General primer polymerase chain reaction in combination with sequence analysis for identification of potentially novel human papillomavirus genotypes in cervical lesions

Molecular detection of human papillomavirus (HPV) in highly fragmented DNA from cervical cancer biopsies using double-nested PCR

Archived Formalin-Fixed Paraffin-Embedded (FFPE) tissue specimens can be a valuable source of human papillomavirus (HPV) nucleic acids for molecular biological analyses in retrospective studies. Although successful amplification with polymerase chain reaction (PCR) is essential for analysis of HPV DNA extracted from cervical FFPE specimens, extensive DNA damage due to cross-linking and fragmentation results in poor yield. Therefore, techniques to improve the diagnostic rate and sensitivity from FFPE tissues through PCR is highly desired and of wider interest. To overcome this, a highly sensitive double-nested PCR methodology was designed and optimized for limited-resource laboratories coupled with an organic extraction of DNA. This method allows the detection of a broad range of HPV genotypes and also allowing the sequencing of the final amplicon. Validation of the new approach developed was done with an automated DNA extraction coupled with Real Time PCR. Results showed that the proposed method achieves 96.3% of HPV detection as compared to 100% Abbott m2000rt used as 'gold standard'. Moreover, the concordance rate between the two methods was equal for detecting HPV -16 or -18 genotypes. Nevertheless, the newly introduced assay has an advantage of: •Simultaneously identifying broad range of HPV genotypes besides HPV-16 and -18 from clinical samples.•It is an easy and cost-effective method that can be beneficial in resource-limited setting and can be employed for various molecular applications.•The method is indicated for highly degraded FFPE samples.

Disparities in Cervical Cancer Incidence and Mortality: Can Epigenetics Contribute to Eliminating Disparities?

Screening for uterine cervical intraepithelial neoplasia (CIN) followed by aggressive treatment has reduced invasive cervical cancer (ICC) incidence and mortality. However, ICC cases and carcinoma in situ (CIS) continue to be diagnosed annually in the United States, with minorities bearing the brunt of this burden. Because ICC peak incidence and mortality are 10-15 years earlier than other solid cancers, the number of potential years of life lost to this cancer is substantial. Screening for early signs of CIN is still the mainstay of many cervical cancer control programs. However, the accuracy of existing screening tests remains suboptimal. Changes in epigenetic patterns that occur as a result of human papillomavirus infection contribute to CIN progression to cancer, and can be harnessed to improve existing screening tests. However, this requires a concerted effort to identify the epigenomic landscape that is reliably altered by HPV infection specific to ICC, distinct from transient changes.

Intrauterine device use, cervical infection with human papillomavirus, and risk of cervical cancer: a pooled analysis of 26 epidemiological studies

BACKGROUND

Intrauterine device (IUD) use has been shown to reduce the risk of endometrial cancer, but little is known about its association with cervical cancer risk. We assessed whether IUD use affects cervical human papillomavirus (HPV) infection and the risk of developing cervical cancer.

METHODS

We did a pooled analysis of individual data from two large studies by the International Agency for Research on Cancer and Institut Català d'Oncologia research programme on HPV and cervical cancer; one study included data from ten case-control studies of cervical cancer done in eight countries, and the other included data from 16 HPV prevalence surveys of women from the general population in 14 countries. 2205 women with cervical cancer and 2214 matched control women without cervical cancer were included from the case-control studies, and 15,272 healthy women from the HPV surveys. Information on IUD use was obtained by personal interview. HPV DNA was tested by PCR-based assays. Odds ratios and 95% CIs were estimated using multivariate unconditional logistic regression for the associations between IUD use, cervical HPV DNA, and cervical cancer.

FINDINGS

After adjusting for relevant covariates, including cervical HPV DNA and number of previous Papanicolaou smears, a strong inverse association was found between ever use of IUDs and cervical cancer (odds ratio 0·55, 95% CI 0·42-0·70; p<0·0001). A protective association was noted for squamous-cell carcinoma (0·56, 0·43-0·72; p<0·0001), adenocarcinoma and adenosquamous carcinoma (0·46, 0·22-0·97; p=0·035), but not among HPV-positive women (0·68, 0·44-1·06; p=0·11). No association was found between IUD use and detection of cervical HPV DNA among women without cervical cancer.

INTERPRETATION

Our data suggest that IUD use might act as a protective cofactor in cervical carcinogenesis. Cellular immunity triggered by the device might be one of several mechanisms that could explain our findings.

