amplification.
As the A7- and A9-targeted systems already are multiplex systems (i.e., they each have more than two primers), the mix of the four group-targeted systems is herein referred to as a “megaplex”.
The megaplex PCR have been tested with the plasmids listed in Table 51, in specificity (Ct; RFU) and in sensitivity (Ct; RFU).
Tables 83-86: Specificity Results for Megaplex EAAH and EBAC
Tables 83-84: Specificity of the Megaplex EAAH

    
    
        Table 83: illustrative megaplex material and method conditions, which can be used for a mix of A5-targeted system E, A6-targeted system A, A7-targeted system A and A9-targeted system H (i.e., megaplex EAAH); these experimental conditions have been used for the results depicted in table 84
        Table 84: specificity results of the EAAH megaplex
    
    


Tables 85-86: Specificity of the Megaplex EBAC

    
    
        Table 85: illustrative megaplex material and method conditions, which can be used for a mix of A5-targeted system E, A6-targeted system B, A7-targeted system A and A9-targeted system C (i.e., megaplex EBAC); these experimental conditions have been used for the results depicted in table 86;
        Table 86: specificity results of the EBAC megaplex

Tables 87-88: Sensitivity Results of the Megaplex EAAH and EBAC

        Table 87: sensitivity results of the megaplex EAAH
        Table 88: sensitivity results of the megaplex EBAC
    
    


Table 89: list of HPV genome sequences.
These tables are followed by a listing of sequences of reference templates.

    
    
        A5 Group=HPV51; HPV26; HPV69; HPV82
        A5 HR HPV=HPV51
        A5 Reference Genome=HPV51 (NC—001533.1; Human HPV, Complete Genome)
    
    









TABLE 12







A5 REFERENCE AMPLICON SEQUENCES (from reference


genome) =











Size
Start and stop positions



Systems
(bp)
within reference genome
SEQ ID NO:













System A
106
772-877
1


System AB
109
772-880
320


System AD
131
772-902
321


System B
145
736-880
2


System BA
142
736-877
322


System BD
167
736-902
323


System C
117
678-794
3


System CA
200
678-877
324


System CB
203
678-880
325


System CD
225
678-902
326


System CE
151
678-828
327


System D
192
711-902
4


System DA
167
711-877
328


System DB
170
711-880
329


System DE
118
711-828
330


System E
125
704-828
5


System EA
174
704-877
331


System EB
177
704-880
332


System ED
199
704-902
333
















TABLE 13







A5 FORWARD PRIMERS















Size
SEQ ID



Name
Sequence
Address
(bp)
NO:















A5E6f1
GGCAGTGGAAAGCAGTGGAGAC
772
22
6



 


A5E6f2
AGCTCCGTGTTGCAGGTGTTC
736
21
7


 


A5E6f3
ATATGCGTGACCAGCTACCAG
678
21
8


 


A5E6f4
GACAGGCTACGTGTTACAGAA
711
21
9


 


A5E6f5
CGGGCTGGACAGGCTACG
704
18
10
















TABLE 14







A5 REVERSE PRIMERS















Size
SEQ ID



Name
Sequence
Address
bp
NO:














A5E6r1
CCATCGCCGTTGCTAGTTGTTC
877
22
11


 


A5E6r2
AGTCCATCGCCGTTGCTAGTTG
880
22
12


 


A5E6r3
TGTCTCCACTGCTTTCCACTG
794
21
13


 


A5E6r4
CCCTCATCCTCTGTACCTTC
902
20
14


 


A5E6r5
TCGCCCATTAACATCTGCTGT
828
21
15
















TABLE 15







A5 PROBES












Corresponding


Size




beacon probes
Sequence
Address
(bp)
SEQ ID NO:





A5E6s1, A5E6s1b
GCTTAGTTCGCCCATTAACATCTGCTG
835
27
16



 


A5E6s2
CGAAGGGTGTCTCCACTGCTTTCCA
801
25
17


 


A5E6s3
ACACGGAGCTTCAATTCTGTAACACG
745
26
18


 


A5E6s4
TAGTACAACTGGCAGTGGAAAGCAGT
762
26
19
















TABLE 16







A5 BEACON PROBES










Name
Sequence (underlined are shown the beacon arms)
Address
SEQ ID NO:














A5E6s1
CCCCCTCGCTTAGTTCGCCCATTAACATCTGCTGGAGGGGG
835
20



 


A5E6s1b
CGCTGCGCTTAGTTCGCCCATTAACATCTGCTGGCAGCG
835
21


 


A5E6s2
CGCGATCCGAAGGGTGTCTCCACTGCTTTCCAGATCGCG
801
22


 


A5E6s3
CGCGATCACACGGAGCTTCAATTCTGTAACACGGATCGCG
745
23


 


A5E6s4
CGCGATCTAGTACAACTGGCAGTGGAAAGCAGTGATCGCG
762
24


 


A5E6s4
CGCGATCTAGTACAACTGGCAGTGGAAAGCAGTGATCGCG
762
24
















TABLE 17







A5 systems; minimal set = one forward primer, one reverse primer, and one probe













HPV51







reference







amplicon
Forward primer
Reverse primer
Probe
Beacon ® Probe















A5
SEQ ID NO:
Name
SEQ ID NO:
Name
SEQ ID NO:
SEQ ID NO:
Name
SEQ ID NO:


















System A
1
A5E6f1
6
A5E6r1
11
16
A5E6s1
20








16
A5E6s1b
21


System AB
320
A5E6f1
6
A5E6r2
12
16
A5E6s1
20








16
A5E6s1b
21


System AD
321
A5E6f1
6
A5E6r4
14
16
A5E6s1
20








16
A5E6s1b
21


System B
2
A5E6f2
7
A5E6r2
12
17
A5E6s2
22








16
A5E6s1
20








16
A5E6s1b
21


System BA
322
A5E6f2
7
A5E6r1
11
16
A5E6s1
20








16
A5E6s1b
21








17
A5E6s2
22


System BD
323
A5E6f2
7
A5E6r4
14
16
A5E6s1
20








16
A5E6s1b
21








17
A5E6s2
22


System C
3
A5E6f3
8
A5E6r3
13
18
A5E6s3
23


System CA
324
A5E6f3
8
A5E6r1
11
16
A5E6s1
20








16
A5E6s1b
21








17
A5E6s2
22








18
A5E6s3
23








19
A5E6s4
24


System CB
325
A5E6f3
8
A5E6r2
12
16
A5E6s1
20








16
A5E6s1b
21








17
A5E6s2
22








18
A5E6s3
23








19
A5E6s4
24


System CD
326
A5E6f3
8
A5E6r4
14
16
A5E6s1
20








16
A5E6s1b
21








17
A5E6s2
22








18
A5E6s3
23








19
A5E6s4
24


System CE
327
A5E6f3
8
A5E6r5
15
18
A5E6s3
23








19
A5E6s4
24


System D
4
A5E6f4
9
A5E6r4
14
19
A5E6s4
24








16
A5E6s1
20








16
A5E6s1b
21








17
A5E6s2
22


System DA
328
A5E6f4
9
A5E6r1
11
16
A5E6s1
20








16
A5E6s1b
21








17
A5E6s2
22








19
A5E6s4
24


System DB
329
A5E6f4
9
A5E6r2
12
16
A5E6s1
20








16
A5E6s1b
21








17
A5E6s2
22








19
A5E6s4
24


System DE
330
A5E6f4
9
A5E6r5
15
19
A5E6s4
24


System D
4
A5E6f4
9
A5E6r4
14
19
A5E6s4
24








16
A5E6s1
20








16
A5E6s1b
21








17
A5E6s2
22


System DA
328
A5E6f4
9
A5E6r1
11
16
A5E6s1
20








16
A5E6s1b
21








17
A5E6s2
22








19
A5E6s4
24


System DB
329
A5E6f4
9
A5E6r2
12
16
A5E6s1
20








16
A5E6s1b
21








17
A5E6s2
22








19
A5E6s4
24


System DE
330
A5E6f4
9
A5E6r5
15
19
A5E6s4
24









    
    
        A6 Group=HPV30; HPV53; HPV56; HPV66
        A6 HR HPV=HPV56
        A6 Reference Genome=HPV56 (NC—001594.1; Human HPV56, Complete Genome)
    
    









TABLE 18







A6 REFERENCE AMPLICON SEQUENCES (from reference genome) =











Size
Start and stop positions 



Systems
(bp)
within reference genome
SEQ ID NO:













System A
100
504-603
25


System AE
288
504-791
334


System B
115
489-603
26


System BE
303
489-791
335


System C
138
413-550
27


System CA
191
413-603
336


System CE
379
413-791
337


System D
102
502-603
28


System DE
290
502-791
338


System E
127
665-791
29
















TABLE 19







A6 FORWARD PRIMERS















Size
SEQ



Name
Sequence
Address
(bp)
ID NO:





A6E6f1
TGGACCGGGTCATGTTTGGG
504
20
30



 


A6E6f2
CTAATAGCACATGGTTGGACCG
489
22
31


 


A6E6f3
AAGGTGCTACAGATGTCAAAG
413
21
32


 


A6E6f4
GTTGGACCGGGTCATGTTTGG
502
21
33


 


A6E6f5
TCAGAGGATGAGGATGAGGATG
665
22
34
















TABLE 20







A6 REVERSE PRIMERS















Size
SEQ



Name
Sequence
Address
bp
ID NO:





A6E6r1
ACGTCTTGCAGCGTTGGTAC
603
20
35



 


A6E6r1
ACGTCTTGCAGCGTTGGTAC
603
20
35


 


A6E6r2
GGTTCTCTAGATGTTTGTCTCC
550
22
36


 


A6E6r1
ACGTCTTGCAGCGTTGGTAC
603
20
35


 


A6E6r3
ACTGCACCACAAACTTACACTC
791
22
37
















TABLE 21







A6 PROBES











Corresponding beacon probes
Sequence
Address
Size (bp)
SEQ ID NO:















A6E6s1
ACATCTAGAGAACCTAGAGAATCTACAGTA
537
30
38



 


A6E6s2, A6E6s2b
GGTCCAACCATGTGCTATTAGATGAA
509
26
39


 


A6E6s3, A6E6s3b
CGGCCACAGCAAGCTAGACA
707
20
40
















TABLE 22







A6 BEACON PROBES










Name
Sequence (underlined are shown the beacon arms)
Address
SEQ ID NO:














A6E6s1
CGCGATCACATCTAGAGAACCTAGAGAATCTACAGTAGATCGCG
537
41



 


A6E6s1
CGCGATCACATCTAGAGAACCTAGAGAATCTACAGTAGATCGCG
537
41


 


A6E6s2
CGCGATCGGTCCAACCATGTGCTATTAGATGAAGATCGCG
509
42


 


A6E6s2b
CGCCTCGGTCCAACCATGTGCTATTAGATGAAGAGGCG
509
43


 


A6E6s1
CGCGATCACATCTAGAGAACCTAGAGAATCTACAGTAGATCGCG
537
41


 


A6E6s3
CGCGACGGCCACAGCAAGCTAGACATCGCG
707
44


 


A6E6s3b
CGCCTCCGGCCACAGCAAGCTAGACAGAGGCG
707
45
















TABLE 23







A6 SYSTEMS; minimal set = one forward primer, one reverse primer, and one probe













HPV56







reference







amplicon
Forward primer
Reverse Primer
Probe
Beacon ® Probe















A6
SEQ ID NO:
Name
SEQ ID NO:
Name
SEQ ID NO: 
SEQ ID NO:
Name
SEQ ID NO:


















System A
25
A6E6f1
30
A6E6r1
35
38
A6E6s1
41


System
334
A6E6f1
30
A6E6r3
37
38
A6E6s1
41


AE





40
A6E6s3
44








40
A6E6s3b
45


System B
26
A6E6f2
31
A6E6r1
35
38
A6E6s1
41


System
335
A6E6f2
31
A6E6r3
37
38
A6E6s1
41


BE





40
A6E6s3
44








40
A6E6s3b
45


System C
27
A6E6f3
32
A6E6r2
36
39
A6E6s2
42








39
A6E6s2b
43


System
336
A6E6f3
32
A6E6r1
35
38
A6E6s1
41


CA





39
A6E6s2
42








39
A6E6s2b
43


System
337
A6E6f3
32
A6E6r3
37
38
A6E6s1
41


CE





39
A6E6s2
42








39
A6E6s2b
43








40
A6E6s3
44








40
A6E6s3b
45


System D
28
A6E6f4
33
A6E6r1
35
38
A6E6s1
41


System
338
A6E6f4
33
A6E6r3
37
38
A6E6s1
41


DE





40
A6E6s3
44








40
A6E6s3b
45


System E
29
A6E6f5
34
A6E6r3
37
40
A6E6s3
44








40
A6E6s3b
45









    
    
        A7 Group=HPV18; HPV39; HPV45; HPV59; HPV68; HPV70; HPV85
        A7 HR HPV=HPV18; HPV39; HPV45; HPV59; HPV68
        A7 Reference Genome=HPV18 (NC—001357.1; Human HPV, Complete Genome)
    
    









TABLE 24







A7 REFERENCE AMPLICON SEQUENCES (from reference


genome) =











Size
Start and stop positions 
SEQ ID


Systems
(bp)
within reference genome
NO:













Systems A, 
198 à 209
1895-2099
46


A1, A2

1895-2102
47




1895-2103
48




1902-2099
49




1902-2102
50




1902-2103
51


System AB
161 à 171
1895-2062
52




1895-2065
53




1902-2062
339




1902-2065
340


Systems
199 à 209
1895-2100
341


AC1, AC2,

1895-2103
48


AC3

1902-2100
342




1902-2103
51


System B
166 à 171
1895-2062
52




1895-2065
53




1896-2062
54




1896-2065
55




1897-2062
56




1897-2065
57


Systems
203 à 209
1895-2099
46


BA1, BA2,

1895-2102
47


BA3

1895-2103
48




1896-2099
343




1896-2102
344




1896-2103
345




1897-2099
346




1897-2102
347




1897-2103
348


Systems
204 à 209
1895-2100
349


BC1, BC2,

1895-2103
48


BC3

1896-2100
350




1896-2103
345




1897-2100
351




1897-2103
352


Systems
113 à 125
1987-2100
58


C, C1

1987-2103
59




1988-2100
60




1988-2103
61




1979-2100
62




1979-2103
63


Systems
112 à 125
1979-2099
353


CA1, CA2

1979-2102
354




1979-2103
63




1987-2099
355




1987-2102
356




1987-2103
59




1988-2099
357




1988-2102
358




1988-2103
61


System D
113 à 129
916-1032
64




916-1044
65




920-1032
66




920-1044
67
















TABLE 25







A7 FORWARD PRIMERS











Name
Sequence
Address
Size (bp)
SEQ ID NO:















A7E16f1a
TGGTATAGAACAGGAATATCAAAT
1895
24
68



 


A7E16f2a
GAACAGGTATATCCAATATTAGTG
1902
24
69


 


A7E16f3a
GAACAGGAATGTCCAATATTAG
1902
22
70


 


A7E115f1a
TGGTATAGAACAGGAATATCAAATAT
1895
26
71


 


A7E115f2a
GTACAGAACAGGAATGTCCAA
1897
21
72


 


A7E115f3d
GGTATCGCACAGGTATATCC
1896
20
73


 


A7E17f1
TGATAGCAATTTTGATTTGTCAG
1987
23
74


 


A7E17f2
GATAGCGTATTTGACCTATCAG
1988
22
75


 


A7E17f3
GGAATAGATGATAGTGTATTTGATC
1979
25
76


 


A7E12f1
GGCCGATCCAGAAGGTACAGAC
 916
22
77


 


A7E12f2
CAATCGTGAAGGTACAGATGG
 920
21
78
















TABLE 26







A7 REVERSE PRIMERS











Name
Sequence
Address
Size bp
SEQ ID NO:















A7E16r1b
CATTGCTGTTGCAGTCTG
2099
18
79



 


A7E16r2b
GCAGCATTACTGTTACAATC
2103
20
80


 


A7E16r3b
CGGCGTTACTATTACTATCTG
2102
21
81


 


A7E115r1a
TGCCATATCGCTTTCATCTG
2062
20
82


 


A7E115r2b
AAATGCTATATCACTTTCATCTG
2065
23
83


 


A7E17r1
GCATTACTGTTGCTGTCTG
2100
19
84


 


A7E17r2
GCGGCATTACTATTACAATCTG
2103
22
85


 


A7E12r2
GCATTTTCATCCTCATCCTCTG
1032
22
86


 


A7E12r3
CCTGTGTCTGTTGCATTTTC
1044
20
87
















TABLE 27







A7 PROBES














Size

Corresponding



Sequence
Address
(bp)
SEQ ID NO:
beacon probes





CAGATGAAAGCGATATGGCATT
2043
22
88
A7E1ZAS61f



 


CAGATGAAAGTGATATTGCATAT
2043
23
89
A7E1ZAS63f


 


CTGATGAAAGTGACATAGCATTT
2043
23
90
A7E1ZAS64f


 


CAGATGAAAGTGATATGGCATTT
2043
23
91
A7E1ZCS40f


 


TGGAATAGATGATAGTGTATTTGAT
1978
25
92
A7E1ZBS74f


 


GATAGCAATTTTGATTTGTCAGA
1988
23
93
A7E1ZBS26f


 


TGGAATAGATGATAGTGTATTTGAT
1978
25
92
A7E1ZBS74f


 


AGTTGATGATAGCGTGTTTGAC
1981
22
94
A7E1ZBS79f


 


AGTTGATGATAGCGTGTTTGAC
1981
22
94
A7E1ZBS80f


 


CGATAGTAATTTTGATTTGTCAGA
1987
24
95
A7E1ZBS27f


 


CAGATGAAAGTGATATGGCATTT
2043
23
91
A7E1ZCS11f


 


CAGATGAAAGTGATATGGCATTT
2043
23
91
A7E1ZCS40f


 


CTGATGAAAGTGACATAGCATTT
2043
23
90
A7E1ZCS45f


 


CAGATGAAAGTGATATTGCATAT
2043
23
89
A7E1ZCS63f


 


AATGAGTTAACAGATGAAAGTGA
2032
23
96
A7E1ZCS90f


 


GTAATGGCTGGTTCTTTGTAGAAACAA
 954
27
97
A7E1ZDS36f


 


GTAACGGCTGGTTTTATGTACAAGCTA
 954
27
98
A7E1ZDS37f


 


GTAATGGATGGTTTTTTGTACAGGCAAT
 954
28
99
A7E1ZDS38f


 


GTAACGGATGGTTTTTTGTACAAGCAAT
 954
28
100 
A7E1ZDS2f


 


GGTGTAATGGCTGGTTCTTTGTAGA
 951
25
101 
A7E1ZDS3f


 


GGTGTAATGGCTGGTTCTTTGTAGA
 951
25
101 
A7E1ZDS4f


 


GGTGTAATGGCTGGTTCTTTGTAGA
 951
25
101 
A7E1ZDS11f
















TABLE 28







A7 BEACON PROBES










Name
Sequence (underlined are shown the beacon arms)
Address
SEQ ID NO:














A7E1ZAS61f
CGACGTCAGATGAAAGCGATATGGCATTACGTCG
2043
102



 


A7E1ZAS63f
CGACGTCAGATGAAAGTGATATTGCATATACGTCG
2043
103


 


A7E1ZAS64f
CGACGTCTGATGAAAGTGACATAGCATTTACGTCG
2043
104


 


A7E1ZCS40f
CCGAGTCAGATGAAAGTGATATGGCATTTACTCGG
2043
105


 


A7E1ZBS74f
ACGTCGTGGAATAGATGATAGTGTATTTGATCGACGT
1978
106


 


A7E1ZBS26f
CGCAGTGATAGCAATTTTGATTTGTCAGAACTGCG
1988
107


 


A7E1ZBS74f
ACGTCGTGGAATAGATGATAGTGTATTTGATCGACGT
1978
106


 


A7E1ZBS79f
ACGTCGAGTTGATGATAGCGTGTTTGACCGACGT
1981
108


 


A7E1ZBS80f
CCGGCTAGTTGATGATAGCGTGTTTGACAGCCGG
1981
109


 


A7E1ZBS27f
CGCAGTCGATAGTAATTTTGATTTGTCAGAACTGCG
1987
110


 


A7E1ZCS11f
CGCAGTCAGATGAAAGTGATATGGCATTTACTGCG
2043
111


 


A7E1ZCS40f
CCGAGTCAGATGAAAGTGATATGGCATTTACTCGG
2043
105


 


A7E1ZCS45f
CGTCGTCTGATGAAAGTGACATAGCATTTACGACG
2043
112


 


A7E1ZCS63f
CGAGGTCAGATGAAAGTGATATTGCATATACCTCG
2043
113


 


A7E1ZCS90f
CCACGTAATGAGTTAACAGATGAAAGTGAACGTGG
2032
114


 


A7E1ZDS36f
CGCGACGTAATGGCTGGTTCTTTGTAGAAACAAGTCGCG
 954
115


 


A7E1ZDS37f
CGCGATCGTAACGGCTGGTTTTATGTACAAGCTAGATCGCG
 954
116


 


A7E1ZDS38f
CGCGATCGTAATGGATGGTTTTTTGTACAGGCAATGATCGCG
 954
117


 


A7E1ZDS2f
CGCGCTGTAACGGATGGTTTTTTGTACAAGCAATAGCGCG
 954
118


 


A7E1ZDS3f
CGCGATGGTGTAATGGCTGGTTCTTTGTAGAATCGCG
 951
119


 


A7E1ZDS4f
CGCGATGGTGTAATGGCTGGTTCTTTGTAGAGATCGCG
 951
120


 


A7E1ZDS11f
CTCGCTCGGTGTAATGGCTGGTTCTTTGTAGAGAGCGAG
 951
121
















TABLE 29







A7 SYSTEMS













HPV18







reference







amplicon
Forward Primers
Reverse Primers
Probes
Beacon ® Probes
















SEQ ID

SEQ ID

SEQ ID
SEQ ID

SEQ ID


A7
NO:
Name
NO:
Name
NO:
NO:
Name
NO:


















System A
46 to 51
A7E16f1a
68
A7E16r1b
79
88
A7E1ZAS61f
102




A7E16f2a
69
A7E16r2b
80
89
A7E1ZAS63f
103




A7E16f3a
70
A7E16r3b
81
90
A7E1ZAS64f
104








91
A7E1ZCS40f
105








92
A7E1ZBS74f
106


System A1
46 to 51
A7E16f1a
68
A7E16r1b
79
93
A7E1ZBS26f
107




A7E16f2a
69
A7E16r2b
80
92
A7E1ZBS74f
106




A7E16f3a
70
A7E16r3b
81
94
A7E1ZBS79f
108








94
A7E1ZBS80f
109








95
A7E1ZBS27f
110


System A2
46 to 51
A7E16f1a
68
A7E16r1b
79
91
A7E1ZCS11f
111




A7E16f2a
69
A7E16r2b
80
91
A7E1ZCS40f
105




A7E16f3a
70
A7E16r3b
81
90
A7E1ZCS45f
112








89
A7E1ZCS63f
113








96
A7E1ZCS90f
114


System AB
52-53-
A7E16f1a
68
A7E115r1a
82
93
A7E1ZBS26f
107



339-340
A7E16f2a
69
A7E115r2b
83
92
A7E1ZBS74f
106




A7E16f3a
70


94
A7E1ZBS79f
108








94
A7E1ZBS80f
109








95
A7E1ZBS27f
110


System AC1
48-51-
A7E16f1a
68
A7E17r1
84
88
A7E1ZAS61f
102



341-342
A7E16f2a
69
A7E17r2
85
89
A7E1ZAS63f
103




A7E16f3a
70


90
A7E1ZAS64f
104








91
A7E1ZCS40f
105








92
A7E1ZBS74f
106


System AC2
48-51-
A7E16f1a
68
A7E17r1
84
93
A7E1ZBS26f
107



341-342
A7E16f2a
69
A7E17r2
85
92
A7E1ZBS74f
106




A7E16f3a
70


94
A7E1ZBS79f
108








94
A7E1ZBS80f 
109








96
A7E1ZBS27f
110


System AC3
48-51-
A7E16f1a
68
A7E17r1
84
91
A7E1ZCS11f
111



341-342
A7E16f2a
69
A7E17r2
85
91
A7E1ZCS40f
105




A7E16f3a
70


90
A7E1ZCS45f
112








89
A7E1ZCS63f
113








96
A7E1ZCS90f
114


System B
52 to −57
A7E115f1a
71
A7E115r1a
82
93
A7E1ZBS26f
107




A7E115f2a
72
A7E115r2b
83
92
A7E1ZBS74f
106




A7E115f3d
73


94
A7E1ZBS79f
108








94
A7E1ZBS80f
109








95
A7E1ZBS27f
110


System BA1
46-47-48-
A7E115f1a
71
A7E16r1b
79
88
A7E1ZAS61f
102



343 to
A7E115f2a
72
A7E16r2b
80
89
A7E1ZAS63f
103



348
A7E115f3d
73
A7E16r3b
81
90
A7E1ZAS64f
104








91
A7E1ZCS40f
105








92
A7E1ZBS74f
106


System BA2
46-47-48-
A7E115f1a
71
A7E16r1b
79
93
A7E1ZBS26f
107



343 to
A7E115f2a
72
A7E16r2b
80
92
A7E1ZBS74f
106



348
A7E115f3d
73
A7E16r3b
81
94
A7E1ZBS79f
108








94
A7E1ZBS80f
109








95
A7E1ZBS27f
110


System BA3
46-47-48-
A7E115f1a
71
A7E16r1b
79
91
A7E1ZCS11f
111



343 to
A7E115f2a
72
A7E16r2b
80
91
A7E1ZCS40f
105



348
A7E115f3d
73
A7E16r3b
81
90
A7E1ZCS45f
112








89
A7E1ZCS63f
113








96
A7E1ZCS90f
114


System BC1
48-345-
A7E115f1a
71
A7E17r1
84
88
A7E1ZAS61f
102



349 to
A7E115f2a
72
A7E17r2
85
89
A7E1ZAS63f
103



352
A7E115f3d
73


90
A7E1ZAS64f
104








91
A7E1ZCS40f
105








92
A7E1ZBS74f
106


System BC2
48-345-
A7E115f1a
71
A7E17r1
84
93
A7E1ZBS26f
107



349 to
A7E115f2a
72
A7E17r2
85
92
A7E1ZBS74f
106



352
A7E115f3d
73


94
A7E1ZBS79f
108








94
A7E1ZBS80f
109








95
A7E1ZBS27f
110


System BC3
48-345-
A7E115f1a
71
A7E17r1
84
91
A7E1ZCS11f
111



349 to
A7E115f2a
72
A7E17r2
85
91
A7E1ZCS40f
105



352
A7E115f3d
73


90
A7E1ZCS45f
112








89
A7E1ZCS63f
113








96
A7E1ZCS90f
114


System C
58 to 63
A7E17f1
74
A7E17r1
84
91
A7E1ZCS11f
111




A7E17f2
75
A7E17r2
85
91
A7E1ZCS40f
105




A7E17f3
76


90
A7E1ZCS45f
112








89
A7E1ZCS63f
113








96
A7E1ZCS90f
114


System C1
58 to 63
A7E17f1
74
A7E17r1
84
88
A7E1ZAS61f
102




A7E17f2
75
A7E17r2
85
89
A7E1ZAS63f
103




A7E17f3
76


90
A7E1ZAS64f
104








91
A7E1ZCS40f
105








96
A7E1ZCS90f
114


System CA1
59-61-63-
A7E17f1
74
A7E16r1b
79
91
A7E1ZCS11f
111



353 to
A7E17f2
75
A7E16r2b
80
91
A7E1ZCS40f
105



358
A7E17f3
76
A7E16r3b
81
90
A7E1ZCS45f
112








89
A7E1ZCS63f
113








96
A7E1ZCS90f
114


System CA2
59-61-63-
A7E17f1
74
A7E16r1b
79
88
A7E1ZAS61f
102



353 to
A7E17f2
75
A7E16r2b
80
89
A7E1ZAS63f
103



358
A7E17f3
76
A7E16r3b
81
90
A7E1ZAS64f
104








91
A7E1ZCS40f
105








96
A7E1ZCS90f
114


System D
64 to 67
A7E12f1
77
A7E12r2
86
97
A7E1ZDS36f
115




A7E12f2
78
A7E12r3
87
98
A7E1ZDS37f
116








99
A7E1ZDS38f
117








100
A7E1ZDS2f
118








101
A7E1ZDS3f
119








101
A7E1ZDS4f
120








101
A7E1ZDS11f
121









    
    
        A9 Group=HPV16; HPV31; HPV33; HPV35; HPV52; HPV58; HPV67
        A9 HR HPV=HPV16; HPV31; HPV33; HPV35; HPV52; HPV58
        A9 Reference Genome=HPV16 (NC—001526.1; Human HPV16, Complete Genome)
    
    









TABLE 30





A9 REFERENCE AMPLICON SEQUENCES (from reference


genome) =





















Amplicons
Forward
Reverse
Start-stop
SEQ 


Systems
size bp
address
address
positions
ID NO:





System C
88
2707
2794
2707-2794
122




2707
2794






2707







2707







2707







2707







2707





System E1
191 à 198
3600
3790
3600-3790
123




3600
3793
3600-3793
124




3600
3791
3600-3791
125





3790
3600-3797
126





3797
3600-3795
127





3795




System E2
190 à 198
3600
3790
3600-3790
123




3601
3793
3600-3793
124




3600
3791
3600-3791
125





3790
3600-3797
126





3797
3600-3795
127





3795
3601-3790
128






3601-3793
129






3601-3791
130






3601-3797
131






3601-3795
132






Amplicons
address 
address 
Start-stop
SEQ 


Systems
size pb
forw
rev
position
ID NO:





System E3
188 à 193
3600
3788
3600-3788
133




3601
3792
3600-3792
134




3600
3792
3600-3790
135





3790
3601-3788
136





3792
3601-3792
137





3792
3601-3790
138





3792







3790




System E4
179 à 186
3607
3788
3607-3788
139




3610
3792
3607-3792
140




3609
3792
3607-3790
141





3790
3610-3788
142





3792
3610-3792
143





3792
3610-3790
144





3792
3609-3788
145





3790
3609-3792
146






3609-3790
147


System E5
181à 191
3607
3790
3607-3790
141




3610
3793
3607-3791
359




3609
3791
3607-3793
360





3790
3607-3795
361





3797
3607-3797
362





3795
3609-3790
363






3609-3791
364






3609-3793
365






3609-3795
366






3609-3797
367






3610-3790
144






3610-3791
368






3610-3793
369






3610-3795
370






3610-3797
371


System E6
189 à 193
3600
3788
3600-3788
133




3600
3792
3600-3790
135




3600
3792
3600-3792
134





3790







3792







3792







3792







3790




System E1 H 
231 à 241
3600
3838
3600-3830
372


Z7, Z8

3600
3831
3600-3831
373




3600
3830
3600-3837
374





3830
3600-3838
375





3838
3600-3839
376





3840
3600-3840
377





3839







3838







3837




System E2H
230 à 241
3600
3838
3600-3830
372


Z7, Z8

3601
3831
3600-3831
373




3600
3830
3600-3837
374





3830
3600-3838
375





3838
3600-3839
376





3840
3600-3840
377





3839
3601-3830
378





3838
3601-3831
379





3837
3601-3837
380






3601-3838
381






3601-3839
382






3601-3840
383


System E4H
224 à 234
3607
3838
3607-3830
384


Z7, Z8

3610
3831
3607-3831
385




3609
3830
3607-3837
386





3830
3607-3838
387





3838
3607-3839
388





3840
3607-3840
389





3839
3609-3830
390





3838
3609-3831
391





3837
3609-3837
392






3609-3838
393






3609-3839
394






3609-3840
395






3610-3830
396






3610-3831
397






3610-3837
398






3610-3838
399






3610-3839
400






3610-3840
401


System F
163 à 172
3626
3788
3626-3788
148




3626
3792
3626-3792
149




3621
3792
3626-3790
150




3625
3790
3621-3788
151





3792
3621-3792
152





3792
3621-3790
153





3792
3625-3788
154





3790
3625-3792
155






3625-3790
156


System FE 
165 à 177
3626
3790
3621-3790
153




3626
3793
3621-3791
402




3621
3791
3621-3793
403




3625
3790
3621-3795
404





3797
3621-3797
405





3795
3625-3790
156






3625-3791
406






3625-3793
407






3625-3795
408






3625-3797
409






3626-3790
150






3626-3791
410






3626-3793
411






3626-3795
412






3626-3797
413


System FH
205 à 220
3626
3838
3621-3830
163


Z7, Z8

3626
3831
3621-3831
162




3621
3830
3621-3837
164




3625
3830
3621-3838
414





3838
3621-3839
415





3840
3621-3840
161





3839
3625-3830
167





3838
3625-3831
166





3837
3625-3837
168






3625-3838
416






3625-3839
417






3625-3840
165






3626-3830
159






3626-3831
158






3626-3837
160






3626-3838
418






3626-3839
419






3626-3840
157


System G Z7,
205 à 220
3626
3840
3626-3840
157


Z8

3626
3831
3626-3831
158




3621
3830
3626-3830
159




3625
3837
3626-3837
160





3840
3621-3840
161





3840
3621-3831
162






3621-3830
163






3621-3837
164






3625-3840
165






3625-3831
166






3625-3830
167






3625-3837
168


System H
132 à 150
3699
3838
3699-3838
169




3691
3831
3699-3831
170




3693
3830
3699-3830
171




3696
3830
3699-3840
172




3695
3838
3699-3839
173




3698
3840
3699-3837
174




3697
3839
3691-3838
175




3699
3838
3691-3831
176




3698
3837
3691-3830
177






3691-3840
178






3691-3839
179






3691-3837
180






3693-3838
181






3693-3831
182






3693-3830
183






3693-3840
184






3693-3839
185






3693-3837
186


System H
132 à 150
3696
3838
3696-3838
187




3695
3831
3696-3831
188




3698
3830
3696-3830
189




3697
3840
3696-3840
190





3839
3696-3839
191





3837
3696-3837
192






3695-3838
193






3695-3831
194






3695-3830
195






3695-3840
196






3695-3839
197






3695-3837
198






3698-3838
199






3698-3831
200






3698-3830
201






3698-3840
202






3698-3839
203






3698-3837
204






3697-3838
205






3697-3831
206






3697-3830
207






3697-3840
208






3697-3839
209






3697-3837
210
















TABLE 31







A9 FORWARD PRIMERS








Forward Primer












Name
5′ Sequence 3′
address
size bp
SEQ ID NO:















A9E1f7
AGGACGTGGTCCAGATTAAGTTT
2707
23
211



 


A9E1f8
AGGACGTGGTGCAGATTAAG
2707
20
212


 


A9E1f9
AGGACGTGGTGCAAATTAAGTTT
2707
23
213


 


A9E1f10
AGGACGTGGTGCAGATTAAATTT
2707
23
214


 


A9E1f11
AGGACGTGGTGCAGATTAGGTTT
2707
23
215


 


A9E1f12
AGGACGTGGTGCAAATTAAATTT
2707
23
216


 


A9E1f13
AGGACGTGGTGCAAATTAGGTTT
2707
23
217


 


A9E2f1
TAGTAACACTACACCCATAGTACAT
3600
25
218


 


A9E2f2
TCTAACGTTGCACCTATCGTG
3600
21
219


 


A9E2f4
TCCTTCTACTGCACCTATAATACA
3600
24
220


 


A9E2f1a
TAGTACCACTACACCCATAGTACAT
3600
25
221


 


A9E2f2a
TCTAACGTTGCACCTATCGTGCAT
3601
24
222


 


A9E2f4a
TCCTTCTACTGCACCTATAATACAC
3600
25
223


 


A9E2Z5Z6f1c
ACTACACCTATAGTACATTTAAAAGG
3607
26
224


 


A9E2Z5Z6f2c
GCACCTATAGTGCATTTAAAAG
3610
22
225


 


A9E2Z5Z6f3b
TGCACCTATAATACACCTAAAAG
3609
23
226


 


A9E21f1az
TAAAAGGTGATGCTAATACTTTAAA
3626
25
227


 


A9E21f2bz
TAAAAGGTGATGCAAATACATTAAA
3626
25
228


 


A9E21f3dz
GCATTTAAAAGGTGAATCAAATAG
3621
24
229


 


A9E21f4cz
CTAAAAGGTGATCCTAATAGTTTAAA
3625
26
230


 


A9E2f5
GTCGTCTACATGGCATTGGA
3699
20
231


 


A9E2f6
CAAGATGCTTCATCTACATGGAG
3691
23
232


 


A9E2f7
AGAAGCGTCATCTACATGGAG
3693
21
233


 


A9E2f8
AGTGTCGTCTACATGGCATTG
3696
21
234


 


A9E2f9
ATATGTCATCTACATGGCATTGG
3695
23
235


 


A9E2f10
TGTCATCCACATGGCATTGG
3698
20
236


 


A9E2f10b
ATGTCATCCACATGGCATTG
3697
20
237


 


A9E2f11
TTCATCTACCTGGAGTTGGAC
3699
21
238


 


A9E2f12
TTTCATCTACATGGAGTTGGAC
3698
22
239
















TABLE 32







A9 REVERSE PRIMERS








Reverse Primer












Name
5′ Sequence 3′
address
size bp
SEQ ID NO:















A9E1r5
TGTCCTGACACACATTTAAACG
2794
22
240



 


A9E1r6
TGTCCTGCACTGCATTTAAAC
2794
21
241


 


A9E2r1
ATTGGTCACGTTGCCATTC
3790
19
242


 


A9E2r2
AAAATTGTTGACGTTGTGTTTC
3793
22
243


 


A9E2r3
AACTGTTGACGTTGTGTTTC
3791
20
244


 


A9E2r4
ACATTTGTCGTTGCGGTTC
3790
19
245


 


A9E2r13
GTCTCTTTGTGATGTACTTATATATG
3797
26
246


 


A9E2r14
CCCTTTGATATTCTGTTGTGTAAG
3795
24
247


 


A9E21r1cz
TGGTCACGTTGCCATTC
3788
17
248


 


A9E21r2az
AAAATCGTCTCTTTGTGATGT
3792
21
249


 


A9E21r3az
AAACATTTGTTGTTGCTGTTC
3792
21
250


 


A9E21r4fz
ATTTATCCCTTTGATATTCTGTTG
3790
24
251


 


A9E21r5az
AAACAGTTGACGTTGTGTTTC
3792
21
252


 


A9E21r6az
AAACTGTTGACGTTGTGTTTC
3792
21
253


 


A9E21r7az
AAATTGTTGACGTTGTGTTTC
3792
21
254


 


A9E21r8az
ACAGTTGTCGTTGTGTTTC
3790
19
255


 


A9E2r7C
AAATCCTGTAGACACTGTAACAGT
3840
24
256


 


A9E2r8
ACTTATTTGCACAGTAGGTGGT
3831
22
257


 


A9E2r10
CTTACTTGCACAGTAGTTGGTA
3830
22
258


 


A9E2r12
ATCCTGTTGACACTGATACTGT
3837
22
259


 


A9E2r12B
TATCCTGTAGACACTGAAACTGTG
3840
24
260


 


A9E2r15
AAATCCAGTAGACACTGTAATAGTT
3840
25
261


 


A9E2r7B
ATCCTGTAGACACTGTAACAGTT
3838
23
262


 


A9E2r8
ACTTATTTGCACAGTAGGTGGT
3831
22
257


 


A9E2r9
CTTACTTGCACAGTAGGTGGTA
3830
22
263


 


A9E2r10
CTTACTTGCACAGTAGTTGGTA
3830
22
258


 


A9E2r12
ATCCTGTTGACACTGATACTGT
3838
22
259


 


A9E2r7C
AAATCCTGTAGACACTGTAACAGT
3840
24
256


 


A9E2r12B
TATCCTGTAGACACTGAAACTGTG
3839
24
264


 


A9E2r15
AAATCCAGTAGACACTGTAATAGTTT
3838
26
261


 


A9E2r16
ACCGTACTTATTTGCACAGTG
3837
21
265
















TABLE 33







A9 PROBES











5′ Sequence 3′
address
size pb
SEQ ID NO:
Corresponding beacon probes















TCCATCGTTTTCCTTGTCCTCT
2738
22
266
A9E1S10 and S10a



 


TCCATCGTTTTCTTTGACCTCT
2738
22
267
A9E1S11 and S11a


 


TCCATCATTTTCTTTGACCTCT
2738
22
268
A9E1S12, S12a and S12b


 


TCTCCATCATTTTCTTTGTCCTCT
2738
24
269
A9E1S13a, S13b and S13c


 


CTCCATCGTTTTCTTTGTCCTC
2739
22
270
A9E1S14a


 


CTCCATCATTTTCTTTGACCTCTC
2737
24
271
A9E1S15a and 15b


 


AGTGTCGTCTACATGGCATTGGAC
3696
24
272
A9E2Z7S1


 


ATATGTCATCCACCTGGCATTGGAC
3695
25
273
A9E2Z7S2 and S2a


 


ATATGTCATCCACCTGGCATTGGA
3695
24
274
A9E2Z7S2b


 


ATGCTTCATCTACATGGAGATGGAC
3695
25
275
A9E2Z7S3 and S3a


 


CAAGTTTCATCTACATGGCATTGGAC
3694
26
276
A9E2Z7S4 and S4a


 


GATAGTGAATGGCAACGTGA
3766
20
277
A9E2Z8S2f, S21f and S28f


 


ATAAGTACATCACAAAGAGACGA
3766
23
278
A9E2Z8S56f, S58f and S61f


 


TAACTGAACAGCAACAACAAATG
3767
23
279
A9E2Z8S101f, 105f and 127f


 


CACAACAGAATATCAAAGGGATAAATT
3765
27
280
A9E2Z8S146f, 155f and 156f


 


CGTACAGTGATGAAACACAAC
3761
21
281
A9E2Z8S210f


 


AACGGAAACACAACGACAAC
3768
20
282
A9E2Z8S231f, 236f and 250f
















TABLE 34







A9 BEACON PROBES








Beacon probe












Name
5′ Sequence 3′
address
size bp
SEQ ID NO:















A9E1S10
CGCGATTCCATCGTTTTCCTTGTCCTCTATCGCG
2738
22
283



 


A9E1S10a
CGCGATCCATCGTTTTCCTTGTCCTCTTCGCG
2738
22
284


 


A9E1S11
CGCGATTCCATCGTTTTCTTTGACCTCTATCGCG
2738
22
285


 


A9E1S11a
CGCGATCCATCGTTTTCTTTGACCTCTTCGCG
2738
22
286


 


A9E1S12
CGCGATTCCATCATTTTCTTTGACCTCTATCGCG
2738
22
287


 


A9E1S12a
CGCGATCCATCATTTTCTTTGACCTCTTCGCG
2738
22
288


 


A9E1S12b
CGCTGTCCATCATTTTCTTTGACCTCTCAGCG
2738
22
289


 


A9E1S13a
CGCGTTCTCCATCATTTTCTTTGTCCTCTACGCG
2738
24
290


 


A9E1S13b
CGCCGTCTCCATCATTTTCTTTGTCCTCTCGGCG
2738
24
291


 


A9E1S13c
CGCGATTCTCCATCATTTTCTTTGTCCTCTATCGCG
2738
24
292


 


A9E1S14a
CGCGATCTCCATCGTTTTCTTTGTCCTCATCGCG
2739
22
293


 


A9E1S15a
CGCCGCTCCATCATTTTCTTTGACCTCTCCGGCG
2737
24
294


 


A9E1S15b
CGCGATCTCCATCATTTTCTTTGACCTCTCATCGCG
2737
24
295


 


A9E2Z7S1
CGCGAAGTGTCGTCTACATGGCATTGGACTCGCG
3696
24
296


 


A9E2Z7S2
CGCTCGATATGTCATCCACCTGGCATTGGACCGAGCG
3695
25
297


 


A9E2Z7S2a
CGCATGATATGTCATCCACCTGGCATTGGACCATGCG
3695
25
298


 


A9E2Z7S2b
CGCATGATATGTCATCCACCTGGCATTGGACATGCG
3695
24
299


 


A9E2Z7S3
CGCACTATGCTTCATCTACATGGAGATGGACAGTGCG
3695
25
300


 


A9E2Z7S3a
CCGACGATGCTTCATCTACATGGAGATGGACCGTCGG
3695
25
301


 


A9E2Z7S4
CGCGATCAAGTTTCATCTACATGGCATTGGACATCGCG
3694
26
302


 


A9E2Z7S4a
CGCGAGCAAGTTTCATCTACATGGCATTGGACCTCGCG
3694
26
303


 


A9E2Z8S2f
CAGCGTGATAGTGAATGGCAACGTGAACGCTG
3766
20
304


 


A9E2Z8S21f
CGGACTGATAGTGAATGGCAACGTGAAGTCCG
3766
20
305


 


A9E2Z8S28f
CTCGCTGATAGTGAATGGCAACGTGAAGCGAG
3766
20
306


 


