A comparison of methylation levels in HPV18, HPV31 and HPV33 genomes reveals similar associations with cervical precancers

BackgroundHigh risk human papillomavirus (HR-HPV) infection is common and only a small minority of infections become persistent and lead to cervical cancers. Women positive for HR-HPV usually require a second test to avoid unnecessary colposcopies and over treatment. Elevated DNA methylation of HR-HPV L1 and L2 genes in high grade disease has emerged as a promising molecular triage tool.ObjectivesOur aim was to accurately measure methylation levels at selected CpG positions in the HPV18, HPV31 and HPV33 genomes. We focused on the L2, L1, URR and E6 regions because these were previously shown to be interesting areas for study.Study designPyrosequencing was used to measure methylation in 208 HPV18, 207 HPV31, and 126 HPV33 positive women selected from a London colposcopy referral population.ResultsAfter adjustment for multiple testing, at FDR 5%, elevated methylation was significantly associated with cervical intraepithelial neoplasia grades 2 or worse (CIN2+) in all investigated CpGs in HPV18 L2 and L1. Two of 6 L2 and 12 of 15 L1 sites in HPV31 and 6 of 8 L2 and 3 of 13 L1 sites in HPV33 showed significantly elevated methylation in CIN2+. Methylation of CpG sites in the URR and E6 region of the HPV types was low and most differences were not significant.ConclusionElevated methylation of CpG sites in the L1 and L2 regions of HPV18, HPV31 and HPV33 is associated with CIN2+ and a panel test may be useful for triage of women with HR-HPV infections.     

The Genomes of Three of Four Novel HPV Types, Defined by Differences of Their L1 Genes, Show High Conservation of the E7 Gene and the URR

The DNA genomes of four new human papillomaviruses, HPV 75, HPV 76, HPV 77, and HPV 80, have been cloned, sequenced, and characterized. HPV 75, HPV 76 (both HPV 49-related), and HPV 77 (HPV 29-related) were isolated from benign cutaneous warts and HPV 80 (HPV 15-related) from histologically normal skin. HPV 77 has also been demonstrated in dysplastic warts and squamous cell carcinomas of the skin. The sequence data presented in this study led to a proposed modification of the definition of a new HPV type. The high degree of DNA sequence similarity between the E7 ORF of HPV 77 and HPV 29 (97.7%), as opposed to the E6 (82.8%) and L1 (85.3%) ORFs, might suggest conservation of a specific function or a possible recombinational event. Only the E6 and L1 ORFs of HPV 75 and HPV 76 have a similarity lower than 90%, whereas the DNA sequences of their upstream regulatory regions (URRs) share a similarity of 93%. The E7, E1, and E4 ORFs, as well as the URR of HPV 15 and HPV 80, share sequence similarities higher than 90%. Such a divergence in the similarity between different segments of the virus genomes of closely related HPV types has not been noted to date. A detailed comparative sequence analysis was performed. HPV 75, HPV 76, and HPV 80 revealed features characteristic of truly cutaneous HPV types, whereas HPV 77 shared several characteristics with the mucosal HPV types, some of which may have functional consequences.     

Trans-regulation and differential cell specificity of human papillomavirus types 16, 18, and 11 cis-acting elements

The noncoding region (ncr) of human papillomavirus (HPV) types 16, 18, and 11 contains promoter and/or enhancer function. We have localized the sequence containing the constitutive enhancers of HPV types 16, 18, and 11 to 315, 230, and 213 bp fragments, respectively, for comparative studies. The region of homology shared between the enhancers of the three viruses is limited to the sequence ATTTTTGGCTT, which is also present in the ncr of HPV 6b and 33. We have also examined the enhancer activity of the HPV ncrs in three human cervical carcinoma cell lines, one noncervical human carcinoma cell line, and one monkey kidney established cell line. We observed cell-specific differences in the constitutive expression of the enhancers in the various cell lines. The conditional enhancer activity of the ncr of the viruses is increased in trans by the E2 gene product of HPV 16. Transactivation by E2 is mediated through the E2 binding motif on HPV enhancer plasmids with a heterologous but not with a homologous promoter. Our preliminary studies also indicate a repressor function for the E7 gene of HPV 16.     