FUNDING

Instituto de Salud Carlos III; Agència de Gestió d'Ajuts Universitaris i Recerca; Marató TV3 Foundation; Bill & Melinda Gates Foundation; International Agency for Research on Cancer; European Community; Fondo de Investigaciones Sanitarias, Spain; Preventiefonds, Netherlands; Programa Interministerial de Investigación y Desarrollo, Spain; Conselho Nacional de Desenvolvimiento Cientifico e Tecnologico, Brazil; and Department of Reproductive Health & Research, WHO.

Inter-laboratory validation of PCR-based HPV detection in pathology specimens

The detection and typing of human papilloma virus (HPV) in pathology specimens is gaining increasingly in importance. In the context of the initiative for quality assurance in pathology (QuIP) of the German Society of Pathology and the Professional Association of German Pathologists, four panel laboratories with experience and expertise in polymerase chain reaction (PCR)-based HPV detection were selected to establish an inter-laboratory trial. In a first step, these laboratories performed an internal testing of their own methodologies, which comprised DNA sequencing, multiplex nested PCR and hybridization techniques. Material from 39 samples including paraffin sections and DNA preparations of tissues and plasmids were evaluated by each panel institute according to their own protocols. Despite the different methodologies, a high degree of inter-laboratory reliability was achieved. In this report, we summarise the results. Pretested specimens are available for the external trail and can be ordered from the steering institute via provitro GmbH Berlin ( http://www.provitro.de ). Supplementary data are online available at http://pathologie-ccm.charite.de (rubric "Forschung"), which includes a web-based photo gallery of HPV-associated lesions and their potential association with specific virus types. The initiative is intended to foster the quality assurance of molecular HPV analysis in pathology and its correlation with morphological changes.

Inactivation of the CDKN2A and the p53 tumour suppressor genes in external genital carcinomas and their precursors

BACKGROUND

p53 has been extensively studied in external genital carcinoma (EGC), and is frequently inactivated, but little is known about the role of the CDKN2A tumour suppressor gene in the oncogenesis of EGC.

OBJECTIVES

To investigate the role of CDKN2A and p53 in the pathogenesis of EGCs and their precursor lesions vulval intraepithelial neoplasia (VIN3), penile intraepithelial neoplasia and lichen sclerosus (LS).

METHODS

By means of CDKN2A and p53 mutation screening (single-strand conformational polymorphism analysis and sequencing), methylation analysis of alternative CDKN2A promoters (methylation-specific polymerase chain reaction) and p53 immununochemistry, we analysed eight invasive EGCs (five from vulva and three from penis) and 25 precancerous lesions (two undifferentiated VIN3 and 23 vulval/penile lesions of LS) from 33 patients.

RESULTS

p53 mutations (mainly transversions) and CDKN2A mutations (including one hot spot) were present in 75% and 50% of invasive tumours, respectively, but were absent in all precancerous lesions. Remarkably, all CDKN2A-mutated tumours also harboured a p53 mutation. CDKN2A or p53 mutations were observed more frequently in LS-derived EGCs than in human papillomavirus-derived EGCs (P = 0.053). A positive anti-p53 staining, but without p53 mutations, was also detected in 30% of LS lesions, suggesting a p53 stabilization in response to inflammation and carcinogenic insult. Methylation of p16(INK4a) and p14(ARF) promoters was not a frequent mechanism of CDKN2A inactivation.

CONCLUSIONS

Our study shows a high prevalence of co-inactivating mutations of p53 and/or CDKN2A genes in EGC, that seem to occur preferentially in LS-derived tumours and late in oncogenesis.

Clinical, histopathological and virological findings in patients with focal epithelial hyperplasia from Colombia

BACKGROUND

Focal epithelial hyperplasia (FEH) is a rare oral HPV-related disease, highly prevalent in certain ethnic communities. A previous study found 7.5% prevalence among school children from the Indian community Embera-Chami in Colombia.

OBJECTIVE

To determine the prevalence and Human Papillomavirus (HPVs)-type in children with FEH.

MATERIALS AND METHODS

One hundred and thirty-eight students were screened. All FEH samples were HPV-tested by two PCR-based systems.

RESULTS

We identified 18 FEH cases. beta-globin amplification was obtained in 15 cases and nine were HPV-55-positive by the HPV-PCR-hybridization method. Nine cases (50%) were HPV-13-positive by the GP5+/GP6+-based method. Twelve cases (80%) were HPV-positive by one or the other method. Forty-four percent and 88% of interviewed parents reported family histories of FEH and toothbrush sharing, respectively.