A9E2Z8S56f
CGAGCTATAAGTACATCACAAAGAGACGAAGCTCG
3766
23
307


 


A9E2Z8S58f
CGCAGTATAAGTACATCACAAAGAGACGAACTGCG
3766
23
308


 


A9E2Z8S61f
CGCGTTATAAGTACATCACAAAGAGACGAAACGCG
3766
23
309


 


A9E2Z8S101f
CGAGGTTAACTGAACAGCAACAACAAATGACCTCG
3767
23
310


 


A9E2Z8S105f
CGCGATTAACTGAACAGCAACAACAAATGATCGCG
3767
23
311


 


A9E2Z8S127f
CCGGCTTAACTGAACAGCAACAACAAATGAGCCGG
3767
23
312


 


A9E2Z8S146f
CGCGATCACAACAGAATATCAAAGGGATAAATTATCGCG
3765
27
313


 


A9E2Z8S155f
CGCACGCACAACAGAATATCAAAGGGATAAATTCGTGCG
3765
27
314


 


A9E2Z8S156f
CCGGCTCACAACAGAATATCAAAGGGATAAATTAGCCGG
3765
27
315


 


A9E2Z8S210f
CCGGCTCGTACAGTGATGAAACACAACAGCCGG
3761
21
316


 


A9E2Z8S231f
CGAGGTAACGGAAACACAACGACAACACCTCG
3768
20
317


 


A9E2Z8S236f
CGCGTTAACGGAAACACAACGACAACAACGCG
3768
20
318


 


A9E2Z8S250f
CGATGCAACGGAAACACAACGACAACGCATCG
3768
20
319
















TABLE 35







A9 SYSTEMS













HPV16 







reference







amplicon
Forward Primer
Reverse Primer
Probe
Beacon Probe















A9
SEQ ID NO:
Name
SEQ ID NO:
Name
SEQ ID NO:
SEQ ID NO:
Name
SEQ ID NO:





System C
122
A9E1f8
212; 214;
A9E1r5
240-241
266-271
A9E1S10
283-295




A9E1f10
216
A9E1r6


A9E1S10a





A9E1f12
(211; 213;



—





(A9E1f7)
215; 217)



A9E1S11





(A9E1f9)




A9E1S11a





(A9E1f11)




—





(A9E1f13)




A9E1S12










A9E1S12a










A9E1S12b










—










A9E1S13a










A9E1S13b










A9E1S13c










—










A9E1S14a










—










A9E1S15a










A9E1S15b



System E1
123 to 127
A9E2f1
218-220
A9E2r1
242-243;
272-276
A9E2Z7S1
296-303




A9E2f2

A9E2r2
245-247

—





A9E2f4

A9E2r4
(244)

A9E2Z7S2







A9E2r13


A9E2Z7S2a







A9E2r14


A9E2Z7S2b







(A9E2r3)


—










A9E2Z7S3










A9E2Z7S3a










—










A9E2Z7S4










A9E2Z7S4a



System E2
123 to 132
A9E2f1a
221-223
A9E2r1
242-243;
272-276
A9E2Z7S1
296-303




A9E2f2a

A9E2r2
246-247

—





A9E2f4a

A9E2r4
(244)

A9E2Z7S2







A9E2r13


A9E2Z7S2a







A9E2r14


A9E2Z7S2b







(A9E2r3)


—










A9E2Z7S3










A9E2Z7S3a










—










A9E2Z7S4










A9E2Z7S4a



System E3
133 to 138
A9E2f1a
221-223
A9E21r1cz
248-252
272-276
A9E2Z7S1
296-303




A9E2f2a

A9E21r2az
(253-255)

—





A9E2f4a

A9E21r3az


A9E2Z7S2







A9E21r4fz


A9E2Z7S2a







A9E21r5az


A9E2Z7S2b







(A9E21r6az)


—







(A9E21r7az)


A9E2Z7S3







(A9E21r8az)


A9E2Z7S3a










—










A9E2Z7S4










A9E2Z7S4a



System E4
139 to 147
A9E2Z5Z6f1c
224-226
A9E21r1cz
248-252
272-276
A9E2Z7S1
296-303




A9E2Z5Z6f2c

A9E21r2az
(253-255)

—





A9E2Z5Z6f3b

A9E21r3az


A9E2Z7S2







A9E21r4fz


A9E2Z7S2a







A9E21r5az


A9E2Z7S2b







(A9E21r6az


—







A9E21r7az


A9E2Z7S3







A9E21r8az)


A9E2Z7S3a










—










A9E2Z7S4










A9E2Z7S4a



System E5
141; 144 and 359
A9E2Z5Z6f1c
224-226
A9E2r1
242-243;
272-276
A9E2Z7S1
296-303



to 371
A9E2Z5Z6f2c

A9E2r2
245-247;

—





A9E2Z5Z6f3b

A9E2r4
(244)

A9E2Z7S2







A9E2r13


A9E2Z7S2a







A9E2r14


A9E2Z7S2b







(A9E2r3)


—










A9E2Z7S3










A9E2Z7S3a










—










A9E2Z7S4










A9E2Z7S4a



System E6
133 to 135
A9E2f1
218-220
A9E21r1cz
248-252;
272-276
A9E2Z7S1
296-303




A9E2f2

A9E21r2az
(253-255)

—





A9E2f4

A9E21r3az


A9E2Z7S2







A9E21r4az


A9E2Z7S2a







A9E21r5az


A9E2Z7S2b







(A9E21r6az)


—







(A9E21r7az)


A9E2Z7S3







(A9E21r8az)


A9E2Z7S3a










—










A9E2Z7S4










A9E2Z7S4a



System
372 to 377
A9E2f1
218-220
(A9E2r7B)
(256; 257; 259; 262; 263); 
272-276
A9E2Z7S1
296-303


E1H Z7

A9E2f2

(A9E2r8)
258; 261; 264; 265

—





A9E2f4

(A9E2r9)


A9E2Z7S2







A9E2r10


A9E2Z7S2a







(A9E2r12)


A9E2Z7S2b







(A9E2r7C)


—







A9E2r12B


A9E2Z7S3







A9E2r15


A9E2Z7S3a







A9E2r16


—










A9E2Z7S4










A9E2Z7S4a



System
372 to 377
A9E2f1
218-220
(A9E2r7B)
(256; 257; 259,
277-282
A9E2Z8S2f
304-319


E1H Z8

A9E2f2

(A9E2r8)
262; 263);

A9E2Z8S21f





A9E2f4

(A9E2r9)
258; 261; 264;

A9E2Z8S28f







A9E2r10
265

—







(A9E2r12)


A9E2Z8S56f







(A9E2r7C)


A9E2Z8S58f







A9E2r12B


A9E2Z8S61f







A9E2r15


—







A9E2r16


A9E2Z8S101f










A9E2Z8S105f










A9E2Z8S127f










—










A9E2Z8S146f










A9E2Z8S155f










A9E2Z8S156f










—










A9E2Z8S210f










—










A9E2Z8S231f










A9E2Z8S236f










A9E2Z8S250f



System
372 to 383
A9E2f1a
221-223
(A9E2r7B)
(256; 257; 259; 262; 263);
272-276
A9E2Z7S1
296-303


E2H Z7

A9E2f2a

(A9E2r8)
258; 261; 264; 265

—





A9E2f4a

(A9E2r9)


A9E2Z7S2







A9E2r10


A9E2Z7S2a







(A9E2r12)


A9E2Z7S2b







(A9E2r7C)


—







A9E2r12B


A9E2Z7S3







A9E2r15


A9E2Z7S3a







A9E2r16


—










A9E2Z7S4










A9E2Z7S4a



System
372 to 383
A9E2f1a
221-223
(A9E2r7B)
(256; 257; 259; 262; 263);
277-282
A9E2Z82f
304-319


E2H Z8

A9E2f2a

(A9E2r8)
258; 261; 264; 265

A9E2Z8S21f





A9E2f4a

(A9E2r9)


A9E2Z8S28f







A9E2r10


—







(A9E2r12)


A9E2Z8S56f







(A9E2r7C)


A9E2Z8S58f







A9E2r12B


A9E2Z8S61f







A9E2r15


—







A9E2r16


A9E2Z8S101f










A9E2Z8S105f










A9E2Z8S127f










—










A9E2Z8S146f










A9E2Z8S155f










A9E2Z8S156f










—










A9E2Z8S210f










—










A9E2Z8S231f










A9E2Z8S236f










A9E2Z8S250f



System 
384 to 401
A9E2Z5Z6f1c
224-226
(A9E2r7B)
(256; 257; 259;
272-276
A9E2Z7S1
296-303


E7H Z7

A9E2Z5Z6f2c

(A9E2r8)
262; 263);

—





A9E2Z5Z6f3b

(A9E2r9)
258; 261; 264;

A9E2Z7S2







A9E2r10
265

A9E2Z7S2a







(A9E2r12)


A9E2Z7S2b







(A9E2r7C)


—







A9E2r12B


A9E2Z7S3







A9E2r15


A9E2Z7S3a







A9E2r16


—










A9E2Z7S4










A9E2Z7S4a



System
384 to 401
A9E2Z5Z6f1c
224-226
(A9E2r7B)
(256; 257; 259; 262; 263);
277-282
A9E2Z8S2f
304-319


E4H Z8

A9E2Z5Z6f2c

(A9E2r8)
258; 261; 264; 265

A9E2Z8S21f





A9E2Z5Z6f3b

(A9E2r9)


A9E2Z8S28f







A9E2r10


—







(A9E2r12)


A9E2Z8S56f







(A9E2r7C)


A9E2Z8S58f







A9E2r12B


A9E2Z8S61f







A9E2r15


—







A9E2r16


A9E2Z8S101f










A9E2Z8S105f










A9E2Z8S127f










—










A9E2Z8S146f










A9E2Z8S155f










A9E2Z8S156f










—










A9E2Z8S210f










—










A9E2Z8S231f










A9E2Z8S236f










A9E2Z8S250f



System F
148 to 156
A9E21f1az
227-230
A9E21r1cz
248-252;
272-276
A9E2Z7S1
296-303




A9E21f2bz

A9E21r2az
(2530255)

—





A9E21f3dz

A9E21r3az


A9E2Z7S2





A9E21f4cz

A9E21r4fz


A9E2Z7S2a







A9E21r5az


A9E2Z7S2b







(A9E21r6az)


—







(A9E21r7az)


A9E2Z7S3







(A9E21r8az)


A9E2Z7S3a










—










A9E2Z7S4










A9E2Z7S4a



System FE
153; 153; 156; 402 to 
A9E21f1az
227-230
A9E2r1
242-243;
272-276
A9E2Z7S1
296-303



413
A9E21f2bz

A9E2r2
(244);

—





A9E21f3dz

(A9E2r3)
245-247

A9E2Z7S2





A9E21f4cz

A9E2r4


A9E2Z7S2a







A9E2r13


A9E2Z7S2b







A9E2r14


—










A9E2Z7S3










A9E2Z7S3a










—










A9E2Z7S4










A9E2Z7S4a



System FH
157 to 168 and 414
A9E21f1az
227-230
(A9E2r7B)
(262);
272-276
A9E2Z7S1
296-303


Z7
to 419
A9E21f2bz

(A9E2r8)
(257);

—





A9E21f3dz

(A9E2r9)
(263);

A9E2Z7S2





A9E21f4cz

(A9E2r12)
(259);

A9E2Z7S2a







(A9E2r7C)
(256);

A9E2Z7S2b







A9E2r10
258;

—







A9E2r12B
264

A9E2Z7S3







A9E2r15
261

A9E2Z7S3a







A9E2r16
265

—










A9E2Z7S4










A9E2Z7S4a



System FH
157 to 168 and 414
A9E21f1az
227-230
(A9E2r7B)
(262);
277-282
A9E2Z8S2f
304-319


Z8
to 419
A9E21f2bz

(A9E2r8)
(257);

A9E2Z8S21f





A9E21f3dz

(A9E2r9)
(263);

A9E2Z8S28f





A9E21f4cz

(A9E2r12)
(259);

—







(A9E2r7C)
(256);

A9E2Z8S56f







A9E2r10
258;

A9E2Z8S58f







A9E2r12B
264

A9E2Z8S61f







A9E2r15
261

—







A9E2r16
265

A9E2Z8S101f










A9E2Z8S105f










A9E2Z8S127f










—










A9E2Z8S146f










A9E2Z8S155f










A9E2Z8S156f










—










A9E2Z8S210f










—










A9E2Z8S231f










A9E2Z8S236f










A9E2Z8S250f



System G
157 to 168
A9E21f1az
227-230
(A9E2r7C)
(256);
272-276
A9E2Z7S1
296-303


Z7

A9E21f2bz

A9E2r8
257-261

—





A9E21f3dz

A9E2r10


A9E2Z7S2





A9E21f4cz

A9E2r12


A9E2Z7S2a







A9E2r12B


A9E2Z7S2b







A9E2r15


—










A9E2Z7S3










A9E2Z7S3a










—










A9E2Z7S4










A9E2Z7S4a



System G
157 to 168
A9E21f1az
227-230
(A9E2r7C)
(256);
277-282
A9E2Z8S2f
304-319


Z8

A9E21f2bz

A9E2r8
257-261

A9E2Z8S21f





A9E21f3dz

A9E2r10


A9E2Z8S28f





A9E21f4cz

A9E2r12


—







A9E2r12B


A9E2Z8S56f







A9E2r15


A9E2Z8S58f










A9E2Z8S61f










—










A9E2Z8S101f










A9E2Z8S105f










A9E2Z8S127f










—










A9E2Z8S146f










A9E2Z8S155f










A9E2Z8S156f










—










A9E2Z8S210f










—










A9E2Z8S231f










A9E2Z8S236f










A9E2Z8S250f



System H
169 to 210
(A9E2f5)
(231);
(A9E2r7B)
(262);
277-282
A9E2Z8S2f
304-319




A9E2f6
232;
(A9E2r8)
(257);

A9E2Z8S21f





(A9E2f7)
(233);
(A9E2r9)
(263);

A9E2Z8S28f





A9E2f8
234;
(A9E2r12)
(259);

—





A9E2f9
235;
(A9E2r7C)
(256);

A9E2Z8S56f





(A9E2f10)
(236);
A9E2r10
258;

A9E2Z8S58f





(A9E2f10b)
(237);
A9E2r12B
264;

A9E2Z8S61f





(A9E2f11)
(238);
A9E2r15
261;

—





(A9E2f12)
(239)
A9E2r16
265

A9E2Z8S101f










A9E2Z8S105f










A9E2Z8S127f










—










A9E2Z8S146f










A9E2Z8S155f










A9E2Z8S156f










—










A9E2Z8S210f










—










A9E2Z8S231f










A9E2Z8S236f










A9E2Z8S250f





Those primers which are between brackets are optional and/or equivalent and/or alternative primers.













TABLE 36







A5 Systems A to C: sequence aligment mismach evaluation


Reference of sequence: HPV 56->ref|NC_001594.1|













System A
System B
System C



















forward
reverse

forward
reverse

forward
reverse





primer
primer
probe
primer
primer
probe
primer
primer
probe




SEQ ID
SEQ ID
SEQ ID
SEQ ID
SEQ ID
SEQ ID
SEQ ID
SEQ ID
SEQ ID




NO: 6
NO: 11
NO: 20
NO: 7
NO: 12
NO: 22
NO: 8
NO: 13
NO: 23


NoHPV
Group
A5E6f1
A5E6r1
A5E6s1
A5E6f2
A5E6r2
A5E6s2
A5E6f3
A5E6r3
A5E6s3




















51
A5
0
0
0
0
0
0
0
0
0


26
A5
7
11
8
7
8
7
5
6
4


69
A5
8
9
8
10
7
9
6
7
6


82
A5
1
4
3
4
4
1
3
0
5


56
A6
12
13
10
9
12
12
10
13
8


30
A6
12
10
8
6
10
15
11
13
8


53
A6
12
11
11
6
11
15
9
13
6


66
A6
12
14
10
8
13
13
10
13
8


18
A7
7
18
11
9
18
7
18
7
13


39
A7
10
16
7
8
16
11
18
10
11


45
A7
9
16
11
10
17
10
19
8
13


59
A7
9
17
7
9
16
12
18
9
12


68
A7
12
16
10
8
16
12
16
11
10


85
A7
9
17
9
11
16
10
17
9
14


70
A7
11
17
11
9
16
11
16
10
12


16
A9
12
13
9
8
14
12
16
12
12


16
A9
12
13
9
8
14
13
16
12
12


31
A9
12
13
9
11
14
13
16
12
14


33
A9
14
15
11
11
15
13
17
13
13


35
A9
14
14
12
9
15
15
16
14
12


52
A9
14
16
10
11
15
11
17
13
13


58
A9
14
14
9
9
14
14
17
14
12


67
A9
13
15
8
10
15
13
17
13
12


54
A 
14
12
14
12
12
15
21
13



42
A1
13
10
10
11
10
15
19
13
13


32
A1
13
11
9
13
11
15
18
13
13


61
A3
11
19
13
9
20
14
18
12
13


72
A3
9
20
14
7
20
13
21
10
14


89
A3
16
18
12
8
18
19
21
16
13


86
A3
12
18
11
11
19
14
21
13
16


87
A3
13
18
12
11
19
15
21
14
16


84
A3
11
18
11
10
19
14
21
12
14


83
A3
13
18
15
9
19
17
21
13
15


71
A3
9
18
8
10
20
11
16
9
16


90
A3
11
18
11
7
19
15
17
12
15


57
A4
11
18
13
9
19
14
20
12
14


57
A4
12
18
13
8
19
14
20
12
14


7
A8
13
13
8
12
13
17
21
13
13


40
A8
14
12
9
10
12
20
21
14
12


91
A8
14
12
13
11
13

15
14
11


6
 A10
12
11
10
12
11
15
19
13
16


6
 A10
12
11
11
12
11
15
19
13
17


6
 A10
12
11
10
12
11
15
19
13
17


11
 A10
10
12
11
12
12
13
20
11
17


44
 A10
10
9
15
10
10
13
16
11
13


55
 A10
10
8
15
10
9
13
16
11
13


74
 A10
12
8
11
10
9
15
16
12
14


13
 A10
10
11
14
9
11
12
16
11
12


34
 A11
13

11
10

14
18
12
10


73
 A11
10

11
12

13
18
10
9
















TABLE 37







A5 Systems D & E: sequence aligment mismach evaluation


Reference of sequence: HPV 56->ref|NC_001594.1|












System D
System E
















forward
reverse

forward
reverse





primer
primer
probe
primer
primer
probe




SEQ ID
SEQ ID
SEQ ID
SEQ ID
SEQ ID
SEQ ID




NO: 9
NO: 14
NO: 24
NO: 10
NO: 15
NO: 24


NoHPV
Group
A5E6f4
A5E6r4
A5E6s4
A5E6f5
A5E6r5
A5E6s4

















51
A5
0
0
0
0
0
0


26
A5
5
3
6
7
4
6


69
A5
6
3
7
7
5
7


82
A5
1
0
3
3
3
3


56
A6
6
5
13
7
6
13


30
A6
8
1
13
10
4
13


53
A6
8
3
12
8
6
12


66
A6
7
5
13
7
6
13


18
A7
15
3
11
13
8
11


39
A7
14
4
11
12
5
11


45
A7
15
4
12
13
6
12


59
A7
16
4
11
12
5
11


68
A7
15
4
11
13
8
11


85
A7
17
4
13
14
6
13


70
A7
14
4
13
12
7
13


16
A9
13
9
14
9
8
14


16
A9
13
9
14
9
8
14


31
A9
12
4
14
8
6
14


33
A9
13
6
15
9
7
15


35
A9
14
6
12
10
9
12


52
A9
12
4
13
7
6
13


58
A9
12
6
16
8
5
16


67
A9
13
6
17
9
7
17


54
A 
18
2
11

14
11


42
A1
42
6
13

7
13


32
A1
12
6
13

8
13


61
A3
15
10
12

8
12


72
A3
16
12
10

9
10


89
A3
18
13
18
11
8
18


86
A3
17
10
14

7
14


87
A3
18
11
14

7
14


84
A3
17
13
13

8
13


83
A3
17
11
14
11
10
14


71
A3
17
15
11

6
11


90
A3
17
13
10

8
10


57
A4
17
14
11

10
11


57
A4
17
14
12

10
12


7
A8
24
3
11

7
11


40
A8
24
4
13

6
13


91
A8
18
1
14

10
14


6
 A10
19
4
12

10
12


6
 A10
20
4
12

10
12


6
 A10
20
4
12

10
12


11
 A10
19
4
10

9
10


44
 A10
21
9
12

11
12


55
 A10
21
9
12

11
12


74
 A10
18
9
15

10
15


13
 A10
32
6
12

10
12


34
 A11
42
15
13
15
9
13


73
 A11
42
15
10
14
9
10
















TABLE 38







A6 Systems A to C: sequence aligment mismach evaluation


Reference of sequence: HPV 56->ref|NC_001594.1|













System A
System B
System C



















forward
reverse

forward
reverse

forward
reverse





primer
primer
probe
primer
primer
probe
primer
primer
probe




SEQ ID
SEQ ID
SEQ ID
SEQ ID
SEQ ID
SEQ ID
SEQ ID
SEQ ID
SEQ ID




NO: 30
NO: 35
NO: 41
NO: 31
NO: 35
NO: 41
NO: 32
NO: 36
NO: 42


NoHPV
Group
A6E6f1
A6E6r1
A6E6s1
A6E6f2
A6E6r1
A6E6s1
A6E6f3
A6E6r2
A6E6s2




















51
A5
9
7
17
8
7
17
3
14
9


26
A5
9
10
19
10
10
19
4
13
11


69
A5
10
11
16
10
11
16
5
11
11


82
A5
10
8
18
9
8
18
4
14
9


56
A6
0
0
0
0
0
0
0
0
0


30
A6
4
8
16
7
8
16
2
10
8


53
A6
5
7
14
7
7
14
2
10
8


66
A6
2
2
6
6
2
6
2
6
6


18
A7
14
7
21
14
7
21
8
22
15


39
A7
11
9
23
10
9
23
8
22
10


45
A7
13
8
22
15
8
22
8
22
16


59
A7
10
9
20
13
9
20
7
22
14


68
A7
12
9
25
11
9
25
9
22
11


85
A7
12
8
22
12
8
22
6
22
13


70
A7
13
8
23
9
8
23
8
22
10


16
A9
6
9
17
10
9
17
8
13
11


16
A9
6
9
17
10
9
17
8
13
11


31
A9
9
6
21
10
6
21
7
16
12


33
A9
8
10
16
11
10
16
6
16
11


35
A9
8
7
18
12
7
18
7
14
13


52
A9
7
10
23
11
10
23
9
14
11


58
A9
8
9
18
10
9
18
8
14
10


67
A9
8
9
23
9
9
23
7
15
9


54
A 
10
10
30
14
10
30
8
18
16


42
A1
9
9

11
9

9
20
12


32
A1
10
5

9
5

9
20
11


61
A3
9
8

11
8

10
21
13


72
A3
10
8

13
8

9
21
15


89
A3
9
10

10
10

9
18
10


86
A3
11
10

9
10

10
18
9


87
A3
11
10

10
10

9
17
12


84
A3
9
9

10
9

9
18
12


83
A3
10
10

10
10

10
18
10


71
A3
10
12

9
12

6
18
9


90
A3
10
8

11
8

8
18
12


57
A4
8
10

10
10

8
18
12


57
A4
8
9

9
9

8
18
11


7
A8
6
7

11
7

6
18
13


40
A8
7
7

10
7

8
18
13


91
A8
10
8

12
8

11
19
14


6
 A10
11
12

14
12

7
16
18


6
 A10
11
12

14
12

7
16
17


6
 A10
11
12

14
12

7
16
18


11
 A10
10
11

13
11

9
16
17


44
 A10
10
12

11
12

9
17
14


55
 A10
10
10

12
10

10
17
14


74
 A14
9
11

12
11

8
16
14


13
 A10
9
9

12
9

9
18
14


34
 A11
9
7
25
6
7
25
6
15
7


73
 A11
8
7
24
6
7
24
6
15
6
















TABLE 39







A6 Systems D & E: sequence aligment mismach evaluation


Reference of sequence: HPV 56->ref|NC_001594.1|












System D
System E
















forward
reverse

forward
reverse





primer
primer
probe
primer
primer
probe




SEQ ID
SEQ ID
SEQ ID
SEQ ID
SEQ ID
SEQ ID




NO: 33
NO: 35
NO: 41
NO: 34
NO: 37
NO: 44


NoHPV
Group
A6E6f4
A6E6r1
A6E6s1
A6E6f5
A6E6r3
A6E6s3

















51
A5
8
7
17

11
9


26
A5
10
10
19

8
9


69
A5
11
11
16

8
8


82
A5
10
8
18

9
9


56
A6
0
0
0

0
0


30
A6
5
8
16

6
1


53
A6
6
7
14

6
2


66
A6
3
2
6

3
0


18
A7
15
7
21

13
12


39
A7
12
9
23

10
13


45
A7
14
8
22

13
15


59
A7
12
9
20

10
15


68
A7
13
9
25

10
12


85
A7
14
8
22

10
12


70
A7
13
8
23

9
12


16
A9
6
9
17

9



16
A9
6
9
17

9



31
A9
9
6
21

9



33
A9
7
10
16

13



35
A9
8
7
18

14



52
A9
6
10
23

15



58
A9
7
9
18

14



67
A9
7
9
23

12



54
A 
10
10
30

13



42
A1
10
9


13



32
A1
10
5


14



61
A3
10
8


11
13


72
A3
11
8


14
14


89
A3
10
10


11
12


86
A3
12
10


13
15


87
A3
12
10


14
13


84
A3
10
9


13
13


83
A3
11
10


16
14


71
A3
10
12


14
16


90
A3
10
8


13
13


57
A4
9
10


12



57
A4
9
9


12



7
A8
7
7


12
14


40
A8
8
7


8
14


91
A8
11
8


14
14


6
 A10
12
12


14



6
 A10
12
12


14



6
 A10
12
12


14



11
 A10
11
11


14



44
 A10
11
12


13



55
 A10
11
10


13



74
 A10
10
11


12



13
 A10
8
9


14



34
 A11
10
7
25

13



73
 A11
10
7
24

12
















TABLE 40





A7 Systems A & B: sequence aligment mismach evaluation


Reference of sequence: HPV 18 ->gi|9626069|ref|NC_001357.1|



















System A













forward primer
reverse primer
probes











SEQ ID NO:





















68
69
70
79
80
81
102
103
104
105
106


NoHPV
Group
6f1a
6f2a
6f3a
6r1b
6r2b
6r3b
A7E1ZAS61f
A7E1ZAS63f
A7E1ZAS64f
A7E1ZCS40f
A7E1ZBS74f





51
A5
4
5
4
7
5
5
5
5
4
4
9


26
A5
7
5
4
7
7
7
4
3
4
3
8


69
A5
5
6
6
7
7
6
4
3
4
3
8


82
A5
3
4
3
7
7
7
6
6
5
5
10


56
A6
5
5
3
5
8
9
5
6
7
6
9


30
A6
8
6
4
7
8
7
4
3
3
3
13


53
A6
8
4
6
6
7
8
6
6
4
5
10


66
A6
5
5
3
5
10
8
5
6
7
6
11


18
A7
0
2
2
1
5
6
0
3
4
1
4


39
A7
4
1
3
3
0
4
4
4
0
3
1


45
A7
2
0
2
1
3
6
1
2
3
0
6


59
A7
3
2
0
6
4
0
3
0
4
2
5


68
A7
1
2
2
4
1
3
2
2
2
1
0


85
A7
1
3
3
5
2
4
5
3
3
4
3


70
A7
3 
5
3
5
2
2
6
4
4
5
2


16
A9
2
2
4
5
7
5
7
4
7
6
9


16
A9
3
3
3
5
7
5
7
4
7
6
9


31
A9
3 
5
2
6
7
6
8
5
7
7
10


33
A9
4
5
3
5
3
5
7
4
5
6
7


35
A9
4
5
3
6
7
5
5
3
5
4
10


52
A9
4
3
3
5
5
6
5
3
3
4
9


58
A9
3
5
3
6
4
4
5
2
4
4
8


67
A9
2
4
2
5
4
5
5
3
4
4
6


54
A 
7
9
8
10
9
9
9
9
9
9
10


42
A1
3
7
5
4
6
6
7
4
4
6
12


32
A1
4
6
6
7
7
7
7
4
5
6
12


61
A3
6
11
9
10
9
12
6
5
7
5
13


72
A3
4
10
7
11
9
13
5
5
6
6
13


89
A3
4
10
7
9
10
13
6
4
5
5
13


86
A3
9
9
9
10
9
12
6
6
7
7
12


87
A3
8
9
8
11
9
11
8
6
5
7
12


84
A3
5
9
7
12
12
14
5
4
6
4
12


83
A3
6
11
10
10
10
10
7
8
7
9
12


71
A3
10
13
12
8
6
7
6
5
7
5
13


90
A3
7
8
7
8
7
7
7
6
8
6
13


57
A4
10
12
11
7
9
12
6
9
8
7
14


57
A4
10
12
11
18
20
21
6
9
8
7
14


7
A8
6
9
7
9
9
8
5
3
4
4
14


40
A8
6
10
7
8
10
10
6
5
6
6
15


91
A8
7
8
8
9
10
9
7
5
5
6
15


6
 A10
4
6
7
9
8
9
7
6
6
6
11


6
 A10
4
6
7
9
8
9
7
6
6
6
11


6
 A10
4
6
7
9
8
9
7
6
6
6
12


11
 A10
4
8
7
6
9
12
6
6
3
5
10


44
 A10
5
6
7
8
11
8
6
5
4
5
12


55
 A10
6
7
8
9
11
9
6
5
4
5
12


74
 A10
8
10
11
8
12
10
6
5
4
5
10


13
 A10
4
5
5
9
9
9
4
6
3
5
9


34
 A11
6
6
7
8
8
9
7
5
6
6
10


73
 A11
4
4
6
9
6
10
7
5
6
6
6














System B













forward primer
reverse primer
probes











SEQ ID NO:




















71
72
73
82
83
107
106
108
109
110


NoHPV
Group
15f1a
15f2a
15f3d
15r1a
15r2b
A7E1ZBS26f
A7E1ZBS74f
A7E1ZBS79f
A7E1ZBS80f
A7E1ZBS27f





51
A5
4
5
6
5
3
6
9
8
8
6


26
A5
7
5
8
4
3
7
8
9
9
7


69
A5
5
6
8
4
3
6
8
8
8
7


82
A5
3
4
6
6
4
7
10
5
5
9


56
A6
5
5
9
5
6
7
9
10
10
7


30
A6
8
5
11
4
3
8
13
10
10
10


53
A6
8
7
7
6
4
10
10
10
10
10


66
A6
5
5
9
5
6
8
11
12
12
8


18
A7
0
3
4
0
2
0
4
6
6
2


39
A7
4
5
0
4
2
8
1
4
4
8


45
A7
2
3
2
1
1
1
6
8
8
0


59
A7
3
0
5
2
2
5
5
0
0
7


68
A7
1
3
4
2
0
6
0
5
5
6


85
A7
1
4
4
4
3
7
3
6
6
7


70
A7
3
3
6
5
4
8
2
5
5
8


16
A9
2
5
4
6
6
7
9
9
9
7


16
A9
3
4
5
6
6
7
9
9
9
7


31
A9
3
1
6
7
7
7
10
10
10
8


33
A9
4
4
7
6
6
8
7
8
8
8


35
A9
4
5
8
4
3
9
10
8
8
10


52
A9
4
4
5
4
3
7
9
8
8
8


58
A9
3
4
7
4
4
9
8
9
9
9


67
A9
2
3
6
4
3
7
6
7
7
7


54
A 
9
6
8
8
9
6
10
9
9
8


42
A1
5
5
6
6
6
7
12
11
11
9


32
A1
6
6
5
6
6
7
12
10
10
8


61
A3
8
6
8
5
6
11
13
13
13
12


72
A3
6
5
8
4
5
13
13
11
11
14


89
A3
6
5
8
5
4
10
13
11
11
12


86
A3
11
6
8
5
6
12
12
12
12
13


87
A3
10
5
9
7
6
10
12
12
12
11


84
A3
7
4
7
4
5
9
12
12
12
10


83
A4
8
6
7
6
8
10
12
13
13
12


71
A3
12
10
11
5
6
8
13
10
10
10


90
A3
9
6
8
6
7
8
13
10
10
10


57
A4
12
8
11
6
8
11
14
12
12
12


57
A4
12
8
11
6
8
11
14
12
12
12


7
A8
8
6
9
4
3
12
14
12
12
13


40
A8
8
6
9
5
5
11
15
10
10
12


91
A8
9
8
9
6
5
10
15
12
12
11


6
 A10
6
7
3
7
6
8
11
11
11
8


6
 A10
6
7
3
7
6
8
11
11
11
8


6
 A10
6
7
3
7
6
8
12
11
11
8


11
 A10
6
6
6
6
4
9
10
11
11
9


44
 A10
7
6
5
6
5
8
12
11
11
10


55
 A10
8
7
6
6
5
9
12
11
11
11


74
 A10
10
10
8
6
5
9
10
12
12
9


13
 A10
6
5
5
4
4
9
9
10
10
9


34
 A11
6
6
8
6
5
10
10
10
10
10


73
 A11
4
7
6
6
5
8
6
7
7
8
















TABLE 41





A7 Systems C & D: sequence aligment mismach evaluation


Reference of sequence: HPV 18 ->gi|9626069|ref|NC_001357.1|



















System C













forward primer
reverse primer
probes











SEQ ID NO:




















74
75
76
84
85
111
105
112
113
114


NoHPV
Group
A7E17f1
A7E17f2
A7E17f3
A7E17r1
A7E17r2
A7E1ZCS11f
A7E1ZCS40f
A7E1ZCS45f
A7E1ZCS63f
A7E1ZCS90f





51
A5
7
7
10
5
5
4
4
4
5
6


26
A5
7
8
9
5
7
3
3
4
3
4


69
A5
7
6
9
5
8
3
3
4
3
4


82
A5
7
6
9
7
7
5
5
5
6
7


56
A6
8
7
9
6
9
6
6
7
6
5


30
A6
9
8
12
6
7
3
3
3
3
3


53
A6
11
8
10
5
8
5
5
4
6
5


66
A6
9
10
11
5
9
6
6
7
6
5


18
A7
0
6
5
1
6
1
1
4
3
3


39
A7
8
2
1
3
2
3
3
0
4
4


45
A7
2
7
7
1
4
0
0
3
2
3


59
A7
5
2
5
4
2
2
2
4
0
2


68
A7
6
2
0
4
1
1
1
2
2
0


85
A7
7
3
3
5
2
4
4
3
3
4


70
A7
8
4
2
3
2
5
5
4
4
4


16
A9
7
7
10
3
6
6
6
7
4
6


16
A9
7
7
10
3
6
6
6
7
4
6


31
A9
7
10
11
4
7
7
7
7
5
6


33
A9
8
8
8
5
3
6
6
5
4
4


35
A9
9
5
10
4
6
4
4
5
3
4


52
A9
8
8
10
6
5
4
4
3
3
4


58
A9
9
9
9
5
3
4
4
4
2
4


67
A9
7
7
7
4
4
4
4
4
3
3


54
A 
7
8
11
9
9
9
9
9
9
10


42
A1
8
8
13
4
6
6
6
4
4
6


32
A1
8
9
13
5
7
6
6
5
4
4


61
A3
11
14
14
10
11
5
5
7
5
3


72
A3
13
11
13
11
12
6
6
6
5
4


89
A3
10
9
12
9
12
5
5
5
4
4


86
A3
12
8
12
10
11
7
7
7
6
4


87
A3
10
8
13
11
10
7
7
5
6
4


84
A3
10
11
13
12
13
4
4
6
4
3


83
A3
10
10
13
10
10
9
9
7
8
9


71
A3
8
8
13
7
6
5
5
7
5
5


90
A3
8
8
13
7
6
6
6
8
6
6


57
A4
11
11
14
8
11
7
7
8
9
8


57
A4
11
11
14
8
11
7
7
8
9
8


7
A8
12
14
15
8
8
4
4
4
3
5


40
A8
11
9
14
8
9
6
6
6
5
7


91
A8
11
12
15
8
9
6
6
5
5
6


6
 A10
9
9
12
9
8
6
6
6
6
7


6
 A10
9
9
12
9
8
6
6
6
6
7


6
 A10
9
9
12
9
8
6
6
6
6
7


11
 A10
9
9
11
8
11
5
5
3
6
7


44
 A10
9
8
13
8
9
5
5
4
5
6


55
 A10
9
9
13
8
10
5
5
4
5
6


74
 A10
10
9
11
7
11
5
5
4
5
6


13
 A10
10
9
10
10
8
5
5
3
6
6


34
 A11
11
7
9
9
8
6
6
6
5
5


73
 A11
8
5
6
8
9
6
6
6
5
5














System D













forward primer
reverse primer
probe











SEQ ID NO:





















77
78
86
87
115
116
117
118
119
120
121


NoHPV
Group
A7E12f1
A7E12f2
A7E12r2
A7E12r3
A7E1ZDS36f
A7E1ZDS37f
A7E1ZDS38f
A7E1ZDS2f
A7E1ZDS3f
A7E1ZDS4f
A7E1ZDS11f





51
A5
8
7
2
4
4
6
4
4
3
3
3


26
A5
9
7
8
7
8
6
8
7
6
6
6


69
A5
8
6
9
8
7
7
7
6
6
6
6


82
A5
8
6
4
5
9
7
7
7
6
6
6


56
A6
6
5
8
11
9
9
6
6
8
8
8


30
A6
6
6
8
9
12
9
9
10
8
8
8


53
A6
6
6
11
12
12
11
9
10
11
11
11


66
A6
6
5
9
9
8
8
7
7
8
8
8


18
A7
1
5
3
0
6
0
5
3
5
5
5


39
A7
3
1
1
1
8
6
3
3
7
7
7


45
A7
2
6
2
2
0
6
5
5
0
0
0


59
A7
3
4
2
1
7
7
2
4
5
5
5


68
A7
5
1
1
3
5
3
2
0
4
4
4


85
A7
3
3
5
6
6
6
2
4
5
5
5


70
A7
5
1
2
1
7
7
4
4
6
6
6


16
A9
6
10
5
5
7
5
4
6
4
4
4


16
A9
6
10
5
5
6
6
5
7
3
3
3


31
A9
3
5
7
9
6
6
6
6
5
5
5


33
A9
3
3
3
7
8
8
8
8
6
6
6


35
A9
4
7


4
6
3
3
3
3
3


52
A9
5
5
1
6
8
7
7
8
7
7
7


58
A9
5
6
4
8
8
7
9
9
6
6
6


67
A9
4
6
2
5
7
7
6
5
6
6
6


54
A 
6
8
6
9
4
6
3
3
3
3
3


42
A1
8
10
4
7
7
6
6
6
5
5
5


32
A1
8
10
2
6
6
7
6
6
5
5
5


61
A3
16
13
9
7
12
12
12
11
11
11
11


72
A3
16
13
9
10
12
11
9
9
11
11
11


89
A3
16
14
13
14
12
11
10
10
10
10
10


86
A3
17
18
9
7
11
11
11
10
10
10
10


87
A3
18
19
11
11
13
13
13
12
12
12
12


84
A3
15
17
10
8
11
11
10
9
10
10
10


83
A3
17
18
11
10
11
12
11
10
11
11
11


71
A3
16
16
9
10
9
8
9
8
9
9
9


90
A3
17
16
11
12
12
10
13
11
12
12
12


57
A4
15
16
10
7
11
11
13
12
10
10
10


57
A4
15
16
11
8
11
11
13
12
10
10
10


7
A8
8
9
8
11
11
10
8
9
7
7
7


40
A8
7
9
9
13
11
10
10
9
8
8
8


91
A8
5
8
10
12
9
9
9
10
7
7
7


6
 A10
8
10
5
10
8
7
7
6
6
6
6


6
 A10
8
10
5
10
8
7
7
6
6
6
6


6
 A10
8
10
5
10
8
7
7
6
6
6
6


11
 A10
8
10
6
10
8
8
7
6
6
6
6


44
 A10
11
13
5
12
11
10
8
9
9
9
9


55
 A10
11
13
6
12
9
10
8
9
6
6
6


74
 A10
11
13
3
9
8
9
8
7
7
7
7


13
 A10
10
11
4
9
11
10
8
9
8
8
8


34
 A11
12
16
8
10
9
7
8
7
7
7
7


73
 A11
12
16
6
9
8
6
7
6
6
6
6
















TABLE 42





A9 System C: sequence aligment mismach evaluation


Reference of sequence: HPV 16 ->gi|9627100|ref|NC_001526.1|




















forward primer
reverse primer



















211
212
213
214
215
216
217
240
241


NoHPV
Group
A9E1f7
A9E1f8
A9E1f9
A9E1f10
A9E1f11
A9E1f12
A9E1f13
A9E1r5
A9E1r6





51
A5
5
6
7
5
5
6
6
2
6


26
A5
5
6
7
5
5
6
6
3
5


69
A5
5
6
7
5
5
6
6
3
5


82
A5
5
6
7
5
5
6
6
2
6


56
A6
1
2
3
1
3
2
4
3
5


30
A6
3
4
5
3
3
4
4
4
6


53
A6
3
4
5
3
3
4
4
4
6


66
A6
2
3
4
2
4
3
5
4
6


18
A7
3
4
5
3
3
4
4
7
4


39
A7
6
5
6
5
4
5
5
2
4


45
A7
3
4
5
3
3
4
4
4
4


59
A7
3
2
3
1
1
2
2
5
7


68
A7
13
12
13
11
13
12
14
16
17


85
A7
2
3
4
2
2
3
3
3
5


70
A7
7
6
5
5
5
4
4
4
4


16
A9
0
1
2
2
2
3
3
0
5


16
A9
0
1
2
2
2
3
3
0
5


31
A9
2
1
2
0
1
1
3
0
5


33
A9
4
3
2
2
3
1
1
6
1


35
A9
2
1
2
0
2
1
3
1
6


52
A9
4
3
2
2
2
1
1
6
1


58
A9
4
3
2
4
2
3
1
6
1


67
A9
5
4
3
3
3
2
2
6
1


54
A 
9
10
11
10
9
11
10
3
7


42
A1
6
7
8
6
6
7
7
5
7


32
A1
6
7
8
6
6
7
7
5
7


61
A3
12
13
14
12
12
13
13
4
6


72
A3
12
13
14
12
12
13
13
4
6


89
A3
9
10
11
9
9
10
10
4
6


86
A3
7
8
9
7
7
8
8
3
5


87
A3
7
8
9
7
7
8
8
3
5


84
A3
8
9
10
8
8
9
9
4
6


83
A3
9
10
11
9
9
10
10
4
6


71
A3
9
10
11
9
9
10
10
4
6


90
A3
9
10
11
9
9
10
10
4
6


57
A4
8
9
10
8
8
9
9
4
6


57
A4
8
9
10
8
8
9
9
4
6


7
A8
9
10
11
9
9
10
10
7
11


40
A8
10
11
12
10
10
11
11
7
11


91
A8
12
13
14
12
12
13
13
6
10


6
 A10
11
12
13
11
11
12
12
5
7


6
 A10
11
12
13
11
11
12
12
5
7


6
 A10
11
12
13
11
11
12
12
5
7


11
 A10
10
11
12
10
10
11
11
5
7


44
 A10
12
13
14
12
12
13
13
5
9


55
 A10
13
14
15
13
13
14
14
5
9


74
 A10
13
14
15
13
13
14
14
5
9


13
 A10
12
13
14
12
12
13
13
6
8


34
 A11
6
7
6
6
6
7
5
3
6


73
 A11
7
8
7
7
7
8
6
3
6














probes























283
284
285
286
287
288
289
290
291
292
293
294
295


NoHPV
Group
A9E1S10
A9E1S10a
A9E1S11
A9E1S11a
A9E1S12
A9E1S12a
A9E1S12b
A9E1S13a
A9E1S13b
A9E1S13c
A9E1S14a
A9E1S15a
A9E1S15b