Use of Probemix and OmniProbe biotinylated cDNA probes for detecting HPV infection in biopsy specimens from the genital tract.

AIMS--To compare two commercially available pan probes for the identification of human papillomavirus (HPV) DNA expression in histological sections and to type the HPV positive cases. METHODS--97 formalin fixed, paraffin wax embedded biopsy specimens from the genital tract were tested for HPV positivity with in situ hybridisation using biotinylated cDNA pan probes--Probemix (Enzo) and OmniProbe (Digene). The HPV positive cases were further tested with HPV types 6/11, 16/18, and 31/33/35/51, and the HPV type was related to the histological diagnosis. Formalin fixed, HeLa cells (10-50 HPV 18 copies per cell) and SiHa cells (1-2 HPV 16 copies per cell) were used as reference cell lines. RESULTS--32% of the specimens gave positive nucleic signals with both Probemix and OmniProbe. Of these, 84% could be further characterised with regard to HPV types 6/11, 16/18, and 31/33/35/51; 4% of all cases were positive with either Probemix or OmniProbe. The concordance of these probes was high, 96% altogether. HeLa cells stained positive but SiHa cells did not. CONCLUSION--There is no difference between Probemix and OmniProbe for the general detection of HPV. The mean detection limit of these probes is about 20 copies a cell.     

HIV合并HPV阳性标本中HPV的型别检测

目的探讨深圳地区人类免疫缺陷病毒（HIV）阳性人群中人乳头瘤病毒（HPV）感染分型情况,为HIV阳性人群中HPV感染的防治提供依据。方法运用荧光PCR方法和反向斑点杂交技术对HPV阳性患者进行HPV分型检测。结果在HIV感染者中。利用反向点杂交分型方法对40例HPV阳性标本进行HPV基因分型。其中单型感染有18例（45．0％）,混合感染有19例（47．5％）,共检出16种HPV型别,其中包括11种高危型（16、18、31、33、35、45、52、56、58、68、73型）和5种低危型（6、11、42、44、54型）。在16种型别中,感染率最高的为16型（25．0％）,其次为52型（17．5％）、58型（15．0％）。结论感染HIV人群中生殖器部位HPV的感染率较高,在HIV阳性人群中检出性病相关的高危HPV16／52／58亚型．对HIV阳性人群中HPV感染的防治有重要指导意义。     

HPV prevalence in women attending cervical screening in rural Malawi using the cartridge-based Xpert® HPV assay

Background and objectivesEarly experience with Cepheid Xpert^® HPV assay (Xpert^® HPV) suggests that its quick turnaround time and ease of application might make it a relevant contender for routine use in low and middle income countries (LMICs). In the context of a cervical screening service in rural Malawi, we aimed to assess practicalities of local laboratory testing with Xpert^® HPV and provide preliminary high-risk HPV (HR-HPV) prevalence data.Study designLiquid-based cytology (LBC) specimens were collected from women attending cervical screening clinics in Nkhoma, Malawi. Xpert^® HPV testing was carried out according to manufacturer’s instructions. Partial genotyping results were obtained immediately (HPV 16, 18/45 and HR-HPV ‘other’). Review of individual channel data provided further breakdown of other HR-HPV types into HPV 31 and related; HPV 51/59 and HPV 39 and related.ResultsValid HR-HPV results were obtained from 750/763 samples. Most samples were from previously unscreened women, with 92.3% aged between 20 and 60 years. Overall HR-HPV positivity was 19.9%, with HR-HPV ‘other’ being more than twice as frequent as HPV 16 or HPV 18/45 and HPV 31-related (HPV 31, 33, 35, 52 or 58) most prevalent. Known HIV status was low (7.3%), but HR-HPV positivity in this group was much higher (43.4%).ConclusionsHR-HPV testing using Xpert^® HPV was practical in a small rural laboratory. The rapid turnaround (within 2 h) could facilitate a ‘see and treat’ programme. Partial genotyping allows assessment of risk beyond HPV 16/18. The high prevalence of HPV 31 and related types warrants further investigation.     