CONCLUSIONS

Human Papillomavirus-DNA was identified in the majority of FEH cases and HPV-13 was the only genotype involved. Frequent familiar infection suggests interfamiliar transmission, genetic predisposition or infection susceptibility among family members.

Denaturing high-performance liquid chromatography for detecting and typing genital human papillomavirus

Human papillomaviruses (HPVs) are important in the development of human cancers, including cervical and oral tumors. However, most existing methods for HPV typing cannot routinely distinguish among the more than 100 distinct types of HPV or the natural HPV intratypic variants that have also been documented. To address this problem, we developed a novel method, general primer-denaturing high-performance liquid chromatography (GP-dHPLC), for the detection and typing of genital HPV using an automated 96-well plate format. GP-dHPLC uses general primer PCR (GP-PCR) to amplify the viral DNA and then analyzes the GP-PCR products by denaturing high-performance liquid chromatography (dHPLC). A number of different primer pairs with homology to most known genital HPV types were tested, and the L1C1-L1C2M pair specific for the L1 region of the viral genome was chosen. A set of HPV standard control patterns, consisting of those for HPV types 16, 18, 31, 33, 39, 45, 51, 52, 56, 58, 59, 6, and 11, was established for genital HPV typing. One hundred eighty-six frozen and formalin-fixed cervical cancer tissue samples were analyzed for the presence of HPV and the HPV type by this method, and 95.8% of them were found to contain HPV DNA. GP-dHPLC accurately discriminated among HPV variants that differed by as little as one nucleotide. Several new variants of HPV types 16, 18, 39, 45, 52, and 59 were identified. Moreover, multiple HPV infections were detected in 26.6% of the samples. Our results indicate that HPV typing by GP-dHPLC permits discrimination of common genital HPV types, detection of multiple HPV infections, and identification of HPV variants in clinical samples.

Detection and genotyping of human papillomavirus DNA by SPF10 and MY09/11 primers in cervical cells taken from women attending a colposcopy clinic

Human papillomavirus (HPV) is the main etiological agent of cervical cancer. There is a large number of HPV genotypes and therefore a need to distinguish the high risk HPV genotypes associated with invasive cancer from the low risk. Because persistence of high risk HPV infection is necessary for progression of a pre-invasive cervical change one needs to identify the individual genotype to see if it persists. PCR amplification of HPV DNA is described using two consensus primer systems from cervical cells. Amplified HPV DNA was genotyped using a reverse hybridization line probe assay (LiPA). HPV DNA was amplified from 42% of samples by MY09/11 and from 80% by SPF10. In 42 samples HPV DNA was detected by both primer sets and in 38 samples only the SPF10 primers detected HPV DNA. The LiPA detected 21 different HPV genotypes (13 high risk) in this cohort of samples. Forty-three percent contained a single HPV genotype and 24% contained multiple infections (2-5 genotypes). Overall, high risk HPV genotypes were detected in 48% of the cervical samples, the most frequent types were 16, 18, 31, and 51. The proportion of high risk HPV genotypes increased with more severe cytological abnormalities. This study demonstrates that the SPF10 primer set is more sensitive than the MY09/11 primer set and that genotyping by LiPA tells us if the HPV infection is caused by a high risk type and if the infection is mixed. Additionally LiPA provides information about the individual genotype when looking for persistence of infection. HPV DNA detection and genotyping is therefore a useful tool in the colposcopy clinic, used in conjunction with cytology.

Vulvar malignant melanoma associated with human papillomavirus DNA: report of two cases and review of literature

Oncogenic human papillomavirus (HPV) types such as HPV 16 are known to play a crucial role in the development of anogenital carcinomas. The etiology of anogenital malignant melanoma is unknown. We report two case of vulvar malignant melanoma in which multiple HPV types including HPV 16 and putative novel HPV types (alb-1, alb-2, alb-7, and alb-10) were identified by degenerated nested polymerase chain techniques (polymerase chain reaction) in both the malignant melanoma and surrounding skin. One melanoma was associated with lichen sclerosus, and the other, with melanoma in situ and pigmented vulvar squamous papillomatosis. These melanomas harbored HPV types alb-7, and HPV 16 as well as alb-1, respectively. HPV types 16, 20, 21, 36, alb-2, and AJ001060 were detected in vulvar skin affected by lichen sclerosus. Vulvar squamous papillomatosis harbored HPV types 28 and alb-10. HPV 16 was physically integrated into the host genome in lichen sclerosus skin and possibly in the melanoma associated with pigmented vulvar squamous papillomatosis. Twenty-two percent (4 of 18) of normal control specimens from skin tumor excisions were found to harbor HPV DNA (HPV types 3, 54, and alb-7); none of these control samples harbored multiple HPV DNA. These findings of multiple HPV DNA and integrated HPV 16 in skin associated with vulvar malignant melanoma indicate that HPV may play a role in the development of vulvar malignant melanoma. The role of HPV could be either direct through infection of melanocytes or indirect as a cofactor with free radicals in chronic fibroinflammatory vulvar disorders such as lichen sclerosus.