51
A5
4
4
4
4
4
4
4
3
3
3
3
4
4


26
A5
6
6
6
6
6
6
6
5
5
5
4
6
6


69
A5
6
6
6
6
6
6
6
5
5
5
4
6
6


82
A5
4
4
4
4
4
4
4
3
3
3
3
4
4


56
A6
3
3
3
3
4
4
4
3
3
3
1
4
4


30
A6
3
3
5
5
6
6
6
5
5
5
3
6
6


53
A6
2
2
4
4
5
5
5
4
4
4
2
5
5


66
A6
3
3
3
3
4
4
4
3
3
3
1
4
4


18
A7
9
9
9
9
10
10
10
10
10
10
9
11
11


39
A7
9
9
9
9
10
10
10
9
9
9
9
10
10


45
A7
9
9
9
9
10
10
10
13
13
13
11
13
13


59
A7
9
9
9
9
8
8
8
8
8
8
9
9
9


68
A7
17
17
17
17
17
17
17
20
20
20
18
22
22


85
A7
5
5
5
5
4
4
4
7
7
7
8
7
7


70
A7
9
9
9
9
10
10
10
8
8
8
8
9
9


16
A9
1
1
3
3
4
4
4
3
3
3
1
4
4


16
A9
1
1
3
3
4
4
4
3
3
3
1
4
4


31
A9
1
1
1
1
2
2
2
1
1
1
0
2
2


33
A9
1
1
3
3
4
4
4
4
4
4
3
4
4


35
A9
3
3
1
1
0
0
0
1
1
1
2
0
0


52
A9
0
0
2
2
3
3
3
3
3
3
2
3
3


58
A9
0
0
2
2
3
3
3
3
3
3
2
3
3


67
A9
1
1
3
3
4
4
4
4
4
4
3
4
4


54
A 
9
9
11
11
11
11
11
12
12
12
11
13
13


42
A1
3
3
5
5
6
6
6
5
5
5
4
7
7


32
A1
4
4
6
6
6
6
6
5
5
5
5
7
7


61
A3
9
9
11
11
11
11
11
20
20
20
20
20
20


72
A3
9
9
11
11
10
10
10
19
19
19
19
19
19


89
A3
8
8
10
10
10
10
10
20
20
20
19
20
20


86
A3
9
9
11
11
11
11
11
21
21
21
19
22
22


87
A3
11
11
13
13
13
13
13
18
18
18
16
18
18


84
A3
11
11
13
13
13
13
13
18
18
18
17
19
19


83
A3
9
9
11
11
11
11
11
19
19
19
18
19
19


71
A3
7
7
9
9
10
10
10
13
13
13
11
14
14


90
A3
6
6
8
8
9
9
9
12
12
12
10
13
13


57
A4
4
4
6
6
7
7
7
11
11
11
10
13
13


57
A4
4
4
6
6
7
7
7
11
11
11
10
13
13


7
A8
7
7
9
9
9
9
9
8
8
8
8
10
10


40
A8
9
9
11
11
11
11
11
10
10
10
9
12
12


91
A8
9
9
9
9
9
9
9
8
8
8
8
10
10


6
 A10
5
5
7
7
7
7
7
8
8
8
8
9
9


6
 A10
5
5
7
7
7
7
7
8
8
8
8
9
9


6
 A10
6
6
8
8
8
8
8
9
9
9
8
10
10


11
 A10
5
5
7
7
7
7
7
8
8
8
8
9
9


44
 A10
6
6
8
8
8
8
8
7
7
7
7
9
9


55
 A10
7
7
9
9
9
9
9
8
8
8
7
10
10


74
 A10
6
6
8
8
8
8
8
7
7
7
7
9
9


13
 A10
7
7
9
9
9
9
9
8
8
8
7
10
10


34
 A11
3
3
5
5
4
4
4
3
3
3
3
4
4


73
 A11
3
3
5
5
4
4
4
3
3
3
3
4
4
















TABLE 43







A9 System E1: sequence aligment mismach evaluation


Reference of sequemce: HPV 16 ->gi||ref|NC_001526.1|













forward primer
reverse primer
probes











SEQ ID NO:



























218
219
220
242
243
244
245
246
247
296
297
298
299
300
301
302
303


NoHPV
Group
A9E2f1
A9E2f2
A9E2f4
A9E2r1
A9E2r2
A9E2r3
A9E2r4
A9E2r13
A9E2r14
A9E2Z7S1
A9E2Z7S2
A9E2Z7S2a
A9E2Z7S2b
A9E2Z7S3
A9E2Z7S3a
A9E2Z7S4
A9E2Z7S4a




























51
A5
10
9
10
8
9
9
7
13
12
6
5
5
5
9
9
6
6


26
A5
11
13
11
9
6
6
9
10
15
5
3
3
3
6
6
4
4


69
A5
11
13
11
8
7
6
8
11
13
3
3
3
3
7
7
3
3


82
A5
9
9
10
8
7
5
5
12
14
3
3
3
3
7
7
3
3


56
A6
6
10
9
8
6
6
6
10
14
8
7
7
7
9
9
7
7


30
A6
6
7
9
8
8
8
10
13
14
6
6
6
6
9
9
7
7


53
A6
6
7
7
7
3
4
5
12
13
7
5
5
5
10
10
8
8


66
A6
8
11
9
7
6
6
7
9
11
9
8
8
8
10
10
8
8


18
A7
4
9
7
9
5
6
7
10
11
7
1
1
1
8
8
6
6


39
A7
4
9
7
7
4
5
6
12
10
8
4
4
4
8
8
6
6


45
A7
4
9
7
11
10
10
9
9
12
6
3
3
3
10
10
6
6


59
A7
4
9
8
7
4
5
8
9
10
6
3
3
3
7
7
5
5


68
A7
4
9
7
7
4
5
6
12
10
8
4
4
4
8
8
6
6


85
A7
5
8
9
8
4
5
5
9
10
7
6
6
6
10
10
5
5


70
A7
4
7
8
7
3
4
5
10
10
8
5
5
5
8
8
6
6


16
A9
0
8
8
0
5
6
8
9
11
0
6
6
6
8
8
4
4


16
A9
0
8
8
2
4
5
8
10
10
1
5
5
5
9
9
5
5


31
A9
7
10
3
8
9
9
10
0
10
2
4
4
4
6
6
1
1


33
A9
7
1
8
9
8
7
2
12
12
5
1
1
1
9
9
7
7


35
A9
3
9
6
6
8
9
9
11
0
8
8
8
8
0
0
6
6


52
A9
8
9
3
5
0
1
6
13
12
5
3
3
3
7
7
2
2


58
A9
9
2
10
8
3
2
3
10
8
5
1
1
1
7
7
5
5


67
A9
6
4
6
7
2
1
4
9
12
5
1
1
1
7
7
4
4


54
A 
4
7
8
8
5
6
9
10
10
6
8
8
8
8
8
5
5


42
A1
9
11
11
9
7
8
7
12
13
5
6
6
6
8
8
4
4


32
A1
8
13
10
8
8
7
7
13
12
6
6
6
6
9
9
5
5


61
A3
7
10
8
8
6
7
9
13
15
6
6
6
6
7
7
5
5


72
A3
7
7
8
10
9
10
12
15
16
5
8
8
8
7
7
5
5


89
A3
5
7
6
8
8
8
11
13
12
6
6
6
6
8
8
7
7


86
A3
10
7
11
10
8
6
9
13
16
7
9
9
9
8
8
9
9


87
A3
9
5
12
10
8
7
10
15
15
7
8
8
8
7
7
8
8


84
A3
9
7
10
11
11
9
11
11
14
8
9
9
9
8
8
10
10


83
A3
9
10
9
7
10
10
9
11
11
7
8
8
8
9
9
8
8


71
A3
7
7
8
9
9
9
12
16
15
7
7
7
7
9
9
7
7


90
A3
9
10
9
12
13
11
11
13
13
9
8
8
8
9
9
9
9


57
A4
13
10
11
9
10
9
12
14
12
8
6
6
6
9
9
8
8


57
A4
13
8
11
9
10
9
12
15
13
8
6
6
6
9
9
8
8


7
A8
7
10
7
8
8
8
9
12
11
10
9
9
9
3
3
8
8


40
A8
8
11
5
9
11
10
9
12
11
10
9
9
9
4
4
9
9


91
A8
5
7
11
10
10
9
9
9
9
5
5
5
5
3
3
5
5


6
 A10
8
9
9
9
6
5
8
11
11
8
7
7
7
11
11
8
8


6
 A10
8
9
9
9
6
5
8
11
11
8
7
7
7
11
11
8
8


6
 A10
8
9
9
9
6
5
8
11
11
8
7
7
7
11
11
8
8


11
 A10
8
9
10
6
4
5
9
11
12
7
9
9
9
10
10
8
8


44
 A10
8
9
10
6
6
5
5
13
13
5
9
9
9
7
7
8
8


55
 A10
8
9
10
4
6
5
7
11
11
5
9
9
9
7
7
8
8


74
 A10
9
9
11
8
5
4
5
12
12
4
7
7
7
8
8
6
6


13
 A10
8
8
9
9
6
6
6
9
10
4
7
7
7
6
6
4
4


34
 A11
9
7
9
8
7
8
9
11
16
6
6
6
6
7
7
5
5


73
 A11
10
6
10
7
7
7
7
13
12
7
6
6
6
8
8
6
6
















TABLE 44







E2: sequence aligment mismach evaluation


Reference of sequence: HPV 16 ->gi||ref|NC_001526.1|













forward primer
reverse primer
probes











SEQ ID NO:



























221
222
223
242
243
244
245
246
247
296
297
298
299
300
301
302
303


NoHPC
Group
A9E2f1a
A9E2f2a
A9E2f4a
A9E2r1
A9E2r2
A9E2r3
A9E2r4
A9E2r13
A9E2r14
A9E2Z7S1
A9E2Z7S2
A9E2Z7S2a
A9E2Z7S2b
A9E2Z7S3
A9E2Z7S3a
A9E2Z7S4
A9E2Z7S4a




























51
A5
11
9
11
8
9
9
7
13
12
6
5
5
5
9
9
6
6


26
A5
13
14
11
9
6
6
9
10
15
5
3
3
3
6
6
4
4


69
A5
12
13
12
8
7
6
8
11
13
3
3
3
3
7
7
3
3


82
A5
10
9
11
8
7
5
5
12
14
3
3
3
3
7
7
3
3


56
A6
7
10
10
8
6
6
6
10
14
8
7
7
7
9
9
7
7


30
A6
7
7
10
8
8
8
10
13
14
6
6
6
6
9
9
7
7


53
A6
7
7
8
7
3
4
5
12
13
7
5
5
5
10
10
8
8


66
A6
9
11
10
7
6
6
7
9
11
9
8
8
8
10
10
8
8


18
A7
5
9
8
9
5
6
7
10
11
7
1
1
1
8
8
6
6


39
A7
5
9
8
7
4
5
6
12
10
8
4
4
4
8
8
6
6


45
A7
6
10
7
11
10
10
9
9
12
6
3
3
3
10
10
6
6


59
A7
6
10
8
7
4
5
8
9
10
6
3
3
3
7
7
5
5


68
A7



7
4
5
6
12
10
8
4
4
4
8
8
6
6


85
A7
7
9
9
8
4
5
5
9
10
7
6
6
6
10
10
5
5


70
A7
5
7
9
7
3
4
5
10
10
8
5
5
5
8
8
6
6


16
A9
1
8
9
0
5
6
8
9
11
0
6
6
6
8
8
4
4


16
A9
1
8
9
2
4
5
8
10
10
1
5
5
5
9
9
5
5


31
A9
7
11
3
8
9
9
10
0
10
2
4
4
4
6
6
1
1


33
A9
8
1
9
9
8
7
2
12
12
5
1
1
1
9
9
7
7


35
A9
2
9
7
6
8
9
9
11
0
8
8
8
8
0
0
6
6


52
A9
9
10
3
5
0
1
6
13
12
5
3
3
3
7
7
2
2


58
A9
10
2
11
8
3
2
3
10
8
5
1
1
1
7
7
5
5


67
A9
7
4
7
7
2
1
4
9
12
5
1
1
1
7
7
4
4


54
A 
6
8
8
8
5
6
9
10
10
6
8
8
8
8
8
5
5


42
A1
10
11
12
9
7
8
7
12
13
5
6
6
6
8
8
4
4


32
A1
10
14
10
8
8
7
7
13
12
6
6
6
6
9
9
5
5


61
A3
9
11
8
8
6
7
9
13
15
6
6
6
6
7
7
5
5


72
A3
8
7
9
10
9
10
12
15
16
5
8
8
8
7
7
5
5


89
A3
7
8
6
8
8
8
11
13
12
6
6
6
6
8
8
7
7


86
A3
12
8
11
10
8
8
9
13
16
7
9
9
9
8
8
9
9


87
A3
11
6
12
10
8
7
10
15
15
7
8
8
8
7
7
8
8


84
A3
11
8
10
11
11
9
11
11
14
8
9
9
9
8
8
10
10


83
A3
11
11
9
7
10
10
9
11
11
7
8
8
8
9
9
8
8


71
A3
9
8
8
9
9
9
12
16
15
7
7
7
7
9
9
7
7


90
A3
11
11
9
12
13
11
11
13
13
9
8
8
8
9
9
9
9


57
A4
15
11
11
9
10
9
12
14
12
8
6
6
6
9
9
8
8


57
A4
15
9
11
9
10
9
12
15
13
8
6
6
6
9
9
8
8


7
A8
9
11
8
8
8
8
9
12
11
10
9
9
9
3
3
8
8


40
A8
8
12
6
9
11
10
9
12
11
10
9
9
9
4
4
9
9


91
A8
7
8
12
10
10
9
9
9
9
5
5
5
5
3
3
5
5


6
 A10
8
10
10
9
6
5
8
11
11
8
7
7
7
11
11
8
8


6
 A10
8
10
10
9
6
5
8
11
11
8
7
7
7
11
11
8
8


6
 A10
8
10
10
9
6
5
8
11
11
8
7
7
7
11
11
8
8


11
 A10
8
10
11
6
4
5
9
11
12
7
9
9
9
10
10
8
8


44
 A10
8
10
11
6
6
5
5
13
13
5
9
9
9
7
7
8
8


55
 A10
8
10
11
4
6
5
7
11
11
5
9
9
9
7
7
8
8


74
 A10
10
10
12
8
5
4
5
12
12
4
7
7
7
8
8
6
6


13
 A10
8
9
10
9
6
6
6
9
10
4
7
7
7
6
6
4
4


34
 A11
10
7
10
8
7
8
9
11
16
6
6
6
6
7
7
5
5


73
 A11
11
6
11
7
7
7
7
13
12
7
6
6
6
8
8
6
6
















TABLE 45





A9 System E3: sequence aligment mismach evaluation


Reference of sequence: HPV 16 ->gi||ref|NC_001526.1|




















forward primer
reverse primer











SEQ ID NO:





















221
222
223
248
249
250
251
252
253
254
255


NoHPV
Group
A9E2f1a
A9E2f2a
A9E2f4a
A9E21r1cz
A9E21r2az
A9E21r3az
A9E21r4fz
A9E21r5az
A9E21r6az
A9E21r7az
A9E21r8az





51
A5
11
9
11
8
10
7
9
9
9
8
9


26
A5
13
14
11
9
7
11
13
7
6
6
8


69
A5
12
13
12
8
9
10
12
6
6
6
7


82
A5
10
9
11
8
10
5
12
6
5
6
7


56
A6
7
10
10
8
8
8
14
6
6
6
5


30
A6
7
7
10
8
11
12
14
9
8
8
10


53
A6
7
7
8
7
10
7
11
5
4
3
5


66
A6
9
11
10
7
8
9
11
6
6
6
6


18
A7
5
9
8
9
8
9
11
7
6
5
6


39
A7
5
9
8
7
9
8
8
6
5
4
6


45
A7
6
10
7
11
10
10
12
10
10
10
9


59
A7
6
10
8
7
8
10
9
6
5
4
6


68
A7













85
A7
7
9
9
8
8
7
8
6
5
4
5


70
A7
5
7
9
7
9
7
9
5
4
3
5


16
A9
1
8
9
0
8
9
10
7
6
5
8


16
A9
1
8
9
2
9
9
9
6
5
4
7


31
A9
7
11
3
8
0
12
11
10
9
9
9


33
A9
8
1
9
9
12
0
11
6
7
8
5


35
A9
2
9
7
6
8
9
0
10
9
8
10


52
A9
9
10
3
5
9
8
13
2
1
0
3


58
A9
10
2
11
8
9
5
11
1
2
3
0


67
A9
7
4
7
7
8
6
12
2
1
2
1


54
A 
6
8
8
8
9
9
10
7
6
5
7


42
A1
10
11
12
9
8
9
12
7
8
7
6


32
A1
10
14
10
8
9
7
10
8
7
8
7


61
A3
9
11
8
8
10
9
13
8
7
6
7


72
A3
8
7
9
10
11
12
15
11
10
9
11


89
A3
7
8
6
8
10
11
11
9
8
7
9


86
A3
12
8
11
10
9
9
16
7
6
7
7


87
A3
11
6
12
10
9
10
16
8
7
8
8


84
A3
11
8
10
10
12
12
15
11
10
11
10


83
A3
11
11
9
7
10
9
10
9
10
9
9


71
A3
9
8
8
9
12
12
13
10
9
8
10


90
A3
11
11
9
12
11
12
12
12
12
12
11


57
A4
15
11
11
9
12
13
13
11
10
9
11


57
A4
15
9
11
9
12
13
14
11
10
9
11


7
A8
9
11
8
8
12
9
12
9
8
7
9


40
A8
8
12
6
9
12
10
12
12
11
11
11


91
A8
7
8
12
10
8
9
10
9
9
10
9


6
 A10
8
10
10
9
10
8
11
6
5
6
6


6
 A10
8
10
10
9
10
8
11
6
5
6
6


6
 A10
8
10
10
9
10
8
11
6
5
6
6


11
 A10
8
10
11
6
11
9
12
6
5
4
7


44
 A10
8
10
11
6
11
5
13
6
5
6
6


55
 A10
8
10
11
4
10
7
11
6
5
6
7


74
 A10
10
10
12
8
10
5
12
5
4
5
4


13
 A10
8
9
10
9
7
6
10
7
6
6
6


34
 A11
10
7
10
8
7
9
13
9
8
7
8


73
 A11
11
6
11
7
9
6
11
8
7
7
7














probes




SEQ ID NO:


















296
297
298
299
300
301
302
303


NoHPV
Group
A9E2Z7S1
A9E2Z7S2
A9E2Z7S2a
A9E2Z7S2b
A9E2Z7S3
A9E2Z7S3a
A9E2Z7S4
A9E2Z7S4a





51
A5
6
5
5
5
9
9
6
6


26
A5
5
3
3
3
6
6
4
4


69
A5
3
3
3
3
7
7
3
3


82
A5
3
3
3
3
7
7
3
3


56
A6
8
7
7
7
9
9
7
7


30
A6
6
6
6
6
9
9
7
7


53
A6
7
5
5
5
10
10
8
8


66
A6
9
8
8
8
10
10
8
8


18
A7
7
1
1
1
8
8
6
6


39
A7
8
4
4
4
8
8
6
6


45
A7
6
3
3
3
10
10
6
6


59
A7
6
3
3
3
7
7
5
5


68
A7
8
4
4
4
8
8
6
6


85
A7
7
6
6
6
10
10
5
5


70
A7
8
5
5
5
8
8
6
6


16
A9
0
6
6
6
8
8
4
4


16
A9
1
5
5
5
9
9
5
5


31
A9
2
4
4
4
6
6
1
1


33
A9
5
1
1
1
9
9
7
7


35
A9
8
8
8
8
0
0
6
6


52
A9
5
3
3
3
7
7
2
2


58
A9
5
1
1
1
7
7
5
5


67
A9
5
1
1
1
7
7
4
4


54
A 
6
8
8
8
8
8
5
5


42
A1
5
6
6
6
8
8
4
4


32
A1
6
6
6
6
9
9
5
5


61
A3
6
6
6
6
7
7
5
5


72
A3
5
8
8
8
7
7
5
5


89
A3
6
6
6
6
8
8
7
7


86
A3
7
9
9
9
8
8
9
9


87
A3
7
8
8
8
7
7
8
8


84
A3
8
9
9
9
8
8
10
10


83
A3
7
8
8
8
9
9
8
8


71
A3
7
7
7
7
9
9
7
7


90
A3
9
8
8
8
9
9
9
9


57
A4
8
6
6
6
9
9
8
8


57
A4
8
6
6
6
9
9
8
8


7
A8
10
9
9
9
3
3
8
8


40
A8
10
9
9
9
4
4
9
9


91
A8
5
5
5
5
3
3
5
5


6
 A10
8
7
7
7
11
11
8
8


6
 A10
8
7
7
7
11
11
8
8


6
 A10
8
7
7
7
11
11
8
8


11
 A10
7
9
9
9
10
10
8
8


44
 A10
5
9
9
9
7
7
8
8


55
 A10
5
9
9
9
7
7
8
8


74
 A10
4
7
7
7
8
8
6
6


13
 A10
4
7
7
7
6
6
4
4


34
 A11
6
6
6
6
7
7
5
5


73
 A11
7
6
6
6
8
8
6
6
















TABLE 46





A9 System E4: sequence aligment mismach evaluation




















forward primer
reverse primer











SEQ ID NO:





















224
225
226
248
249
250
251
252
253
254
255


NoHPV
Group
A9E2Z5Z6f1c
A9E2Z5Z6f2c
A9E2Z5Z6f3b
A9E21r1cz
A9E21r2az
A9E21r3az
A9E21r4fz
A9E21r5az
A9E21r6az
A9E21r7az
A9E21r8az





51
A5
5
3
7
8
10
7
9
9
9
8
9


26
A5
7
7
5
9
7
11
13
7
6
6
8


69
A5
5
5
7
8
9
10
12
6
6
6
7


82
A5
5
4
7
8
10
5
12
6
5
6
7


56
A6
2
4
6
8
8
8
14
6
6
6
5


30
A6
2
2
6
8
11
12
14
9
8
8
10


53
A6
3
3
4
7
10
7
11
5
4
3
5


66
A6
4
5
6
7
8
9
11
6
6
6
6


18
A7
2
4
4
9
8
9
11
7
6
5
6


39
A7
2
4
4
7
9
8
8
6
5
4
6


45
A7
3
5
3
11
10
10
12
10
10
10
9


59
A7
3
5
3
7
8
10
9
6
5
4
6


68
A7













85
A7
4
4
4
8
8
7
8
6
5
4
5


70
A7
1
1
5
7
9
7
9
5
4
3
5


16
A9
1
3
5
0
8
9
10
7
6
5
8


16
A9
1
3
5
2
9
9
9
6
5
4
7


31
A9
2
4
2
8
0
12
11
10
9
9
9


33
A9
4
0
4
9
12
0
11
6
7
8
5


35
A9
0
2
4
6
8
9
0
10
9
8
10


52
A9
4
4
0
5
9
8
13
2
1
0
3


58
A9
5
2
6
8
9
5
11
1
2
3
0


67
A9
2
0
4
7
8
6
12
2
1
2
1


54
A 
3
3
5
8
9
9
10
7
6
5
7


42
A1
6
6
7
9
8
9
12
7
8
7
6


32
A1
6
8
6
8
9
7
10
8
7
8
7


61
A3
6
6
2
8
10
9
13
8
7
6
7


72
A3
4
2
2
10
11
12
15
11
10
9
11


89
A3
6
6
2
8
10
11
11
9
8
7
9


86
A3
8
5
4
10
9
9
16
7
6
7
7


87
A3
9
5
4
10
9
10
16
8
7
8
8


84
A3
7
6
3
10
12
12
15
11
10
11
10


83
A3
8
7
4
7
10
9
10
9
10
9
9


71
A3
8
7
3
9
12
12
13
10
9
8
10


90
A3
10
9
5
12
11
12
12
12
12
12
11


57
A4
12
10
7
9
12
13
13
11
10
9
11


57
A4
12
10
7
9
12
13
14
11
10
9
11


7
A8
6
7
4
8
12
9
12
9
8
7
9


40
A8
4
5
4
9
12
10
12
12
11
11
11


91
A8
5
5
7
10
8
9
10
9
9
10
9


6
 A10
6
5
8
9
10
8
11
6
5
6
6


6
 A10
6
5
8
9
10
8
11
6
5
6
6


6
 A10
6
5
8
9
10
8
11
6
5
6
6


11
 A10
7
6
7
6
11
9
12
6
5
4
7


44
 A10
6
6
8
6
11
5
13
6
5
6
6


55
 A10
6
6
8
4
10
7
11
6
5
6
7


74
 A10
5
5
7
8
10
5
12
5
4
5
4


13
 A10
4
4
6
9
7
6
10
7
6
6
6


34
 A11
5
3
5
8
7
9
13
9
8
7
8


73
 A11
6
2
6
7
9
6
11
8
7
7
7














probes




SEQ ID NO:


















296
297
298
299
300
301
302
303


NoHPV
Group
A9E2Z7S1
A9E2Z7S2
A9E2Z7S2a
A9E2Z7S2b
A9E2Z7S3
A9E2Z7S3a
A9E2Z7S4
A9E2Z7S4a





51
A5
6
5
5
5
9
9
6
6


26
A5
5
3
3
3
6
6
4
4


69
A5
3
3
3
3
7
7
3
3


82
A5
3
3
3
3
7
7
3
3


56
A6
8
7
7
7
9
9
7
7


30
A6
6
6
6
6
9
9
7
7


53
A6
7
5
5
5
10
10
8
8


66
A6
9
8
8
8
10
10
8
8


18
A7
7
1
1
1
8
8
6
6


39
A7
8
4
4
4
8
8
6
6


45
A7
6
3
3
3
10
10
6
6


59
A7
6
3
3
3
7
7
5
5


68
A7
8
4
4
4
8
8
6
6


85
A7
7
6
6
6
10
10
5
5


70
A7
8
5
5
5
8
8
6
6


16
A9
0
6
6
6
8
8
4
4


16
A9
1
5
5
5
9
9
5
5


31
A9
2
4
4
4
6
6
1
1


33
A9
5
1
1
1
9
9
7
7


35
A9
8
8
8
8
0
0
6
6


52
A9
5
3
3
3
7
7
2
2


58
A9
5
1
1
1
7
7
5
5


67
A9
5
1
1
1
7
7
4
4


54
A 
6
8
8
8
8
8
5
5


42
A1
5
6
6
6
8
8
4
4


32
A1
6
6
6
6
9
9
5
5


61
A3
6
6
6
6
7
7
5
5


72
A3
5
8
8
8
7
7
5
5


89
A3
6
6
6
6
8
8
7
7


86
A3
7
9
9
9
8
8
9
9


87
A3
7
8
8
8
7
7
8
8


84
A3
8
9
9
9
8
8
10
10


83
A3
7
8
8
8
9
9
8
8


71
A3
7
7
7
7
9
9
7
7


90
A3
9
8
8
8
9
9
9
9


57
A4
8
6
6
6
9
9
8
8


57
A4
8
6
6
6
9
9
8
8


7
A8
10
9
9
9
3
3
8
8


40
A8
10
9
9
9
4
4
9
9


91
A8
5
5
5
5
3
3
5
5


6
 A10
8
7
7
7
11
11
8
8


6
 A10
8
7
7
7
11
11
8
8


6
 A10
8
7
7
7
11
11
8
8


11
 A10
7
9
9
9
10
10
8
8


44
 A10
5
9
9
9
7
7
8
8


55
 A10
5
9
9
9
7
7
8
8


74
 A10
4
7
7
7
8
8
6
6


13
 A10
4
7
7
7
6
6
4
4


34
 A11
6
6
6
6
7
7
5
5


73
 A11
7
6
6
6
8
8
6
6
















TABLE 47





A9 System F: sequence aligment mismach evaluation




















forward primer
reverse primer











SEQ ID NO:






















227
228
229
230
248
249
250
251
252
253
254
255


NoHPV
Group
A9E21f1az
A9E21f2bz
A9E21f3dz
A9E21f4cz
A9E21r1cz
A9E21r2az
A9E21r3az
A9E21r4fz
A9E21r5az
A9E21r6az
A9E21r7az
A9E21r8az





51
A5
4
4
3
4
8
10
7
9
9
9
8
9


26
A5
3
3
5
2
9
7
11
13
7
6
6
8


69
A5
4
4
4
4
8
9
10
12
6
6
6
7


82
A5
6
6
4
6
8
10
5
12
6
5
6
7


56
A6
5
5
4
4
8
8
8
14
6
6
6
5


30
A6
6
4
2
5
8
11
12
14
9
8
8
10


53
A6
6
4
4
7
7
10
7
11
5
4
3
5


66
A6
3
3
3
4
7
8
9
11
6
6
6
6


18
A7
6
6
5
6
9
8
9
11
7
6
5
6


39
A7
6
6
5
6
7
9
8
8
6
5
4
6


45
A7
7
7
6
7
11
10
10
12
10
10
10
9


59
A7
9
8
6
9
7
8
10
9
6
5
4
6


68
A7














85
A7
5
3
5
4
8
8
7
8
6
5
4
5


70
A7
6
6
4
6
7
9
7
9
5
4
3
5


16
A9
0
2
5
3
0
8
9
10
7
6
5
8


16
A9
0
2
5
3
2
9
9
9
6
5
4
7


31
A9
3
1
5
5
8
0
12
11
10
9
9
9


33
A9
4
4
0
4
9
12
0
11
6
7
8
5


35
A9
2
0
4
5
6
8
9
0
10
9
8
10


52
A9
2
4
6
0
5
9
8
13
2
1
0
3


58
A9
4
4
2
3
8
9
5
11
1
2
3
0


67
A9
3
5
3
2
7
8
6
12
2
1
2
1


54
A 
4
4
5
5
8
9
9
10
7
6
5
7


42
A1
7
8
6
6
9
8
9
12
7
8
7
6


32
A1
6
7
7
5
8
9
7
10
8
7
8
7


61
A3
4
2
6
3
8
10
9
13
8
7
6
7


72
A3
5
4
3
5
10
11
12
15
11
10
9
11


89
A3
7
6
8
8
8
10
11
11
9
8
7
9


86
A3
8
9
7
7
10
9
9
16
7
6
7
7


87
A3
8
8
6
6
10
9
10
16
8
7
8
8


84
A3
8
8
5
7
10
12
12
15
11
10
11
10


83
A3
7
5
6
6
7
10
9
10
9
10
9
9


71
A3
7
6
8
8
9
12
12
13
10
9
8
10


90
A3
8
6
10
7
12
11
12
12
12
12
12
11


57
A4
7
7
8
7
9
12
13
13
11
10
9
11


57
A4
6
6
9
6
9
12
13
14
11
10
9
11


7
A8
5
6
9
5
8
12
9
12
9
8
7
9


40
A8
6
6
6
7
9
12
10
12
12
11
11
11


91
A8
5
5
9
8
10
8
9
10
9
9
10
9


6
 A10
6
8
5
6
9
10
8
11
6
5
6
6


6
 A10
6
8
5
6
9
10
8
11
6
5
6
6


6
 A10
7
8
5
7
9
10
8
11
6
5
6
6


11
 A10
6
7
7
5
6
11
9
12
6
5
4
7


44
 A10
3
5
7
4
6
11
5
13
6
5
6
6


55
 A10
4
6
7
3
4
10
7
11
6
5
6
7


74
 A10
6
6
6
5
8
10
5
12
5
4
5
4


13
 A10
6
8
6
6
9
7
6
10
7
6
6
6


34
 A11
6
6
5
6
8
7
9
13
9
8
7
8


73
 A11
7
6
4
7
7
9
6
11
8
7
7
7














probes




SEQ ID NO:


















296
297
298
299
300
301
302
303


NoHPV
Group
A9E2Z7S1
A9E2Z7S2
A9E2Z7S2a
A9E2Z7S2b
A9E2Z7S3
A9E2Z7S3a
A9E2Z7S4
A9E2Z7S4a





51
A5
5
5
5
5
9
9
6
6


26
A5
4
3
3
3
6
6
4
4


69
A5
2
3
3
3
7
7
3
3


82
A5
2
3
3
3
7
7
3
3


56
A6
7
7
7
7
9
9
7
7


30
A6
5
6
6
6
9
9
7
7


53
A6
7
5
5
5
10
10
8
8


66
A6
8
8
8
8
10
10
8
8


18
A7
6
1
1
1
8
8
6
6


39
A7
7
4
4
4
8
8
6
6


45
A7
5
3
3
3
10
10
6
6


59
A7
5
3
3
3
7
7
5
5


68
A7

4
4
4
8
8
6
6


85
A7
6
6
6
6
10
10
5
5


70
A7
7
5
5
5
8
8
6
6


16
A9
0
6
6
6
8
8
4
4


16
A9
1
5
5
5
9
9
5
5


31
A9
1
4
4
4
6
6
1
1


33
A9
5
1
1
1
9
9
7
7


35
A9
7
8
8
8
0
0
6
6


52
A9
4
3
3
3
7
7
2
2


58
A9
4
1
1
1
7
7
5
5


67
A9
4
1
1
1
7
7
4
4


54
A 
5
8
8
8
8
8
5
5


42
A1
4
6
6
6
8
8
4
4


32
A1
5
6
6
6
9
9
5
5


61
A3
5
6
6
6
7
7
5
5


72
A3
4
8
8
8
7
7
5
5


89
A3
5
6
6
6
8
8
7
7


86
A3
6
9
9
9
8
8
9
9


87
A3
6
8
8
8
7
7
8
8


84
A3
7
9
9
9
8
8
10
10


83
A3
6
8
8
8
9
9
8
8


71
A3
6
7
7
7
9
9
7
7


90
A3
8
8
8
8
9
9
9
9


57
A4
7
6
6
6
9
9
8
8


57
A4
7
6
6
6
9
9
8
8


7
A8
9
9
9
9
3
3
8
8


40
A8
9
9
9
9
4
4
9
9


91
A8
4
5
5
5
3
3
5
5


6
 A10
7
7
7
7
11
11
8
8


6
 A10
7
7
7
7
11
11
8
8


6
 A10
7
7
7
7
11
11
8
8


11
 A10
6
9
9
9
10
10
8
8


44
 A10
5
9
9
9
7
7
8
8


55
 A10
5
9
9
9
7
7
8
8


74
 A10
4
7
7
7
8
8
6
6


13
 A10
3
7
7
7
6
6
4
4


34
 A11
5
6
6
6
7
7
5
5


73
 A11
6
6
6
6
8
8
6
6
















TABLE 48





A9 System GZ7: sequence aligment mismach evaluation




















forward primer
reverse primer











SEQ ID NO:


















No

227
228
229
230
256
257
258
259
260
261


HPV
Group
A9E21f1az
A9E21f2bz
A9E21f3dz
A9E21f4cz
A9E2r7C
A9E2r8
A9E2r10
A9E2r12
A9E2r12B
A9E2r15





51
A5
4
4
3
4
8
11
11
8
12
9


26
A5
3
3
5
2
14
12
12
13
17
13


69
A5
4
4
4
4
14
11
11
13
17
14


82
A5
6
6
4
6
8
10
8
9
12
9


56
A6
5
5
4
4
14
8
7
13
14
16


30
A6
6
4
2
5
13
9
10
12
14
13


53
A6
6
4
4
7
12
10
10
9
12
14


66
A6
3
3
3
4
14
6
6
13
14
16


18
A7
6
6
5
6
13
8
8
11
13
15


39
A7
6
6
5
6
13
10
8
10
13
15


45
A7
7
7
6
7
12
11
10
10
11
14


59
A7
9
8
6
9
13
8
8
13
14
14


68
A7




13
10
8
10
13
15


85
A7
5
3
5
4
9
10
7
11
11
10


70
A7
6
6
4
6
10
7
7
10
11
12


16
A9
0
2
5
3
2
11
9
6
6
0


16
A9
0
2
5
3
2
11
9
6
6
0


31
A9
3
1
5
5
5
13
10
0
2
8


33
A9
4
4
0
4
8
0
2
10
11
9


35
A9
2
0
4
5
3
12
10
4
2
6


52
A9
2
4
6
0
12
6
3
11
14
15


58
A9
4
4
2
3
10
1
3
12
12
11


67
A9
3
5
3
2
13
5
7
14
14
14


54
A 
4
4
5
5
12
11
12
9
13
13


42
A1
7
8
6
6
13
12
12
13
14
12


32
A1
6
7
7
5
14
12
12
15
15
13


61
A3
4
2
6
3
12
12
10
12
13
13


72
A3
5
4
3
5
14
13
11
13
14
13


89
A3
7
6
8
8
17
13
10
16
18
18


86
A3
8
9
7
7
14
15
12
13
15
14


87
A3
8
8
6
6
16
17
14
15
16
15


84
A3
8
8
5
7
16
15
12
15
17
14


83
A3
7
5
6
6
14
14
11
14
16
15


71
A3
7
6
8
8
14
18
15
11
14
15


90
A3
8
6
10
7
17
15
12
15
16
16


57
A4
7
7
8
7
14
14
11
14
15
16


57
A4
6
6
9
6
14
14
11
14
15
16


7
A8
5
6
9
5
12
10
9
15
15
12


40
A8
6
6
6
7
16
11
9
14
17
15


91
A8
5
5
9
8
9
12
11
11
11
9


6
 A10
6
8
5
6
12
10
10
14
16
12


6
 A10
6
8
5
6
13
10
10
15
17
13


6
 A10
7
8
5
7
13
12
12
14
16
13


11
 A10
6
7
7
5
14
12
12
16
16
14


44
 A10
3
5
7
4
12
11
11
11
12
12


55
 A10
4
6
7
3
11
11
11
10
11
11


74
 A10
6
6
6
5
14
14
12
14
14
13


13
 A10
6
8
6
6
12
12
12
11
15
12


34
 A11
6
6
5
6
7
10
9
4
7
7


73
 A11
7
6
4
7
9
10
9
8
9
9














probes




SEQ ID NO:
















No

296
297
298
299
300
301
302
303


HPV
Group
A9E2Z7S1
A9E2Z7S2
A9E2Z7S2a
A9E2Z7S2b
A9E2Z7S3
A9E2Z7S3a
A9E2Z7S4
A9E2Z7S4a





51
A5
5
5
5
5
9
9
6
6


26
A5
4
3
3
3
6
6
4
4


69
A5
2
3
3
3
7
7
3
3


82
A5
2
3
3
3
7
7
3
3


56
A6
7
7
7
7
9
9
7
7


30
A6
5
6
6
6
9
9
7
7


53
A6
7
5
5
5
10
10
8
8


66
A6
8
8
8
8
10
10
8
8


18
A7
6
1
1
1
8
8
6
6


39
A7
7
4
4
3
8
8
6
6


45
A7
5
3
3
3
10
10
6
6


59
A7
5
3
3
3
7
7
5
5


68
A7










85
A7
6
6
6
5
10
10
5
5


70
A7
7
5
5
4
8
8
6
6


16
A9
0
6
6
6
8
8
4
4


16
A9
1
5
5
5
9
9
5
5


31
A9
1
4
4
4
6
6
1
1


33
A9
5
1
1
1
9
9
7
7


35
A9
7
8
8
8
0
0
6
6


52
A9
4
3
3
3
7
7
2
2


58
A9
4
1
1
1
7
7
5
5


67
A9
4
1
1
1
7
7
4
4


54
A 
5
8
8
8
8
8
5
5


42
A1
4
6
6
6
8
8
4
4


32
A1
5
6
6
6
9
9
5
5


61
A3
5
6
6
6
7
7
5
5


72
A3
4
8
8
8
7
7
5
5


89
A3
5
6
6
6
8
8
7
7


86
A3
6
9
9
9
8
8
9
9


87
A3
6
8
8
8
7
7
8
8


84
A3
7
9
9
9
8
8
10
10


83
A3
6
8
8
8
9
9
8
8


71
A3
6
7
7
7
9
9
7
7


90
A3
8
8
8
8
9
9
9
9


57
A4
7
6
6
6
9
9
8
8


57
A4
7
6
6
6
9
9
8
8


7
A8
9
9
9
9
3
3
8
8


40
A8
9
9
9
9
4
4
9
9


91
A8
4
5
5
5
3
3
5
5


6
 A10
7
7
7
7
11
11
8
8


6
 A10
7
7
7
7
11
11
8
8


6
 A10
7
7
7
7
11
11
8
8


11
 A10
6
9
9
9
10
10
8
8


44
 A10
5
9
9
9
7
7
8
8


55
 A10
5
9
9
9
7
7
8
8


74
 A10
4
7
7
7
8
8
6
6


13
 A10
3
7
7
7
6
6
4
4


34
 A11
5
6
6
6
7
7
5
5


73
 A11
6
6
6
6
8
8
6
6
















TABLE 49





A9 System GZ8: sequence aligment mismach evaluation





















forward primer
reverse primer
probes











SEQ ID NO:























227
228
229
230
256
257
258
259
264
261
304
305
306


NoHPV
Group
A9E21f1az
A9E21f2bz
A9E21f3dz
A9E21f4cz
A9E2r7C
A9E2r8
A9E2r10
A9E2r12
A9E2r12B
A9E2r15
A9E2Z8S2f
A9E2Z8S21f
A9E2Z8S28f





51
A5
4
4
3
4
8
11
11
8
12
9
6
6
6


26
A5
3
3
5
2
14
12
12
13
17
13
8
8
8


69
A5
4
4
4
4
14
11
11
13
17
14
4
4
4


82
A5
6
6
4
6
8
10
8
9
12
9
6
6
6


56
A6
5
5
4
4
14
8
7
13
14
16
9
9
9


30
A6
6
4
2
5
13
9
10
12
14
13
10
10
10


53
A6
6
4
4
7
12
10
10
9
12
14
9
9
9


66
A6
3
3
3
4
14
6
6
13
14
16
8
8
8


18
A7
6
6
5
6
13
8
8
11
13
15
8
8
8


39
A7
6
6
5
6
13
10
8
10
13
15
9
9
9


45
A7
7
7
6
7
12
11
10
10
11
14
8
8
8


59
A7
9
8
6
9
13
8
8
13
14
14
9
9
9


68
A7




13
10
8
10
13
15





85
A7
5
3
5
4
9
10
7
11
11
10
9
9
9


70
A7
6
6
4
6
10
7
7
10
11
12
8
8
8


16
A9
0
2
5
3
2
11
9
6
6
0
0
0
0


16
A9
0
2
5
3
2
11
9
6
6
0
1
1
1


31
A9
3
1
5
5
5
13
10
0
2
8
9
9
9


33
A9
4
4
0
4
8
0
2
10
11
9
8
8
8


35
A9
2
0
4
5
3
12
10
4
2
6
9
9
9


52
A9
2
4
6
0
12
6
3
11
14
15
8
8
8


58
A9
4
4
2
3
10
1
3
12
12
11
10
10
10


67
A9
3
5
3
2
13
5
7
14
14
14
7
7
7


54
A 
4
4
5
5
12
11
12
9
13
13
9
9
9


42
A1
7
8
6
6
13
12
12
13
14
12
9
9
9


32
A1
6
7
7
5
14
12
12
15
15
13
7
7
7


61
A3
4
2
6
3
12
12
10
12
13
13
9
9
9


72
A3
5
4
3
5
14
13
11
13
14
13
13
13
13


89
A3
7
6
8
8
17
13
10
16
18
18
9
9
9


86
A3
8
9
7
7
14
15
12
13
15
14
13
13
13


87
A3
8
8
6
6
16
17
14
15
16
15
13
13
13


84
A3
8
8
5
7
16
15
12
15
17
14
10
10
10


83
A3
7
5
6
6
14
14
11
14
16
15
7
7
7


71
A3
7
6
8
8
14
18
15
11
14
15
8
8
8


90
A3
8
6
10
7
17
15
12
15
16
16
8
8
8


57
A4
7
7
8
7
14
14
11
14
15
16
9
9
9


57
A4
6
6
9
6
14
14
11
14
15
16
9
9
9


7
A8
5
6
9
5
12
10
9
15
15
12
9
9
9


40
A8
6
6
6
7
16
11
9
14
17
15
8
8
8


91
A8
5
5
9
8
9
12
11
11
11
9
7
7
7


6
 A10
6
8
5
6
12
10
10
14
16
12
8
8
8


6
 A10
6
8
5
6
13
10
10
15
17
13
8
8
8


6
 A10
7
8
5
7
13
12
12
14
16
13
7
7
7


11
 A10
6
7
7
5
14
12
12
16
16
14
8
8
8


44
 A10
3
5
7
4
12
11
11
11
12
12
7
7
7


55
 A10
4
6
7
3
11
11
11
10
11
11
4
4
4


74
 A10
6
6
6
5
14
14
12
14
14
13
8
8
8


13
 A10
6
8
6
6
12
12
12
11
16
12
9
9
9


34
 A11
6
6
5
6
7
10
9
4
7
7
10
10
10


73
 A11
7
6
4
7
9
10
9
8
9
9
9
9
9












probes



SEQ ID NO:























307
308
309
310
311
312
313
314
315
316
317
318
319


NoHPV
Group
A9E2Z8S56f
A9E2Z8S58f
A9E2Z8S61f
A9E2Z8S101f
A9E2Z8S105f
A9E2Z8S127f
A9E2Z8S146f
A9E2Z8S155f
A9E2Z8S156f
A9E2Z8S210f
A9E2Z8S231f
A9E2Z8S236f
A9E2Z8S250f