Detection and identification of human papilloma viral DNA, types 16, 18, and 33, by a combination of polymerase chain reaction and a colorimetric solid phase capture hybridisation assay

A colorimetric microplate hybridization assay was developed previously to simplify detection procedures of DNA fragments resulting from polymerase chain reactions (PCR). This format has now been adapted for the simultaneous detection and identification of three human papillomavirus (HPV), types 16, 18 and 33, associated frequently with cervical cancer. This post-PCR detection system uses three type-specific capture oligonucleotides linked covalently to a single microplate well and three type-specific multibiotinylated oligonucleotidic probes for detection. It therefore offers a double specificity; the first is conferred by pairs of primers, specific of each type of virus tested, and the second, by the sets of capture and detection probes which are complementary to internal regions of the amplified DNA fragments. The detection format outperformed agarose gel electrophoresis of amplified DNA products in sensitivity and specificity. The rapidity and simplicity of this hybridisation system would justify its use in routine diagnostic examination of cervical specimens (smears and biopsies).

DNA-EIA to detect high and low risk HPV genotypes in cervical lesions with E6/E7 primer mediated multiplex PCR

BACKGROUND

Oncogenicity of human papillomavirus (HPV) DNA in premalignant and malignant uterine cervical diseases is mainly induced by E6/E7 open reading frame (ORF). The presence of an oncogenic HPV DNA may be a diagnostic marker for the detection of cytologically negative smears.

AIMS

To evaluate an original polymerase chain reaction enzyme immunoassay (PCR-EIA) for the detection and typing of oncogenic and non-oncogenic HPV types.

METHODS

The test was an original multiplex labelled PCR-EIA for the detection and typing of oncogenic and non-oncogenic HPV using three consensus sequence primers within the oncogenic E6/E7 ORF. One primer was dinitrophenyl (DNP) labelled and the DNP labelled amplimers could be further hybridised with specific biotinylated oligoprobes mixed in only two cocktails: oncogenic (16, 18, 31, 33, 35, 52, and 58) and non-oncogenic (6 and 11) HPV types in only two wells; then biotinylated oligoprobes were deposited in streptavidin-coated microplates. The PCR-EIA was validated on HPV plasmids (types 6, 11, 16, 18, 31, 35, 52, and 58) and used to evaluate cervical scrapes from 181 patients (median age 32 years) at high risk for cervical cancer.

RESULTS

HPV were detected in the cervical scrapes of 88 of 181 patients (48.6%); nine with non-oncogenic HPV (5.0%) and 79 with oncogenic HPV (43.6%) including 29 coinfections with oncogenic and non-oncogenic HPV. The number of oncogenic HPV infections increased with the presence of high grade lesions: 95.8% of the cervical scrapes from patients with high grade lesions contained oncogenic HPV compared with 32.1% of the specimens from patients without any lesions detectable by colposcopy and/or by cytological examination of the cervical smears. Moreover, 60% of cervical scrapes exhibiting low grade lesions contained oncogenic HPV.

CONCLUSIONS

This test is simple, specific, sensitive, safe, fast, reproducible, and easy to use in routine practice. Thus, it is possible to detect simultaneously on a simple cervical scrape, two kinds of HPV--oncogenic and non-oncogenic--in just two microplate wells with non-isotopic oligoprobes.