51
A5
12
12
12
10
10
10
11
11
11
12
10
10
10


26
A5
9
9
9
14
14
14
14
14
14
9
9
9
9


69
A5
12
12
12
13
13
13
14
14
14
7
8
8
8


82
A5
12
12
12
8
8
8
14
14
14
12
9
9
9


56
A6
11
11
11
12
12
12
15
15
15
5
7
7
7


30
A6
13
13
13
15
15
15
15
15
15
8
11
11
11


53
A6
12
12
12
10
10
10
12
12
12
6
6
6
6


66
A6
10
10
10
12
12
12
12
12
12
5
7
7
7


18
A7
10
10
10
12
12
12
12
12
12
6
7
7
7


39
A7
13
13
13
11
11
11
10
10
10
10
6
6
6


45
A7
11
11
11
13
13
13
13
13
13
9
10
10
10


59
A7
9
9
9
13
13
13
10
10
10
7
6
6
6


68
A7















85
A7
10
10
10
9
9
9
10
10
10
8
5
5
5


70
A7
11
11
11
9
9
9
10
10
10
6
5
5
5


16
A9
10
10
10
12
12
12
12
12
12
9
9
9
9


16
A9
11
11
11
12
12
12
11
11
11
9
8
8
8


31
A9
0
0
0
13
13
13
12
12
12
10
9
9
9


33
A9
13
13
13
0
0
0
13
13
13
11
6
6
6


35
A9
10
10
10
11
11
11
0
0
0
10
9
9
9


52
A9
12
12
12
12
12
12
13
13
13
0
5
5
5


58
A9
11
11
11
7
7
7
11
11
11
6
0
0
0


67
A9
10
10
10
9
9
9
14
14
14
7
3
3
3


54
A 
10
10
10
12
12
12
11
11
11
8
8
8
8


42
A1
12
12
12
13
13
13
14
14
14
7
9
9
9


32
A1
12
12
12
10
10
10
12
12
12
9
9
9
9


61
A3
12
12
12
11
11
11
15
15
15
9
8
8
8


72
A3
14
14
14
15
15
15
17
17
17
11
13
13
13


89
A3
12
12
12
14
14
14
13
13
13
10
10
10
10


86
A3
12
12
12
13
13
13
17 
17
17
8
10
10
10


87
A3
13
13
13
15
15
15
16
16
16
9
11
11
11


84
A3
10
10
10
12
12
12
16
16
16
12
10
10
10


83
A3
11
11
11
11
11
11
12
12
12
13
10
10
10


71
A3
14
14
14
15
15
15
15
15
15
12
11
11
11


90
A3
12
12
12
14
14
14
14
14
14
12
12
12
12


57
A4
11
11
11
14
14
14
13
13
13
10
11
11
11


57
A4
12
12
12
15
15
15
14
14
14
10
12
12
12


7
A8
13
13
13
12
12
12
13
13
13
8
10
10
10


40
A8
12
12
12
12
12
12
13
13
13
8
12
12
12


91
A8
10
10
10
12
12
12
12
12
12
10
11
11
11


6
 A10
12
12
12
11
11
11
13
13
13
10
8
8
8


6
 A10
12
12
12
11
11
11
13
13
13
10
8
8
8


6
 A10
12
12
12
11
11
11
13
13
13
10
8
8
8


11
 A10
12
12
12
12
12
12
13
13
13
8
8
8
8


44
 A10
14
14
14
8
8
8
15
15
15
7
9
9
9


55
 A10
12
12
12
9
9
9
13
13
13
8
9
9
9


74
 A10
13
13
13
8
8
8
14
14
14
8
6
6
6


13
 A10
8
8
8
7
7
7
12
12
12
9
6
6
6


34
 A11
9
9
9
12
12
12
15
15
15
12
9
9
9


73
 A11
11
11
11
7
7
7
12
12
12
11
6
6
6
















TABLE 50





A9 System H




















forward primer
reverse primer











SEQ ID NO:





















232
232
233
234
235
236
237
238
239
262
257


NoHPV
Group
A9E2f5
A9E2f6
A9E2f7
A9E2f8
A9E2f9
A9E2f10
A9E2f10b
A9E2f11
A9E2f12
A9E2r7B
A9E2r8





51
A5
4
8
8
5
6
4
5
5
6
8
11


26
A5
3
7
8
4
3
3
4
3
4
13
12


69
A5
2
8
6
2
3
2
3
3
4
14
11


82
A5
2
6
4
2
3
2
3
3
4
8
10


56
A6
6
10
11
7
6
5
6
8
7
13
8


30
A6
3
10
11
5
4
5
5
7
6
13
9


53
A6
6
12
13
7
7
4
5
6
7
12
10


66
A6
7
10
11
8
7
6
7
9
8
13
6


18
A7
4
7
8
6
3
2
2
4
5
12
8


39
A7
5
7
9
6
3
4
4
4
5
12
10


45
A7
4
10
9
5
5
3
3
5
6
11
11


59
A7
3
7
9
5
3
4
4
3
4
13
8


68
A7
5
7
9
6
3
4
4
4
5
12
10


85
A7
5
9
8
6
4
4
4
6
6
9
10


70
A7
5
6
8
6
3
4
4
5
5
10
7


16
A9
0
8
6
0
4
2
3
5
4
2
11


16
A9
1
8
6
1
5
1
2
6
5
2
11


31
A9
1
5
3
1
2
1
2
4
3
5
13


33
A9
3
10
10
5
3
1
1
4
5
9
0


35
A9
5
0
2
7
6
6
7
2
2
3
12


52
A9
3
8
8
4
3
3
3
2
3
12
6


58
A9
2
9
9
4
1
0
0
5
4
11
1


67
A9
2
8
8
4
1
0
0
5
4
13
5


54
A 
4
7
6
4
6
4
5
7
7
12
11


42
A1
3
7
6
3
4
3
3
6
5
13
12


32
A1
5
9
7
5
6
3
4
8
7
13
12


61
A3
4
7
6
4
5
2
3
6
6
12
12


72
A3
3
7
6
3
5
4
5
6
6
14
13


89
A3
3
7
7
4
5
2
3
7
7
17
13


86
A3
5
9
8
6
10
6
7
6
7
14
15


87
A3
5
9
8
6
9
6
7
6
7
15
17


84
A3
5
9
9
7
10
6
7
6
7
15
15


83
A3
4
10
10
6
8
4
5
7
7
14
14


71
A3
5
10
9
5
7
4
5
7
8
14
18


90
A3
8
12
11
7
9
6
7
7
8
15
15


57
A4
5
10
10
6
7
4
5
6
8
13
14


57
A4
5
10
10
6
7
4
5
6
8
13
14


7
A8
6
5
7
9
7
7
8
3
3
11
10


40
A8
6
8
9
9
7
7
8
4
4
15
11


91
A8
3
5
5
4
3
3
4
4
3
9
12


6
 A10
6
11
10
6
6
4
4
7
7
13
10


6
 A10
6
11
10
6
6
4
4
7
7
14
10


6
 A10
6
11
10
6
6
4
4
7
7
14
12


11
 A10
5
9
8
5
8
5
6
7
8
15
12


44
 A10
4
8
7
5
9
6
6
6
6
11
11


55
 A10
4
8
7
5
9
5
6
6
6
10
11


74
 A10
3
10
9
4
7
3
4
6
6
13
14


13
 A10
2
8
7
3
5
3
4
4
4
12
12


34
 A11
4
8
9
5
4
4
5
6
5
6
10


73
 A11
5
8
9
6
5
4
5
7
6
7
10















reverse primer
probes











SEQ ID NO:





















263
258
259
256
264
261
265
304
305
306
307


NoHPV
Group
A9E2r9
A9E2r10
A9E2r12
A9E2r7C
A9E2r12B
A9E2r15
A9E2r16
A9E2Z8S2f
A9E2Z8S21f
A9E2Z8S28f
A9E2Z8S56f





51
A5
10
11
8
8
12
9
14
6
6
6
12


26
A5
11
12
13
14
17
13
15
8
8
8
9


69
A5
10
11
13
14
17
14
13
4
4
4
12


82
A5
8
8
9
8
12
9
12
6
6
6
12


56
A6
7
7
13
14
14
16
10
9
9
9
11


30
A6
9
10
12
13
14
13
11
10
10
10
13


53
A6
9
10
9
12
12
14
14
9
9
9
12


66
A6
5
6
13
14
14
16
11
8
8
8
10


18
A7
8
8
11
13
13
15
10
8
8
8
10


39
A7
8
8
10
13
13
15
12
9
9
9
13


45
A7
11
10
10
12
11
14
10
8
8
8
11


59
A7
9
8
13
13
14
14
8
9
9
9
9


68
A7
8
8
10
13
13
15
12






85
A7
8
7
11
9
11
10
10
9
9
9
10


70
A7
6
7
10
10
11
12
11
8
8
8
11


16
A9
10
9
6
2
6
0
10
0
0
0
10


16
A9
10
9
6
2
6
0
10
1
1
1
11


31
A9
11
10
0
5
2
8
11
9
9
9
0


33
A9
1
2
10
8
11
9
2
8
8
8
13


35
A9
11
10
4
3
2
6
11
9
9
9
10


52
A9
4
3
11
12
14
15
8
8
8
8
12


58
A9
2
3
12
10
12
11
0
10
10
10
11


67
A9
6
7
14
13
14
14
5
7
7
7
10


54
A 
11
12
9
12
13
13
15
9
9
9
10


42
A1
12
12
13
13
14
12
13
9
9
9
12


32
A1
11
12
15
14
15
13
13
7
7
7
12


61
A3
11
10
12
12
13
13
12
9
9
9
12


72
A3
12
11
13
14
14
13
12
13
13
13
14


89
A3
11
10
16
17
18
18
14
9
9
9
12


86
A3
13
12
13
14
15
14
16
13
13
13
12


87
A3
15
14
15
16
16
15
18
13
13
13
13


84
A3
13
12
15
16
17
14
15
10
10
10
10


83
A3
12
11
14
14
16
15
15
7
7
7
11


71
A3
16
15
11
14
14
15
17
8
8
8
14


90
A3
13
12
15
17
16
16
16
8
8
8
12


57
A4
12
11
14
14
15
16
14
9
9
9
11


57
A4
12
11
14
14
15
16
14
9
9
9
12


7
A8
10
9
15
12
15
12
11
9
9
9
13


40
A8
10
9
14
16
17
15
12
8
8
8
12


91
A8
12
11
11
9
11
9
13
7
7
7
10


6
 A10
9
10
14
12
16
12
14
8
8
8
12


6
 A10
9
10
15
13
17
13
15
8
8
8
12


6
 A10
11
12
14
13
16
13
16
7
7
7
12


11
 A10
11
12
16
14
16
14
15
8
8
8
12


44
 A10
10
11
11
12
12
12
14
7
7
7
14


55
 A10
10
11
10
11
11
11
13
4
4
4
12


74
 A10
13
12
14
14
14
13
16
8
8
8
13


13
 A10
11
12
11
12
15
12
14
9
9
9
8


34
 A11
8
9
4
7
7
7
13
10
10
10
9


73
 A11
8
9
8
9
9
9
12
9
9
9
11














probes




SEQ ID NO:






















308
309
310
311
312
313
314
315
316
317
318
319


NoHPV
Group
A9E2Z8S58f
A9E2Z8S61f
A9E2Z8S101f
A9E2Z8S105f
A9E2Z8S127f
A9E2Z8S146f
A9E2Z8S155f
A9E2Z8S156f
A9E2Z8S210f
A9E2Z8S231f
A9E2Z8S236f
A9E2Z8S250f





51
A5
12
12
10
10
10
11
11
11
12
10
10
10


26
A5
9
9
14
14
14
14
14
14
9
9
9
9


69
A5
12
12
13
13
13
14
14
14
7
8
8
8


82
A5
12
12
8
8
8
14
14
14
12
9
9
9


56
A6
11
11
12
12
12
15
15
15
5
7
7
7


30
A6
13
13
15
15
15
15
15
15
8
11
11
11


53
A6
12
12
10
10
10
12
12
12
6
6
6
6


66
A6
10
10
12
12
12
12
12
12
5
7
7
7


18
A7
10
10
12
12
12
12
12
12
6
7
7
7


39
A7
13
13
11
11
11
10
10
10
10
6
6
6


45
A7
11
11
13
13
13
13
13
13
9
10
10
10


59
A7
9
9
13
13
13
10
10
10
7
6
6
6


68
A7














85
A7
10
10
9
9
9
10
10
10
8
5
5
5


70
A7
11
11
9
9
9
10
10
10
6
5
5
5


16
A9
10
10
12
12
12
12
12
12
9
9
9
9


16
A9
11
11
12
12
12
11
11
11
9
8
8
8


31
A9
0
0
13
13
13
12
12
12
10
9
9
9


33
A9
13
13
0
0
0
13
13
13
11
6
6
6


35
A9
10
10
11
11
11
0
0
0
10
9
9
9


52
A9
12
12
12
12
12
13
13
13
0
5
5
5


68
A9
11
11
7
7
7
11
11
11
6
0
0
0


67
A9
10
10
9
9
9
14
14
14
7
3
3
3


54
A 
10
10
12
12
12
11
11
11
8
8
8
8


42
A1
12
12
13
13
13
14
14
14
7
9
9
9


32
A1
12
12
10
10
10
12
12
12
9
9
9
9


61
A3
12
12
11
11
11
15
15
15
9
8
8
8


72
A3
14
14
15
15
15
17
17
17
11
13
13
13


89
A3
12
12
14
14
14
13
13
13
10
10
10
10


86
A3
12
12
13
13
13
17
17
17
8
10
10
10


87
A3
13
13
15
15
15
16
16
16
9
11
11
11


84
A3
10
10
12
12
12
16
16
16
12
10
10
10


83
A3
11
11
11
11
11
12
12
12
13
10
10
10


71
A3
14
14
15
15
15
15
15
15
12
11
11
11


90
A3
12
12
14
14
14
14
14
14
12
12
12
12


57
A4
11
11
14
14
14
13
13
13
10
11
11
11


57
A4
12
12
15
15
15
14
14
14
10
12
12
12


7
A8
13
13
12
12
12
13
13
13
8
10
10
10


40
A8
12
12
12
12
12
13
13
13
8
12
12
12


91
A8
10
10
12
12
12
12
12
12
10
11
11
11


6
 A10
12
12
11
11
11
13
13
13
10
8
8
8


6
 A10
12
12
11
11
11
13
13
13
10
8
8
8


6
 A10
12
12
11
11
11
13
13
13
10
8
8
8


11
 A10
12
12
12
12
12
13
13
13
8
8
8
8


44
 A10
14
14
8
8
8
15
15
15
7
9
9
9


55
 A10
12
12
9
9
9
13
13
13
8
9
9
9


74
 A10
13
13
8
8
8
14
14
14
8
6
6
6


13
 A10
8
8
7
7
7
12
12
12
9
6
6
6


34
 A11
9
9
12
12
12
15
15
15
12
9
9
9


73
 A11
11
11
7
7
7
12
12
12
11
6
6
6
















TABLE 51







list of HPV plasmids












Name
Group
Plasmid size kb
Insert size kb
Source
Publications















pHPV 16
A9
2.961
7.904
ATCC 45113



pHPV 6B
A10
2.686
7.900
ATCC 45150
The EMBO Journal vol2 no12 p.2341-2348 (1983)


pHPV 18
A7
4.363
7.857
ATCC 45152
J. Mol. Biol. (1987) 193 p.599-608


pHPV 31
A9
4.363
8.000
ATCC 65446
J Virol 58: 225-229, 1986


pHPV 11
A10
4.363
7.931
ATCC 45151
Virology 151 124-130 (1986)


pHPV 35 cl 2A
A9
4.363
3.750
ATCC 40330
U.S. Pat. 4,849,332


pHPV 35 cl 2B
A9
4.363
4.100
ATCC 40331
U.S. Pat. 4,849,332


pHPV 56 cl 2A
A6
2.818
5.100
ATCC 40341
U.S. Pat. 4,908,306


pHPV 56 cl 2C
A6
2.818
7.900
ATCC 40549
U.S. Pat. 4,908,306


pHPV 56 cl 2B
A6
2.818
3.100
ATCC 40379
U.S. Pat. 4,908,306


pHPV 43 cl 2A
A8
2.812
6.300
ATCC 40338
U.S. Pat. 4,849,334


pHPV 43 cl 2B
A8
2.812
2.850
ATCC 40339
U.S. Pat. 4,849,334


pHPV 44 cl 2
A10
2.818
7.800
ATCC 40353
U.S. Pat. 4,849,331


pHPV 7cl 7/4
A8
2.686
3.905
DKFZ


pHPV 7cl 7/5
A8
2.686
4.131
DKFZ


pHPV 13 cl 13
A10
2.686
7.241
DKFZ


pHPV 30 cl 30
A6
4.36
7.157
DKFZ


pHPV 40 cl 40
A8
2.686
7.296
DKFZ


pHPV 53 cl 53
A8
3.939
7.154
DKFZ


pHPV 57 cl 57
A4
2.686
7.235
DKFZ


pHPV 72 cl 72
A3
2.961
7.307
DKFZ


pHPV 73 cl 73
A11
2.961
7.005
DKFZ


pHPV 45 cl 45
A7
2.871
7.149
DKFZ


pHPV 51
A5
2.68
7.800
DKFZ
J. of Virology 1998 p1452-1455/aug.1991







p.4216-4225


pHPV 26
A5
2.686
7.100
DKFZ


pHPV 52
A9
2.686
7.940
DKFZ


pHPV 89 Frag 1
A3
3.015
0.700
DKFZ
The Journal of infectious diseases 2002 185: 1794-7


pHPV 89 Frag 2
A3
3.015
1.100
DKFZ
The Journal of infectious diseases 2002 185: 1794-7


pHPV 89 Frag 3
A3
3.015
2000
DKFZ
The Journal of infectious diseases 2002 185: 1794-7


pHPV 89 Frag 4
A3
3.015
5.100
DKFZ
The Journal of infectious diseases 2002 185: 1794-7


pHPV 62 Frag 1
A3
3.015
3.325
DKFZ


pHPV 62 Frag 2
A3
3.015
4.040
DKFZ


pHPV 62 Frag 3
A3
3.015
1.268
DKFZ


pHPV 84 Frag 1
A3
3.015
0.700
DKFZ
Virology 279, 109-115, 2001


pHPV 84 Frag 2
A3
3.015
4.500
DKFZ
Virology 279, 109-115, 2001


pHPV 84 Frag 3
A3
3.015
1000
DKFZ
Virology 279, 109-115, 2001


pHPV 84 Frag 4
A3
3.015
1.800
DKFZ
Virology 279, 109-115, 2001


pHPV 84 Frag 5
A3
3.015
0.600
DKFZ
Virology 279, 109-115, 2001


pHPV 90 Frag 1
A3
3.015
4.200
DKFZ
The Journal of infectious diseases 2002 185: 1794-7


pHPV 90 Frag 2
A3
3.015
1.700
DKFZ
The Journal of infectious diseases 2002 185: 1794-7


pHPV 90 Frag 3
A3
3.015
2.500
DKFZ
The Journal of infectious diseases 2002 185: 1794-7


pHPV 86 Frag 1
A3
3.015
3.900
DKFZ
J Gen Virol 2001, 82, 2035-2040


pHPV 86 Frag 2
A3
3.015
5.800
DKFZ
J Gen Virol 2001, 82, 2035-2040


pHPV 86 Frag 3
A3
3.015
0.140
DKFZ
J Gen Virol 2001, 82, 2035-2040


pHPV 91 Frag 1
A8
3.015
3.200
DKFZ
The Journal of infectious diseases 2002 185: 1794-7


pHPV 91 Frag 2
A8
3.015
1.500
DKFZ
The Journal of infectious diseases 2002 185: 1794-7


pHPV 91 Frag 3
A8
3.015
1.400
DKFZ
The Journal of infectious diseases 2002 185: 1794-7


pHPV 91 Frag 4
A8
3.015
2.500
DKFZ
The Journal of infectious diseases 2002 185: 1794-7


pHPV 33
A9
4.363
7.093
CNCM I-450


pHPV 39
A7
3.005
7.160
CNCM I-507
JCM mar 1996, 738-744


pHPV 42
A1
3.030
7.107
CNCM I-508


pHPV 54
A4
3.030
7.107
CNCM I-756


pHPV 23
B1
4.363
7.324
CNCM I-391
J Virol, december 1984, 52, 1013-1018


pHPV 68
A7
4.363
6.042
CNCM I-1540
JCM march 1996, 738-744/U.S. Pat. 5,981,173


pHPV 66
A6
4.363
7.158
CNCM I-951
J virol, 1986, 57, 688-692


pHPV 87 L1 E1 16
A3
3.015
1.014
DKFZ
Journal of Virology déc. 2001 p11913-11919


pHPV 87 L1 f
A3
3.015
0.974
DKFZ
Journal of Virology déc. 2001 p11913-11919


pHPV 87 MY 16
A3
3.015
0.448
DKFZ
Journal of Virology déc. 2001 p11913-11919


pHPV 87 E1 L1 11/2
A3
3.015
2.794
DKFZ
Journal of Virology déc. 2001 p11913-11919


pHPV 87 L1 E1 37
A3
3.015
1.227
DKFZ
Journal of Virology déc. 2001 p11913-11919


pHPV 87 E11 E2 as
A3
3.015
1.130
DKFZ
Journal of Virology déc. 2001 p11913-11919


pHPV 58
A8
3.800
7.824
DKFZ
Virology (1990) 177: 833-836


pHPV 59
A7
2.695
7.896
DKFZ
Int. J. Cancer (1995) 61: 13-22


pHPV 87
A9
2.695
7.801
DKFZ
Int. J. Cancer (1995) 61: 13-22


pHPV 81
A3
3.204
4.759
DKFZ
Virology (2001) 283: 139-147


pHPV 82
A5
3.204
7.871
DKFZ
Clin. Diagn. Lab. Immu. (2000) 7: 91-95


pHPV 85
A7
3.500
7.812
DKFZ
Journal of General Virology (1999) 80, 2923-2929





DKFZ is Deusches Kresbsorschungszentrum; Tumorvirologie; ATV0660; Im Neuenheimer Feld 242; DE-Heidelberg; Germany;


CNCM is Collection Nationale de Cultures de Microorganisme; Institut Pasteur; 25, rue du Docteur Roux; F-75724 Paris Cedex 15; France;


ATCC is American Type Culture Collection; 10801 University Blvd.; Manassas, Virginia 20110-2209; U.S.A.


All HPV strains are available from DKFZ.













TABLE 52





A5 and A6 Systems PCR simplex probe conditions


















Kit
Kit Quantitect probe PCR



MgCl2
6 mM



Plasmid concentration
108 cop de plasmides/PCR















forward
reverse




primer
primer
probes















Thermoprofile
Name
μM
Name
μM
Name
μM










A5 System A. B. C. D. E: PCR simplex probe conditions














System A
55° C.
A5E6f1
0.4
A5E6r1
0.4
A5E6S1
0.3


System A
53° C.
A5E6f1
0.4
A5E6r1
0.4
A5E6S1b
0.2


System B
55° C.
A5E6f2
0.3
A5E6r2
0.3
A5E6S2
0.4


System C
55° C.
A5E6f3
0.6
A5E6r3
0.6
A5E6S3
0.3


System D
56° C.
A5E6f4
0.3
A5E6r4
0.3
A5E6S4
0.3


System E
55° C.
A5E6f5
0.6
A5E6r5
0.6
A5E6S4
0.2







A6 System A. B. C. D. E: PCR simplex probe conditions














System A
58° C.
A6E6f1
0.4
A6E6r1
0.4
A6E6S1
0.3


System B
57° C.
A6E6f2
0.6
A6E6r1
0.6
A6E6S1
0.4


System C
55° C.
A6E6f3
0.6
A6E6r2
0.6
A6E6S2
0.3


System C
57° C.
A6E6f3
0.6
A6E6r2
0.6
A6E6S2b
0.2


System D
58° C.
A6E6f4
0.5
A6E6r1
0.5
A6E6S1
0.4


System E
57° C.
A6E6f5
0.4
A6E6r3
0.4
A6E6S3
0.3


System E
56° C.
A6E6f5
0.4
A6E6r3
0.4
A6E6S3b
0.2
















TABLE 53







A5 System A, B, C, D, E, specificity
















Syt A
Syt A
Syt B
Syt C
Syt D
Syt E




A5E6S1b
A5E6S1
A5E6S2
A5E6S3
A5E6S4
A5E6S4




















N° HPV
Group
CT
RFU
CT
RFU
CT
RFU
CT
RFU
CT
RFU
CT
RFU























51
A5
22.2*
500
10.95
600
9.9
350
9.9
500
10.5
1200
9.6
1700


26
A5
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND


69
A5
NT
NT
NT
NT
NT
NT
NT
NT
NT
NT
NT
NT


82
A5
ND
ND
ND
ND
22.5
200
ND
ND
ND
ND
ND
ND



















Other HPV
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND


DNA sample
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND


H2O sample
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND





*Plasmid concentration: 5 · 105 copies of plasmids/PCR


ND: no Detection


NT: no test













TABLE 54







A6 System A, B, C, D, E, specificity

















Syt A
Syt B
Syt C
Syt C
Syt D
Syt E
Syt E




A6E6S1
A6E6S1
A6E6S2
A6E6S2b
A6E6S1
A5E6S3
A5E6S3b






















N° HPV
Group
CT
RFU
CT
RFU
CT
RFU
CT
RFU
CT
RFU
CT
RFU
CT
RFU





56
A6
14.3
250
13.0
500
13.6
3200
19.9*
700
14.3
550
12.3 
350
18.5*
900


30
A6
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND


53
A6
NT
NT
NT
NT
NT
NT
NT
NT
NT
NT
NT
NT
NT
NT


66
A6
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
22.6*
450
24.9*
820





















Other HPV
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND


DNA sample
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND


H2O sample
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND





*Plasmid concentration: 5 106 copies of plasmids/PCR


ND: no Detection


NT: no test













TABLE 55





A7 System A. B. C. D: PCR simplex probe and PCR multiplex probes conditions


















Kit
Kit Quantitect probe PCR



MgCl2
6 mM



Plasmid concentration
106 cop de plasmides/PCR















forward primer
reverse primer
probes















Thermoprofile
Name
μM
Name
μM
Name
μM





System A
53° C.
A7E16f1a
0.3
A7E16r1b
0.2
A7E1ZAS61f
0.2




A7E16f2a
0.3
A7E16r2b
0.3
A7E1S63f
0.2




A7E16f3a
0.3
A7E16r3b
0.3
A7E1S64f
0.2








A7E1S40f
0.2








A7E1ZBS74f
0.2


System B
52° C.
A7E115f1a
0.3
A7E115r1a
0.2
A7E1ZBS26f
0.2




A7E115f2a
0.3
A7E115r2b
0.3
A7E1ZBS74f
0.2




A7E115f3d
0.3


A7E1ZBS80f
0.2


System C
51° C.
A7E17f1
0.4
A7E17r1
0.3
A7E1ZCS11f
0.2




A7E17f2
0.4
A7E17r2
0.4
A7E1ZCS45f
0.2




A7E17f3
0.4


A7E1ZCS63f
0.2








A7E1ZCS90f
0.2


System D
53° C.
A7E12f1
0.3
A7E12r2
0.3
A7E1S36f
0.2




A7E12f2
0.3
A7E12r3
0.1
A7E1S37f
0.2








A7E1S38f
0.2








A7E1ZDS2f
0.2
















TABLE 56







A7 System A. specificity





















Multiplex









A7E1ZAS61f









A7E1ZAS63f




Simplex
Simplex
Simplex
Simplex
Simplex
A7E1ZCS40f



Probe
A7E1ZAS61f
A7E1ZAS63f
A7E1ZAS64f
A7E1ZCS40f
A7E1ZBS74f
A7E1ZBS74f




















N° HPV 
Group
CT
RFU
CT
RFU
CT
RFU
CT
RFU
CT
RFU
CT
RFU























18
A7
22.5
175
ND
ND
ND
ND
ND
ND
ND
ND
22.5
168


39
A7
ND
ND
ND
ND
22.1
145
ND
ND
22.8
248
21.0
263


45
A7
ND
ND
ND
ND
ND
ND
25.5
115
ND
ND
20.3
160


59
A7
ND
ND
20.5
62.5
ND
ND
ND
ND
ND
ND
20.2
188


68
A7
ND
ND
ND
ND
ND
ND
ND
ND
26.2
125
25.9
31


85
A7
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND


70
A7
NT
NT
NT
NT
NT
NT
NT
NT
NT
NT
NT
NT



















Other HPV
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
NT
NT


DNA sample
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND


H2O sample
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND





ND: no Detection


NT: no test













TABLE 57





A7 System B. specificity























Simplex
Simplex
Simplex
Simplex
Simplex



Probe
A7E1ZBS74f
A7E1ZBS79f
A7E1ZBS80f
A7E1ZBS26f
A7E1ZBS27f


















N° HPV
Groupe
CT
RFU
CT
RFU
CT
RFU
CT
RFU
CT
RFU





18
A7
ND
ND
ND
ND
ND
ND
22.9
770
22.5
43


39
A7
24.2 
900
ND
ND
ND
ND
ND
ND
ND
ND


45
A7
ND
ND
ND
ND
ND
ND
25.6
312
21.7
665


59
A7
ND
ND
18.6
2525
21.2
845
ND
ND
ND
ND


68
A7
25.7 
77
ND
ND
ND
ND
ND
ND
ND
ND


85
A7
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND


70
A7
NT
NT
NT
NT
NT
NT 
NT
NT
NT
NT

















Other HPV 
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND


DNA sample
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND


H2O sample 
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
























Multiplex







Multiplex
Multiplex
A7E1ZBS26f







A7E1ZBS26f
A7E1ZBS26f 
A7E1ZBS74f







A7E1ZBS74f
A7E1ZBS74f 
A7E1ZBS80f






Probe
A7E1ZBS79f 
A7E1ZBS80f
A7E1ZBS27f




















N° HPV
Groupe
CT
RFU
CT
RFU
CT
RFU








18
A7
22.3
215
20.9
248
20.3
318





39
A7
34.8
155
26.7
375
32.9
213





45
A7
26
72
26.3
98
26.2
173





59
A7
24
505
21.7
338
21.5
308





68
A7
34.5
128
22.8
163
27.1
135





85
A7
ND
ND
ND
ND
ND
ND





70
A7
NT
NT
NT
NT
NT
NT



















DNA sample
ND
ND
ND
ND
ND
ND





H2O sample 
ND
ND
ND
ND
ND 
ND





ND: no Detection


NT: no test













TABLE 58







A7 System C. specificity






















Multiplex
Multiplex









A7E1ZCS40f
A7E1ZCS11f









A7E1ZCS45f
A7E1ZCS45f




Simplex
Simplex
Simplex
Simplex
Simplex
A7E1ZCS63f
A7E1ZCS63f



Probe
A7E1ZCS11f
A7E1ZCS40f
A7E1ZCS45f
A7E1ZCS63f
A7E1ZCS90f
A7E1ZCS90f
A7E1ZCS90f






















N° HPV
Groupe
CT
RFU
CT
RFU
CT
RFU
CT
RFU
CT
RFU
CT
RFU
CT
RFU

























18
A7
22.0
247
23.4
200
ND
ND
ND
ND
ND
ND
22.6
231
22.0
239


39
A7
ND
ND
ND
ND
21.9
350
ND
ND
ND
ND
21.7
649
21.1
451


45
A7
21.9
349
24.0
325
ND
ND
ND
ND
ND
ND
25.6
319
24.7
192


59
A7
ND
ND
24.4
35
ND
ND
22.4
400
ND
ND
24.4
491
25.3
309


68
A7
ND
ND
ND
ND
ND
ND
ND
ND
26.2
250
24.5
344
25.3
181


85
A7
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND


70
A7
NT
NT
NT
NT
NT
NT
NT
NT
NT
NT
NT
NT
NT
NT





















Other HPV
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
NT
NT
NT
NT


DNA sample
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND


H2O sample
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND





ND: no Detection


NT: no test













TABLE 59







A7 System D. specificity






















Multiplex
Multiplex









A7E1S36f
A7E1S3f









A7E1S37f
A7E1S37f




Simplex
Simplex
Simplex
Simplex
Simplex
A7E1S38f
A7E1S38f



Probe
A7E1ZDS37f
A7E1ZDS38f
A7E1S36 f
A7E1ZDS2f
A7E1ZDS3f
A7E1ZDS2f
A7E1ZDS2f






















N° HPV
Groupe
CT
RFU
CT
RFU
CT
RFU
CT
RFU
CT
RFU
CT
RFU
CT
RFU

























18
A7
23.0
230
ND
ND
ND
ND
ND
ND
ND
ND
21.1
357
21.8
420


39
A7
ND
ND
23.9
269
ND
ND
25.1
323
ND
ND
22.5
233
22.3
310


45
A7
ND
ND
ND
ND
27.2
426
ND
ND
23.0
1545
26.6
295
23.5
508


59
A7
ND
ND
23.8
592
ND
ND
ND
ND
ND
ND
22.6
135
22.6
230


68
A7
ND
ND
ND
ND
ND
ND
22.9
897
ND
ND
23.4
363
23.5
548


85
A7
ND
ND
31.8
262
ND
ND
ND
ND
ND
ND
32.6
63
29.2
103


70
A7
NT
NT
NT
NT
NT
NT
NT
NT
NT
NT
NT
NT
NT
NT





















Other HPV
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
NT
NT
NT
NT


DNA sample
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND


H2O sample
ND 
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND





ND: no Detection


NT: no test













TABLE 60





A9 Systems: PCR simplex and PCR multiplex probes conditions


















Kit
Kit Quantitect probe PCR



MgCl2
5 mM



Plasmid concentration
106 cop/PCR















forward primer
reverse primer
probes















Thermoprofile
Name
μM
Name
μM
Name
μM





System C
51° C.
A9E1f8
0.4
A9E1r5
0.4
A9E1S10a
0.2




A9E1f10
0.4
A9E1r6
0.4
A9E1S12a
0.2




A9E1f12
0.2


System E2
52° C.
A9E2f1a
0.4
A9E2r1
0.4
A9E2Z7S1
0.2




A9E2f2a
0.6
A9E2r2
0.4
A9E2Z7S2
0.2




A9E2f4a
0.4
A9E2r4
0.6
A9E2Z7S3a
0.2






A9E2r13
0.4
A9E2Z7S4a
0.2






A9E2r14
0.4


System E3
52° C.
A9E2f1a
0.4
A9E21r1cz
0.4
A9E2Z7S1
0.2




A9E2f2a
0.4
A9E21r2az
0.4
A9E2Z7S2
0.2




A9E2f4a
0.4
A9E21r3az
0.4
A9E2Z7S3a
0.2






A9E21r4fz

A9E2Z7S4a
0.2






A9E21r5az


System E4
52° C.
A9E2Z5Z6f1c
0.4
A9E21r1cz
0.4
A9E2Z7S1
0.2




A9E2Z5Z6f2c
0.4
A9E21r2az
0.4
A9E2Z7S2
0.2




A9E2Z5Z6f3b
0.4
A9E21r3az
0.4
A9E2Z7S3a
0.2






A9E21r4fz

A9E2Z7S4a
0.2






A9E21r5az


System F
52° C.
A9E2-1f1az
0.4
A9E2-1r1cz
0.4
A9E2Z7S1
0.2




A9E2-1f2bz
0.5
A9E2-1r2az
0.4
A9E2Z7S2
0.2




A9E2-1f3dz
0.4
A9E2-1r3az
0.4
A9E2Z7S3a
0.2




A9E2-1f4cz
0.4
A9E2-1r4fz
0.4
A9E2Z7S4a
0.2






A9E2-1r5az
0.4


System G Z7
52° C.
A9E2-1f1az
0.4
A9E2r8
0.4
A9E2Z7S1
0.2




A9E2-1f2bz
0.4
A9E2r10
0.4
A9E2Z7S2a
0.2




A9E2-1f3dz
0.4
A9E2r12
0.4
A9E2Z7S3a
0.2




A9E2-1f4cz
0.5
A9E2r12B
0.4
A9E2Z7S4a
0.2






A9E2r15
0.4


System G Z8
52° C.
A9E2-1f1az
0.6
A9E2r8
0.4
A9E2Z8S2f
0.2




A9E2-1f2bz
0.4
A9E2r10
0.4
A9E2Z8S61f
0.2




A9E2-1f3dz
0.4
A9E2r12
0.4
A9E2Z8S127f
0.2




A9E2-1f4cz
0.5
A9E2r12B
0.4
A9E2Z8S156f
0.2






A9E2r15
0.6
A9E2Z8S210f
0.2








A9E2Z8S250f
0.2


System H
53° C.
A9E2f6
0.4
A9E2r10
0.4
A9E2Z8S2f
0.2




A9E2f8
0.4
A9E2r12B
0.4
A9E2Z8S61f
0.2




A9E2f9
0.4
A9E2r15
0.4
A9E2Z8S127f
0.2






A9E2r16
0.4
A9E2Z8S156f
0.2








A9E2Z8S210f
0.2








A9E2Z8S231f
0.2








A9E2Z8S250f
0.2
















TABLE 61







A9 System C specificity

























Multiplex




Simplex
Simplex
Simplex
Simplex
Simplex
Simplex
Simplex
A9E2S10a



Probes
A9E1S10*
A9E1S10a
A9E1S11*
A9E1S11a*
A9E1S12*
A9E1S12a
A9E1S12b*
A9E2S12a
























N° HPV
Group
CT
RFU
CT
RFU
CT
RFU
CT
RFU
CT
RFU
CT
RFU
CT
RFU
CT
RFU



























16
A9
22.3
1125
21.9
492
NT
NT
NT
NT
NT
NT
ND
ND
NT
NT
21.0
442


31
A9
27.3
625
23.0
469
25.7
679
24.6
415
39.4
14.5
26.6
103
ND
ND
20.8
458


33
A9
25.8
450
22.9
374
NT
NT
NT
NT
NT
NT
ND
ND
NT
NT
22.3
327


35
A9
33.0
181
24.9
188
27.2
342
26.4
234
26.5
224
23.2
502
26.9
241
23.0
435


52
A9
23.4
1059
22.7
599
NT
NT
23.8
215
NT
NT
ND
ND
NT
NT
21.7
581


58
A9
23.5
1435
23.7
582
NT
NT
24.3
278
NT
NT
ND
ND
NT
NT
23.7
525


67
A9
25.0
334
22.4
294
NT
NT
NT
NT
NT
NT
ND
ND
NT
NT
21.9
279


53
A6
NT
NT
29.7
449
NT
NT
NT
NT
NT
NT
ND
ND
NT
NT
31.1
263























Other HPV
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND


DNA sample
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND


H2O sample
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND





*Probes tested only with some A9 plasmids (i.e.. those A9 plasmids. which are indicated in this table)


ND: not detected


NT: not tested













TABLE 62







A9 System E2 specificity



















Multiplex








A9E2S1








A9E2S2




Simplex
Simplex 
Simplex
Simplex
A9E2S3a



Probes
A9E2Z7S1
A9E2Z7S2
A9E2Z7S3a
A9E2Z7S4a
A9E2S4a


















N° HPV
Group
CT
RFU
CT
RFU
CT
RFU
CT
RFU
CT
RFU





















16
A9
21.35
806
ND
ND
ND
ND
22.85
113
20.55
333


31
A9
23.8
485
ND
ND
ND
ND
23.5
295
25.3
238


33
A9
32.1
73
27.7 
1415
ND
ND
27.5
45
31.45
256


35
A9
ND
ND 
ND
ND
27.8
840
ND
ND
30.1
160


52
A9
25.2
80
22.4
186
ND
ND
21.45
278
21.7
115


58
A9
24.45
130
22.1
435
ND
ND
23.55
94
24.1
113


67
A9
30.2
173
28.7
447
ND
ND
29.35
123
31.9
125

















Other HPV
ND
ND
ND
ND
ND
ND
ND
ND
NT
NT


DNA sample
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND


H2O sample
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND





ND: not detected


NT: not tested













TABLE 63







A9 System E3 specificity



















Multiplex








A9E2S1








A9E2S2




Simplex
Simplex
Simplex
Simplex
A9E2S3a



Probes
A9E2Z7S1
A9E2Z7S2
A9E2Z7S3a
A9E2Z7S4a
A9E2S4a


















N° HPV
Group
CT
RFU
CT
RFU
CT
RFU
CT
RFU
CT
RFU





















16
A9
20.5
2000
ND
ND
ND
ND
21.85
520
21
546


31
A9
22.35
1200
ND
ND
ND
ND
22.65
660
25.2
336


33
A9
27.05
250
20.7
1600
ND
ND
24.8
135
22.2
496


35
A9
ND
ND
ND
ND
26.95
750
ND
ND
31.5
79


52
A9
25.35
300
21.7
370
ND
ND
21.65
220
21.7
169


58
A9
32.6
100
22.05
200
ND
ND
23.6
180
22.7
189


67
A9
30.05
150
28.95
420
ND
ND
29.95
120 
NT
NT

















Other HPV
ND
ND
ND
ND
ND
ND
ND
ND
NT
NT


DNA sample
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND


H2O sample
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND





ND: not detected


NT: not tested













TABLE 64







A9 System E4 specificity



















Multiplex








A9E2S1








A9E2S2




Simplex
Simplex
Simplex
Simplex
A9E2S3a



Probes
A9E2Z7S1
A9E2Z7S2
A9E2Z7S3a
A9E2Z7S4a
A9E2S4a


















N° HPV
Group
CT
RFU
CT
RFU
CT
RFU
CT
RFU
CT
RFU





















16
A9
21.05
600.24
ND
ND
ND
ND
23.25 
139.94
23.55 
473.54


31
A9
22.0 
461.14
ND
ND
ND
ND
22.5 
447.6
23.65
524.07


33
A9
25.95 
68.73
21.65
3190.34
ND
ND
24.95
108.385
23.2
800.33


35
A9
ND
ND
ND
ND
21.6
1355.5
ND
ND
23.4
348.45


52
A9
26.9 
26.58
22.85
314.81
ND
ND
21.5 
320.785
22.4 
207.195


58
A9
26.25
104.23
24.1
899.37
ND
ND
24.8
158.91
24.9
357.445


67
A9
24.6 
134.345
22.9
1275.03 
ND
ND
23.85
188.72
NT
NT

















Other HPV
ND
ND
ND
ND
ND
ND
ND
ND
NT
NT


DNA sample
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND


H2O sample
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND





ND: not detected


NT: not tested













TABLE 65







A9 System F specificity



















Multiplex








A9E2S1








A9E2S2




Simplex
Simplex
Simplex
Simplex
A9E2S3a



Probes
A9E2Z7S1
A9E2Z7S2
A9E2Z7S3a
A9E2Z7S4a
A9E2S4a


















N° HPV
Group
CT
RFU
CT
RFU
CT
RFU
CT
RFU
CT
RFU





















16
A9
21.75
765
ND
ND
ND
ND
23.95
77
21.1
335


31
A9
22.4
510
ND
ND
ND
ND
22.05
287
22.7
235


33
A9
27.0
117
21.1
1298.5 
ND
ND
24.4
61.5
21.1
443


35
A9
ND
ND
ND
ND
21.0
1542.5
ND
ND
22.8
164


52
A9
30.95
78.5 
25.3
180
ND
ND
22.45
399
22.3
199


58
A9
26.05
187.5 
23.1
538.5
ND
ND
23.05
178
22.2
280


67
A9
25.15 
190.5
23.0
569.5 
ND
ND
23.1
185.5
NT
NT

















Other HPV
ND
ND
ND
ND
ND
ND
ND
ND
NT
NT


DNA sample
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND


H2O sample
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND





ND: not detected


NT: not tested













TABLE 66







A9 System G Z7 specificity



















Multiplex








A9E2S1








A9E2S2a




Simplex
Simplex
Simplex
Simplex
A9E2S3a



Probes
A9E2Z7S1
A9E2Z7S2a
A9E2Z7S3a
A9E2Z7S4a
A9E2S4a


















N° HPV
Group
CT
RFU
CT
RFU
CT
RFU
CT
RFU
CT
RFU





















16
A9
20.3
600
ND
ND
ND
ND
24.6
56
21
658


31
A9
20.6
303.5
ND
ND
ND
ND
22.7
167
23.1
501


33
A9
22.9
80
ND
ND
ND
ND
22.1
280
20.4
920


35
A9
ND
ND
ND
ND
22.2
1330
ND
ND
23.9
254


52
A9
24.1
53
23
371.5
ND
ND
23
284
22.9
519


58
A9
23.1
150
21.6
739
ND
ND
23.8
124
21.9
779


67
A9
21.9
191.5
21.7
692
ND
ND
23.6
156.5 
NT
NT

















Other HPV
ND
ND
ND
ND
ND
ND
ND
ND
NT
NT


DNA sample
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND


H2O sample
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND





ND: not detected


NT: not tested













TABLE 67





A9 system G Z8 specificity
























Simplex
Simplex
Simplex
Simplex
Simplex
Simplex



Probes
A9E2Z8S2f
A9E2Z8S61f
A9E2Z8S127f 
A9E2Z8S156f
A9E2Z8S210f 
A9E2Z8S250f




















N° HPV
Group 
CT
RFU
CT
RFU
CT
RFU
CT
RFU
CT
RFU
CT
RFU





16
A9
21.5
261
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND


31
A9
ND
ND
21.9
291
ND
ND
ND
ND
ND
ND
ND
ND


33
A9
ND
ND
ND
ND
20.5
677
ND
ND
ND
ND
ND
ND


35
A9
ND
ND
ND
ND
ND
ND
22.6
333.5
ND
ND
ND
ND


52
A9
ND
ND
ND
ND
ND
ND
ND
ND
23.0
115
ND
ND


58
A9
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
20.0 
1348


67
A9
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
22.1
351.5



















Other HPV
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND


DNA sample
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND


H2O sample
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND

















Multiplex
Multiplex





A9E2Z8S2f
A9E2Z8S2f**





A9E2Z8S61f
A9E2Z8S61f





A9E2Z8S127f
A9E2Z8S127f





A9E2Z8S156f
A9E2Z8S156f





A9E2Z8S210f
A9E2Z8S210f**




Probes
A9E2Z8S250f*
A9E2Z8S250f*














N° HPV
Group 
CT
RFU
CT
RFU






16
A9
22.4
27
22.4
22



31
A9
23.6
73.5
24
42



33
A9
21.8
83.5
20.9
110



35
A9
22.7
42
23.6
45



52
A9
25.8
25
24
30



58
A9
19.3
169
19.6
201



67
A9
21.6
57
NT
NT













DNA sample
ND
ND
ND
ND



H2O sample
ND
ND
ND
ND





*probe at 0.1 μM in these tests


**probes at 0.3 μM in this test


ND: not detected


NT: not tested













TABLE 68





A9 SystemH specificity

























Simplex
Simplex
Simplex
Simplex
Simplex
Simplex
Simplex



Probes
A9E2Z8S2f
A9E2Z8S61f
A9E2Z8S127f
A9E2Z8S156f
A9E2Z8S210f
A9E2Z8S231f
A9E2Z8S250f






















N° HPV
Group
CT
RFU
CT
RFU
CT
RFU
CT
RFU
CT
RFU
CT
RFU
CT
RFU





16
A9
21.7
665
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND


31
A9
ND
ND
22.1
307
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND


33
A9
ND
ND
ND
ND
21.4
889
ND
ND
ND
ND
ND
ND
ND
ND


35
A9
ND
ND
ND
ND
ND
ND
22.2
155
ND
ND
ND
ND
ND
ND


52
A9
ND
ND
ND
ND
ND
ND
ND
ND
23.9
270
ND
ND
ND
ND


58
A9
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
21.3
345
19.8
2690


67
A9
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
27.0
82.5
27.1 
276





















Other HPV
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND


DNA sample
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND


H2O sample
ND
ND 
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND



























Multiplex
Multiplex
Multiplex
Multiplex









A9E2Z8S2f
A9E2Z8S2f
A9E2Z8S2f
A9E2Z8S2f









A9E2Z8S61f
A9E2Z8S61f
A9E2Z8S61f
A9E2Z8S61f









A9E2Z8S127f
A9E2Z8S127f
A9E2Z8S127f 
A9E2Z8S127f









A9E2Z8S156f
A9E2Z8S156f
A9E2Z8S156f
A9E2Z8S156f









A9E2Z8S210f 
A9E2Z8S210f
A9E2Z8S210f
A9E2Z8S210f








Probes
A9E2Z8S250f
A9E2Z8S231f
A9E2Z8S250f
A9E2Z8S231f


























N° HPV
Group
CT
RFU
CT
RFU
CT
RFU
CT
RFU










16
A9
21.9
143
21.9
167
21.7 
106
22.9
98







31
A9
21.5
81
21.9
101
21.6
50
22.5
62







33
A9
22.7
114
22.5
155
22.2
93
22.2
158







35
A9
22.5
63
22.4
70
22.4
46
22.9
48







52
A9
23.7
44
25.4
50
24.6
15
25.0
39







58
A9
19.7
403
19.9
280
19.1
398
19.7
255







67
A9
29.0
29
29.1
26
27.6
16
27.0
38

























DNA sample
ND
ND
ND
ND
ND
ND
ND
ND







H2O sample
ND
ND
ND
ND
ND
ND
ND
ND





ND: not detected


NT: not tested













TABLE 69





A5 Systems A, B, C, D, E/sensitivity



















System A
System B
System C












A5E6S1/HPV51
A5E6S1b/HPV51
A5E6S2/HPV51
A5E6S3/HPV51
















Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs





103 cop/PCR
27.95
2700
25.65
1100
27.3
180
24.3
430


102 cop/PCR
31.3
2500
29.75
1000
31.0
180
26.85
380


10 cop/PCR
34.85
2200
34.3
700
35.7
160
30.0
280


1 cop/PCR
36.95
1700
36.65
450
38.85
150
33.1
180


H2O sample
ND
ND
ND
ND
ND
ND
ND
ND


ADN Sample
ND
ND
ND
ND
ND
ND
ND
ND











r2/slope/PCR efficiency
0.997/−2.988/116.1%
0.997/−3.647/88% 
0.990/−3.924/79.8%
0.997/−2.955/118%





















System D
System E






Copy number HPV
A5E6S4/HPV51
A5E6S4/HPV51



















plasmid/PCR
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs









103 cop/PCR
31.45
750
24.55
500






102 cop/PCR
35.1
700
27.45
450






10 cop/PCR
39.7
500
31.15
450






1 cop/PCR
43.2
250
33.75
500






H2O sample
ND
ND
ND
ND






ADN Sample
ND
ND
ND
ND















r2/slope/PCR fficiency
0.994/−3.990/78.1%
0.997/−3.128/108.8%





ND: No Detection


NT: Not tested













TABLE 70





A6 Systems A, B, C, D, E/sensitivity



















System A
System B
System C











Copy number HPV
A6E6S1/HPV56
A6E6S1/HPV56
A6E6S2/HPV56
A6E6S2b/HPV56















plasmid/PCR
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs





103 cop/PCR
27.25
400
27.1
600
33.955
1700
29.55
650


102 cop/PCR
27.8
450
27.9
700
35.78
1500
33.1
550


 10 cop/PCR
30.8
450
30.75
700
38.89
1200
38.25
300


  1 cop/PCR
34.25
350
34.15
450
43.09
600
ND
ND


H2O sample
ND
ND
ND
ND
ND
ND
ND
ND


ADN Sample
ND
ND
ND
ND
ND
ND
ND
ND











r2/slope/PCR
0.974/−3.228/104.1%
0.997/−3.16/107%
0.989/−3.270/102.2%
0.998/−3.699/86.4%


efficiency















System D

System E
















Copy number HPV
A6E6S1/HPV56

A6E6S3/HPV56

A6E6S3b/HPV56
















plasmid/PCR
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs







103 cop/PCR
28.95
750
26.1
600
27.5
750



102 cop/PCR
30.75
750
27.45
650
30.35
750



 10 cop/PCR
33.65
800
30.45
550
33.9
600



  1 cop/PCR
35.4
700
32.15
550
ND
ND



H2O sample
ND
ND
ND
ND
ND
ND



ADN Sample
ND
ND
ND
ND
ND
ND















r2/slope/PCR
0.987/−2.461/154.8%

0.986/−2.126/195.4%

0.990/−3.183/106.1%




efficiency







ND: No detection



NT: Not tested













TABLE 71





A7 System A, sensitivity



















copy number HPV plasmid/
A7E1ZAS61f HPV 18
A7E1S63f HPV 59
A7E1S64f HPV 39
A7E1S40f HPV 45















PCR
Moy Ct
Moy RFU
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Ecart-type
Moy RFUs





106 cop/PCR
22.7
165
21.7
125
22.1
240
24.6
305


105 cop/PCR
25.95
170
24.6
95
25.0
310
27.45
320


104 cop/PCR
29.15
180
27.1
125
28.3
320
30.6
310


103 cop/PCR
32.6
180
31.0
105
31.1
350
33.85
272.5


102 cop/PCR
35.2
170
33.95
70
34.15
290
36.9
282.5


H2O sample
ND
ND
ND
ND
ND
ND
ND
ND


ADN sample
ND
ND
ND
ND
ND
ND
ND
ND











r2/slope/efficiency PCR
0.997/−3.16/107%
0.993/−3.1/110%
0.996/−3.19/106%
0.995/−3.27/102%
















copy number HPV plasmid/
A7E1ZBS74f HPV 68

A7E1ZBS74f HPV 39














PCR
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs







106 cop/PCR
24.2
597.585
22.5
1095.195



105 cop/PCR
26.85
611.52
25.25
1182.205



104 cop/PCR
31.15
557.525
28.05
1062.505



103 cop/PCR
35.35
496.425
32.45
1005.26



102 cop/PCR
39.5
473.395
40.6
804



H2O sample
ND
ND
ND
ND



ADN sample
ND
ND
ND
ND













r2/slope/efficiency PCR
0.995/−3.919/80%

0.972/−3.271/102.2%







ND: no Detection



NT: no test













TABLE 72





A7 System B. sensitivity



















copy number HPV plasmid/
A7E1ZBS26f HPV 18
A7E1ZBS26f HPV 45
A7E1ZBS74f HPV 68
A7E1ZBS74f HPV 39















PCR
Moy Ct
Moy RFU
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Ecart-type
Moy RFUs





106 cop/PCR
21.35
222.5
22.1
115
21.2
705
24.85
892.5


105 cop/PCR
23.05
252.5
24.75
130
24.7
690
27.0
852.5


104 cop/PCR
26.5
225
28.05
115
28.15
645
31.2
632.5


103 cop/PCR
28.6
180
29.7
112.5
30.85
540
32.65
445


102 cop/PCR
31.35
155
30.85
112.5
33.25
390
31.85
660.5


H2O sample
ND
ND
ND
ND
42.5
64
42.5
64


ADN sample
ND
ND
ND
ND
ND
23
ND
23











r2/slope/efficiency PCR
0.987/−2.55/146%
0.970/−2.24/179%
0.995/−3.02/114%
0.887/−1.96/223%














copy number HPV plasmid/
A7E1ZBS80f HPV 59
A7E1ZBS79f HPV 59
A7E1ZBS27f HPV 45
A7E1ZBS27f HPV 18















PCR
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs





106 cop/PCR
19.65
952.5
18.85
387.5
20.3
675
20.9
112.5


105 cop/PCR
21.85
1025
21.5
427.5
23.25
595
24.35
117.5


104 cop/PCR
23.75
997.5
24.1
405
26.3
557.5
28
122.5


103 cop/PCR
27.1
952.5
26.25
412.5
27.8
502.5
31.7
137.5


102 cop/PCR
31.7
907.5
29.0
377.5
33.05
440
31.05
157.5


H2O sample
ND
ND
ND
ND
ND
ND
ND
ND


ADN sample
ND
ND
ND
ND
ND
ND
ND
ND











r2/slope/efficiency PCR
0.981/−2.94/119%
0.976/−2.51/150%
0.973/−3.01/115%
0.934/−2.718/133.3%





ND: no Detection


NT: no test













TABLE 73





A7 System C. sensitivity



















copy number HPV plasmid/
A7E1ZCS11f/HPV 45
A7E1ZCS45f/HPV 39
A7E1ZCS63f/HPV 59
A7E1ZCS90f/HPV 68















PCR
Moy Ct
Moy RFU
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Ecart-type
Moy RFUs





106 cop/PCR
21.95
349.45
20.35
649.815
23.1
256.71
24.05
234.305


105 cop/PCR
24.7
344.81
23.4
623.445
26.4
224.625
27.0
200


104 cop/PCR
28.35
274.81
26.95
502.52
28.9
178.505
30.5
140.205


103 cop/PCR
31.6
154.565
30.35
364.095
33.0
107.145
33.4
92.505


102 cop/PCR
35.1
48.72
33.45
173.17
35.3
49.965
37.15
46.65


H2O sample
ND
ND
ND
ND
ND
ND
ND
ND


ADN sample
ND
ND
ND
ND
ND
ND
ND
ND











r2/slope/efficiency PCR
0.997/−3.321/100%
0.998/−3.322/100%
0.993/−3.111/109.9%
0.998/−3.255/102.9%














copy number HPV plasmid/
A7E1ZCS11f/HPV 18
A7E1ZCS40f/HPV 18
A7E1ZCS40f/HPV 45
A7E1ZCS40f/HPV 59















PCR
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs





106 cop/PCR
22.05
247.645
23.6
65.31
23.65
161.135
22.25
9.985


105 cop/PCR
24.45
230.285
26.25
79.255
27.5
138.725
22.65
27.19


104 cop/PCR
27.1
197.085
29.95
56.015
29.85
107.025
28.7
11.595


103 cop/PCR
31.35
94.76
34.2
29.31
37.9
14
N/A
ND


102 cop/PCR
35.0
12.61
N/A
ND
N/A
ND
N/A
ND


H2O sample
ND
ND
ND
ND
ND
ND
ND
ND


ADN sample
ND
ND
ND
ND
ND
ND
ND
ND











r2/slope/efficiency PCR
0.993/−3.275/102%
0.986/−3.55/91.3%
0.988/−3.079/111.3%
0.922/−4.269/71.5%





ND: no Detection


NT: no test













TABLE 74





A7 System D. sensitivity



















copy number HPV plasmid/
A7E1ZDS36f HPV 45
A7E1ZDS37f HPV 18
A7E1ZDS38f HPV 59
A7E1ZDS38f HPV 39















PCR
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs





106 cop/PCR
26.0
705
21.9
305
21.05
525
24.2
190


105 cop/PCR
29.5
645
25.55
302.5
25.35
487.5
27.8
192.5


104 cop/PCR
33.25
537.5
27.1
292.5
29.2
402.5
32.25
155


103 cop/PCR
36.95
440
30.95
265
32.5
335
35.95
147.5


102 cop/PCR
40.0
332.5
32.45
247.5
33.7
342.5
39.2
140


H2O sample
ND
ND
ND
ND
ND
ND
ND
ND


ADN sample
ND
ND
ND
ND
ND
ND
ND
ND











r2/slope/efficiency PCR
0.998/−3.622/88.8%
0.978/−2.652/138.3%
0.981/−3.253/103%
0.995/−3.805/83.2%


















copy number HPV plasmid/
A7E1ZDS2f HPV 68

A7E1ZDS2f HPV 39

A7E1ZDS3f HPV 45
















PCR
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs







106 cop/PCR
23.1
942
21.15
113.5
21.85
2075



105 cop/PCR
26.8
898.5
25.55
97.5
24.9
1875



104 cop/PCR
30.5
842.5
28.8
87.5
27.75
1617.5



103 cop/PCR
33.15
677.5
32.25
79
31.05
1250



102 cop/PCR
36.65
635
31.75
80
34.2
1007.5



H2O sample
ND
ND
ND
ND
ND
ND



ADN sample
ND
ND
36.1
ND
ND
ND















r2/slope/efficiency PCR
0.995/−3.334/99.5%

0.941/−2.797/127.8%

0.999/−3.086/110.9%







ND: no Detection



NT: no test













TABLE 75





A9 System C, sensitivity



















copy number HPV plasmid/
A9E1S10a/HPV 16
A9E1S10a/HPV 31
A9E1S10a/HPV 33
A9E1S10a/HPV 35















PCR
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs





106 cop/PCR
22.4
457.5
22.15
477
22.5
410
24.4
233.5


105 cop/PCR
27.2
402.5
26.45
360
28.2
344
29.0
202


104 cop/PCR
30.85
341
29.9
342
31.0
306.5
32.65
192


103 cop/PCR
34.3
322.5
33.2
316.5
34.35
272
36.25
167


102 cop/PCR
37.35
320
36.7
259.5
37.1
227.5
39.45
135.5


H2O sample
ND
ND
ND
ND
ND
ND
ND
ND


ADN sample
ND
ND
ND
ND
ND
ND
ND
ND











r2/slope/efficiency PCR
0.996/−3.705/86.2%
0.998/−3.586/90.0%
0.987/−3.536/91.8%
0.997/−3.735/85.2%


















copy number HPV plasmid/
A9E1S10a/HPV 52

A9E1S10a/HPV 58

A9E1S10a/HPV 67
















PCR
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs







106 cop/PCR
21.85
650
23.65
620
22.0
351



105 cop/PCR
26.4
507
28.3
558.5
25.95
339



104 cop/PCR
29.9
474.5
32.3
484
29.75
304



103 cop/PCR
33.55
429.5
35.95
422.5
33.05
261.5



102 cop/PCR
36.7
350.5
39.35
271.5
36.45
222.5



H2O sample
ND
ND
ND
ND
ND
ND



ADN sample
ND
ND
ND
ND
ND
ND















r2/slope/efficiency PCR
0.997/−3.680/87.0%

0.997/−3.915/80.1%

0.999/−3.594/89.8%

















copy number HPV plasmid/
A9E1S12a/HPV 31

A9E1S12a/HPV 35














PCR
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs







106 cop/PCR
26.45
61
22.45
504



105 cop/PCR
31.3
53.5
27.6
469.5



104 cop/PCR
32.2
67
31.3
452



103 cop/PCR
36.25
56
34.25
419.5



102 cop/PCR
39.45
51
37.7
356.5



H2O sample
ND
ND
ND
ND



ADN sample
ND
ND
ND
ND













r2/slope/efficiency PCR
0.971/−3.099/110.2%

0.994/−3.719/85.7%







ND: not detected



NT: not tested













TABLE 76





A9 System E2, sensitivity



















copy number HPV plasmid/
A9E2Z7S1/HPV 16
A9E2Z7S1/HPV 31
A9E2Z7S1/HPV 33
A9E2Z7S1/HPV 52















PCR
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs





106 cop/PCR
19.8
795
23.05
485
31.35
88.5
24.25
86


105 cop/PCR
24.1
765
26.5
425
34.4
83.5
27.05
82.5


104 cop/PCR
27.3
705
29.8
385
38.1
65
30.8
78.5


103 cop/PCR
31.5
610
33.0
342.5
42.8
35
33.85
77.5


102 cop/PCR
34.95
287.5
37.25
177.5
38.9
41.5
36.2
82.5


H2O sample
ND
ND
ND
ND
ND
ND
ND
ND


ADN sample
ND
ND
ND
ND
ND
ND
ND
ND











r2/slope/efficiency PCR
0.996/−3.767/84.3%
0.998/−3.492/93.4%
0.869/−2.762/130.2%
0.996/−3.069/111.7%





copy number HPV plasmid/
A9E2Z7S1/HPV 58
A9E2Z7S1/HPV 67
A9E1Z7S2/HPV 33
A9E1Z7S2/HPV 58















PCR
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs





106 cop/PCR
23.4
145
29.35
120.5
26.4
1257.5
20.95
485


105 cop/PCR
26.4
140
32.85
105
30.0
1120
24.35
395


104 cop/PCR
30.45
125
36.9
77.5
33.6
877.5
28.15
340


103 cop/PCR
34.35
95
42.4
37.5
37.05
520
31.85
310


102 cop/PCR
37.05
91
ND
ND
40.0
107.5
34.7
257.5


H2O sample
ND
ND
ND
ND
ND
ND
ND
ND


ADN sample
ND
ND
ND
ND
ND
ND
ND
ND











r2/slope/efficiency PCR
0.99/−3.525/90.2%
0.991/−4.333/70.1%
0.993/−3.431/95.7%
0.999/−3.508/92.8%


















copy number HPV plasmid/
A9E1Z7S2/HPV 52

A9E1Z7S2/HPV 67

A9E1Z7S3a/HPV 35
















PCR
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs







106 cop/PCR
21.1
182.5
26.6
473
27.25
825



105 cop/PCR
24.65
197.5
30.4
430
30.85
807.5



104 cop/PCR
28.15
192.5
33.2
390
34.5
505



103 cop/PCR
31.85
182.5
35.7
200
37.9
82.5



102 cop/PCR
34.95
162.5
40.3
115
40.4
47.5



H2O sample
ND
ND
ND
ND
ND
ND



ADN sample
ND
ND
ND
ND
ND
ND















r2/slope/efficiency PCR
0.999/−3.480/92.8%

0.989/−3.279/101.8%

0.990/−3.396/97%







copy number HPV plasmid/
A9E2Z7S4a/HPV 31

A9E2Z7S4a/HPV 52

A9E2Z7S4a/HPV 16
















PCR
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs







106 cop/PCR
23.2
460
21.45
485
21.85
182.5



105 cop/PCR
26.5
452.5
24.5
425
25.6
177.5



104 cop/PCR
29.85
435
28.35
385
29.8
147.5



103 cop/PCR
34.05
322.5
31.65
340
33.75
135



102 cop/PCR
38.0
165
35.55
280
36.2
145



H2O sample
ND
ND
ND
ND
ND
ND



ADN sample
ND
ND
ND
ND
ND
ND















r2/slope/efficiency PCR
0.998/−3.720/85.7%

0.996/−3.517/92.5%

0.996/−3.687/86.7%







copy number HPV plasmid/
A9E2Z7S4a/HPV 33

A9E2Z7S4a/HPV 58

A9E2Z7S4a/HPV 67
















PCR
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs







106 cop/PCR
32.0
57.5
23.6
115
28.45
177.5



105 cop/PCR
35.0
57.5
27.2
122.5
32.0
140



104 cop/PCR
43.6
31
31.5
87.5
36.3
107.5



103 cop/PCR
ND
ND
34.1
90
42.8
42.5



102 cop/PCR
ND
ND
40.4
50
46.7
20



H2O sample
ND
ND
ND
ND
ND
ND



ADN sample
ND
ND
ND
ND
ND
ND















r2/slope/efficiency PCR
0.938/−5.797/48..8%

0.980/−4.047/76.6%

0.981/−4.736/62.6%







ND: not detected



NT: not tested













TABLE 77





A9 System E3, sensitivity



















copy number HPV plasmid/
A9E2Z7S1/HPV 16
A9E2Z7S1/HPV 31
A9E2Z7S1/HPV 33
A9E2Z7S1/HPV 52















PCR
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs





106 cop/PCR
18.0
725
19.7
457
22.8
69
20.3
59


105 cop/PCR
20.3
754
23.7
428
26.9
58
22.7
77


104 cop/PCR
23.3
692
25.5
390
30.2
55
24.7
97


103 cop/PCR
26.2
611
29.4
322
34.1
48
28.4
73


102 cop/PCR
30.0
476
32.6
208
37.2
29
32.2
65


H2O sample
ND
ND
ND
ND
ND
ND
ND
ND


ADN sample
ND
ND
ND
ND
ND
ND
ND
ND











r2/slope/efficiency PCR
0.994/−2.994/115.8%
0.994/−3.148/107.8%
0.988/−3.647/88%
0.987/−2.952/118.2%





copy number HPV plasmid/
A9E2Z7S1/HPV 58
A9E2Z7S1/HPV 67
A9E1Z7S2/HPV 33
A9E1Z7S2/HPV 58















PCR
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs





106 cop/PCR
20.8
117
27.5
111
16.7
1741
20.8
636


105 cop/PCR
22.5
113
29.4
110
19.2
1767
22.5
537


104 cop/PCR
24.9
123
33.1
99
22.7
1574
24.9
693


103 cop/PCR
28.4
117
36.9
70
26.9
1473
28.4
465


102 cop/PCR
31.3
104
41.3
30
29.6
1172
31.3
357


H2O sample
ND
ND
ND
ND
ND
ND
ND
ND


ADN sample
ND
ND
ND
ND
ND
ND
ND
ND











r2/slope/efficiency PCR
0.987/−2.296/134.9%
0.990/−3.509/92.7%
0.995/−3.318/100.1%
0.772/−2.474/153.6%

















copy number HPV plasmid/
A9E1Z7S2/HPV 52

A9E1Z7S2/HPV67

A9E1Z7S3a/HPV 35















PCR
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs







106 cop/PCR
18.6
393
25.3
433
25.3
869



105 cop/PCR
21.1
303
28.8
375
27.6
611



104 cop/PCR
25.1
274
31.8
299
31.6
509



103 cop/PCR
28.0
260
35.4
214
34.7
294



102 cop/PCR
32.4
152
ND
ND
ND
ND



H2O sample
ND
ND
ND
ND
ND
ND



ADN sample
ND
ND
ND
ND
ND
ND















r2/slope/efficiency PCR
0.994/−3.523/92.3%

0.997/−3.323/99.9%

0.993/−3.328/104.1%







copy number HPV plasmid/
A9E2Z7S4a/HPV 31

A9E2Z7S4a/HPV 52

A9E2Z7S4a/HPV 16
















PCR
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs







106 cop/PCR
19.2
494
18.1
427
18.9
79



105 cop/PCR
22.8
451
20.2
473
21.0
199



104 cop/PCR
26.0
360
23.7
460
23.7
170



103 cop/PCR
29.5
283
27.5
419
27.2
166



102 cop/PCR
33.4
82
31.0
273
31.3
37



H2O sample
ND
ND
ND
ND
ND
ND



ADN sample
ND
ND
ND
ND
ND
ND















r2/slope/efficiency PCR
0.998/−3.510/92.7%

0.995/−3.312/100.4%

0.989/−3.006/115.1%







copy number HPV plasmid/
A9E2Z7S4a/HPV 33

A9E2Z7S4a/HPV 58

A9E2Z7S4a/HPV 67
















PCR
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs







106 cop/PCR
21.0
66
19.7
105
27.2
494



105 cop/PCR
24.2
62
22.8
108
30.5
451



104 cop/PCR
27.5
56
25.8
108
36.1
360



103 cop/PCR
30.8
53
30.3
78
45.4
283



102 cop/PCR
ND
22
35.6
57
ND
ND



H2O sample
ND
ND
ND
ND
ND
ND



ADN sample
ND
ND
ND
ND
ND
ND















r2/slope/efficiency PCR
0.994/−3.257/102.8%

0.976/−3.920/79.9%

0.959/−5.655/50.3%







ND: not detected



NT: not tested













TABLE 78





A9 System E4, sensitivity



















copy number HPV plasmid/
A9E2Z7S1/HPV 16
A9E2Z7S1/HPV 31
A9E2Z7S1/HPV 52
A9E2Z7S1/HPV 33















PCR
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs





106 cop/PCR
19.8
915
21.45
795
24.25
65
24.35
105


105 cop/PCR
23.25
940
24.3
717.5
31.1
47.5
28.65
90


104 cop/PCR
26.75
840
28.25
540
37.8
27
37.8
83


103 cop/PCR
30.85
615
32.5
412.5
35.15
40
36.15
75


102 cop/PCR
34.95
507.5
35.0
272.5
37.3
37.5
38.95
47.5


H2O sample
ND
ND
ND
ND
ND
ND
ND
ND


ADN sample
ND
ND
ND
ND
ND
ND
ND
ND











r2/slope/efficiency PCR
0.993/−3.789/83.7%
0.996/−3.509/92.8%
0.889/−3.017/114.5%
0.996/−3.664/87.5%





copy number HPV plasmid/
A9E2Z7S1/HPV 58
A9E2Z7S1/HPV 67
A9E1Z7S2/HPV 33
A9E1Z7S2/HPV 58















PCR
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs





106 cop/PCR
23.8
157.5
22.9
207.5
22.0
2871.625
22.75
903.92


105 cop/PCR
27.6
167.5
26.45
190
25.7
2916.84
25.95
822.335


104 cop/PCR
37.8
128
37.8
160
29.95
2525.075
29.55
731.815


103 cop/PCR
36.0
90
34.25
122.5
33.55
1574.41
33.95
614.88


102 cop/PCR
39.8
45
39.8
52.5
37.45
1675.46
37.35
155.27


H2O sample
ND
ND
ND
ND
ND
ND
ND
ND


ADN sample
ND
ND
ND
ND
ND
ND
ND
ND











r2/slope/efficiency PCR
0.999/−4.075/75.9%
0.996/−4.075/75.9%
0.998/−3.866/81.4%
0.998/−3.725/85.5%


















copy number HPV plasmid/
A9E1Z7S2/HPV 52

A9E1Z7S2/HPV67

A9E1Z7S3a/HPV 35
















PCR
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs







106 cop/PCR
20.4
372.5
21.3
1225
22.6
1085.81



105 cop/PCR
23.6
360
24.35
1157.5
26.1
1037.5



104 cop/PCR
27.2
345
27.9
1055
29.6
932.32



103 cop/PCR
30.85
347.5
31.75
935
33.75
730.08



102 cop/PCR
34.65
310
35.85
757.5
38.55
501.76



H2O sample
ND
ND
ND
ND
ND
ND



ADN sample
ND
ND
ND
ND
ND
ND















r2/slope/efficiency PCR
0.997/−3.586/90.1%

0.998/−3.641/88.2%

0.997/−3.960/78.9%







copy number HPV plasmid/
A9E2Z7S4a/HPV 31

A9E2Z7S4a/HPV 52

A9E2Z7S4a/HPV 16
















PCR
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs







106 cop/PCR
21.8
800
20.45
640
22.35
267.5



105 cop/PCR
25.2
747.5
24.0
600
25.0
260



104 cop/PCR
28.4
665
27.5
562.5
29.55
240



103 cop/PCR
33.3
505
30.95
532.5
32.75
210



102 cop/PCR
37.2
335
34.4
422.5
33.55
207.5



H2O sample
ND
ND
ND
ND
ND
ND



ADN sample
ND
ND
ND
ND
ND
ND















r2/slope/efficiency PCR
0.996/−3.872/81.2%

1/−3.476/94%

0.976/−3.010/114.9%







copy number HPV plasmid/
A9E2Z7S4a/HPV 33

A9E2Z7S4a/HPV 58

A9E2Z7S4a/HPV 67
















PCR
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs







106 cop/PCR
24.45
212.5
24.2
340
23.25
415



105 cop/PCR
27.3
230
27.45
305
25.55
407.5



104 cop/PCR
31.1
205
31.2
250
30.5
312.5



103 cop/PCR
35.1
162.5
34.35
187.5
33.75
277.5



102 cop/PCR
36.8
127.5
38.9
117.5
38.2
145



H2O sample
ND
ND
ND
ND
ND
ND



ADN sample
ND
ND
ND
ND
ND
ND















r2/slope/efficiency PCR
0.991/−3.264/102.5%

0.998/−3.632/88.5%

0.989/−3.810/83%







ND: not detected



NT: not tested













TABLE 79





A9 System F, sensitivity



















copy number HPV plasmid/
A9E2Z7S1/HPV 16
A9E2Z7S1/HPV 31
A9E2Z7S1/HPV 33
A9E2Z7S1/HPV 52















PCR
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs





106 cop/PCR
19.45
1815
19.85
1227.5
23.85
63
25.25
40


105 cop/PCR
22.25
1727.5
22.95
1215
27.1
63
28.55
41.5


104 cop/PCR
26.1
1665
26.75
1150
30.55
62.5
31.6
37.5


103 cop/PCR
26.65
1535
29.6
1055
33.9
62
35.4
41


102 cop/PCR
33.15
1312.5
35.2
753.5
37.8
47.5
38.25
34


H2O sample
ND
ND
ND
ND
ND
ND
ND
ND


ADN sample
ND
ND
ND
ND
ND
ND
ND
ND











r2/slope/efficiency PCR
0.969/−3.202/105.2%
0.990/−3.739/85.1%
0.999/−3.487/93.5%
0.998/−3.651/87.9%





copy number HPV plasmid/
A9E2Z7S1/HPV 58
A9E2Z7S1/HPV 67
A9E1Z7S2/HPV 33
A9E1Z7S2/HPV 58















PCR
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs





106 cop/PCR
22.8
132.5
22.85
138
20.2
3013.235
21.75
1330.945


105 cop/PCR
26.1
125
25.95
127.5
23.4
3085.8
24.85
1292.96


104 cop/PCR
29.55
120
29.6
120
26.7
2967.135
28.35
1266.585


103 cop/PCR
33.45
107
33.65
96
30.45
2499.875
32.25
973.095


102 cop/PCR
37.4
100
35.85
100
33.8
2129.57
35.55
841.57


H2O sample
ND
ND
ND
ND
ND
ND
ND
ND


ADN sample
ND
ND
ND
ND
ND
ND
ND
ND











r2/slope/efficiency PCR
0.998/−3.651/87.9%
0.993/−3.366/98.20%
0.999/−3.435/95.5%
0.999/−3.502/93%





copy number HPV plasmid/
A9E1Z7S3a/HPV 35
A9E2Z7S4a/HPV 31
A9E2Z7S4a/HPV 52
A9E2Z7S4a/HPV 58















PCR
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs





106 cop/PCR
22.1
1337.995
21.85
705
21.75
1022.5
22.1
522.5


105 cop/PCR
25.05
1354.145
24.1
730
24.25
992.5
24.55
460


104 cop/PCR
29.4
1254.22
27.9
665
27.65
1002.5
28.9
455


103 cop/PCR
33.25
1018.5
30.5
560
31.05
957.5
31.5
465


102 cop/PCR
37.0
678.815
35.25
430
34.7
650
35.2
382.5


H2O sample
ND
ND
ND
ND
ND
ND
ND
ND


ADN sample
ND
ND
ND
ND
ND
ND
ND
ND











r2/slope/efficiency PCR
0.996/−3.799/83.3%
0.989/−3.332/99.6%
0.996/−3.273/102.1%
0.994/−3.317/100.2%


















copy number HPV plasmid/
A9E2Z7S4a/HPV 67

A9E2Z7S4a/HPV 16

A9E2Z7S4a/HPV 33
















PCR
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs







106 cop/PCR
22.15
570
21.95
195
22.45
240



105 cop/PCR
24.2
670
24.65
227.5
25.15
245



104 cop/PCR
28.75
555
29.2
196
29.7
255



103 cop/PCR
31.2
460
32.6
187.5
32.55
187.5



102 cop/PCR
32.7
447.5
35.7
185
36.45
165



H2O sample
ND
ND
ND
ND
ND
ND



ADN sample
ND
ND
ND
ND
ND
ND















r2/slope/efficiency PCR
0.964/−2.805/127.3%

0.994/−3.487/93.5%

0.995/−3.538/91.7%







ND: not detected



NT: not tested













TABLE 80





A9 System G Z7, sensitivity



















copy number HPV plasmid/
A9E2Z7S1/HPV 16
A9E2Z7S1/HPV 31
A9E2Z7S1/HPV 33
A9E2Z7S1/HPV 52















PCR
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs





106 cop/PCR
20.25
771
20.85
468
22.85
113
23.2
82


105 cop/PCR
23.55
713.5
24.5
419.5
26.4
119
26.45
75


104 cop/PCR
27.0
654
27.6
375.5
30.8
79.5
29.65
65


103 cop/PCR
30.75
527
31.15
289
33.6
71
33.35
48.5


102 cop/PCR
34.45
296.5
35.1
186
37.3
44.5
37.05
30.5


H2O sample
ND
ND
ND
ND
ND
ND
ND
ND


ADN sample
ND
ND
ND
ND
ND
ND
ND
ND











r2/slope/efficiency PCR
0.999/−3.557/91%
0.998/−3.520/92.3%
0.996/−3.612/89.2%
0.998/−3.452/94.9%





copy number HPV plasmid/
A9E2Z7S1/HPV 58
A9E2Z7S1/HPV 67
A9E1Z7S2a/HPV 33
A9E1Z7S2a/HPV 58















PCR
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs





106 cop/PCR
22.15
187.5
21.8
207
19.8
1165
20.65
717


105 cop/PCR
25.75
165.5
24.9
199
23.1
1080.5
23.75
682


104 cop/PCR
28.8
147
27.35
182.5
26.3
1015.5
27.35
603.5


103 cop/PCR
32.45
100
32.05
128.5
30.05
844
30.9
426


102 cop/PCR
35.35
63
35.4
78.5
33.65
605.5
34.8
234


H2O sample
ND
ND
ND
ND
ND
ND
ND
ND


ADN sample
ND
ND
ND
ND
ND
ND
ND
ND











r2/slope/efficiency PCR
0.998/−3.313/100.4%
0.993/−3.425/95.9%
0.998/−3.469/94.2%
0.998/−3.558/91%





copy number HPV plasmid/
A9E1Z7S3a/HPV 35
A9E2Z7S4a/HPV 31
A9E2Z7S4a/HPV 52
A9E2Z7S4a/HPV 58















PCR
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs





106 cop/PCR
22.15
883.5
21.7
187.5
21.65
257
22.35
145


105 cop/PCR
25.3
795
25.95
180.5
26.45
268
26.05
136.5


104 cop/PCR
29.0
674.5
29.7
157.5
29.8
220
29.3
116


103 cop/PCR
32.2
546
33.4
128.5
33.6
155
33.65
80


102 cop/PCR
35.2
300
36.65
71
37.9
69
37.3
40


H2O sample
ND
ND
ND
ND
ND
ND
ND
ND


ADN sample
ND
ND
ND
ND
ND
ND
ND
ND











r2/slope/efficiency PCR
0.999/−3.656/87.7%
0.999/−3.727/85.5%
0.997/−3.967/78.7%
0.998/−3.751/84.7%


















copy number HPV plasmid/
A9E2Z7S4a/HPV 67

A9E2Z7S4a/HPV 16

A9E2Z7S4a/HPV 33
















PCR
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs







106 cop/PCR
22.4
159
22.4
67
22.65
69.5



105 cop/PCR
26.5
155.5
27.7
63
27.0
60



104 cop/PCR
30.1
134
31.0
60
30.25
58.5



103 cop/PCR
34.35
90.5
34.6
46
33.4
51.5



102 cop/PCR
38.55
33
38.4
23.5
37.8
32.5



H2O sample
ND
ND
ND
ND
ND
ND



ADN sample
ND
ND
ND
ND
ND
ND















r2/slope/efficiency PCR
0.996/−4.035/76.9%

0.996/−3.894/80.6%

0.996/−3.670/87.3%







ND: not detected



NT: not tested













TABLE 81





A9 System G Z8, sensitivity



















copy number HPV plasmid/
A9E2Z8S2f/HPV16
A9E2Z8S61f/HPV 31
A9E2Z8S127f/HPV 33
A9E2Z8S156f/HPV35















PCR
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs





106 cop/PCR
20.9
275
20.8
439.5
20.4
357
21.85
347.5


105 cop/PCR
24.65
274.5
25.25
382
24.95
322
25.75
334.5


104 cop/PCR
27.85
270
29.1
328
28.75
300.5
29.25
331.5


103 cop/PCR
31.55
217
32.3
242
31.6
261.5
32.8
243


102 cop/PCR
35.3
107.5
36.3
86
37.0
98
36.45
121


H2O sample
ND
ND
ND
ND
ND
ND
ND
ND


ADN sample
ND
ND
ND
ND
ND
ND
ND
ND











r2/slope/efficiency PCR
0.995/−3.587/90%
0.995/−3.799/83.3%
0.995/−3.990/78.1%
0.997/−3.639/88.3%


















copy number HPV plasmid/
A9E2Z8S210f/HPV52

A9E2AZ8S250f/HPV58

A9E2AZ8S250f/HPV67
















PCR
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs







106 cop/PCR
22.05
32
19.3
728
21.2
173



105 cop/PCR
25.65
57
22.6
663
26.2
152



104 cop/PCR
27.45
54.5
26.0
728
29.6
157



103 cop/PCR
32.7
31
29.7
627
32.6
149



102 cop/PCR
37.75
14
32.9
457
36.6
98



H2O sample
ND
ND
ND
ND
ND
ND



ADN sample
ND
ND
ND
ND
ND
ND















r2/slope/efficiency PCR
0.976/−3.880/81%

0.999/−3.425/95.9%

0.994/−3.701/86.3%







ND: not detected



NT: not tested













TABLE 82





A9 System H, sensitivity



















copy number HPV plasmid/
A9E2Z8S2f/HPV16
A9E2Z8S61f/HPV 31
A9E2Z8S127f/HPV 33
A9E2Z8S156f/HPV35















PCR
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs





106 cop/PCR
20.55
567.5
20.55
570
20.25
550
21.2
435


105 cop/PCR
23.7
530
23.25
530
23.7
490
24.55
437.5


104 cop/PCR
27.2
465
27.05
507.5
27.4
482.5
28.1
375


103 cop/PCR
31.85
395
29.8
400
31.5
450
32.95
250


102 cop/PCR
34.3
220
34.05
247.5
35.35
212.5
37.05
172.5


H2O sample
ND
ND
ND
ND
ND
ND
ND
ND


ADN sample
ND
ND
ND
ND
ND
ND
ND
ND











r2/slope/efficiency PCR
0.99/−3.570/90.6%
0.995/−3.352/98.8%
0.988/−3.805/83.2%
0.995/−4.011/77.5%


















copy number HPV plasmid/
A9E2Z8S210f/HPV52

A9E2AZ8S250f/HPV58

A9E2AZ8S250f/HPV67
















PCR
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs







106 cop/PCR
21.65
240
20.15
2300
27.5
150



105 cop/PCR
25.95
225
23.0
2405
32.3
100



104 cop/PCR
30.2
170
26.6
2350
35.2
62.5



103 cop/PCR
34.3
100
30.55
1800
37.55
82.5



102 cop/PCR
36.65
75
33.45
1387.5
40.2
52.5



H2O sample
ND
ND
ND
ND
ND
ND



ADN sample
ND
ND
ND
ND
ND
ND















r2/slope/efficiency PCR
0.988/−3.837/82.2%

0.993/−3.425/95.9%

0.976/−3.131/108.6%

















copy number HPV plasmid/
A9E2AZ8S231f/HPV58

A9E2AZ8S231f/HPV67














PCR
Moy Ct
Moy RFUs
Moy Ct
Moy RFUs







106 cop/PCR
19.75
295
25.45
47.5



105 cop/PCR
22.95
287.5
29.4
47.5



104 cop/PCR
26.4
272.5
33.1
38.5



103 cop/PCR
30.35
210
35.8
28.5



102 cop/PCR
33.65
147.5
36.15
28.5



H2O sample
ND
ND
ND
ND



ADN sample
ND
ND
ND
ND













r2/slope/efficiency PCR
0.996/−3.525/92.2%

0.945/−2.778/129.1%







ND: not detected



NT: not tested













TABLE 83





Megaplex A5 E A6 A A7 A A9 H


















Kit
Kit Quantitect probe PCR



MgCl2
5 mM



Plasmid concentration
106 cop/PCR



Thermoprofile
52° C.



Taq
7U/well



Cycling
42x















forward primer
reverse primer
probes














Name
μM
Name
μM
Name
μM





A5
A5E6f5
0.4
A5E6r5
0.4
A5E6s4
0.2


System E


A6
A6E6f1
0.4
A6E6r1
0.4
A6E6s1
0.2


System A


A7
A7E1-6f1a
0.3
A7E1-6r1b
0.3
A7E1ZCS40f
0.2


System A
A7E1-6f2a
0.3
A7E1-6r2b
0.3
A7E1ZAS61f
0.2



A7E1-6f3a
0.3
A7E1-6r3b
0.3
A7E1ZAS63f
0.2







A7E1ZBS74f
0.2


A9
A9E2f6
0.4
A9E2r10
0.6
A9E2Z8S2f
0.2


System H
A9E2f8
0.4
A9E2r12B
0.4
A9E2Z8S61f
0.2



A9E2f9
0.6
A9E2r15
0.4
A9E2Z8S127f
0.2





A9E2r16
0.4
A9E2Z8S156f
0.2







A9E2Z8S210f
0.2







A9E2Z8S250f
0.1
















TABLE 84







specificity of megaplex EAAH













Megaplex












N° HPV
Group
CT
RFU
















51
A5
21.9
226



26

ND
ND



69

NT
NT



82

ND
ND



56
A6 
24.4
220



30

ND
ND



53

ND
ND



66

ND
ND



18
A7
23.3
148



39

22.1 
182



45

23.1
215



59

24.8
194



68

24.1
169



85

ND
ND



70

NT
NT



16
A9
24.0
136



16

24.0
136



31

22.5
121



33

22.6
173



35

23.6
94



52

24.1
102



58

21.7
268



67

32.7
25











DNA sample
ND
ND



H2O sample
ND
ND







ND: no detection



NT: not tested













TABLE 85





Megaplex A5 E A6 B A7 A A9 C


















Kit
Kit Quantitect probe PCR



MgCl2
5 mM



Plasmid concentration
106 cop/PCR



Thermoprofile
52° C.