Intratype variation in 12 human papillomavirus types: a worldwide perspective

In this study, we have examined intratype human papillomavirus (HPV) sequence variation in a worldwide collection of cervical specimens. Twelve different HPV types including HPV-18, HPV-33, HPV-35, HPV-39, HPV-45, HPV-51, HPV-52, HPV-58, HPV-59, HPV-68 (ME180), MM9/PAP238A (recently designated HPV-73), and a novel partial genomic HPV sequence designated MM4/Wl3B were analyzed in this study. Cervical specimens were collected as part of epidemiological investigations conducted in New Mexico and an international study of invasive cervical cancer (IBSCC). Specimens from several countries including Argentina, Brazil, Bolivia, Benin, Cuba, Colombia, Chile, Germany, Mali, Panama, Paraguay, Spain, Algeria, Uganda, Guinea, Tanzania, Indonesia, Philippines, Thailand, and the United States were evaluated. Specimen DNAs were subjected to amplification with the MY09/11 L1 consensus PCR system. The PCR products were cloned, and an approximately 410-bp region in the L1 open reading frame was sequenced from 146 specimens (approximately 60,000 bp). Within a single HPV type, nucleotide diversity varied between 0.2 and 2.9% (i.e., between any pair of variants) and the majority of nucleotide changes were synonymous (amino acid conserving). These data provide information pertinent to HPV diagnostic probe development and are potentially relevant to future rational vaccine strategies. Similarly, amino acid diversity varied between 0 and 5.1%. Some of these amino acid changes may represent markers of intertype evolutionary relationships. Presuming that HPVs have evolved under the same constraints as their corresponding hosts, the limited genetic diversity observed for all HPVs studied to date may reflect an evolutionary bottleneck occurring in both virus and host populations.

Two novel genital human papillomavirus (HPV) types, HPV68 and HPV70, related to the potentially oncogenic HPV39

The genomes of two novel human papillomavirus (HPV) types, HPV68 and HPV70, were cloned from a low-grade cervical intraepithelial neoplasia and a vulvar papilloma, respectively, and partially sequenced. Both types are related to HPV39, a potentially oncogenic virus. HPV68 and HPV70 were also detected in genital intraepithelial neoplasia from three patients and one patient, respectively. Comparison with sequence data in the literature indicates that the subgenomic ME180-HPV DNA fragment, cloned from a carcinoma cell line, corresponds to an HPV68 subtype and that several HPV DNA fragments amplified by PCR from genital neoplasia represent worldwide distributed variants of HPV68 and HPV70.

Prevalence of human papillomavirus in cervical scrapes, as analyzed by PCR, in a population-based sample of women with and without cervical dysplasia

HPV is suspected of being a major cause of cancer of the uterine cervix. To understand the risk of disease in the general population of women, it is important to estimate the prevalence of HPV infection in a random population-based sample of women without disease. In this study, a total of 231 randomly selected women without dysplasia (controls) were examined, and compared with 103 women with histologically confirmed CIN II-III (patients). The prevalence of HPV DNA in cervical scrapes was determined by general nested PCR, which was expected to detect any relevant HPV type commonly found in cervical samples. The nested positive samples were typed with type-specific PCR. In the general nested PCR, 15% of the controls were positive, compared to 91% of the patients. In the population-based sample, 2.2% had HPV types 6 and 11 and 10% had types 16, 18, 31, and 33. In both groups, HPV DNA was observed less frequently in women above than below the age of 30. The results are among the few population-based figures on the prevalence of HPV in women, and provide a baseline for understanding the risk of developing cancer of the uterine cervix, and determining the proportion of women to be included in intervention studies.

Genital papillomavirus in Greek women with high-grade cervical intraepithelial neoplasia and cervical carcinoma

Fifty biopsies from high-grade squamous intraepithelial lesions (HG-SIL) and 14 cervical carcinoma biopsies from Greek women were screened for the presence of human papillomavirus (HPV) DNA sequences by Southern blot hybridization and by the polymerase chain reaction (PCR) for the presence of different HPV types. In high-grade SIL, HPV DNA sequences were detected in 44 of 50 biopsies with the following distribution: 36% HPV 16, 12% HPV 18, 6% HPV 31, 6% HPV 33, 4% HPV 51, and 24% unclassified HPV types. In cervical carcinoma biopsies, 13 of 14 specimens were positive for HPV DNA sequences. Six biopsies were positive for HPV 16, three were positive for HPV 18, and four contained unclassified HPV types. Overall, of the total 64 biopsies, 57 (89%) were positive for HPV DNA sequences. Of these, Southern blot hybridization alone detected HPV DNA sequences in 39 cases, whereas by PCR 18 additional specimens were found to be positive for HPV. Among the HPV 16-positive biopsies, two samples produced a Pstl banding pattern very similar but not identical to that of HPV 16 prototype and were referred to as HPV 16 isolates. One HPV 16 isolate appears to carry a mutation within the carboxy-terminal half of the L2 gene that results in the loss of a Pstl site. The other HPV 16 isolate had a similar Pstl banding pattern to that previously reported as HPV 16 "variant" found in Cape Town [Williamson et al., 1989, Journal of Medical Virology 28: 146-149, 1994, Journal of Medical Virology 43: 231-237.] and in Italy [Li Vigni et al., 1994, 2nd International Congress of Papillomavirus in Human Pathology (Abstracts), p 100.].

Detection of genital human papillomavirus by single-tube nested PCR and type-specific oligonucleotide hybridization

Cervical cancer is, on a global scale, the second most common form of cancer in women. Development of cervical carcinoma is strongly associated with infection by certain types of human papillomavirus (HPV). To facilitate the detection and molecular typing of HPV in clinical samples, nested-PCR amplification systems were developed for regions of the E1 and L1 genes. The nested amplifications were performed in a single reaction tube, and shifting between inner and outer primer pairs was achieved by a two-phase amplification with different annealing temperatures. This method eliminates cross-contamination between samples during transfer from the first to the second amplification step. A set of type-specific oligonucleotide probes were designed for the E1 system and used to distinguish 19 genital HPV types. The sensitivities of our amplification systems compare favorably with that for the L1 system on the basis of the MY09-MY11 primer pair (M.M. Manos, Y. Ting, D. K. Wright, A. J. Lewis, T. R. Broker, and S. M. Wolinsky, Cancer Cells 7:209-214, 1989) and our systems can be used on materials such as HPV-infected cell lines, cytobrush samples, cancer biopsies, and recent as well as archival Papanicolaou (Pap) smears. The high sensitivity coupled with the effective elimination of contamination in the transfer between the two amplification steps of the nested PCR makes these systems suitable for research as well as clinical analyses.

HPV prevalence in cytomorphologically normal cervical scrapes of pregnant women as determined by PCR: the age-related pattern

Diverging data exist on human papillomavirus (HPV) prevalence in cytomorphologically normal scrapes during pregnancy. The prevalence of HPV was therefore investigated by polymerase chain reaction method (PCR) in cytomorphologically normal scrapes of 709 pregnant women and 3,948 non-pregnant women visiting the same hospital during the same time period. The prevalence of all types of HPV among pregnant women was 9.6% (68/709) and the high risk HPV types of 16 and 18 were found in 3.1% (22/709). In the non-pregnant women the prevalence of all types of HPV was 10.9% (432/3,948) with 2.9% (116/3,948) HPV types 16 and 18. The highest prevalence of HPV was present in women at younger ages in both groups. With increasing age the prevalence declines from about 19% (15-25 yrs) to 5% (40-49 yrs). The age-adjusted odds ratio of prevalence of all types of HPV in pregnant versus non-pregnant women was 0.73 (95% CI 0.56-0.96, P = 0.025) and statistically significant. When HPV types 16 and 18 were considered, significant differences were not found. HPV of all types and types 16/18 prevalence was higher in the second half of pregnancy than in the first part but did not reach statistical significance. High HPV copy numbers in the scrapes were found during the first half of the pregnancy and not during the second half using a semi-quantitative HPV 16/18 PCR detection method. Since the difference in HPV prevalence between non-pregnant and pregnant women is very small, it is concluded that HPV prevalence in cytomorphologically normal smears is hardly influenced by pregnancy.

A novel human papillomavirus sequence based on L1 general primers

Over 65 human papillomaviruses (HPVs) have been identified. The majority have been isolated on the basis of cloning systems in bacteria. Recently, general consensus or degenerate primers from the L1 region have been used in PCR to identify novel genotypes. In this fashion, we employed general primers in the L1 region followed by DNA sequencing to identify a novel HPV sequence in association with esophageal squamous cell carcinoma.