Taq
7U/well



Cycling
42x


















Name
μM
Name
μM
Name
μM





A5 System E
A5E6f5
0.4
A5E6r5
0.4
A5E6s4
0.2


A6 System B
A6E6f1
0.6
A6E6r1
0.6
A6E6s1
0.4


A7
A7E1-6f1a
0.5
A7E1-6r1b
0.3
A7E1ZCS40f
0.2


System A
A7E1-6f2a
0.3
A7E1-6r2b
0.5
A7E1ZAS61f
0.2



A7E1-6f3a
0.3
A7E1-6r3b
0.3
A7E1ZAS63f
0.2







A7E1ZBS74f
0.2


A9 System C
A9E1-f8
0.6
A9E1-r5
0.6
A9E1s10a
0.2



A9E1-f10
0.6
A9E1-r6
0.6
A9E1s12a
0.2



A9E1-f12
0.2



A9E1-f13
0.4
















TABLE 86







specificity of meqaplex EBAC













Megaplex












N° HPV
Group
CT
RFU
















51
A5
23.3
229



26

ND
ND



69

NT
NT



82

ND
ND



56
A6
24
458



30

ND
ND



53

36
170



66

ND
ND



18
A7
23.7
110



39

23.8
185



45

23.8
205



59

29
47



68

28.3
107



85

ND
ND



70

NT
NT



16
A9
24.0
333



16

24.0
333



31

24.1
321



33

23.3
364



35

24.6
347



52

22.7
390



58

22
395



67

22.8
303











DNA sample
ND
ND



H2O sample
ND
ND







ND: no Detection



NT: not tested













TABLE 87







Megaplex A5 E/A6 A/A7 A/A9 H; HPV16 and 18 sensitivity









copy number HPV plasmid/
HPV 16
HPV 18











PCR
Moy Ct
Moy RFU
Moy Ct
Moy RFUs





106 cop/PCR
25.5
50
25.2
33


105 cop/PCR
28.1
87
27.9
79


104 cop/PCR
31.3
106 
31.1
72


103 cop/PCR
35.0
98
34.3
53


102 cop/PCR
37.9
51
37.9
27


H2O sample
ND
ND
ND
ND


ADN sample
ND
ND
ND
ND









r2/slope/efficiency PCR
0.989/−3.16/107%
0.989/−3.17/107%





ND: not detected


NT: not tested













TABLE 88







Megaplex A5 E/A6 B/A7 A/A9 C; HPV16 and 18 sensitivity









copy number HPV plasmid/
HPV 16
HPV 18











PCR
Moy Ct
Moy RFU
Moy Ct
Moy RFUs





106 cop/PCR
24.3
278
24.3
 55


105 cop/PCR
26.8
475
28.1
154


104 cop/PCR
29.9
410
31.5
190


103 cop/PCR
31.2
412
34.3
271


102 cop/PCR
35.8
277
38.0
148


H2O sample
ND
ND
ND
ND


ADN sample
ND
ND
ND
ND









r2/slope/efficiency PCR
0.984/−2.76/130%
0.995/−3.36/98.5%





ND: not detected


NT: not tested













TABLE 89







list of HPV sequences









Organism
Type
Accession number





human
 1 a
NC_001356


human
 2 a
NC_001352


human
 3
NC_001588


human
 4
NC_001457


human
 5
NC_001531


human
 5 b
NC_001444


human
 6
NC_000904


human
 6 a
NC_001668


human
 6 b
NC_001355


human
 7
NC_001595


human
 8
NC_001532


human
 9
NC_001596


human
10
NC_001576


human
11
NC_001525


human
12
NC_001577


human
13
NC_001349


human
14 D
NC_001578


human
15
NC_001579


human
16
AF472509


human
16
NC_001526


human
17
NC_001580


human
18
NC_001357


human
19
NC_001581


human
20
NC_001679


human
21
NC_001680


human
22
NC_001681


human
23
NC_001682


human
24
NC_001683


human
25
NC_001582


human
26
NC_001583


human
27
NC_001584


human
28
NC_001684


human
29
NC_001685


human
30
NC_001585


human
31
NC_001527


human
32
NC_001586


human
33
NC_001528


human
34
NC_001587


human
35
NC_001529


human
36
NC_001686


human
37
NC_001687


human
38
NC_001688


human
39
NC_001535


human
40
NC_001589


human
41
NC_001354


human
42
NC_001534


human
44
NC_001689


human
45
NC_001590


human
47
NC_001530


human
48
NC_001690


human
49
NC_001591


human
50
NC_001691


human
51
NC_001533


human
52
NC_001592


human
53
NC_001593


human
54
NC_001676


human
55
NC_001692


human
56
NC_001594


human
57
NC_001353


human
57 b
HPU37537


human
58
NC_001443


human
59
NC_001635


human
60
NC_001693


human
61
NC_001694


human
63
NC_001458


human
65
NC_001459


human
66
NC_001695


human
67
D21208


human
68
M73258


human
69
NC_002171


human
70
NC_001711


human
71
NC_002644


human
72
X94164 partial




E6; 7; 1; 2; 4; L2; 1


human
73
X94165 partial




E6; 7; 1; 2; 4; L2; 1


human
74
NC_004501


human
82
NC_002172


human
83
NC_000856


human
84
NC_002676


human
85
AF131950


human
86
NC_003115


human
87
NC_002627


human
89
NC_004103


human
90
NC_004104


human
91
NC_004085


human
92
NC_004500


bovine
BPV
NC_001522


bovine
BPV2
NC_001521


bovine
BPV3
NC_004197


bovine
BPV4
X05817 D00146




X59063


bovine
BPV5
NC_004195


canine
Canine oral papillomavirus
NC_001619


chimpanzee
Common chimpanzee
NC_001838



papillomavirus


rabbit
Cottontail rabbit papillomavirus
NC_001541


Deer
Deer papillomavirus
NC_001523


Equinus
Equinus papillomavirus
NC_004194


Equus
Equus caballus papillomavirus
NC_003748



type 1


elk
European elk papillomavirus
NC_001524


Felis
Felis domesticus papillomavirus
AF480454



type 1


coelebs
Fringilla coelebs papillomavirus
NC_004068


Hamster
Hamster papovavirus
NC_001663


Monkey
Monkey B-lymphotropic
NC_001536



papovavirus


rat
Multimammate rat papillomavirus
NC_001605


Ovine
Ovine papillomavirus 2
NC_001790


Ovine
Ovine papillomavirus 1
NC_001789


Phocoena
Phocoena spinipinnis
NC_003348



papillomavirus


Psittacus
Psittacus erithacus papillomavirus
NC_003973


Chimpanzee
Pygmy Chimpanzee papilloma
X62844 S43934



virus type 1


Rabbit
Rabbit oral papillomavirus
NC_002232


Reindeer
Reindeer papillomavirus
NC_004196









Sequences of the Reference Template Sequences:









<SEQ25; DNA; Human papillomavirus>



tggaccgggtcatgttt ggggtgctgg agacaaacat ctagagaacc


tagagaatct acagtataat catgcatggt aaagtaccaa


cgctgcaaga cgt


 


<SEQ334; DNA; Human papillomavirus>


tggaccgggtcatgttt ggggtgctgg agacaaacat ctagagaacc


tagagaatct acagtataat catgcatggt aaagtaccaa


cgctgcaaga cgttgtatta gaactaacac ctcaaacaga


aattgaccta cagtgcaatg agcaattgga cagctcagag


gatgaggatg aggatgaagt agaccatttg caggagcggc


cacagcaagc tagacaagct aaacaacata cgtgttacct


aatacacgta ccttgttgtg agtgtaagtt tgtggtgcag t


 


<SEQ26; DNA; Human papillomavirus>


ctaatagcacat ggttggaccg ggtcatgttt ggggtgctgg


agacaaacat ctagagaacc tagagaatct acagtataat


catgcatggt aaagtaccaa cgctgcaaga cgt


 


<SEQ335; DNA; Human papillomavirus>


ctaatagcacat ggttggaccg ggtcatgttt ggggtgctgg


agacaaacat ctagagaacc tagagaatct acagtataat


catgcatggt aaagtaccaa cgctgcaaga cgttgtatta


gaactaacac ctcaaacaga aattgaccta cagtgcaatg


agcaattgga cagctcagag gatgaggatg aggatgaagt


agaccatttg caggagcggc cacagcaagc tagacaagct


aaacaacata cgtgttacct aatacacgta ccttgttgtg


agtgtaagtt tgtggtgcag t


 


<SEQ27;DNA; Human papillomavirus>


aaggtgctacagatgtca aagtccgtta actccggagg


aaaagcaatt gcattgtgac agaaaaagac gatttcatct


aatagcacat ggttggaccg ggtcatgttt ggggtgctgg


agacaaacat ctagagaacc


 


<SEQ336; DNA; Human papillomavirus>


aaggtgctacagatgtca aagtccgtta actccggagg


aaaagcaatt gcattgtgac agaaaaagac gatttcatct


aatagcacat ggttggaccg ggtcatgttt ggggtgctgg


agacaaacat ctagagaacc tagagaatct acagtataat


catgcatggt aaagtaccaa cgctgcaaga cgt


 


<SEQ337; DNA; Human papillomavirus>


aaggtgctacagatgtca aagtccgtta actccggagg


aaaagcaatt gcattgtgac agaaaaagac gatttcatct


aatagcacat ggttggaccg ggtcatgttt ggggtgctgg


agacaaacat ctagagaacc tagagaatct acagtataat


catgcatggt aaagtaccaa cgctgcaaga cgttgtatta


gaactaacac ctcaaacaga aattgaccta cagtgcaatg


agcaattgga cagctcagag gatgaggatg aggatgaagt


agaccatttg caggagcggc cacagcaagc tagacaagct


aaacaacata cgtgttacct aatacacgta ccttgttgtg


agtgtaagtt tgtggtgcag t


 


<SEQ28; DNA; Human papillomavirus>


gttggaccgggtcatgttt ggggtgctgg agacaaacat


ctagagaacc tagagaatct acagtataat catgcatggt


aaagtaccaa cgctgcaaga cgt


 


<SEQ338; DNA; Human papillomavirus>


gttggaccg ggtcatgttt ggggtgctgg agacaaacat


ctagagaacc tagagaatct acagtataat catgcatggt


aaagtaccaa cgctgcaaga cgttgtatta gaactaacac


ctcaaacaga aattgaccta cagtgcaatg agcaattgga


cagctcagag gatgaggatg aggatgaagt agaccatttg


caggagcggc cacagcaagc tagacaagct aaacaacata


cgtgttacct aatacacgta ccttgttgtg agtgtaagtt


tgtggtgcag t


 


<SEQ29; DNA; Human papillomavirus>


tcagaggatgaggatg aggatgaagt agaccatttg caggagcggc


cacagcaagc tagacaagct aaacaacata cgtgttacct


aatacacgta ccttgttgtg agtgtaagtt tgtggtgcag t


 


<SEQ1; DNA; Human papillomavirus>


ggcagtggaaagcagtgga gacacccttc gcgttgtaca


gcagatgtta atgggcgaac taagcctggt ttgcccgtgt


tgtgcgaaca actagcaacg gcgatgg


 


<SEQ320; DNA; Human papillomavirus>


ggcagtggaaagcagtgga gacacccttc gcgttgtaca


gcagatgtta atgggcgaac taagcctggt ttgcccgtgt


tgtgcgaaca actagcaacg gcgatggact


 


<SEQ321; DNA; Human papillomavirus>


ggcagtggaaagcagtgga gacacccttc gcgttgtaca


gcagatgtta atgggcgaac taagcctggt ttgcccgtgt


tgtgcgaaca actagcaacg gcgatggact gtgaaggtac


agaggatgag gg


 


<SEQ2; DNA; Human papillomavirus>


agctccgtgttgcag gtgttcaagt gtagtacaac tggcagtgga


aagcagtgga gacacccttc gcgttgtaca gcagatgtta


atgggcgaac taagcctggt ttgcccgtgt tgtgcgaaca


actagcaacg gcgatggact


 


<SEQ322; DNA; Human papillomavirus>


agctccgtgttgcag gtgttcaagt gtagtacaac tggcagtgga


aagcagtgga gacacccttc gcgttgtaca gcagatgtta


atgggcgaac taagcctggt ttgcccgtgt tgtgcgaaca


actagcaacg gcgatgg


 


<SEQ323; DNA; Human papillomavirus>


agctccgtgttgcag gtgttcaagt gtagtacaac tggcagtgga


aagcagtgga gacacccttc gcgttgtaca gcagatgtta


atgggcgaac taagcctggt ttgcccgtgt tgtgcgaaca


actagcaacg gcgatggact gtgaaggtac agaggatgag gg


 


<SEQ3; DNA; Human papillomavirus>


atatgcgtgacca gctaccagaa ag/acgggctg gacaggctac


gtgttacaga attgaagctc cgtgttgcag gtgttcaagt


gtagtacaac tggcagtgga aagcagtgga gaca


 


<SEQ324; DNA; Human papillomavirus>


atatgcgtgacca gctaccagaa agacgggctg gacaggctac


gtgttacaga attgaagctc cgtgttgcag gtgttcaagt


gtagtacaac tggcagtgga aagcagtgga gacacccttc


gcgttgtaca gcagatgtta atgggcgaac taagcctggt


ttgcccgtgt tgtgcgaaca actagcaacg gcgatgg


 


<SEQ325; DNA; Human papillomavirus>


atatgcgtgacca gctaccagaa agacgggctg gacaggctac


gtgttacaga attgaagctc cgtgttgcag gtgttcaagt


gtagtacaac tggcagtgga aagcagtgga gacacccttc


gcgttgtaca gcagatgtta atgggcgaac taagcctggt


ttgcccgtgt tgtgcgaaca actagcaacg gcgatggact


 


(SEQ326; DNA; Human papillomavirus>


atatgcgtgacca gctaccagaa agacgggctg gacaggctac


gtgttacaga attgaagctc cgtgttgcag gtgttcaagt


gtagtacaac tggcagtgga aagcagtgga gacacccttc


gcgttgtaca gcagatgtta atgggcgaac taagcctggt


ttgcccgtgt tgtgcgaaca actagcaacg gcgatggact


gtgaaggtac agaggatgag gg


 


<SEQ327; DNA; Human papillomavirus>


atatgcgtgacca gctaccagaa .agacgggctg gacaggctac


gtgttacaga attgaagctc cgtgttgcag gtgttcaagt


gtagtacaac tggcagtgga aagcagtgga gacacccttc


gcgttgtaca gcagatgtta atgggcga


 


<SEQ4; DNA; Human papillomavirus>


gacaggctacgtgttacaga attgaagctc cgtgttgcag


gtgttcaagt gtagtacaac tggcagtgga aagcagtgga


gacacccttc gcgttgtaca gcagatgtta atgggcgaac


taagcctggt ttgcccgtgt tgtgcgaaca actagcaacg


gcgatggact gtgaaggtac agaggatgag gg


 


<SEQ328; DNA; Human papillomavirus>


gacaggctac gtgttacaga attgaagctc cgtgttgcag


gtgttcaagt gtagtacaac tggcagtgga aagcagtgga


gacacccttc gcgttgtaca gcagatgtta atgggcgaac


taagcctggt ttgcccgtgt tgtgcgaaca actagcaacg


gcgatgg


 


<SEQ329; DNA; Human papillomavirus>


gacaggctac gtgttacaga attgaagctc cgtgttgcag


gtgttcaagt gtagtacaac tggcagtgga aagcagtgga


gacacccttc gcgttgtaca gcagatgtta atgggcgaac


taagcctggt ttgcccgtgt tgtgcgaaca actagcaacg


gcgatggact


 


<SEQ330; DNA; Human papillomavirus>


gacaggctac gtgttacaga attgaagctc cgtgttgcag


gtgttcaagt gtagtacaac tggcagtgga aagcagtgga


gacacccttc gcgttgtaca gcagatgtta atgggcga


 


<SEQ5; DNA; Human papillomavirus>


cgggctggacaggctac gtgttacaga attgaagctc cgtgttgcag


gtgttcaagt gtagtacaac tggcagtgga aagcagtgga


gacacccttc gcgttgtaca gcagatgtta atgggcga


 


<SEQ331; DNA; Human papillomavirus>


cgggctggacaggctac gtgttacaga attgaagctc cgtgttgcag


gtgttcaagt gtagtacaac tggcagtgga aagcagtgga


gacacccttc gcgttgtaca gcagatgtta atgggcgaac


taagcctggt ttgcccgtgt tgtgcgaaca actagcaacg


gcgatgg


 


<SEQ332; DNA; Human papillomavirus>


cgggctggacaggctac gtgttacaga attgaagctc cgtgttgcag


gtgttcaagt gtagtacaac tggcagtgga aagcagtgga


gacacccttc gcgttgtaca gcagatgtta atgggcgaac


taagcctggt ttgcccgtgt tgtgcgaaca actagcaacg


gcgatggact


 


<SEQ333; DNA; Human papillomavirus>


cgggctggacaggctac gtgttacaga attgaagctc cgtgttgcag


gtgttcaagt gtagtacaac tggcagtgga aagcagtgga


gacacccttc gcgttgtaca gcagatgtta atgggcgaac


taagcctggt ttgcccgtgt tgtgcgaaca actagcaacg


gcgatggact gtgaaggtac agaggatgag gg


 


<SEQ122; DNA; Human papillomavirus>


ggacgtggtccaga ttaagtttgc acgaggacga ggacaaggaa


aacgatggag actctttgcc aacgtttaaa tgtgtgtcag gaca


 


<SEQ123; DNA; Human papillomavirus>


tagtaacacta cacccatagt acatttaaaa ggtgatgcta


atactttaaa atgtttaaga tatagattta aaaagcattg


tacattgtat actgcagtgt cgtctacatg gcattggaca


ggacataatg taaaacataa aagtgcaatt gttacactta


catatgatag tgaatggcaa cgtgaccaat


 


<SEQ124; DNA; Human papillomavirus>


tagtaacacta cacccatagt acatttaaaa ggtgatgcta


atactttaaa atgtttaaga tatagattta aaaagcattg


tacattgtat actgcagtgt cgtctacatg gcattggaca


ggacataatg taaaacataa aagtgcaatt gttacactta


catatgatag tgaatggcaa cgtgaccaat ttt


 


<SEQ125; DNA; Human papillomavirus>


tagtaacacta cacccatagt acatttaaaa ggtgatgcta


atactttaaa atgtttaaga tatagattta aaaagcattg


tacattgtat actgcagtgt cgtctacatg gcattggaca


ggacataatg taaaacataa aagtgcaatt gttacactta


catatgatag tgaatggcaa cgtgaccaat t


 


<SEQ126; DNA; Human papillomavirus>


tagtaacacta cacccatagt acatttaaaa ggtgatgcta


atactttaaa atgtttaaga tatagattta aaaagcattg


tacattgtat actgcagtgt cgtctacatg gcattggaca


ggacataatg taaaacataa aagtgcaatt gttacactta


catatgatag tgaatggcaa cgtgaccaat ttttgtc


 


<SEQ127; DNA; Human papillomavirus>


tagtaacacta cacccatagt acatttaaaa ggtgatgcta


atactttaaa atgtttaaga tatagattta aaaagcattg


tacattgtat actgcagtgt cgtctacatg gcattggaca


ggacataatg taaaacataa aagtgcaatt gttacactta


catatgatag tgaatggcaa cgtgaccaat ttttg


 


<SEQ128; DNA; Human papillomavirus>


agtaacacta cacccatagt acatttaaaa ggtgatgcta


atactttaaa atgtttaaga tatagattta aaaagcattg


tacattgtat actgcagtgt cgtctacatg gcattggaca


ggacataatg taaaacataa aagtgcaatt gttacactta


catatgatag tgaatggcaa cgtgaccaat


 


<SEQ129; DNA; Human papillomavirus>


agtaacacta cacccatagt acatttaaaa ggtgatgcta


atactttaaa atgtttaaga tatagattta aaaagcattg


tacattgtat actgcagtgt cgtctacatg gcattggaca


ggacataatg taaaacataa aagtgcaatt gttacactta


catatgatag tgaatggcaa cgtgaccaat ttt


 


<SEQ130; DNA; Human papillomavirus>


agtaacacta cacccatagt acatttaaaa ggtgatgcta


atactttaaa atgtttaaga tatagattta aaaagcattg


tacattgtat actgcagtgt cgtctacatg gcattggaca


ggacataatg taaaacataa aagtgcaatt gttacactta


catatgatag tgaatggcaa cgtgaccaat t


 


<SEQ131; DNA; Human papillomavirus>


agtaacacta cacccatagt acatttaaaa ggtgatgcta


atactttaaa atgtttaaga tatagattta aaaagcattg


tacattgtat actgcagtgt cgtctacatg gcattggaca


ggacataatg taaaacataa aagtgcaatt gttacactta


catatgatag tgaatggcaa cgtgaccaat ttttgtc


 


<SEQ132; DNA; Human papillomavirus>


agtaacacta cacccatagt acatttaaaa ggtgatgcta


atactttaaa atgtttaaga tatagattta aaaagcattg


tacattgtat actgcagtgt cgtctacatg gcattggaca


ggacataatg taaaacataa aagtgcaatt gttacactta


catatgatag tgaatggcaa cgtgaccaat ttttg


 


<SEQ133; DNA; Human papillomavirus>


tagtaacacta cacccatagt acatttaaaa ggtgatgcta


atactttaaa atgtttaaga tatagattta aaaagcattg


tacattgtat actgcagtgt cgtctacatg gcattggaca


ggacataatg taaaacataa aagtgcaatt gttacactta


catatgatag tgaatggcaa cgtgacca


 


<SEQ134; DNA; Human papillomavirus>


tagtaacacta cacccatagt acatttaaaa ggtgatgcta


atactttaaa atgtttaaga tatagattta aaaagcattg


tacattgtat actgcagtgt cgtctacatg gcattggaca


ggacataatg taaaacataa aagtgcaatt gttacactta


catatgatag tgaatggcaa cgtgaccaat tt


 


<SEQ135; DNA; Human papillomavirus>


tagtaacacta cacccatagt acatttaaaa ggtgatgcta


atactttaaa atgtttaaga tatagattta aaaagcattg


tacattgtat actgcagtgt cgtctacatg gcattggaca


ggacataatg taaaacataa aagtgcaatt gttacactta


catatgatag tgaatggcaa cgtgaccaat


 


<SEQ136; DNA; Human papillomavirus>


agtaacacta cacccatagt acatttaaaa ggtgatgcta


atactttaaa atgtttaaga tatagattta aaaagcattg


tacattgtat actgcagtgt cgtctacatg gcattggaca


ggacataatg taaaacataa aagtgcaatt gttacactta


catatgatag tgaatggcaa cgtgacca


 


<SEQ137; DNA; Human papillomavirus>


agtaacacta cacccatagt acatttaaaa ggtgatgcta


atactttaaa atgtttaaga tatagattta aaaagcattg


tacattgtat actgcagtgt cgtctacatg gcattggaca


ggacataatg taaaacataa aagtgcaatt gttacactta


catatgatag tgaatggcaa cgtgaccaat tt


 


<SEQ138; DNA; Human papillomavirus>


agtaacacta cacccatagt acatttaaaa ggtgatgcta


atactttaaa atgtttaaga tatagattta aaaagcattg


tacattgtat actgcagtgt cgtctacatg gcattggaca


ggacataatg taaaacataa aagtgcaatt gttacactta


catatgatag tgaatggcaa cgtgaccaat


 


<SEQ139; DNA; Human papillomavirus>


actacacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgacca


 


<SEQ140; DNA; Human papillomavirus>


actacacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat tt


 


<SEQ141; DNA; Human papillomavirus>


actacacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat


 


<SEQ142; DNA; Human papillomavirus>


acacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgacca


 


<SEQ143; DNA; Human papillomavirus>


acacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat tt


 


<SEQ144; DNA; Human papillomavirus>


acacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat


 


<SEQ145; DNA; Human papillomavirus>


tacacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgacca


 


<SEQ146; DNA; Human papillomavirus>


tacacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat tt


 


<SEQ147; DNA; Human papillomavirus>


tacacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat


 


<SEQ359; DNA; Human papillomavirus>


actacacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat t


 


<SEQ360; DNA; Human papillomavirus>


actacacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat ttt


 


<SEQ361; DNA; Human papillomavirus>


actacacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat ttttg


 


<SEQ362; DNA; Human papillomavirus>


actacacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat ttttgtc


 


<SEQ363; DNA; Human papillomavirus>


tacacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat


 


<SEQ364; DNA; Human papillomavirus>


tacacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat t


 


<SEQ365; DNA; Human papillomavirus>


tacacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat ttt


 


<SEQ366; DNA; Human papillomavirus>


tacacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat ttttg


 


<SEQ367; DNA; Human papillomavirus>


tacacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat ttttgtc


 


<SEQ144; DNA; Human papillomavirus>


acacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat


 


<SEQ368; DNA; Human papillomavirus>


acacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat t


 


<SEQ369; DNA; Human papillomavirus>


acacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat ttt


 


<SEQ370; DNA; Human papillomavirus>


acacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat ttttg


 


<SEQ371; DNA; Human papillomavirus>


acacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat ttttgtc


 


<SEQ372; DNA; Human papillomavirus>


t agtaacacta cacccatagt acatttaaaa ggtgatgcta


atactttaaa atgtttaaga tatagattta aaaagcattg


tacattgtat actgcagtgt cgtctacatg gcattggaca


ggacataatg taaaacataa aagtgcaatt gttacactta


catatgatag tgaatggcaa cgtgaccaat ttttgtctca


agttaaaata ccaaaaacta ttacagtgtc


 


<SEQ373; DNA; Human papillomavirus>


t agtaacacta cacccatagt acatttaaaa ggtgatgcta


atactttaaa atgtttaaga tatagattta aaaagcattg


tacattgtat actgcagtgt cgtctacatg gcattggaca


ggacataatg taaaacataa aagtgcaatt gttacactta


catatgatag tgaatggcaa cgtgaccaat ttttgtctca


agttaaaata ccaaaaacta ttacagtgtc t


 


<SEQ374; DNA; Human papillomavirus>


t agtaacacta cacccatagt acatttaaaa ggtgatgcta


atactttaaa atgtttaaga tatagattta aaaagcattg


tacattgtat actgcagtgt cgtctacatg gcattggaca


ggacataatg taaaacataa aagtgcaatt gttacactta


catatgatag tgaatggcaa cgtgaccaat ttttgtctca


agttaaaata ccaaaaacta ttacagtgtc tactgga


 


<SEQ375; DNA; Human papillomavirus>


t agtaacacta cacccatagt acatttaaaa ggtgatgcta


atactttaaa atgtttaaga tatagattta aaaagcattg


tacattgtat actgcagtgt cgtctacatg gcattggaca


ggacataatg taaaacataa aagtgcaatt gttacactta


catatgatag tgaatggcaa cgtgaccaat ttttgtctca


agttaaaata ccaaaaacta ttacagtgtc tactggat


 


<SEQ376; DNA; Human papillomavirus>


t agtaacacta cacccatagt acatttaaaa ggtgatgcta


atactttaaa atgtttaaga tatagattta aaaagcattg


tacattgtat actgcagtgt cgtctacatg gcattggaca


ggacataatg taaaacataa aagtgcaatt gttacactta


catatgatag tgaatggcaa cgtgaccaat ttttgtctca


agttaaaata ccaaaaacta ttacagtgtc tactggatt


 


<SEQ377; DNA; Human papillomavirus>


t agtaacacta cacccatagt acatttaaaa ggtgatgcta


atactttaaa atgtttaaga tatagattta aaaagcattg


tacattgtat actgcagtgt cgtctacatg gcattggaca


ggacataatg taaaacataa aagtgcaatt gttacactta


catatgatag tgaatggcaa cgtgaccaat ttttgtctca


agttaaaata ccaaaaacta ttacagtgtc tactggattt


 


<SEQ378; DNA; Human papillomavirus>


agtaacacta cacccatagt acatttaaaa ggtgatgcta


atactttaaa atgtttaaga tatagattta aaaagcattg


tacattgtat actgcagtgt cgtctacatg gcattggaca


ggacataatg taaaacataa aagtgcaatt gttacactta


catatgatag tgaatggcaa cgtgaccaat ttttgtctca


agttaaaata ccaaaaacta ttacagtgtc


 


<SEQ379; DNA; Human papillomavirus>


agtaacacta cacccatagt acatttaaaa ggtgatgcta


atactttaaa atgtttaaga tatagattta aaaagcattg


tacattgtat actgcagtgt cgtctacatg gcattggaca


ggacataatg taaaacataa aagtgcaatt gttacactta


catatgatag tgaatggcaa cgtgaccaat ttttgtctca


agttaaaata ccaaaaacta ttacagtgtc t


 


<SEQ380; DNA; Human papillomavirus>


agtaacacta cacccatagt acatttaaaa ggtgatgcta


atactttaaa atgtttaaga tatagattta aaaagcattg


tacattgtat actgcagtgt cgtctacatg gcattggaca


ggacataatg taaaacataa aagtgcaatt gttacactta


catatgatag tgaatggcaa cgtgaccaat ttttgtctca


agttaaaata ccaaaaacta ttacagtgtc tactgga


 


<SEQ381; DNA; Human papillomavirus>


agtaacacta cacccatagt acatttaaaa ggtgatgcta


atactttaaa atgtttaaga tatagattta aaaagcattg


tacattgtat actgcagtgt cgtctacatg gcattggaca


ggacataatg taaaacataa aagtgcaatt gttacactta


catatgatag tgaatggcaa cgtgaccaat ttttgtctca


agttaaaata ccaaaaacta ttacagtgtc tactggat


 


<SEQ382; DNA; Human papillomavirus>


agtaacacta cacccatagt acatttaaaa ggtgatgcta


atactttaaa atgtttaaga tatagattta aaaagcattg


tacattgtat actgcagtgt cgtctacatg gcattggaca


ggacataatg taaaacataa aagtgcaatt gttacactta


catatgatag tgaatggcaa cgtgaccaat ttttgtctca


agttaaaata ccaaaaacta ttacagtgtc tactggatt


 


<SEQ383; DNA; Human papillomavirus>


agtaacacta cacccatagt acatttaaaa ggtgatgcta


atactttaaa atgtttaaga tatagattta aaaagcattg


tacattgtat actgcagtgt cgtctacatg gcattggaca


ggacataatg taaaacataa aagtgcaatt gttacactta


catatgatag tgaatggcaa cgtgaccaat ttttgtctca


agttaaaata ccaaaaacta ttacagtgtc tactggattt


 


<SEQ384; DNA; Human papillomavirus>


actacacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat ttttgtctca agttaaaata


ccaaaaacta ttacagtgtc


 


<SEQ385; DNA; Human papillomavirus>


actacacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat ttttgtctca agttaaaata


ccaaaaacta ttacagtgtc t


 


<SEQ386; DNA; Human papillomavirus>


actacacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat ttttgtctca agttaaaata


ccaaaaacta ttacagtgtc tactgga


 


<SEQ387; DNA; Human papillomavirus>


actacacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat ttttgtctca agttaaaata


ccaaaaacta ttacagtgtc tactggat


 


<SEQ388; DNA; Human papillomavirus>


actacacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat ttttgtctca agttaaaata


ccaaaaacta ttacagtgtc tactggatt


 


<SEQ389; DNA; Human papillomavirus>


actacacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat ttttgtctca agttaaaata


ccaaaaacta ttacagtgtc tactggattt


 


<SEQ390; DNA; Human papillomavirus>


tacacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat ttttgtctca agttaaaata


ccaaaaacta ttacagtgtc


 


<SEQ391; DNA; Human papillomavirus>


tacacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat ttttgtctca agttaaaata


ccaaaaacta ttacagtgtc t


 


<SEQ392; DNA; Human papillomavirus>


tacacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagactta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat ttttgtctca agttaaaata


ccaaaaacta ttacagtgtc tactgga


 


<SEQ393; DNA; Human papillomavirus>


tacacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat ttttgtctca agttaaaata


ccaaaaacta ttacagtgtc tactggat


 


<SEQ394; DNA; Human papillomavirus>


tacacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat ttttgtctca agttaaaata


ccaaaaacta ttacagtgtc tactggatt


 


<SEQ395; DNA; Human papillomavirus>


tacacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat ttttgtctca agttaaaata


ccaaaaacta ttacagtgtc tactggattt


 


<SEQ396; DNA; Human papillomavirus>


acacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat ttttgtctca agttaaaata


ccaaaaacta ttacagtgtc


 


<SEQ397; DNA; Human papillomavirus>


acacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat ttttgtctca agttaaaata


ccaaaaacta ttacagtgtc t


 


<SEQ398; DNA; Human papillomavirus>


acacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat ttttgtctca agttaaaata


ccaaaaacta ttacagtgtc tactgga


 


<SEQ399; DNA; Human papillomavirus>


acacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat ttttgtctca agttaaaata


ccaaaaacta ttacagtgtc tactggat


 


<SEQ400; DNA; Human papillomavirus>


acacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat ttttgtctca agttaaaata


ccaaaaacta ttacagtgtc tactggatt


 


<SEQ401; DNA; Human papillomavirus>


acacccatagt acatttaaaa ggtgatgcta atactttaaa


atgtttaaga tatagattta aaaagcattg tacattgtat


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat ttttgtctca agttaaaata


ccaaaaacta ttacagtgtc tactggattt


 


<SEQ148; DNA; Human papillomavirus>


taaaaggtgatgcta atactttaaa atgtttaaga tatagattta


aaaagcattg tacattgtat actgcagtgt cgtctacatg


gcattggaca ggacataatg taaaacataa aagtgcaatt


gttacactta catatgatag tgaatggcaa cgtgacca


 


<SEQ149; DNA; Human papillomavirus>


taaaaggtgatgcta atactttaaa atgtttaaga tatagattta


aaaagcattg tacattgtat actgcagtgt cgtctacatg


gcattggaca ggacataatg taaaacataa aagtgcaatt


gttacactta catatgatag tgaatggcaa cgtgaccaat tt


 


<SEQ150; DNA; Human papillomavirus>


taaaaggtgatgcta atactttaaa atgtttaaga tatagattta


aaaagcattg tacattgtat actgcagtgt cgtctacatg


gcattggaca ggacataatg taaaacataa aagtgcaatt


gttacactta catatgatag tgaatggcaa cgtgaccaat


 


<SEQ151; DNA; Human papillomavirus>


acatttaaaa ggtgatgcta atactttaaa atgtttaaga


tatagattta aaaagcattg tacattgtat actgcagtgt


cgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgacca


 


<SEQ152; DNA; Human papillomavirus>


acatttaaaa ggtgatgcta atactttaaa atgtttaaga


tatagattta aaaagcattg tacattgtat actgcagtgt


cgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat tt


 


<SEQ153; DNA; Human papillomavirus>


acatttaaaa ggtgatgcta atactttaaa atgtttaaga


tatagattta aaaagcattg tacattgtat actgcagtgt


cgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat


 


<SEQ154; DNA; Human papillomavirus>


ttaaaaggtgatgcta atactttaaa atgtttaaga tatagattta


aaaagcattg tacattgtat actgcagtgt cgtctacatg


gcattggaca ggacataatg taaaacataa aagtgcaatt


gttacactta catatgatag tgaatggcaa cgtgacca


 


<SEQ155; DNA; Human papillomavirus>


ttaaaaggtgatgcta atactttaaa atgtttaaga tatagattta


aaaagcattg tacattgtat actgcagtgt cgtctacatg


gcattggaca ggacataatg taaaacataa aagtgcaatt


gttacactta catatgatag tgaatggcaa cgtgaccaat tt


 


<SEQ156; DNA; Human papillomavirus>


ttaaaaggtgatgcta atactttaaa atgtttaaga tatagattta


aaaagcattg tacattgtat actgcagtgt cgtctacatg


gcattggaca ggacataatg taaaacataa aagtgcaatt


gttacactta catatgatag tgaatggcaa cgtgaccaat


 


<SEQ402; DNA; Human papillomavirus>


acatttaaaa ggtgatgcta atactttaaa atgtttaaga


tatagattta aaaagcattg tacattgtat actgcagtgt


cgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat t


 


<SEQ403; DNA; Human papillomavirus>


acatttaaaa ggtgatgcta atactttaaa atgtttaaga


tatagattta aaaagcattg tacattgtat actgcagtgt


cgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat ttt


 


<SEQ404; DNA; Human papillomavirus>


acatttaaaa ggtgatgcta atactttaaa atgtttaaga


tatagattta aaaagcattg tacattgtat actgcagtgt


cgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat ttttg


 


<SEQ405; DNA; Human papillomavirus>


acatttaaaa ggtgatgcta atactttaaa atgtttaaga


tatagattta aaaagcattg tacattgtat actgcagtgt


cgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat ttttgtc


 


<SEQ406; DNA; Human papillomavirus>


ttaaaaggtgatgcta atactttaaa atgtttaaga tatagattta


aaaagcattg tacattgtat actgcagtgt cgtctacatg


gcattggaca ggacataatg taaaacataa aagtgcaatt


gttacactta catatgatag tgaatggcaa cgtgaccaat t


 


<SEQ407; DNA; Human papillomavirus>


ttaaaaggtgatgcta atactttaaa atgtttaaga tatagattta


aaaagcattg tacattgtat actgcagtgt cgtctacatg


gcattggaca ggacataatg taaaacataa aagtgcaatt


gttacactta catatgatag tgaatggcaa cgtgaccaat ttt


 


<SEQ408; DNA; Human papillomavirus>


ttaaaaggtgatgcta atactttaaa atgtttaaga tatagattta


aaaagcattg tacattgtat actgcagtgt cgtctacatg


gcattggaca ggacataatg taaaacataa aagtgcaatt


gttacactta catatgatag tgaatggcaa cgtgaccaat ttttg


 


<SEQ409; DNA; Human papillomavirus>


ttaaaaggtgatgcta atactttaaa atgtttaaga tatagattta


aaaagcattg tacattgtat actgcagtgt cgtctacatg


gcattggaca ggacataatg taaaacataa aagtgcaatt


gttacactta catatgatag tgaatggcaa cgtgaccaat


ttttgtc


 


<SEQ410; DNA; Human papillomavirus>


taaaaggtgatgcta atactttaaa atgtttaaga tatagattta


aaaagcattg tacattgtat actgcagtgt cgtctacatg


gcattggaca ggacataatg taaaacataa aagtgcaatt


gttacactta catatgatag tgaatggcaa cgtgaccaat t


 


<SEQ411; DNA; Human papillomavirus>


taaaaggtgatgcta atactttaaa atgtttaaga tatagattta


aaaagcattg tacattgtat actgcagtgt cgtctacatg


gcattggaca ggacataatg taaaacataa aagtgcaatt


gttacactta catatgatag tgaatggcaa cgtgaccaat ttt


 


<SEQ412; DNA; Human papillomavirus>


taaaaggtgatgcta atactttaaa atgtttaaga tatagattta


aaaagcattg tacattgtat actgcagtgt cgtctacatg


gcattggaca ggacataatg taaaacataa aagtgcaatt


gttacactta catatgatag tgaatggcaa cgtgaccaat ttttg


 


<SEQ413; DNA; Human papillomavirus>


taaaaggtgatgcta atactttaaa atgtttaaga tatagattta


aaaagcattg tacattgtat actgcagtgt cgtctacatg


gcattggaca ggacataatg taaaacataa aagtgcaatt


gttacactta catatgatag tgaatggcaa cgtgaccaat


ttttgtc


 


<SEQ163; DNA; Human papillomavirus>


acatttaaaa ggtgatgcta atactttaaa atgtttaaga


tatagattta aaaagcattg tacattgtat actgcagtgt


cgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat ttttgtctca agttaaaata ccaaaaacta


ttacagtgtc


 


<SEQ162; DNA; Human papillomavirus>


acatttaaaa ggtgatgcta atactttaaa atgtttaaga


tatagattta aaaagcattg tacattgtat actgcagtgt


cgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat ttttgtctca agttaaaata ccaaaaacta


ttacagtgtc t


 


<SEQ164; DNA; Human papillomavirus>


acatttaaaa ggtgatgcta atactttaaa atgtttaaga


tatagattta aaaagcattg tacattgtat actgcagtgt


cgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat ttttgtctca agttaaaata ccaaaaacta


ttacagtgtc tactgga


 


<SEQ414; DNA; Human papillomavirus>


acatttaaaa ggtgatgcta atactttaaa atgtttaaga


tatagattta aaaagcattg tacattgtat actgcagtgt


cgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat ttttgtctca agttaaaata ccaaaaacta


ttacagtgtc tactggat


 


<SEQ415; DNA; Human papillomavirus>


acatttaaaa ggtgatgcta atactttaaa atgtttaaga


tatagattta aaaagcattg tacattgtat actgcagtgt


cgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat ttttgtctca agttaaaata ccaaaaacta


ttacagtgtc tactggatt


 


<SEQ161; DNA; Human papillomavirus>


acatttaaaa ggtgatgcta atactttaaa atgtttaaga


tatagattta aaaagcattg tacattgtat actgcagtgt


cgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat ttttgtctca agttaaaata ccaaaaacta


ttacagtgtc tactggattt


 


<SEQ167; DNA; Human papillomavirus>


ttaaaaggtgatgcta atactttaaa atgtttaaga tatagattta


aaaagcattg tacattgtat actgcagtgt cgtctacatg


gcattggaca ggacataatg taaaacataa aagtgcaatt


gttacactta catatgatag tgaatggcaa cgtgaccaat


ttttgtctca agttaaaata ccaaaaacta ttacagtgtc


 


<SEQ165; DNA; Human papillomavirus>


ttaaaaggtgatgcta atactttaaa atgtttaaga tatagattta


aaaagcattg tacattgtat actgcagtgt cgtctacatg


gcattggaca ggacataatg taaaacataa aagtgcaatt


gttacactta catatgatag tgaatggcaa cgtgaccaat


ttttgtctca agttaaaata ccaaaaacta ttacagtgtc t


 


<SEQ168; DNA; Human papillomavirus>


ttaaaaggtgatgcta atactttaaa atgtttaaga tatagattta


aaaagcattg tacattgtat actgcagtgt cgtctacatg


gcattggaca ggacataatg taaaacataa aagtgcaatt


gttacactta catatgatag tgaatggcaa cgtgaccaat


ttttgtctca agttaaaata ccaaaaacta ttacagtgtc


tactgga


 


<SEQ416; DNA; Human papillomavirus>


ttaaaaggtgatgcta atactttaaa atgtttaaga tatagattta


aaaagcattg tacattgtat actgcagtgt cgtctacatg


gcattggaca ggacacaatg taaaacataa aagtgcaatt


gttacactta catatgatag tgaatggcaa cgtgaccaat


ttttgtctca agttaaaata ccaaaaacta ttacagtgtc


tactggat


 


<SEQ417; DNA; Human papillomavirus>


ttaaaaggtgatgcta atactttaaa atgtttaaga tatagattta


aaaagcattg tacattgtat actgcagtgt cgtctacatg


gcattggaca ggacataatg taaaacataa aagtgcaatt


gttacactta catatgatag tgaatggcaa cgtgaccaat


ttttgtctca agttaaaata ccaaaaacta ttacagtgtc


tactggatt


 


<SEQ165; DNA; Human papillomavirus>


ttaaaaggtgatgcta atactttaaa atgtttaaga tatagattta


aaaagcattg tacattgtat actgcagtgt cgtctacatg


gcattggaca ggacataatg taaaacataa aagtgcaatt


gttacactta catatgatag tgaatggcaa cgtgaccaat


ttttgtctca agttaaaata ccaaaaacta ttacagtgtc


tactggattt


 


<SEQ159; DNA; Human papillomavirus>


taaaaggtgatgcta atactttaaa atgtttaaga tatagattta


aaaagcattg tacattgtat actgcagtgt cgtctacatg


gcattggaca ggacataatg taaaacataa aagtgcaatt


gttacactta catatgatag tgaatggcaa cgtgaccaat


ttttgtctca agttaaaata ccaaaaacta ttacagtgtc


 


<SEQ158; DNA; Human papillomavirus>


taaaaggtgatgcta atactttaaa atgtttaaga tatagattta


aaaagcattg tacattgtat actgcagtgt cgtctacatg


gcattggaca ggacataatg taaaacataa aagtgcaatt


gttacactta catatgatag tgaatggcaa cgtgaccaat


ttttgtctca agttaaaata ccaaaaacta ttacagtgtc t


 


<SEQ160; DNA; Human papillomavirus>


taaaaggtgatgcta atactttaaa atgtttaaga tatagattta


aaaagcattg tacattgtat actgcagtgt cgtctacatg


gcattggaca ggacataatg taaaacataa aagtgcaatt


gttacactta catatgatag tgaatggcaa cgtgaccaat


ttttgtctca agttaaaata ccaaaaacta ttacagtgtc


tactgga


 


<SEQ418; DNA; Human papillomavirus>


taaaaggtgatgcta atactttaaa atgtttaaga tatagattta


aaaagcattg tacattgtat actgcagtgt cgtctacatg


gcattggaca ggacataatg taaaacataa aagtgcaatt


gttacactta catatgatag tgaatggcaa cgtgaccaat


ttttgtctca agttaaaata ccaaaaacta ttacagtgtc


tactggat


 


<SEQ419; DNA; Human papillomavirus>


taaaaggtgatgcta atactttaaa atgtttaaga tatagattta


aaaagcattg tacattgtat 8ctgcagtgt cgtctacatg


gcattggaca ggacataatg taaaacataa aagtgcaatt


gttacactta catatgatag tgaatggcaa cgtgaccaat


ttttgtctca agttaaaata ccaaaaacta ttacagtgtc


tactggatt


 