Group-specific differentiation between high- and low-risk human papillomavirus genotypes by general primer-mediated PCR and two cocktails of oligonucleotide probes

In recent years, general primer-mediated PCR assays have been developed to detect a broad spectrum of human papillomavirus (HPV) genotypes. In this study, a procedure enabling a simple group-specific differentiation of high-risk (HPV-16, -18, -31, -33, -35, -39, -45, -51, -52, -54, -56, and -58) and low risk (HPV-6, -11, -34, -40, -42, -43, and 44) HPVs following an HPV general primer-mediated (GP5+/GP6+) PCR is presented. By computer-assisted sequence analysis, oligonucleotides (30-mers) specific for 19 different HPV genotypes were selected from the internal part of the 150-bp GP5+/GP6(+)-amplified region. These oligo probes were tested for specificity in a Southern blot analysis of PCR products derived from the same panel of HPV types. No cross-hybridizations were found. The sensitivities of the oligo probes varied from the femtogram level for the well-amplified HPV types like HPV-16 and -18 to the picogram level for the less-well amplified HPV types like HPV-39 and -51. These sensitivities were reached when the oligo probes were applied both individually and in a cocktail. On the basis of these results, two cocktail oligo probes that enabled a specific and sensitive differentiation between low- and high-risk HPV types were composed.

Analysis of cytomorphologically abnormal cervical scrapes for the presence of 27 mucosotropic human papillomavirus genotypes, using polymerase chain reaction

The aim of this study was to investigate the distribution of 27 mucosotropic human papillomavirus (HPV) genotypes (HPV 6, 11, 13, 16, 18, 30, 31, 32, 33, 35, 39, 40, 42, 43, 44, 45, 51, 52, 53, 54, 55, 56, 57, 58, 59, 61 and 66) in cytomorphologically abnormal cervical scrapes (Pap IIIa-Pap IV; n = 1,373) using the polymerase chain reaction (PCR) method on crude cell suspensions. The scrapes were analyzed for the presence of HPV DNA by HPV general-primer-mediated PCR (GP-PCR), which allows the detection of a broad spectrum of HPV types at the subpicogram level. Subsequently, 2 HPV typing procedures based on either type-specific PCR (for HPV 6, 11, 16, 18, 31 and 33) or characterization of GP-PCR products by hybridization (for HPV 13, 30, 32, 35, 39, 40, 43, 44, 45, 51, 52, 53, 54, 55, 56, 57, 58, 59, 61 and 66) were applied. Increasing total HPV prevalence was found with increasing severity of dysplasia from 71% in Pap IIIa to 100% in Pap IV scrapes (carcinoma in situ). The scrapes which were positive by type-specific PCR included 47% cases of Pap IIIa, 71% cases of Pap IIIb and 90% cases of Pap IV. Moreover, 12% of Pap IIIa scrapes, 6% of Pap IIIb scrapes and 8% of Pap IV scrapes revealed positivity for one or more of the remaining HPV types, as determined by successive hybridizations of the GP-PCR products. Taking the typing data together, we noted that the level of HPV heterogeneity decreased from 22 different HPV types (HPV 6, 11, 16, 18, 31, 33, 35, 39, 40, 42, 43, 44, 45, 51, 52, 54, 55, 56, 58, 59, 61 and 66) detected in the group of Pap IIIa scrapes to 13 (HPV 6, 11, 16, 18, 31, 33, 35, 45, 51, 52, 58, 59 and 61) and 10 HPV genotypes (HPV 6, 16, 18, 31, 33, 45, 51, 52, 54 and 58) in the Pap IIIb and Pap IV classes, respectively. An increasing prevalence rate from Pap IIIa to Pap IV was found for HPV 16, 18, 31, 33, 45 and 54. The prevalence rate of identified HPV genotypes increased from 59% in Pap IIIa to 98% in Pap IV, indicating that almost all high-risk HPV genotypes related to cervical cancer in The Netherlands have been characterized.

Human papillomavirus testing in the clinical laboratory. Part I: squamous lesions of the cervix

The aim of this study was twofold: (1) to evaluate the contribution of viral (HPV) testing for improving the sensitivity of cervical cytology and (2) to correlate HPV types with the histology of the detected cervical cancer precursors, particularly the low-grade, CIN I variant. We used the dot blot hybridization technique (ViraPap) and polymerase chain reaction (PCR) in 63 women referred to our colposcopy clinic for evaluation of an abnormal Pap test. Histopathologic samples obtained by multiple colposcope-directed punch biopsies were used for a diagnostic gold standard. Among the 53 women with histologically proven CIN, precolposcopy cytology was positive in 38 (72%) compared to 53% and 60% HPV positivity by ViraPap and PCR, respectively (p less than 0.01). When the yields of ViraPap/PCR and cytology were combined, however, the detection rate of CIN was 91%, a significant improvement over cytology alone (p less than 0.02). HPV DNA was found either by ViraPap or PCR in 45 of 63 (71%) biopsy specimens, and 37 of 38 (97%) HPV-positive CIN, including the low-grade CIN I variant, contained oncogenic HPV types. HPV type 16 was present in 22 of 38 (58%) CIN lesions and mixed with HPV 6/11, 18, or the 30s group in 6 of 38 (16%) of the cases. HPV 6/11 alone was found only in 1 case of CIN I (2.7%). HPV testing by molecular technology increases the sensitivity of cytology.(ABSTRACT TRUNCATED AT 250 WORDS)

Human papillomavirus and cutaneous warts in meat handlers

The association of papillomavirus and hand warts in meat handlers was examined. Human papillomavirus (HPV) DNA was found in 23 (88%) of 26 cutaneous warts, with HPV 7 (27%) and a yet unidentified HPV (HPV X) (42%) being the predominant types. HPV 2 was found in two (7.5%) patients, and HPV 4 was found in three (11.5%) patients. No bovine papillomavirus sequences were detected. In most patients, the warts developed in less than 2 years after they started working with meat. A possible HPV transmission route by protection gloves and professional equipment is suggested.

Pathogenesis of genital HPV infection

Clinical, subclinical, and latent human papillomavirus (HPV) infections are distinguished from HPV-associated neoplasia. Besides HPV additional cofactors are necessary to transform HPV infected tissue to intraepithelial or invasive neoplasia. Risk factors for the presence of HPV are high number of sexual partners, early cohabitarche, young age at first delivery, suppression and alteration of immune status, young age and hormonal influences. While the fact of a high number of sexual partners exclusively increases the risk of HPV infection, it is not known whether the other factors lead to either an increased risk for HPV infection and/or to HPV-associated neoplasia. Subclinical and latent genital HPV infections are highly prevalent. The prevalence rate depends on the sensitivity of the HPV detection system used, on age and sexual activity of the population screened, and on the number of subsequent examinations performed for each subject. Sexual transmission is the main pathway for genital HPV's, however, vertical, peripartal, and oral transmission are also possible. Seroreactivity against genital HPV may be due to an active infection or the result of contact with HPV earlier in life. Antibodies against the HPV 16 E7 protein indicate an increased risk for cervical cancer. Compared with humoral response cellular immune response is probably more important for regression of genital HPV infection: impaired cellular response is characterized by depletion of T helper/inducer cells and/or Langerhans cells and impaired function of natural killer cells and/or the infected keratinocyte. In condylomata replication and transcription of viral nucleic acids and antigen production coincide with cellular differentiation. However, the interaction between HPV and the keratinocyte on a molecular level in subclinical and latent disease is not well understood. Regression or persistence of subclinical and latent genital HPV infections as observed in longitudinal investigations show a constant come-and-go of HPV presence. Subclinical or latent cervical infections with high-risk HPV types (such as HPV 16 and 18) have an increased risk for the development of HPV-associated neoplasia.

Prevalence of HPV in cytomorphologically normal cervical smears, as determined by the polymerase chain reaction, is age-dependent

The prevalence of human papillomavirus (HPV) genotypes in relation to age was investigated by the polymerase chain reaction (PCR) method in cytologically normal smears from 4 different groups of women. Group A consisted of young women from a district population, aged 15-34 years, using oral contraceptives and visiting general practitioners for a check-up (n = 156); group B were asymptomatic women, aged 35-55, in a district population participating in a triennial screening program for cervical cancer (n = 1555); group C and D consisted of women, seen at the gynecological outpatient department for a wide spectrum of gynecological complaints or for control of their hormonal contraception, aged 15-34 years (n = 2320), and aged 35-55 years (n = 1826) respectively. An HPV (all types) prevalence of 14.1%, 4.1%, 13.9% and 6.6% and an HPV 16/18 prevalence of 3.8%, 0.9%, 3.3% and 1.5% were found in groups A, B, C and D respectively. Statistically significant differences (p value < 0.001) in HPV prevalence were found between women aged 15-34 years and women aged 35-55 years in the district population and in the hospital population. No statistically significant differences in HPV 16/18 were observed after age-matching between women in corresponding age-classes of both populations. In a 5-year interval analysis a strong age-dependent relationship was demonstrated, with a maximum between 20 and 24 years. After the age of 35 a constant level of 1-2% HPV 16/18 was observed. These results indicate that genital HPV infections are age-dependent and suggest that HPV infections at young age can be transient. The implications of these findings in the context of cervical cancer screening are discussed.