<SEQ157; DNA; Human papillomavirus>


taaaaggtgatgcta atactttaaa atgtttaaga tatagattta


aaaagcattg tacattgtat actgcagtgt cgtctacatg


gcattggaca ggacataatg taaaacataa aagtgcaatt


gttacactta catatgatag tgaatggcaa cgtgaccaat


ttttgtctca agttaaaata ccaaaaacta ttacagtgtc


tactggattt


 


<SEQ169; DNA; Human papillomavirus>


gtcgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat ttttgtctca agttaaaata ccaaaaacta


ttacagtgtc tactggat


 


<SEQ170; DNA; Human papillomavirus>


gtcgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat ttttgtctca agttaaaata ccaaaaacta


ttacagtgtc t


 


<SEQ171; DNA; Human papillomavirus>


gtcgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat ttttgtctca agttaaaata ccaaaaacta


ttacagtgtc


 


<SEQ172; DNA; Human papillomavirus>


gtcgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat ttttgtctca agttaaaata ccaaaaacta


ttacagtgtc tactggattt


 


<SEQ173; DNA; Human papillomavirus>


gtcgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgt9accaat ttttgtctca agttaaaata ccaaaaacta


ttacagtgtc tactggatt


 


<SEQ174; DNA; Human papillomavirus>


gtcgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat ttttgtctca agttaaaata ccaaaaacta


ttacagtgtc tactgga


 


<SEQ175; DNA; Human papillomavirus>


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat ttttgtctca agttaaaata


ccaaaaacta ttacagtgtc tactggat


 


<SEQ176; DNA; Human papillomavirus>


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat ttttgtctca agttaaaata


ccaaaaacta ttacagtgtc t


 


<SEQ177; DNA; Human papillomavirus>


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat ttttgtctca agttaaaata


ccaaaaacta ttacagtgtc


 


<SEQ178; DNA; Human papillomavirus>


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat ttttgtctca agttaaaata


ccaaaaacta ttacagtgtc tactggattt


 


<SEQ179; DNA; Human papillomavirus>


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat ttttgtctca agttaaaata


ccaaaaacta ttacagtgtc tactggatt


 


<SEQ180; DNA; Human papillomavirus>


actgcagtgt cgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat ttttgtctca agttaaaata


ccaaaaacta ttacagtgtc tactgga


 


<SEQ181; DNA; Human papillomavirus>


tgcagtgtcgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat ttttgtctca agttaaaata


ccaaaaacta ttacagtgtc tactggat


 


<SEQ182; DNA; Human papillomavirus


tgcagtgtcgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat ttttgtctca agttaaaata


ccaaaaacta ttacagtgtc t


 


<SEQ183; DNA; Human papillomavirus>


tgcagtgtcgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat ttttgtctca agttaaaata


ccaaaaacta ttacagtgtc


 


<SEQ184; DNA; Human papillomavirus>


tgcagtgtcgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat ttttgtctca agttaaaata


ccaaaaacta ttacagtgtc tactggattt


 


<SEQ185; DNA; Human papillomavirus>


tgcagtgtcgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat ttttgtctca agttaaaata


ccaaaaacta ttacagtgtc tactggatt


 


<SEQ186; DNA; Human papillomavirus>


tgcagtgtcgtctacatg gcattggaca ggacataatg


taaaacataa aagtgcaatt gttacactta catatgatag


tgaatggcaa cgtgaccaat ttttgtctca agttaaaata


ccaaaaacta ttacagtgtc tactgga


 


<SEQ187; DNA; Human papillomavirus>


agtgtcgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat ttttgtctca agttaaaata ccaaaaacta


ttacagtgtc tactggat


 


<SEQ188; DNA; Human papillomavirus>


agtgtcgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat ttttgtctca agttaaaata ccaaaaacta


ttacagtgtc t


 


<SEQ189; DNA; Human papillomavirus>


agtgtcgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat ttttgtctca agttaaaata ccaaaaacta


ttacagtgtc


 


<SEQ190; DNA; Human papillomavirus>


agtgtcgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat ttttgtctca agttaaaata ccaaaaacta


ttacagtgtc tactggattt


 


<SEQ191;DNA; Human papillomavirus>


agtgtcgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat ttttgtctca agttaaaata ccaaaaacta


ttacagtgtc tactggatt


 


<SEQ192; DNA; Human papillomavirus>


agtgtcgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat ttttgtctca agttaaaata ccaaaaacta


ttacagtgtc tactgga


 


<SEQ193; DNA; Human papillomavirus>


cagtgtcgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat ttttgtctca agttaaaata ccaaaaacta


ttacagtgtc tactggat


 


<SEQ194; DNA; Human papillomavirus>


cagtgtcgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat ttttgtctca agttaaaata ccaaaaacta


ttacagtgtc t


 


<SEQ195; DNA; Human papillomavirus>


cagtgtcgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat ttttgtctca agttaaaata ccaaaaacta


ttacagtgtc


 


<SEQ196; DNA; Human papillomavirus>


cagtgtcgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat ttttgtctca agttaaaata ccaaaaacta


ttacagtgtc tactggattt


 


<SEQ197; DNA; Human papillomavirus>


cagtgtcgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat ttttgtctca agttaaaata ccaaaaacta


ttacagtgtc tactggatt


 


<SEQ198; DNA; Human papillomavirus>


cagtgtcgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat ttttgtctca agttaaaata ccaaaaacta


ttacagtgtc tactgga


 


<SEQ199; DNA; Human papillomavirus>


tgtcgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat ttttgtctca agttaaaata ccaaaaacta


ttacagtgtc tactggat


 


<SEQ200; DNA; Human papillomavirus>


tgtcgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat ttttgtctca agttaaaata ccaaaaacta


ttacagtgtc t


 


<SEQ201; DNA; Human papillomavirus>


tgtcgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat ttttgtctca agttaaaata ccaaaaacta


ttacagtgtc


 


<SEQ202; DNA; Human papillomavirus>


tgtcgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat ttttgtctca agttaaaata ccaaaaacta


ttacagtgtc tactggattt


 


<SEQ203; DNA; Human papillomavirus>


tgtcgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat ttttgtctca agttaaaata ccaaaaacta


ttacagtgtc tactggatt


 


<SEQ204; DNA; Human papillomavirus>


tgtcgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat ttttgtctca agttaaaata ccaaaaacta


ttacagtgtc tactgga


 


<SEQ205; DNA; Human papillomavirus>


gtgtcgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat ttttgtctca agttaaaata ccaaaaacta


ttacagtgtc tactggat


 


<SEQ206; DNA; Human papillomavirus>


gtgtcgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat ttttgtctca agttaaaata ccaaaaacta


ttacagtgtc t


 


<SEQ207; DNA; Human papillomavirus>


gtgtcgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat ttttgtctca agttaaaata ccaaaaacta


ttacagtgtc


 


<SEQ208; DNA; Human papillomavirus>


gtgtcgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat ttttgtctca agttaaaata ccaaaaacta


ttacagtgtc tactggattt


 


<SEQ209; DNA; Human papillomavirus>


gtgtcgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat ttttgtctca agttaaaata ccaaaaacta


ttacagtgtc tactggatt


 


<SEQ210; DNA; Human papillomavirus>


gtgtcgtctacatg gcattggaca ggacataatg taaaacataa


aagtgcaatt gttacactta catatgatag tgaatggcaa


cgtgaccaat ttttgtctca agttaaaata ccaaaaacta


ttacagtgtc tactgga


 


<SEQ46; DNA; Human papillomavirus>


tggtatagaacaggaa tatcaaatat tagtgaagta atgggagaca


cacctgagtg gatacaaaga cttactatta tacaacatgg


aatagatgat agcaattttg atttgtcaga aatggtacaa


tgggcatttg ataatgagct gacagatgaa agcgatatgg


catttgaata tgccttatta gcagacagca acagcaatg


 


<SEQ47; DNA; Human papillomavirus>


tggtatagaacaggaa tatcaaatat tagtgaagta atgggagaca


cacctgagtg gatacaaaga cttactatta tacaacatgg


aatagatgat agcaattttg atttgtcaga aatggtacaa


tgggcatttg ataatgagct gacagatgaa agcgatatgg


catttgaata tgccttatta gcagacagca acagcaatgc ag


 


<SEQ48; DNA; Human papillomavirus>


tggtatagaacaggaa tatcaaatat tagtgaagta atgggagaca


cacctgagtg gatacaaaga cttactatta tacaacatgg


aatagatgat agcaattttg atttgtcaga aatggtacaa


tgggcatttg ataatgagct gacagatgaa agcgatatgg


catttgaata tgccttatta gcagacagca atagcaatgc agc


 


<SEQ49; DNA; Human papillomavirus>


gaacaggaatatcaaatat tagtgaagta atgggagaca


cacctgagtg gatacaaaga cttactatta tacaacatgg


aatagatgat agcaattttg atttgtcaga aatggtacaa


tgggcatttg ataatgagct gacagatgaa agcgatatgg


catttgaata tgccttatta gcagacagca acagcaatg


 


<SEQ50; DNA; Human papillomavirus>


gaacaggaatatcaaatat tagtgaagta atgggagaca


cacctgagtg gatacaaaga cttactatta tacaacatgg


aatagatgat agcaattttg atttgtcaga aatggtacaa


tgggcatttg ataatgagct gacagatgaa agcgatatgg


catttgaata tgccttatta gcagacagca acagcaatgc ag


 


<SEQ51; DNA; Human papillomavirus>


gaacaggaatatcaaatat tagtgaagta atgggagaca


cacctgagtg gatacaaaga cttactatta tacaacatgg


aatagatgat agcaattttg atttgtcaga aatggtacaa


tgggcatttg ataatgagct gacagatgaa agcgatatgg


catttgaata tgccttatta gcagacagca acagcaatgc agc


 


<SEQ52; DNA; Human papillomavirus>


tggtatagaacaggaa tatcaaatat tagtgaagta atgggagaca


cacctgagtg gatacaaaga cttactatta tacaacatgg


aatagatgat agcaattttg atttgtcaga aatggtacaa


tgggcatttg ataatgagct gacagatgaa agcgatatgg ca


 


<SEQ53; DNA; Human papillomavirus>


tggtatagaacaggaa tatcaaatat tagtgaagta atgggagaca


cacctgagtg gatacaaaga cttactatta tacaacatgg


aatagatgat agcaattttg atttgtcaga aatggtacaa


tgggcatttg ataatgagct gacagatgaa agcgatatgg cattt


 


<SEQ339; DNA; Human papillomavirus>


gaacaggaa tatcaaatat tagtgaagta atgggagaca


cacctgagtg gatacaaaga cttactatta tacaacatgg


aatagatgat agcaattttg atttgtcaga aatggtacaa


tgggcatttg ataatgagct gacagatgaa agcgatatgg ca


 


<SEQ340; DNA; Human papillomavirus>


gaacaggaatatcaaatat tagtgaagta atgggagaca


cacctgagtg gatacaaaga cttactatta tacaacatgg


aatagatgat agcaattttg atttgtcaga aatggtacaa


tgggcatttg ataatgagct gacagatgaa agcgatatgg cattt


 


<SEQ341; DNA; Human papillomavirus>


tggtatagaacaggaa tatcaaatat tagtgaagta atgggagaca


cacctgagtg gatacaaaga cttactatta tacaacatgg


aatagatgat agcaattttg atttgtcaga aatggtacaa


tgggcatttg ataatgagct gacagatgaa agcgatatgg


catttgaata tgccttatta gcagacagca acagcaatgc


 


<SEQ342; DNA; Human papillomavirus>


gaacaggaatatcaaatat tagtgaagta atgggagaca


cacctgagtg gatacaaaga cttactatta tacaacatgg


aatagatgat agcaattttg atttgtcaga aatggtacaa


tgggcatttg ataatgagct gacagatgaa agcgatatgg


catttgaata tgccttatta gcagacagca acagcaatgc


 


<SEQ54; DNA; Human papillomavirus>


ggtatagaacaggaa tatcaaatat tagtgaagta atgggagaca


cacctgagtg gatacaaaga cttactatta tacaacatgg


aatagatgat agcaattttg atttgtcaga aatggtacaa


tgggcatttg ataatgagct gacagatgaa agcgatatgg ca


 


<SEQ55; DNA; Human papillomavirus>


ggtatagaacaggaa tatcaaatat tagtgaagta atgggagaca


cacctgagtg gatacaaaga cttactatta tacaacatgg


aatagatgat agcaattttg atttgtcaga aatggtacaa


tgggcatttg ataatgagct gacagatgaa agcgatatgg cattt


 


<SEQ56; DNA; Human papillomavirus>


gtatagaacaggaa tatcaaatat tagtgaagta atgggagaca


cacctgagtg gatacaaaga cttactatta tacaacatgg


aatagatgat agcaattttg atttgtcaga aatggtacaa


tgggcatttg ataatgagct gacagatgaa agcgatatgg ca


 


<SEQ57; DNA; Human papillomavirus>


gtatagaacaggaa tatcaaatat tagtgaagta atgggagaca


cacctgagtg gatacaaaga cttactatta tacaacatgg


aatagatgat agcaattttg atttgtcaga aatggtacaa


tgggcatttg ataatgagct gacagatgaa agcgatatgg cattt


 


<SEQ343; DNA; Human papillomavirus>


ggtatagaacaggaa tatcaaatat tagtgaagta atgggagaca


cacctgagtg gatacaaaga cttactatta tacaacatgg


aatagatgat agcaattttg atttgtcaga aatggtacaa


tgggcatttg ataatgagct acagatgaa agcgatatgg


catttgaata tgccttatta gcagacagca acagcaatg


 


<SEQ344; DNA; Human papillomavirus>


ggtatagaacaggaa tatcaaatat tagtgaagta atgggagaca


cacctgagtg gatacaaaga cttactatta tacaacatgg


aatagatgat agcaattttg atttgtcaga aatggtacaa


tgggcatttg ataatgagct gacagatgaa agcgatatgg


catttgaata tgccttatta gcagacagca acagcaatgc ag


 


<SEQ345; DNA; Human papillomavirus>


ggtatagaacaggaa tatcaaatat tagtgaagta atgggagaca


cacctgagtg gatacaaaga cttactatta tacaacatgg


aatagatgat agcaattttg atttgtcaga aatggtacaa


tgggcatttg ataatgagct gacagatgaa agcgatatgg


catttgaata tgccttatta gcagacagca acagcaatgc agc


 


<SE0346; DNA; Human papillomavirus>


gtatagaacaggaa tatcaaatat tagtgaagta atgggagaca


cacctgagtg gatacaaaga cttactatta tacaacatgg


aatagatgat agcaattttg atttgtcaga aatggtacaa


tgggcatttg ataatgagct gacagatgaa agcgatatgg


catttgaata tgccttatta gcagacagca acagcaatg


 


<SEQ347; DNA; Human papillomavirus>


gtatagaacaggaa tatcaaatat tagtgaagta atgggagaca


cacctgagtg gatacaaaga cttactatta tacaacatgg


aatagatgat agcaattttg atttgtcaga aatggtacaa


tgggcatttg ataatgagct gacagatgaa agcgatatgg


catttgaata tgccttatta gcagacagca acagcaatgc ag


 


<SEQ348; DNA; Human papillomavirus>


gtatagaacaggaa tatcaaatat tagtgaagta atgggagaca


cacctgagtg gatacaaaga cttactatta tacaacatgg


aatagatgat agcaattttg atttgtcaga aatggtacaa


tgggcatttg ataatgagct gacagatgaa agcgatatgg


catttgaata tgccttatta gcagacagca acagcaatgc agc


 


<SEQ349; DNA; Human papillomavirus>


tggtatagaacaggaa tatcaaatat tagtgaagta atgggagaca


cacctgagtg gatacaaaga cttactatta tacaacatgg


aatagatgat agcaattttg atttgtcaga aatggtacaa


tgggcatttg ataatgagct gacagatgaa agcgatatgg


catttgaata tgccttatta gcagacagca acagcaatgc


 


<SEQ350; DNA; Human papillomavirus>


ggtatagaacaggaa tatcaaatat tagtgaagta atgggagaca


cacctgagtg gatacaaaga cttactatta tacaacatgg


aatagatgat agcaattttg atttgtcaga aatggtacaa


tgggcatttg ataatgagct gacagatgaa agcgatatgg


catttgaata tgccttatta gcagacagca acagcaatgc


 


<SEQ345; DNA; Human papillomavirus>


ggtatagaacaggaa tatcaaatat tagtgaagta atgggagaca


cacctgagtg gatacaaaga cttactatta tacaacatgg


aatagatgat agcaattttg atttgtcaga aatggtacaa


tgggcatttg ataatgagct gacagatgaa agcgatatgg


catttgaata tgccttatta gcagacagca acagcaatgc agc


 


<SEQ351; DNA; Human papillomavirus>


gtatagaacaggaa tatcaaatat tagtgaagta atgggagaca


cacctgagtg gatacaaaga ettactatta tacaacatgg


aatagatgat agcaattttg atttgtcaga aatggtacaa


tgggcatttg ataatgagct gacagatgaa agcgatatgg


catttgaata tgccttatta gcagacagca acagcaatgc


 


<SEQ352; DNA; Human papillomavirus>


gtatagaacaggaa tatcaaatat tagtgaagta atgggagaca


cacctgagtg gatacaaaga cttactatta tacaacatgg


aatagatgat agcaattttg atttgtcaga aatggtacaa


tgggcatttg ataatgagct gacagatgaa agcgatatgg


catttgaata tgccttatta gcagacagca acagcaatgc agc


 


<SEQ58; DNA; Human papillomavirus>


tgatagcaattttg atttgtcaga aatggtacaa tgggcatttg


ataatgagct gacagatgaa agcgatatgg catttgaata


tgccttatta gcagacagca acagcaatgc


 


<SEQ59; DNA; Human papillomavirus>


tgatagcaattttg atttgtcaga aatggtacaa tgggcatttg


ataatgagct gacagatgaa agcgatatgg catttgaata


tgccttatta gcagacagca acagcaatgc agc


 


<SEQ60; DNA; Human papillomavirus>


gatagcaattttg atttgtcaga aatggtacaa tgggcatttg


ataatgagct gacagatgaa agcgatatgg catttgaata


tgccttatta gcagacagca acagcaatgc


 


<SEQ61; DNA; Human papillomavirus>


gatagcaattttg atttgtcaga aatggtacaa tgggcatttg


ataatgagct gacagatgaa agcgatatgg catttgaata


tgccttatta gcagacagca acagcaatgc agc


 


<SEQ62; DNA; Human papillomavirus>


ggaatagatgat agcaattttg atttgtcaga aatggtacaa


tgggcatttg ataatgagct gacagatgaa agcgatatgg


catttgaata tgccttatta gcagacagca acagcaatgc


 


<SEQ63; DNA; Human papillomavirus>


ggaatagatgat agcaattttg atttgtcaga aatggtacaa


tgggcatttg ataatgagct gacagatgaa agcgatatgg


catttgaata tgccttatta gcagacagca acagcaatgc agc


 


<SEQ353; DNA; Human papillomavirus>


ggaatagatgat agcaattttg atttgtcaga aatggtacaa


tgggcatttg taatgagct gacagatgaa agcgatatgg


catttgaata tgccttatta gcagacagca acagcaatg


 


<SEQ354; DNA; Human papillomavirus>


ggaatagatgat agcaattttg atttgtcaga aatggtacaa


tgggcatttg ataatgagct gacagatgaa agcgatatgg


catttgaata tgccttatta gcagacagca acagcaatgc ag


 


<SEQ355; DNA; Human papillomavirus>


tgatagcaattttg atttgtcaga aatggtacaa tgggcatttg


ataatgagct gacagatgaa agcgatatgg catttgaata


tgccttatta gcagacagca acagcaatg


 


<SEQ356; DNA; Human papillomavirus>


tgatagcaattttg atttgtcaga aatggtacaa tgggcatttg


ataatgagct gacagatgaa agcgatatgg catttgaata


tgccttatta gcagacagca acagcaatgc ag


 


<SEQ59; DNA; Human papillomavirus>


tgatagcaattttg atttgtcaga aatggtacaa tgggcatttg


ataatgagct gacagatgaa agcgatatgg catttgaata


tgccttatta gcagacagca acagcaatgc agc


 


<SEQ357; DNA; Human papillomavirus>


gatagcaattttg atttgtcaga aatggtacaa tgggcatttg


ataatgagct gacagatgaa agcgatatgg catttgaata


tgccttatta gcagacagca acagcaatg


 


<SEQ358; DNA; Human papillomavirus>


gatagcaattttg atttgtcaga aatggtacaa tgggcatttg


ataatgagct gacagatgaa agcgatatgg catttgaata


tgccttatta gcagacagca acagcaatgc ag


 


<SEQ64; DNA; Human papillomavirus>


ggctgatccagaagg tacagacggg gagggcacgg gttgtaacgg


ctggttttat gtacaagcta ttgtagacaa aaaaacagga


gatgtaatat cagatgacga ggacgaaaat gc


 


<SEQ65; DNA; Human papillomavirus>


ggctgatccagaagg tacagacggg gagggcacgg gttgtaacgg


ctggttttat gtacaagcta ttgtagacaa aaaaacagga


gatgtaatat cagatgacga ggacgaaaat gcaacagaca cagg


 


<SEQ66; DNA; Human papillomavirus>


gatccagaagg tacagacggg gagggcacgg gttgtaacgg


ctggttttat gtacaagcta ttgtagacaa aaaaacagga


gatgtaatat cagatgacga ggacgaaaat gc


 


<SEQ67; DNA; Human papillomavirus>


gatccagaagg tacagacggg gagggcacgg gttgtaacgg


ctggttttat gtacaagcta ttgtagacaa aaaaacagga


gatgtaatat cagatgacga ggacgaaaat gcaacagaca cagg

## Claims

1. A process for detecting in a sample at least one HPV, which can be oncogenic for the mucosal epithelia, wherein said detection comprises the determination of whether at least one amplicon has been, or is, produced from said sample, or from nucleic acid material thereof, by amplification by means of amplification primers, whereby the production of at least one amplicon indicates that at least one HPV, which can be oncogenic for the mucosal epithelia, is present in said sample, wherein said amplification primers comprise
at least two primers of 14-30 nucleotides, the sequences of which are suitable for use as primers in the amplification of at least one target template sequence, wherein said at least one target template sequence is at least one of the HPV16 fragments, which comprise the sequence of SEQ ID NO: 122 or the complementary sequence thereof or a fragment of said sequence of SEQ ID NO: 122 or complementary sequence, wherein said HPV16 fragments differ by at most 5 nucleotides in length from said sequence of SEQ ID NO: 122 or complementary sequence,
wherein said at least two primers of 14-30 nucleotides anneal to the 5′ terminal end of said at least one target template sequence and to the 5′ terminal end of the sequence that is complementary to said at least one target template sequence;
and wherein said amplification primers further comprise
at least two primers of 14-30 nucleotides, the sequences of which are suitable for use as primers in the amplification of at least one target template sequence, wherein said at least one target template sequence is at least one of the following HPV18 fragments:
the HPV18 fragments, which comprise the sequence of SEQ ID NO: 64 or the complementary sequence thereof or a fragment of said sequence of SEQ ID NO: 64 or complementary sequence, wherein said HPV18 fragments differ by at most 5 nucleotides in length from said sequence of SEQ ID NO: 64 or complementary sequence,
the HPV18 fragments, which comprise the sequence of SEQ ID NO: 65 or the complementary sequence thereof or a fragment of said sequence of SEQ ID NO: 65 or complementary sequence, wherein said HPV18 fragments differ by at most 5 nucleotides in length from said sequence of SEQ ID NO: 65 or complementary sequence,
the HPV18 fragments, which comprise the sequence of SEQ ID NO: 66 or the complementary sequence thereof or a fragment of said sequence of SEQ ID NO: 66 or complementary sequence, wherein said HPV18 fragments differ by at most 5 nucleotides in length from said sequence of SEQ ID NO: 66 or complementary sequence, and
the HPV18 fragments, which comprise the sequence of SEQ ID NO: 67 or the complementary sequence thereof or a fragment of said sequence of SEQ ID NO: 67 or complementary sequence, wherein said HPV18 fragments differ by at most 5 nucleotides in length from said sequence of SEQ ID NO: 67 or complementary sequence,
wherein said at least two primers of 14-30 nucleotides anneal to the 5′ terminal end of said at least one target template sequence and to the 5′ terminal end of the sequence that is complementary to said at least one target template sequence.

2. The process of claim 1, wherein said amplification primers comprise primers of 14-30 nucleotides, the sequences of which are suitable for use as primers in the amplification of at least two target template sequences, which are HPV18 fragments selected from two different groups among the following four groups i. to iv.:
i. the HPV18 fragments, which comprise the sequence of SEQ ID NO: 64 or the complementary sequence thereof or a fragment of said sequence of SEQ ID NO: 64 or complementary sequence, wherein said HPV18 fragments differ by at most 5 nucleotides in length from said sequence of SEQ ID NO: 64 or complementary sequence,
ii. the HPV18 fragments, which comprise the sequence of SEQ ID NO: 65 or the complementary sequence thereof or a fragment of said sequence of SEQ ID NO: 65 or complementary sequence, wherein said HPV18 fragments differ by at most 5 nucleotides in length from said sequence of SEQ ID NO: 65 or complementary sequence,
iii. the HPV18 fragments, which comprise the sequence of SEQ ID NO: 66 or the complementary sequence thereof or a fragment of said sequence of SEQ ID NO: 66 or complementary sequence, wherein said HPV18 fragments differ by at most 5 nucleotides in length from said sequence of SEQ ID NO: 66 or complementary sequence,
iv. the HPV18 fragments, which comprise the sequence of SEQ ID NO: 67 or the complementary sequence thereof or a fragment of said sequence of SEQ ID NO: 67 or complementary sequence, wherein said HPV18 fragments differ by at most 5 nucleotides in length from said sequence of SEQ ID NO: 67 or complementary sequence,
wherein said primers of 14-30 nucleotides anneal to the 5′ terminal end of at least one of said at least two target template sequences or to the 5′ terminal end of at least one of the sequences that are complementary to said at least two target template sequences.

3. The process of claim 1, wherein said amplification primers comprise more than two primers of 14-30 nucleotides, the sequences of which are suitable for use as primers in the amplification of at least one target template sequence, wherein said at least one target template sequence is at least one of the HPV16 fragments, which comprise the sequence of SEQ ID NO: 122 or the complementary sequence thereof or a fragment of said sequence of SEQ ID NO: 122 or complementary sequence, wherein said HPV16 fragments differ by at most 5 nucleotides in length from said sequence of SEQ ID NO: 122 or complementary sequence, wherein said more than two primers of 14-30 nucleotides anneal to the 5′ terminal end of said at least one target template sequence or to the 5′ terminal end of the sequence that is complementary to said at least one target template sequence.

4. The process of claim 1, wherein said fragment differs by at most 4 nucleotides or at most 3 nucleotides or at most 2 nucleotides or at most 1 nucleotide in length from said SEQ ID or complementary sequence.

5. The HPV detection process of claim 1, wherein said amplification primers comprise at least two primers of 14-30 nucleotides, the sequences of which are suitable for use as primers in the amplification of at least one target template sequence, which is at least one of the sequences of SEQ ID NOs: 64-65 and the sequences complementary to SEQ ID NOs: 64-65, wherein said at least two primers of 14-30 nucleotides anneal to the 5′ terminal end of said at least one target template sequence and to the 5′ terminal end of the sequence that is complementary to said at least one target template sequence.

6. The HPV detection process of claim 1, wherein said at least two primers, the sequences of which are suitable for use as primers in the amplification of at least one target template sequence, which is a fragment of HPV16, are suitable for use as primers in the amplification of at least one nucleic acid of 80-260 nucleotides from the target region consisting of the E1 and E2 genes from each of the following HPV: HPV16, HPV33 and HPV31.

7. The HPV detection process of claim 1, wherein said at least two primers, the sequences of which are suitable for use as primers in the amplification of at least one target template sequence, which is a fragment of HPV16, are suitable for use as primers in the amplification of at least one nucleic acid of 80-260 nucleotides from the target region consisting of the E1 and E2 genes from each of the following HPV: HPV16, HPV58, HPV33, HPV52, HPV35 and HPV31.

8. The HPV detection process of claim 1, wherein said at least two primers, the sequences of which are suitable for use as primers in the amplification of at least one target template sequence, which is a fragment of HPV16, are suitable for use as primers in the amplification of at least one nucleic acid of 80-260 nucleotides from the target region consisting of the E1 and E2 genes of HPV16, HPV58, HPV33, HPV52, HPV35, HPV31 and HPV67.

9. The HPV detection process of claim 1, wherein said at least two primers, the sequences of which are suitable for use as primers in the amplification of at least one target template sequence, which is a fragment of HPV18, are suitable for use as primers in the amplification of at least one nucleic acid of 100-220 nucleotides from the target region consisting of the E1 gene from each of the following HPV: HPV45 and HPV18.

10. The HPV detection process of claim 1, wherein said at least two primers, the sequences of which are suitable for use as primers in the amplification of at least one target template sequence, which is a fragment of HPV18, are suitable for use as primers in the amplification of at least one nucleic acid of 100-220 nucleotides from the target region consisting of the E1 gene from each of the following HPV: HPV45, HPV18, HPV68, HPV39 and HPV59.

11. The HPV detection process of claim 1, wherein said at least two primers, the sequences of which are suitable for use as primers in the amplification of at least one target template sequence, which is a fragment of HPV18, are suitable for use as primers in the amplification of at least one nucleic acid of 100-220 nucleotides from the target region consisting of the E1 gene from each of the following HPV: HPV45, HPV18, HPV68, HPV39, HPV59 and HPV85.

12. The HPV detection of claim 1, wherein said amplification primers comprise:
at least two primers, the sequences of which are suitable for use as primers in the amplification of at least one nucleic acid of 80-260 nucleotides from the target region consisting of the E1 and E2 genes from each of the following HPV: HPV16, HPV33 and HPV31; and
at least two primers, the sequences of which are suitable for use as primers in the amplification of at least one nucleic acid of 100-220 nucleotides from the target region consisting of the E1 gene from each of the following HPV: HPV45 and HPV18.

13. The HPV detection process of claim 1, wherein said amplification primers comprise:
at least two primers, the sequences of which are suitable for use as primers in the amplification of at least one nucleic acid of 80-260 nucleotides from the target region consisting of the E1 and E2 genes from each of the following HPV: HPV16, HPV33 and HPV31; and
at least two primers, the sequences of which are suitable for use as primers in the amplification of at least one nucleic acid of 100-220 nucleotides from the target region consisting of the E1 gene from each of the following HPV: HPV45 and HPV18; and
wherein said amplification primers further comprise:
at least two primers, the sequences of which are suitable for use as primers in the amplification of at least one nucleic acid of 90-390 nucleotides from the target region consisting of the E6 and E7 genes of HPV56.

14. The HPV detection process of claim 1, wherein said amplification primers comprise:
at least two primers, the sequences of which are suitable for use as primers in the amplification of at least one nucleic acid of 80-260 nucleotides from the target region consisting of the E1 and E2 genes from each of the following HPV: HPV16, HPV33, and HPV31; and
wherein said amplification primers further comprise:
at least two primers, the sequences of which are suitable for use as primers in the amplification of at least one nucleic acid of 100-220 nucleotides from the target region consisting of the E1 gene from each of the following HPV: HPV45 and HPV18; and
wherein said amplification primers further comprise:
at least two primers, the sequences of which are suitable for use as primers in the amplification of at least one nucleic acid of 90-240 nucleotides from the target region consisting of the E7 and E1 genes of each of HPV51 and HPV82.

15. The HPV detection process of claim 1, wherein said amplification primers comprise:
at least two primers, the sequences of which are suitable for use as primers in the amplification of at least one nucleic acid of 80-260 nucleotides from the target region consisting of the E1 and E2 genes from each of the following HPV: HPV16, HPV33 and HPV31; and
at least two primers, the sequences of which are suitable for use as primers in the amplification of at least one nucleic acid of 100-220 nucleotides from the target region consisting of the E1 gene from each of the following HPV: HPV45 and HPV18; and
wherein said amplification primers further comprise:
at least two primers, the sequences of which are suitable for use as primers in the amplification of at least one nucleic acid of 90-390 nucleotides from the target region consisting of the E6 and E7 genes of HPV56;
and
at least two primers, the sequences of which are suitable for use as primers in the amplification of at least one nucleic acid of 90-240 nucleotides from the target region consisting of the E7 and E1 genes of HPV51.

16. The HPV detection process of claim 1, wherein:
the oligonucleotide sequence of one of said at least two primers is at least 80% identical to the sequence of the same length that is the 5′ terminal end of said target template sequence, and
the oligonucleotide sequence of the other of said at least two primers is at least 80% identical to the sequence of the same length that is the 5′ terminal end of the sequence that is complementary to said target template sequence.

17. The HPV detection process of claim 1, wherein:
the oligonucleotide sequence of one of said at least two primers is at least 85% identical to the sequence of the same length that is the 5′ terminal end of said target template sequence, and
the oligonucleotide sequence of the other of said at least two primers is at least 85% identical to the sequence of the same length that is the 5′ terminal end of the sequence that is complementary to said target template sequence.

18. The HPV detection process of claim 1, wherein:
the oligonucleotide sequence of one of said at least two primers is 100% identical to the sequence of the same length that is the 5′ terminal end of said target template sequence, and
the oligonucleotide sequence of the other of said at least two primers is 100% identical to the sequence of the same length that is the 5′ terminal end of the sequence that is complementary to said target template sequence.

19. The HPV detection process of claim 1, wherein at least two primers are oligonucleotides of 17-25 nucleotides.

20. The HPV detection process of claim 1, wherein said at least two primers, the sequences of which are suitable for use as primers in the amplification of at least one target template sequence, which is a fragment of HPV16, comprise at least one oligonucleotide of SEQ ID NOs: 211-217 and 240-241.

21. The HPV detection process of claim 1, wherein said at least two primers, the sequences of which are suitable for use as primers in the amplification of at least one target template sequence, which is a fragment of HPV16, comprise at least one oligonucleotide of SEQ ID NOs: 240-241.

22. The HPV detection process of claim 1, wherein said at least two primers, the sequences of which are suitable for use as primers in the amplification of at least one target template sequence, which is a fragment of HPV18, comprise at least one oligonucleotide of SEQ ID NOs: 77, 78, 86 and 87.

23. The HPV detection process of claim 1, wherein said at least two primers, the sequences of which are suitable for use as primers in the amplification of at least one target template sequence, which is a fragment of HPV18, comprise at least one oligonucleotide of SEQ ID NOs: 86-87.

24. The HPV detection process of claim 1, wherein said amplification primers comprise
at least one of SEQ ID NOs: 211-217 and at least one of SEQ ID NOs: 240-241; and
at least one of SEQ ID NOs: 77-78 and at least one of SEQ ID NOs: 86-87.

25. The HPV detection process of claim 1, wherein said amplification primers comprises the primers of SEQ ID NOs: 211-217 and 240-241.

26. The HPV detection process of claim 1, wherein said amplification primers comprises the primers of SEQ ID NOs: 77-78 and 86-87.

27. The HPV detection process of claim 1, wherein said amplification primers comprises the primers of SEQ ID NOs: 211-217 and 240-241, and the primers of SEQ ID NOs: 77-78 and 86-87.

28. The process of claim 1, wherein said detecting comprises contacting a nucleic acid product of said amplification with at least one HPV-specific probe.

29. The HPV detection process of claim 1, wherein said determination of whether at least one amplicon is produced is carried out by using in real-time amplification at least one probe, the oligonucleotide sequence of which is one of SEQ ID NOs: 266-271, or one of the complementary sequences thereof, or a sequence, which differs by at most 5 nucleotides in length from said SEQ ID or complementary sequence and which is at least 90% identical to said SEQ ID or complementary sequence, said probe being optionally linked to at least one detection label and/or to two complementary nucleotide sequences of 3 to 10 nucleotides, one of said two complementary nucleotide sequences of 3 to 10 nucleotides being linked at the 5′ end of said probe, the other of said two complementary nucleotide sequences of 3 to nucleotides being linked at the 3′ end of said probe.

30. The HPV detection process of claim 1, wherein said determination of whether at least one amplicon is produced is carried out by using in real-time amplification at least one probe, the oligonucleotide sequence of which is one of SEQ ID NOs: 266 and 268, or one of the complementary sequences thereof, or a sequence, which differs by at most 5 nucleotides in length from said SEQ ID or complementary sequence and which is at least 90% identical to said SEQ ID or complementary sequence, said probe being optionally linked to at least one detection label and/or to two complementary nucleotide sequences of 3 to 10 nucleotides, one of said two complementary nucleotide sequences of 3 to 10 nucleotides being linked at the 5′ end of said probe, the other of said two complementary nucleotide sequences of 3 to nucleotides being linked at the 3′ end of said probe.

31. The HPV detection process of claim 30, wherein said determination of whether at least one amplicon is produced is carried out by using in real-time amplification at least one probe, the sequence of which is one of SEQ ID NOs: 283, 284, 287, 288 and 289, or one of the complementary sequences thereof.

32. The HPV detection of claim 1, wherein the determination of whether at least one amplicon is produced is carried out by using in real-time amplification at least one probe, which is one of SEQ ID NOs: 97-101 or one of the complementary sequences thereof, or a sequence, which differs by at most 5 nucleotides in length from said SEQ ID or complementary sequence and which is at least 90% identical to said SEQ ID sequence, said probe being optionally linked to at least one detection label and/or to two complementary nucleotide sequences of 3 to 10 nucleotides, one of said two complementary nucleotide sequences of 3 to 10 nucleotides being linked at the 5′ end of said probe, the other of said two complementary nucleotide sequences of 3 to 10 nucleotides being linked at the 3′ end of said probe.

33. The HPV detection of claim 1, wherein the determination of whether at least one amplicon is produced is carried out by using in real-time amplification at least one probe, which is one of SEQ ID NOs: 98, 100 and 101, or one of the complementary sequences thereof, or a sequence, which differs by at most 5 nucleotides in length from said SEQ ID or complementary sequence and which is at least 90% identical to said SEQ ID sequence, said probe being optionally linked to at least one detection label and/or to two complementary nucleotide sequences of 3 to nucleotides, one of said two complementary nucleotide sequences of 3 to 10 nucleotides being linked at the 5′ end of said probe, the other of said two complementary nucleotide sequences of 3 to 10 nucleotides being linked at the 3′ end of said probe.

34. The HPV detection process of claim 33, wherein the determination of whether at least one amplicon is produced is carried out by using in real-time amplification at least one probe, the sequence of which is one of SEQ ID NOs: 116, 118 and 119-121, or one of the complementary sequences thereof.

35. The HPV detection process of claim 1, wherein said amplification primers further comprise:
at least two primers, the sequences of which are suitable for use as primers in the amplification of at least one nucleic acid of 90-390 nucleotides from the target region consisting of the E6 and E7 genes of HPV56; and/or
at least two primers, the sequences of which are suitable for use as primers in the amplification of at least one nucleic acid of 90-240 nucleotides from the target region consisting of the E7 and E1 genes of HPV51.

36. The HPV detection process of claim 1, wherein said amplification primers further comprise:
at least two primers of 14-30 nucleotides, the sequences of which are suitable for use as primers in the amplification of at least one target template sequence, which is a fragment of HPV56, wherein said fragment comprises
one of the sequences of SEQ ID NOs: 25-29 and 334-338, or
the complementary sequence thereof, or
a fragment of said SEQ ID or complementary sequence,
wherein said HPV56 fragment differs by at most 5 nucleotides in length from said SEQ ID or complementary sequence,
wherein the sequences of said at least two primers anneal to the 5′ terminal end of said at least one target template sequence and to the 5′ terminal end of the sequence that is complementary to said at least one target template sequence;
and/or
at least two primers of 14-30 nucleotides, the sequences of which are suitable for use as primers in the amplification of at least one target template sequence, which is a fragment of HPV51, wherein said fragment comprises
one of the sequences of SEQ ID NOs: 1-5 and 320-333, or
the complementary sequence thereof, or
a fragment of said SEQ ID or complementary sequence,
wherein said HPV51 fragment differs by at most 5 nucleotides in length from said SEQ ID or complementary sequence,
wherein the sequences of said at least two primers anneal to the 5′ terminal end of said at least one target template sequence and to the 5′ terminal end of the sequence that is complementary to said at least one target template sequence.

37. The HPV detection process of claim 1, wherein said amplification primers further comprise at least one of SEQ ID NOs: 30-34 and at least one of SEQ ID NOs: 35-37.

38. The HPV detection process of claim 1, wherein said amplification primers further comprise at least one of SEQ ID NOs: 6-10 and at least one of SEQ ID NOs: 11-15.

39. The HPV detection process of claim 35, which further comprises the determination of whether at least one amplicon is produced is carried out by using in real-time amplification at least one probe, which is one of SEQ ID NOs: 38-40, or one of the complementary sequences thereof, or a sequence, which differs by at most 5 nucleotides in length from said SEQ ID or complementary sequence and which is at least 90% identical to said SEQ ID or complementary sequence, said probe being optionally linked to at least one detection label and/or to two complementary nucleotide sequences of 3 to 10 nucleotides, one of said two complementary nucleotide sequences of 3 to 10 nucleotides being linked at the 5′ end of said probe, the other of said two complementary nucleotide sequences of 3 to 10 nucleotides being linked at the 3′ end of said probe.

40. The HPV detection process of claim 35, which further comprises the determination of whether at least one amplicon is produced is carried out by using in real-time amplification at least one probe, the sequence of which is one of SEQ ID NOs: 41-45, or one of the complementary sequences thereof.

41. The HPV detection process of claim 35, which further comprises the determination of whether at least one amplicon is produced is carried out by using in real-time amplification at least one probe, which is one of SEQ ID NOs: 16-19, or one of the complementary sequences thereof, or a sequence, which differs by at most 5 nucleotides in length from said SEQ ID or complementary sequence and which is at least 90% identical to said SEQ ID or complementary sequence, said probe being optionally linked to at least one detection label and/or to two complementary nucleotide sequences of 3 to 10 nucleotides, one of said two complementary nucleotide sequences of 3 to 10 nucleotides being linked at the 5′ end of said probe, the other of said two complementary nucleotide sequences of 3 to 10 nucleotides being linked at the 3′ end of said probe.

42. The HPV detection process of claim 35, which further comprises the determination of whether at least one amplicon is produced is carried out by using in real-time amplification at least one probe, the sequence of which is one of SEQ ID NOs: 20-24, or one of the complementary sequences thereof.

43. The HPV detection process of claim 1, wherein said at least one HPV, which can be oncogenic for the mucosal epithelia is an oncogenic anogenital HPV or an oncogenic cervical HPV.

44. The HPV detection process of claim 1, wherein said at least one HPV, which can be oncogenic for the mucosal epithelia, is at least one of HPV16, HPV58, HPV33, HPV52, HPV35, HPV31 and HPV67 and/or at least one of HPV18, HPV45, HPV59, HPV85, HPV39 and HPV68.

45. The process of claim 1, wherein said at least one HPV, which can be oncogenic for the mucosal epithelia, is one or several of HPV18, HPV45, HPV16, HPV31 and HPV33.

46. The process of claim 1, wherein said at least one HPV, which can be oncogenic for the mucosal epithelia, is one or several of HPV18, HPV45, HPV59, HPV39, HPV68, HPV16, HPV31, HPV33, HPV35, HPV52 and HPV58.

47. The HPV detection process of claim 35, wherein said at least one HPV, which can be oncogenic for the mucosal epithelia, is:
at least one of HPV16, HPV58, HPV33, HPV52, HPV35, HPV31, HPV67, HPV68, HPV39, HPV85, HPV59, HPV45 and HPV18;
and
at least one of HPV56, HPV66, HPV 51.

48. The HPV detection process of claim 35, wherein said at least one HPV, which can be oncogenic for the mucosal epithelia, is:
at least one of HPV16, HPV58, HPV33, HPV52, HPV35, HPV31 and HPV67, and
at least one of HPV 68, HPV39, HPV85, HPV59, HPV45 and HPV18, and
at least one of HPV51 and HPV82;
or
at least one of HPV16, HPV58, HPV33, HPV52, HPV35, HPV31 and HPV67, and
at least one of HPV 68, HPV39, HPV85, HPV59, HPV45 and HPV18, and
at least one of HPV56 and HPV66;
or
at least one of HPV16, HPV58, HPV33, HPV52, HPV35, HPV31 and HPV67, and
at least one of HPV 68, HPV39, HPV85, HPV59, HPV45 and HPV18, and at least one of HPV56 and HPV66, and at least one of HPV51 and HPV82.

49. The HPV detection process of claim 1, wherein said amplification is a real-time amplification.

50. The HPV detection process of claim 1, wherein said amplification is a real-time multiplex amplification.

51. The HPV detection process of claim 1, wherein said amplification is a quantitative real-time multiplex amplification.

52. The HPV detection process of claim 1, wherein said amplification is a multiplex amplification.

53. The HPV detection process of claim 1, wherein said amplification is a PCR.

54. The HPV detection process of claim 1, wherein said primers are in the same amplification tube.

55. A set of oligonucleotides, which comprises
at least one probe, which is one of SEQ ID NOs: 266 and 268 or the complementary sequence thereof, or a sequence, which differs by at most 5 nucleotides in length from said SEQ ID or complementary sequence and which is at least 90% identical to said SEQ ID or complementary sequence, said probe being optionally linked to least one detection label and/or each of the 5′ and 3′ ends of said probe being optionally directly linked to an oligonucleotide of 3-10 nucleotides, said 5′ oligonucleotide and said 3′ end oligonucleotide imparting a hairpin structure to said probe when said probe is unhybridized; and/or
at least one probe, which is one of SEQ ID NOs: 98, 100 and 101 or the complementary sequence thereof, or a sequence, which differs by at most 5 nucleotides in length from said SEQ ID or complementary sequence and which is at least 90% identical to said SEQ ID or complementary sequence, said probe being optionally linked to least one detection label and/or each of the 5′ and 3′ ends of said probe being optionally directly linked to an oligonucleotide of 3-10 nucleotides, said 5′ oligonucleotide and said 3′ end oligonucleotide imparting a hairpin structure to said probe when said probe is unhybridized;
and which further comprises

at least two primers of 14-30 nucleotides, the sequences of which are suitable for annealing to HPV16 at such positions that they target on HPV16 at least one HPV16 fragment, which comprises the sequence of SEQ ID NO: 122 or the complementary sequence thereof or a fragment of said sequence of SEQ ID NO: 122 or complementary sequence, wherein said HPV16 fragment differs by at most 5 nucleotides in length from said sequence of SEQ ID NO: 122 or complementary sequence, wherein said at least two primers of 14-30 nucleotides anneal to the 5′ terminal end of said at least one HPV16 fragment and to the 5′ terminal end of the sequence that is complementary to said at least one HPV16 fragment, and/or
at least two primers of 14-30 nucleotides, the sequences of which are suitable for annealing to HPV18 at such positions that they target on HPV18 at least one HPV18 fragment, which comprises at least one of the sequences of SEQ ID NOs: 64-67 or at least one of the complementary sequences thereof or a fragment of said at least one SEQ ID or complementary sequence, wherein said HPV18 fragment differs by at most 5 nucleotides in length from said at least one SEQ ID or complementary sequence, wherein said at least two primers of 14-30 nucleotides anneal to the 5′ terminal end of said at least one HPV18 fragment and to the 5′ terminal end of the sequence that is complementary to said at least one HPV18 fragment.

56. A set of oligonucleotides, which comprises more than two primers of 14-30 nucleotides, the sequences of which are suitable for annealing to HPV16 at such positions that they target on HPV16 at least one HPV16 fragment, which comprises the sequence of SEQ ID NO: 122 or the complementary sequence thereof or a fragment of said sequence of SEQ ID NO: 122 or complementary sequence, wherein said HPV16 fragment differs by at most 5 nucleotides in length from said sequence of SEQ ID NO: 122 or complementary sequence, wherein said more than two primers of 14-30 nucleotides anneal to the 5′ terminal end of said at least one HPV16 fragment and to the 5′ terminal end of the sequence that is complementary to said at least one HPV16 fragment and wherein said more than two primers are suitable for use as primers in the amplification of at least one nucleic acid of 80-260 nucleotides from the target region consisting of the E1 and E2 genes from each of the following HPV: HPV16, HPV33 and HPV31.

57. The set of claim 56, wherein said more than two primers are suitable for use as primers in the amplification of at least one nucleic acid of 80-260 nucleotides from the target region consisting of the E1 and E2 genes from each of the following HPV: HPV16, HPV58, HPV33, HPV52, HPV35 and HPV31.

58. The set of claim 56, wherein said more than two primers are suitable for use as primers in the amplification of at least one nucleic acid of 80-260 nucleotides from the target region consisting of the E1 and E2 genes of HPV16, HPV58, HPV33, HPV52, HPV35, HPV31 and HPV67.

59. The set of claim 56, wherein said fragment differs by at most 4 nucleotides or at most 3 nucleotides or at most 2 nucleotides or at most 1 nucleotide in length from said SEQ ID or complementary sequence.

60. A set of oligonucleotides, which comprises more than two primers of 14-30 nucleotides, the sequences of which are suitable for annealing to HPV18 at such positions that they target on HPV18 at least one HPV18 fragment, which comprises at least one of the sequences of SEQ ID NOs: 64-67 or at least one of the complementary sequences thereof or at least one fragment of said SEQ ID or complementary sequence, wherein said HPV18 fragment differs by at most 5 nucleotides in length from said at least one SEQ ID or complementary sequence, wherein said more than two primers of 14-30 nucleotides anneal to the 5′ terminal end of said at least one HPV18 fragment and to the 5′ terminal end of the sequence that is complementary to said at least one HPV18 fragment and wherein said more than two primers are suitable for use as primers in the amplification of at least one nucleic acid of 100-220 nucleotides from the target region consisting of the E1 gene from each of the following HPV: HPV45 and HPV18.

61. The set of claim 60, wherein said more than two primers are suitable for use as primers in the amplification of at least one nucleic acid of 100-220 nucleotides from the target region consisting of the E1 gene from each of the following HPV: HPV68, HPV39, HPV59, HPV45 and HPV18.

62. The set of claim 60, wherein said more than two primers are suitable for use as primers in the amplification of at least one nucleic acid of 100-220 nucleotides from the target region consisting of the E1 gene from each of the following HPV: HPV68, HPV39, HPV59, HPV45, HPV18 and HPV85.

63. The set of claim 60, wherein said fragment differs by at most 4 nucleotides or at most 3 nucleotides or at most 2 nucleotides or at most 1 nucleotide in length from said SEQ ID or complementary sequence.

64. A set of oligonucleotides, which comprises primers of 14-30 nucleotides, the sequences of which are suitable for annealing to HPV18 at such positions that they target on HPV18 at least one HPV18 fragment from two different groups among the following four groups i. to iv.:
i. the group of the HPV18 fragments, which comprise the sequence of SEQ ID NO: 64 or the complementary sequence thereof or a fragment of said SEQ ID or complementary sequence, wherein said HPV18 fragments differ by at most 5 nucleotides in length from said SEQ ID or complementary sequence;
ii. the group of the HPV18 fragments, which comprise the sequence of SEQ ID NO: 65 or the complementary sequence thereof or a fragment of said SEQ ID or complementary sequence, wherein said HPV18 fragments differ by at most 5 nucleotides in length from said SEQ ID or complementary sequence;
iii. the group of the HPV18 fragments, which comprise the sequence of SEQ ID NO: 66 or the complementary sequence thereof or a fragment of said SEQ ID or complementary sequence, wherein said HPV18 fragments differ by at most 5 nucleotides in length from said SEQ ID or complementary sequence;
iv. the group of the HPV18 fragments, which comprise the sequence of SEQ ID NO: 67 or the complementary sequence thereof or a fragment of said SEQ ID or complementary sequence, wherein said HPV18 fragments differ by at most 5 nucleotides in length from said SEQ ID or complementary sequence,
wherein said primers of 14-30 nucleotides anneal to the 5′ terminal end of said at least one HPV18 fragment and to the 5′ terminal end of the sequence that is complementary to said at least one HPV18 fragment.

65. The set of claim 64, wherein said fragment differs by at most 4 nucleotides or at most 3 nucleotides or at most 2 nucleotides or at most 1 nucleotide in length from said SEQ ID or complementary sequence.

66. A kit for the diagnosis or prognosis of a cervical neoplasia or cancer, comprising:
at least one oligonucleotide set of claim 55, and/or
at least one oligonucleotide set of claim 56 or 60 or 64,
optionally, instructions for the use thereof and/or nucleotides.

67. A set of polynucleotides, which comprises:
at least one polynucleotide, the sequence of which consists of the sequence of SEQ ID NO: 122 or the complementary sequence thereof, or of a sequence, which differs by at most 5 nucleotides in length from said SEQ ID or complementary sequence and which is at least 80% identical to said SEQ ID or complementary sequence; and/or
at least one polynucleotide, the sequence of which consists of one the sequences of SEQ ID NOs: 64-67 or the complementary sequence thereof, or of a sequence, which differs by at most 5 nucleotides in length from said SEQ ID or complementary sequence and which is at least 80% identical to said SEQ ID or complementary sequence.

68. A set of polynucleotides, which comprises at least two, at least three or at least four polynucleotides, the respective sequences of which consist of one the sequences of SEQ ID NOs: 64-67 or the complementary sequence thereof, or of a sequence, which differs by at most 5 nucleotides in length from said SEQ ID or complementary sequence and which is at least 80% identical to said SEQ ID or complementary sequence.

69. A process of production of HPV primers, which comprises producing at least two oligonucleotides, the respective sequences of which consist of 14-30 nucleotides each and are suitable for use as primers in the amplification of at least one target template sequence,
wherein said at least one reference template sequence is a HPV16 fragment comprising the sequence of SEQ ID NO: 122 or the complementary sequence thereof or a fragment of said sequence of SEQ ID NO: 122 or complementary sequence, wherein said HPV16 fragment differs by at most 5 nucleotides in length from said sequence of SEQ ID NO: 122 or complementary sequence,
wherein said each of said at least two primers anneal to the 5′ terminal end of said at least one target template sequence or to the 5′ terminal end of the sequence that is complementary to said at least one target template sequence,
wherein said at least two primers anneal to at least two HPVs selected from the group consisting of HPV16, HPV31, HPV33, HPV35, HPV52, HPV58 and HPV67.

70. The process of claim 69, wherein said at least two primers anneal to at least HPV16, HPV31 and HPV33.

71. A process of production of HPV primers, which comprises producing at least two oligonucleotides, the respective sequences of which consist of 14-30 nucleotides each and are suitable for use as primers in the amplification of at least one target template sequence,
wherein said at least one reference template sequence is at least one HPV18 fragment comprising one of the sequences of SEQ ID NOs: 64-67 or the complementary sequence thereof or a fragment of said SEQ ID or complementary sequence, wherein said fragment differs by at most 5 nucleotides in length from said SEQ ID or complementary sequence,
wherein said each of said at least two primers anneal to the 5′ terminal end of said at least one target template sequence or to the 5′ terminal end of the sequence that is complementary to said at least one target template sequence,
wherein said at least two primers anneal to at least two HPVs selected from the group consisting of HPV18, HPV45, HPV59, HPV39, HPV68 and HPV85.

72. The process of claim 71, wherein said at least two primers anneal to at least HPV18 and HPV45.

73. The process of claim 1, wherein said amplification primers comprise primers of 14-30 nucleotides, the sequences of which are suitable for use as primers in the amplification of at least four target template sequences, which are HPV18 fragments selected from each one of the following four groups i. to iv.:
i. the HPV18 fragments, which comprise the sequence of SEQ ID NO: 64 or the complementary sequence thereof or a fragment of said sequence of SEQ ID NO: 64 or complementary sequence, wherein said HPV18 fragments differ by at most 5 nucleotides in length from said sequence of SEQ ID NO: 64 or complementary sequence,
ii. the HPV18 fragments, which comprise the sequence of SEQ ID NO: 65 or the complementary sequence thereof or a fragment of said sequence of SEQ ID NO: 65 or complementary sequence, wherein said HPV18 fragments differ by at most 5 nucleotides in length from said sequence of SEQ ID NO: 65 or complementary sequence,
iii. the HPV18 fragments, which comprise the sequence of SEQ ID NO: 66 or the complementary sequence thereof or a fragment of said sequence of SEQ ID NO: 66 or complementary sequence, wherein said HPV18 fragments differ by at most 5 nucleotides in length from said sequence of SEQ ID NO: 66 or complementary sequence,
iv. the HPV18 fragments, which comprise the sequence of SEQ ID NO: 67 or the complementary sequence thereof or a fragment of said sequence of SEQ ID NO: 67 or complementary sequence, wherein said HPV18 fragments differ by at most 5 nucleotides in length from said sequence of SEQ ID NO: 67 or complementary sequence,
wherein each one of said at least four target template sequences and of the sequences that are complementary to said at least four target template sequences is annealed at its 5′ terminal end by the sequence of at least one of said primers of 14-30 nucleotides.

74. The HPV detection process of claim 1, wherein said amplification primers further comprise primers annealing to HPV56 and/or primers annealing to HPV51.

75. The HPV detection process of claim 1, wherein said amplification primers further comprise:
at least two primers of 14-30 nucleotides, the sequences of which are suitable for use as primers in the amplification of at least one target template sequence, which is a fragment of HPV56, wherein said fragment comprises
the sequence of SEQ ID NO: 26, or
the complementary sequence thereof, or
a fragment of said SEQ ID or complementary sequence,
wherein said HPV56 fragment differs by at most 5 nucleotides in length from said SEQ ID or complementary sequence,
wherein the sequences of said at least two primers anneal to the 5′ terminal end of said at least one target template sequence and to the 5′ terminal end of the sequence that is complementary to said at least one target template sequence;
and/or
at least two primers of 14-30 nucleotides, the sequences of which are suitable for use as primers in the amplification of at least one target template sequence, which is a fragment of HPV51, wherein said fragment comprises
the sequence of SEQ ID NO: 5, or
the complementary sequence thereof, or
a fragment of said SEQ ID or complementary sequence,
wherein said HPV51 fragment differs by at most 5 nucleotides in length from said SEQ ID or complementary sequence,
wherein the sequences of said at least two primers anneal to the 5′ terminal end of said at least one target template sequence and to the 5′ terminal end of the sequence that is complementary to said at least one target template sequence.

76. The HPV detection process of claim 1, wherein said amplification primers further comprise at least one of SEQ ID NO: 31 and at least one of SEQ ID NO: 35, and/or further comprise at least one of SEQ ID NO: 10 and at least one of SEQ ID NO: 15.

77. The HPV detection process of claim 1, which further comprises the determination of whether at least one amplicon is produced is carried out by using in real-time amplification at least one probe, which is one of SEQ ID NOs: 19 and 38, or one of the complementary sequences thereof, or a sequence, which differs by at most 5 nucleotides in length from said SEQ ID or complementary sequence and which is at least 90% identical to said SEQ ID or complementary sequence, said probe being optionally linked to at least one detection label and/or to two complementary nucleotide sequences of 3 to 10 nucleotides, one of said two complementary nucleotide sequences of 3 to 10 nucleotides being linked at the 5′ end of said probe, the other of said two complementary nucleotide sequences of 3 to 10 nucleotides being linked at the 3′ end of said probe.

78. The set of claim 55, which comprises at least two primer pairs.

79. The set of claim 55, which comprises at least four primer pairs.

80. The set of claim 55, which comprises at least two probes.

81. The set of claim 55, wherein said HPV16 fragment differs by at most 4, or at most 3, or at most 2 nucleotides in length from said at least one SEQ ID or complementary sequence.

82. The set of claim 55, wherein said HPV18 fragment differs by at most 4, or at most 3, or at most 2 nucleotides in length from said at least one SEQ ID or complementary sequence.

83. The set of claim 55, wherein said HPV16 fragment differs by at most 1 nucleotide in length from said at least one SEQ ID or complementary sequence.

84. The set of claim 55, wherein said HPV18 fragment differs by at most 1 nucleotide in length from said at least one SEQ ID or complementary sequence.

85. The set of claim 55, wherein:
the oligonucleotide sequence of one of said at least two primers is at least 80% identical to the sequence of the same length that is the 5′ terminal end of said at least one HPV16 fragment, and
the oligonucleotide sequence of the other of said at least two primers is at least 80% identical to the sequence of the same length that is the 5′ terminal end of the sequence that is complementary to said at least one HPV16 fragment.

86. The set of claim 55, wherein:
the oligonucleotide sequence of one of said at least two primers is at least 85% identical to the sequence of the same length that is the 5′ terminal end of said at least one HPV16 fragment, and
the oligonucleotide sequence of the other of said at least two primers is at least 85% identical to the sequence of the same length that is the 5′ terminal end of the sequence that is complementary to said at least one HPV16 fragment.

87. The set of claim 55, wherein:
the oligonucleotide sequence of one of said at least two primers is at least 100% identical to the sequence of the same length that is the 5′ terminal end of said at least one HPV16 fragment, and
the oligonucleotide sequence of the other of said at least two primers is at least 100% identical to the sequence of the same length that is the 5′ terminal end of the sequence that is complementary to said at least one HPV16 fragment.

88. The set of claim 55, wherein:
the oligonucleotide sequence of one of said at least two primers is at least 80% identical to the sequence of the same length that is the 5′ terminal end of said at least one HPV18 fragment, and
the oligonucleotide sequence of the other of said at least two primers is at least 80% identical to the sequence of the same length that is the 5′ terminal end of the sequence that is complementary to said at least one HPV18 fragment.

89. The set of claim 55, wherein:
the oligonucleotide sequence of one of said at least two primers is at least 85% identical to the sequence of the same length that is the 5′ terminal end of said at least one HPV18 fragment, and
the oligonucleotide sequence of the other of said at least two primers is at least 85% identical to the sequence of the same length that is the 5′ terminal end of the sequence that is complementary to said at least one HPV18 fragment.

90. The set of claim 55, wherein said at least two primers are oligonucleotides of 17-25 nucleotides.

91. The set of claim 55, wherein said at least two primers comprise at least one of SEQ ID NOs: 211-217 and at least one of SEQ ID NOs: 240-241.

92. The set of claim 55, wherein said at least two primers comprise the primers of SEQ ID NOs: 240 and 241, and at least three primers selected from the primers of SEQ ID NOs: 211-217.

93. The set of claim 55, wherein said at least two primers comprise at least one of SEQ ID NOs: 77 and 78 and at least one of SEQ ID NOs: 86 and 87.

94. The set of claim 55, wherein said at least two primers comprise the four primers of SEQ ID NOs: 77, 78, 86 and 87.

95. The set of claim 55, which comprises primers, the sequences of which are suitable for annealing to HPV18 and HPV45.

96. The set of claim 55, which comprises primers, the sequences of which are suitable for annealing to HPV16, HPV31 and HPV33.

97. The set of claim 55, which further comprises primers, the sequences of which are suitable for annealing to HPV56 and/or primers, the sequences of which are suitable for annealing to HPV51.

98. The set of claim 55, which further comprises:
at least two primers of 14-30 nucleotides, the sequences of which are suitable for use as primers in the amplification of at least one target template sequence, which is a fragment of HPV56, wherein said fragment comprises
the sequence of SEQ ID NO: 26, or
the complementary sequence thereof, or
a fragment of said SEQ ID or complementary sequence,
wherein said HPV56 fragment differs by at most 5 nucleotides in length from said SEQ ID or complementary sequence,
wherein the sequences of said at least two primers anneal to the 5′ terminal end of said at least one target template sequence and to the 5′ terminal end of the sequence that is complementary to said at least one target template sequence;
and/or
at least two primers of 14-30 nucleotides, the sequences of which are suitable for use as primers in the amplification of at least one target template sequence, which is a fragment of HPV51, wherein said fragment comprises
the sequence of SEQ ID NO: 5, or
the complementary sequence thereof, or
a fragment of said SEQ ID or complementary sequence,
wherein said HPV51 fragment differs by at most 5 nucleotides in length from said SEQ ID or complementary sequence,
wherein the sequences of said at least two primers anneal to the 5′ terminal end of said at least one target template sequence and to the 5′ terminal end of the sequence that is complementary to said at least one target template sequence.

99. The set of claim 55, which further comprises primers of SEQ ID NOs: 31 and 35, and/or which further comprises primers of SEQ ID NOs: 10 and 15.

100. The set of claim 55, which further comprises at least one probe, which is one of SEQ ID NOs: 19 and 38, or one of the complementary sequences thereof, or a sequence, which differs by at most 5 nucleotides in length from said SEQ ID or complementary sequence and which is at least 90% identical to said SEQ ID or complementary sequence, said probe being optionally linked to at least one detection label and/or to two complementary nucleotide sequences of 3 to 10 nucleotides, one of said two complementary nucleotide sequences of 3 to 10 nucleotides being linked at the 5′ end of said probe, the other of said two complementary nucleotide sequences of 3 to nucleotides being linked at the 3′ end of said probe.

101. The set of claim 56, which comprises at least two primer pairs.

102. The set of claim 56, which comprises at least four primer pairs.

103. The set of claim 56, wherein said HPV16 fragment differs by at most 1 nucleotide in length from said at least one SEQ ID or complementary sequence.

104. The set of claim 56, wherein:
the oligonucleotide sequence of at least one of said more than two primers is at least 80% identical to the sequence of the same length that is the 5′ terminal end of said at least one HPV16 fragment, and
the oligonucleotide sequence of at least another one of said more than two primers is at least 80% identical to the sequence of the same length that is the 5′ terminal end of the sequence that is complementary to said at least one HPV16 fragment.

105. The set of claim 56, wherein:
the oligonucleotide sequence of at least one of said more than two primers is at least 85% identical to the sequence of the same length that is the 5′ terminal end of said at least one HPV16 fragment, and
the oligonucleotide sequence of at least another one of said more than two primers is at least 85% identical to the sequence of the same length that is the 5′ terminal end of the sequence that is complementary to said at least one HPV16 fragment.

106. The set of claim 56, wherein:
the oligonucleotide sequence of at least one of said more than two primers is at least 100% identical to the sequence of the same length that is the 5′ terminal end of said at least one HPV16 fragment, and
the oligonucleotide sequence of at least another one of said more than two primers is at least 100% identical to the sequence of the same length that is the 5′ terminal end of the sequence that is complementary to said at least one HPV16 fragment.

107. The set of claim 56, wherein the oligonucleotide sequence of said more than two primers is at least 80% identical to the sequence of the same length that is the 5′ terminal end of said at least one HPV16 fragment, or at least 80% identical to the sequence of the same length that is the 5′ terminal end of the sequence that is complementary to said at least one HPV16 fragment.

108. The set of claim 56, wherein the oligonucleotide sequence of said more than two primers is at least 85% identical to the sequence of the same length that is the 5′ terminal end of said at least one HPV16 fragment, or at least 85% identical to the sequence of the same length that is the 5′ terminal end of the sequence that is complementary to said at least one HPV16 fragment.

109. The set of claim 56, wherein said more than two primers are oligonucleotides of 17-25 nucleotides.

110. The set of claim 56, wherein said more than two primers comprise the two primers of SEQ ID NOs: 240 and 241 and at least three primers selected from the primers of SEQ ID NOs: 211-217.

111. The set of claim 56, wherein said more than two primers comprise the primers of SEQ ID NOs: 212, 214, 216, 240 and 241.

112. The set of claim 56, wherein said more than two primers are suitable for annealing to HPV16, HPV31 and HPV33.

113. The set of claim 56, wherein said more than two primers are suitable for annealing to HPV16, HPV31, HPV35, HPV52, HPV33 and HPV58.

114. The set of claim 56, which further comprises primers, the sequences of which are suitable for annealing to HPV18.

115. The set of claim 56, which further comprises primers, the sequences of which are suitable for annealing to HPV18 and HPV45.

116. The set of claim 56, which further comprises at least two primers of 14-30 nucleotides, the sequences of which are suitable for annealing to HPV18 at such positions that they target on HPV18 at least one HPV18 fragment, which comprises at least one of the sequences of SEQ ID NOs: 64-67 or at least one of the complementary sequences thereof or at least one fragment of said SEQ ID or complementary sequence, wherein said HPV18 fragment differs by at most 5 nucleotides in length from said at least one SEQ ID or complementary sequence, wherein said at least two primers of 14-30 nucleotides anneal to the 5′ terminal end of said at least one HPV18 fragment and to the 5′ terminal end of the sequence that is complementary to said at least one HPV18 fragment.

117. The set of claim 56, which further comprises primers, the sequences of which are suitable for annealing to HPV56 and/or primers, the sequences of which are suitable for annealing to HPV51.

118. The set of claim 56, which further comprises:
at least two primers of 14-30 nucleotides, the sequences of which are suitable for use as primers in the amplification of at least one target template sequence, which is a fragment of HPV56, wherein said fragment comprises
the sequence of SEQ ID NO: 26, or
the complementary sequence thereof, or
a fragment of said SEQ ID or complementary sequence,
wherein said HPV56 fragment differs by at most 5 nucleotides in length from said SEQ ID or complementary sequence,
wherein the sequences of said at least two primers anneal to the 5′ terminal end of said at least one target template sequence and to the 5′ terminal end of the sequence that is complementary to said at least one target template sequence;
and/or
at least two primers of 14-30 nucleotides, the sequences of which are suitable for use as primers in the amplification of at least one target template sequence, which is a fragment of HPV51, wherein said fragment comprises
the sequence of SEQ ID NO: 5, or
the complementary sequence thereof, or
a fragment of said SEQ ID or complementary sequence,
wherein said HPV51 fragment differs by at most 5 nucleotides in length from said SEQ ID or complementary sequence,
wherein the sequences of said at least two primers anneal to the 5′ terminal end of said at least one target template sequence and to the 5′ terminal end of the sequence that is complementary to said at least one target template sequence.

119. The set of claim 56, which further comprises primers of SEQ ID NOs: 31 and 35, and/or which further comprises primers of SEQ ID NOs: 10 and 15.

120. The set of claim 56, which further comprises at least one probe, which is one of SEQ ID NOs: 19 and 38, or one of the complementary sequences thereof, or a sequence, which differs by at most 5 nucleotides in length from said SEQ ID or complementary sequence and which is at least 90% identical to said SEQ ID or complementary sequence, said probe being optionally linked to at least one detection label and/or to two complementary nucleotide sequences of 3 to 10 nucleotides, one of said two complementary nucleotide sequences of 3 to 10 nucleotides being linked at the 5′ end of said probe, the other of said two complementary nucleotide sequences of 3 to nucleotides being linked at the 3′ end of said probe.

121. The set of claim 60, which comprises at least two primer pairs.

122. The set of claim 60, which comprises at least four primer pairs.

123. The set of claim 60, wherein said HPV18 fragment differs by at most 1 nucleotide in length from said at least one SEQ ID or complementary sequence.

124. The set of claim 60, wherein:
the oligonucleotide sequence of at least one of said more than two primers is at least 80% identical to the sequence of the same length that is the 5′ terminal end of said at least one HPV18 fragment, and
the oligonucleotide sequence of at least another one of said more than two primers is at least 80% identical to the sequence of the same length that is the 5′ terminal end of the sequence that is complementary to said at least one HPV18 fragment.

125. The set of claim 60, wherein:
the oligonucleotide sequence of at least one of said more than two primers is at least 85% identical to the sequence of the same length that is the 5′ terminal end of said at least one HPV18 fragment, and
the oligonucleotide sequence of at least another one of said more than two primers is at least 85% identical to the sequence of the same length that is the 5′ terminal end of the sequence that is complementary to said at least one HPV18 fragment.

126. The set of claim 60, wherein the oligonucleotide sequence of said more than two primers is at least 80% identical to the sequence of the same length that is the 5′ terminal end of said at least one HPV18 fragment, or at least 80% identical to the sequence of the same length that is the 5′ terminal end of the sequence that is complementary to said at least one HPV18 fragment.

127. The set of claim 60, wherein the oligonucleotide sequence of said more than two primers is at least 85% identical to the sequence of the same length that is the 5′ terminal end of said at least one HPV18 fragment, or at least 85% identical to the sequence of the same length that is the 5′ terminal end of the sequence that is complementary to said at least one HPV18 fragment.

128. The set of claim 60, wherein said more than two primers are oligonucleotides of 17-25 nucleotides.

129. The set of claim 60, wherein said more than two primers comprise the primers of SEQ ID NOs: 77, 78, 86 and 87.

130. The set of claim 60, wherein said more than two primers are suitable for annealing to HPV18 and HPV45.

131. The set of claim 60, wherein said more than two primers are suitable for annealing to HPV18, HPV45, HPV59, HPV39 and HPV68.

132. The set of claim 60, which further comprises primers, the sequences of which are suitable for annealing to HPV16.

133. The set of claim 60, which further comprises primers, the sequences of which are suitable for annealing to HPV16 and HPV31.

134. The set of claim 60, which further comprises primers, the sequences of which are suitable for annealing to HPV16 and HPV33.

135. The set of claim 60, which further comprises primers, the sequences of which are suitable for annealing to HPV16, HPV31 and HPV33.

136. The set of claim 60, which further comprises at least two primers of 14-30 nucleotides, the sequences of which are suitable for annealing to HPV16 at such positions that they target on HPV16 at least one HPV16 fragment, which comprises the sequence of SEQ ID NO: 122 or the complementary sequence thereof or a fragment of said sequence of SEQ ID NO: 122 or complementary sequence, wherein said HPV16 fragment differs by at most 5 nucleotides in length from said sequence of SEQ ID NO: 122 or complementary sequence, wherein said at least two primers of 14-30 nucleotides anneal to the 5′ terminal end of said at least one HPV16 fragment and to the 5′ terminal end of the sequence that is complementary to said at least one HPV16 fragment.

137. The set of claim 60, which further comprises primers, the sequences of which are suitable for annealing to HPV56 and/or primers, the sequences of which are suitable for annealing to HPV51.

138. The set of claim 60, which further comprises:
at least two primers of 14-30 nucleotides, the sequences of which are suitable for use as primers in the amplification of at least one target template sequence, which is a fragment of HPV56, wherein said fragment comprises
the sequence of SEQ ID NO: 26, or
the complementary sequence thereof, or
a fragment of said SEQ ID or complementary sequence,
wherein said HPV56 fragment differs by at most 5 nucleotides in length from said SEQ ID or complementary sequence,
wherein the sequences of said at least two primers anneal to the 5′ terminal end of said at least one target template sequence and to the 5′ terminal end of the sequence that is complementary to said at least one target template sequence;
and/or
at least two primers of 14-30 nucleotides, the sequences of which are suitable for use as primers in the amplification of at least one target template sequence, which is a fragment of HPV51, wherein said fragment comprises
the sequence of SEQ ID NO: 5, or
the complementary sequence thereof, or
a fragment of said SEQ ID or complementary sequence,
wherein said HPV51 fragment differs by at most 5 nucleotides in length from said SEQ ID or complementary sequence,
wherein the sequences of said at least two primers anneal to the 5′ terminal end of said at least one target template sequence and to the 5′ terminal end of the sequence that is complementary to said at least one target template sequence.

139. The set of claim 60, which further comprises primers of SEQ ID NOs: 31 and 35, and/or which further comprises primers of SEQ ID NOs: 10 and 15.

140. The set of claim 60, which further comprises at least one probe, which is one of SEQ ID NOs: 19 and 38, or one of the complementary sequences thereof, or a sequence, which differs by at most 5 nucleotides in length from said SEQ ID or complementary sequence and which is at least 90% identical to said SEQ ID or complementary sequence, said probe being optionally linked to at least one detection label and/or to two complementary nucleotide sequences of 3 to 10 nucleotides, one of said two complementary nucleotide sequences of 3 to 10 nucleotides being linked at the 5′ end of said probe, the other of said two complementary nucleotide sequences of 3 to nucleotides being linked at the 3′ end of said probe.

141. The set of claim 64, which comprises at least two primer pairs.

142. The set of claim 64, which comprises at least four primer pairs.

143. The set of claim 64, wherein said HPV18 fragment differs by at most 1 nucleotide in length from said at least one SEQ ID or complementary sequence.

144. The set of claim 64, wherein:
the oligonucleotide sequence of at least one of said primers is at least 80% identical to the sequence of the same length that is the 5′ terminal end of said at least one HPV18 fragment, and
the oligonucleotide sequence of at least one other of said primers is at least 80% identical to the sequence of the same length that is the 5′ terminal end of the sequence that is complementary to said at least one HPV18 fragment.

145. The set of claim 64, wherein:
the oligonucleotide sequence of at least one of said primers is at least 85% identical to the sequence of the same length that is the 5′ terminal end of said at least one HPV18 fragment, and
the oligonucleotide sequence of at least one other of said primers is at least 85% identical to the sequence of the same length that is the 5′ terminal end of the sequence that is complementary to said at least one HPV18 fragment.

146. The set of claim 64, wherein said primers are oligonucleotides of 17-nucleotides.

147. The set of claim 64, wherein said primers comprise the primers of SEQ ID NOs: 77, 78, 86 and 87.

148. The set of claim 64, wherein said primers are suitable for annealing to HPV18 and HPV45.

149. The set of claim 64, wherein said primers are suitable for annealing to HPV18, HPV45, HPV59, HPV39 and HPV68.

150. The set of claim 64, which further comprises primers, the sequences of which are suitable for annealing to HPV16.

151. The set of claim 64, which further comprises primers, the sequences of which are suitable for annealing to HPV16 and HPV31.

152. The set of claim 64, which further comprises primers, the sequences of which are suitable for annealing to HPV16 and HPV33.

153. The set of claim 64, which further comprises primers, the sequences of which are suitable for annealing to HPV16, HPV31 and HPV33.

154. The set of claim 64, which further comprises at least two primers of 14-30 nucleotides, the sequences of which are suitable for annealing to HPV16 at such positions that they target on HPV16 at least one HPV16 fragment, which comprises the sequence of SEQ ID NO: 122 or the complementary sequence thereof or a fragment of said sequence of SEQ ID NO: 122 or complementary sequence, wherein said HPV16 fragment differs by at most 5 nucleotides in length from said sequence of SEQ ID NO: 122 or complementary sequence, wherein said at least two primers of 14-30 nucleotides anneal to the 5′ terminal end of said at least one HPV16 fragment and to the 5′ terminal end of the sequence that is complementary to said at least one HPV16 fragment.

155. The set of claim 64, which further comprises primers, the sequences of which are suitable for annealing to HPV56 and/or primers, the sequences of which are suitable for annealing to HPV51.

156. The set of claim 64, which further comprises:
at least two primers of 14-30 nucleotides, the sequences of which are suitable for use as primers in the amplification of at least one target template sequence, which is a fragment of HPV56, wherein said fragment comprises
the sequence of SEQ ID NO: 26, or
the complementary sequence thereof, or
a fragment of said SEQ ID or complementary sequence,
wherein said HPV56 fragment differs by at most 5 nucleotides in length from said SEQ ID or complementary sequence,
wherein the sequences of said at least two primers anneal to the 5′ terminal end of said at least one target template sequence and to the 5′ terminal end of the sequence that is complementary to said at least one target template sequence;
and/or
at least two primers of 14-30 nucleotides, the sequences of which are suitable for use as primers in the amplification of at least one target template sequence, which is a fragment of HPV51, wherein said fragment comprises
the sequence of SEQ ID NO: 5, or
the complementary sequence thereof, or
a fragment of said SEQ ID or complementary sequence,
wherein said HPV51 fragment differs by at most 5 nucleotides in length from said SEQ ID or complementary sequence,
wherein the sequences of said at least two primers anneal to the 5′ terminal end of said at least one target template sequence and to the 5′ terminal end of the sequence that is complementary to said at least one target template sequence.

157. The set of claim 64, which further comprises primers of SEQ ID NOs: 31 and 35, and/or which further comprises primers of SEQ ID NOs: 10 and 15.

158. The set of claim 64, which further comprises at least one probe, which is one of SEQ ID NOs: 19 and 38, or one of the complementary sequences thereof, or a sequence, which differs by at most 5 nucleotides in length from said SEQ ID or complementary sequence and which is at least 90% identical to said SEQ ID or complementary sequence, said probe being optionally linked to at least one detection label and/or to two complementary nucleotide sequences of 3 to 10 nucleotides, one of said two complementary nucleotide sequences of 3 to 10 nucleotides being linked at the 5′ end of said probe, the other of said two complementary nucleotide sequences of 3 to nucleotides being linked at the 3′ end of said probe.

159. A kit for the diagnosis or prognosis of cervical neoplasia or cancer, comprising:
at least one oligonucleotide set of claim 103,
optionally, instructions for the use thereof and/or nucleotides.

160. A kit for the diagnosis or prognosis of cervical neoplasia or cancer, comprising:
at least one oligonucleotide set of claim 104,
optionally, instructions for the use thereof and/or nucleotides.

161. A kit for the diagnosis or prognosis of cervical neoplasia or cancer, comprising:
at least one oligonucleotide set of claim 110,
optionally, instructions for the use thereof and/or nucleotides.

162. A kit for the diagnosis or prognosis of cervical neoplasia or cancer, comprising:
at least one oligonucleotide set of claim 111,
optionally, instructions for the use thereof and/or nucleotides.

163. A kit for the diagnosis or prognosis of cervical neoplasia or cancer, comprising:
at least one oligonucleotide set of claim 112,
optionally, instructions for the use thereof and/or nucleotides.

164. A kit for the diagnosis or prognosis of cervical neoplasia or cancer, comprising:
at least one oligonucleotide set of claim 113,
optionally, instructions for the use thereof and/or nucleotides.

165. A kit for the diagnosis or prognosis of cervical neoplasia or cancer, comprising:
at least one oligonucleotide set of claim 114,
optionally, instructions for the use thereof and/or nucleotides.

166. A kit for the diagnosis or prognosis of cervical neoplasia or cancer, comprising:
at least one oligonucleotide set of claim 117,
optionally, instructions for the use thereof and/or nucleotides.

167. A kit for the diagnosis or prognosis of cervical neoplasia or cancer, comprising:
at least one oligonucleotide set of claim 123,
optionally, instructions for the use thereof and/or nucleotides.

168. A kit for the diagnosis or prognosis of cervical neoplasia or cancer, comprising:
at least one oligonucleotide set of claim 124,
optionally, instructions for the use thereof and/or nucleotides.

169. A kit for the diagnosis or prognosis of cervical neoplasia or cancer, comprising:
at least one oligonucleotide set of claim 129,
optionally, instructions for the use thereof and/or nucleotides.

170. A kit for the diagnosis or prognosis of cervical neoplasia or cancer, comprising:
at least one oligonucleotide set of claim 130,
optionally, instructions for the use thereof and/or nucleotides.

171. A kit for the diagnosis or prognosis of cervical neoplasia or cancer, comprising:
at least one oligonucleotide set of claim 131,
optionally, instructions for the use thereof and/or nucleotides.

172. A kit for the diagnosis or prognosis of cervical neoplasia or cancer, comprising:
at least one oligonucleotide set of claim 132,
optionally, instructions for the use thereof and/or nucleotides.

173. A kit for the diagnosis or prognosis of cervical neoplasia or cancer, comprising:
at least one oligonucleotide set of claim 137,
optionally, instructions for the use thereof and/or nucleotides.

174. A kit for the diagnosis or prognosis of cervical neoplasia or cancer, comprising:
at least one oligonucleotide set of claim 143,
optionally, instructions for the use thereof and/or nucleotides.

175. A kit for the diagnosis or prognosis of cervical neoplasia or cancer, comprising:
at least one oligonucleotide set of claim 144,
optionally, instructions for the use thereof and/or nucleotides.

176. A kit for the diagnosis or prognosis of cervical neoplasia or cancer, comprising:
at least one oligonucleotide set of claim 148,
optionally, instructions for the use thereof and/or nucleotides.

177. A kit for the diagnosis or prognosis of cervical neoplasia or cancer, comprising:
at least one oligonucleotide set of claim 149,
optionally, instructions for the use thereof and/or nucleotides.

178. A set of polynucleotides, which comprises:
at least one polynucleotide, the sequence of which consists of the sequence of SEQ ID NO: 122 or the complementary sequence thereof, or of a sequence, which differs by at most 5 nucleotides in length from said SEQ ID or complementary sequence and which is at least 80% identical to said SEQ ID or complementary sequence; and
at least one polynucleotide, the sequence of which consists of the sequence of SEQ ID NO: 64 or the complementary sequence thereof, or of a sequence, which differs by at most 5 nucleotides in length from said SEQ ID or complementary sequence and which is at least 80% identical to said SEQ ID or complementary sequence.

179. A set of polynucleotides, which comprises:
at least one polynucleotide, the sequence of which consists of the sequence of SEQ ID NO: 122 or the complementary sequence thereof, or of a sequence, which differs by at most 5 nucleotides in length from said SEQ ID or complementary sequence and which is at least 80% identical to said SEQ ID or complementary sequence; and
at least one polynucleotide, the sequence of which consists of the sequence of SEQ ID NO: 65 or the complementary sequence thereof, or of a sequence, which differs by at most 5 nucleotides in length from said SEQ ID or complementary sequence and which is at least 80% identical to said SEQ ID or complementary sequence.

180. A set of polynucleotides, which comprises:
at least one polynucleotide, the sequence of which consists of the sequence of SEQ ID NO: 122 or the complementary sequence thereof, or of a sequence, which differs by at most 5 nucleotides in length from said SEQ ID or complementary sequence and which is at least 80% identical to said SEQ ID or complementary sequence; and
at least one polynucleotide, the sequence of which consists of the sequence of SEQ ID NO: 66 or the complementary sequence thereof, or of a sequence, which differs by at most 5 nucleotides in length from said SEQ ID or complementary sequence and which is at least 80% identical to said SEQ ID or complementary sequence.

181. A set of polynucleotides, which comprises:
at least one polynucleotide, the sequence of which consists of the sequence of SEQ ID NO: 122 or the complementary sequence thereof, or of a sequence, which differs by at most 5 nucleotides in length from said SEQ ID or complementary sequence and which is at least 80% identical to said SEQ ID or complementary sequence; and
at least one polynucleotide, the sequence of which consists of the sequence of SEQ ID NO: 67 or the complementary sequence thereof, or of a sequence, which differs by at most 5 nucleotides in length from said SEQ ID or complementary sequence and which is at least 80% identical to said SEQ ID or complementary sequence.

182. The process of claim 69, wherein said at least two primers anneal to HPV16, HPV31, HPV33, HPV35, HPV52 and HPV58.

183. The process of claim 69, wherein said at least two primers anneal to HPV16, HPV31, HPV33, HPV35, HPV52, HPV58 and HPV67.

184. The process of claim 69, which comprises producing at least two primer pairs.

185. The process of claim 69, which comprises producing at least four primer pairs.

186. The process of claim 69, wherein said HPV16 fragment differs by at most 4, or at most 3, or at most 2 nucleotides in length from said at least one SEQ ID or complementary sequence.

187. The process of claim 69, wherein said HPV16 fragment differs by at most 1 nucleotide in length from said at least one SEQ ID or complementary sequence.

188. The process of claim 69, wherein:
the oligonucleotide sequence of one of said at least two primers is at least 80% identical to the sequence of the same length that is the 5′ terminal end of said at least one HPV16 fragment, and
the oligonucleotide sequence of the other of said at least two primers is at least 80% identical to the sequence of the same length that is the 5′ terminal end of the sequence that is complementary to said at least one HPV16 fragment.

189. The process of claim 69, wherein:
the oligonucleotide sequence of one of said at least two primers is at least 85% identical to the sequence of the same length that is the 5′ terminal end of said at least one HPV16 fragment, and
the oligonucleotide sequence of the other of said at least two primers is at least 85% identical to the sequence of the same length that is the 5′ terminal end of the sequence that is complementary to said at least one HPV16 fragment.

190. The process of claim 69, wherein:
the oligonucleotide sequence of one of said at least two primers is at least 100% identical to the sequence of the same length that is the 5′ terminal end of said at least one HPV16 fragment, and
the oligonucleotide sequence of the other of said at least two primers is at least 100% identical to the sequence of the same length that is the 5′ terminal end of the sequence that is complementary to said at least one HPV16 fragment.

191. The process of claim 69, wherein said at least two primers are oligonucleotides of 17-25 nucleotides.

192. The process of claim 71, wherein said at least two primers anneal to HPV18, HPV45, HPV59, HPV39 and HPV68.

193. The process of claim 71, wherein said at least two primers anneal to HPV18, HPV45, HPV59, HPV39, HPV68 and HPV85.

194. The process of claim 71, which comprises producing at least two primer pairs.

195. The process of claim 71, which comprises producing at least four primer pairs.

196. The process of claim 71, wherein said HPV16 fragment differs by at most 4, or at most 3, or at most 2 nucleotides in length from said at least one SEQ ID or complementary sequence.

197. The process of claim 71, wherein said HPV16 fragment differs by at most 1 nucleotide in length from said at least one SEQ ID or complementary sequence.

198. The process of claim 71, wherein:
the oligonucleotide sequence of one of said at least two primers is at least 80% identical to the sequence of the same length that is the 5′ terminal end of said at least one HPV18 fragment, and
the oligonucleotide sequence of the other of said at least two primers is at least 80% identical to the sequence of the same length that is the 5′ terminal end of the sequence that is complementary to said at least one HPV18 fragment.

199. The process of claim 71, wherein:
the oligonucleotide sequence of one of said at least two primers is at least 85% identical to the sequence of the same length that is the 5′ terminal end of said at least one HPV18 fragment, and
the oligonucleotide sequence of the other of said at least two primers is at least 85% identical to the sequence of the same length that is the 5′ terminal end of the sequence that is complementary to said at least one HPV18 fragment.

200. The process of claim 71, wherein said at least two primers are oligonucleotides of 17-25 nucleotides.