HPV genotype distribution according to severity of cervical neoplasia using the digene HPV genotyping LQ test

A new genotyping-based DNA assay (Digene LQ^®) was developed recently. The primary aim was to assess the distribution of HPV types using this new assay in atypical squamous cells of undeterminate significance (ASCUS). The secondary aim was to correlate the HPV types with the severity of the disease. The study population comprised 376 ASCUS women. The women were all Hybrid Capture II (HCII) positive and were admitted in three European referral gynecology clinics between 2007 and 2010. A colposcopy with histological examination was performed in all these patients. HPV 16 was typed in 40 % of patients, HPV 18 in 7 %, and HPV 31 in 17 %, and 18 % of patients had mixed genotypes. Patients aged over 30 more often had the HPV 16 genotype than patients aged under 30 (29 % vs. 11 %, chi-square test p < 0.001). The risk of cervical intra-epithelial neoplasia of grade 2 or more (CIN2 +) when HPV 18 positive is lower than the probability associated with HPV 16 or HPV 31: 28 % vs. 58 % and 52 %, respectively (chi-square test, p = 0.005 and p = 0.05, respectively). The Digene LQ^®, a new sequence-specific hybrid capture sample preparation, is fast and efficient and allows high-throughput genotyping of 18 HR HPV types by PCR compared to traditional non-sequence-specific sample preparation methods.     

不孕患者中宫颈HPV高危型别感染率及病毒载量的调查

目的调查高危型人乳头瘤病毒（HPV）在不孕患者宫颈细胞中的感染情况,探讨HPV病毒型别及其载量（viral load）对不孕发生的影响。方法对临床130份不孕患者的宫颈脱落细胞标本和在门诊体检的150份对照组的宫颈脱落细胞标本采用多通道实时荧光定量PCR仪进行八种高危HPvDNA分型及定量检测,该八种高危HPV型别为主要高危型：HPV16,18,45,31和次要高危型HPv33,52,58,67。结果不孕组阳性率为25．38％（33／130）,对照组的阳性率为11．33％（17／150）,两组间的阳性率差异有统计学意义。不孕组的33份阳性标本中病毒载量≥10^6为24例,病毒载量〈10^6为9例;对照组的17份阳性标本中,病毒载量≥10^6为4份,病毒载量〈10^6为13份,两组间的病毒载量有显著性差异。结论不孕组高危型HPV感染率比正常人群（对照组）高。对不孕组病毒载量的分析表明：不孕组人群中其病毒载量明显高于正常人群。此外,本研究还为分泌物核酸检测的定量设置了内标（β-球蛋白）,提出可供临床使用的分泌物取样的核酸定量检测方法。     

Distribution of 14 high risk HPV types in cervical intraepithelial neoplasia detected by a non-radioactive general primer PCR mediated enzyme immunoassay.

AIM: To evaluate the presence of high risk human papillomaviruses (HPV) in cervical smears showing intraepithelial neoplasia (CIN). METHODS: The presence of 14 high risk HPV was evaluated in 114 cervical smears with CIN of different degrees, by comparing a non-radioactive polymerase chain reaction (PCR) enzyme immunoassay (EIA) with conventional PCR followed by radioactive Southern blot hybridisation. General primer PCR amplicons detecting low risk and high risk HPV were typed for 14 different high risk HPV types (HPV 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, and 68) by a non-radioactive PCR-EIA. Virus load of HPV 16 positive CIN was assessed using the semiquantitative PCR-EIA. RESULTS: Histological evaluation confirmed CIN I in 49 cases (mean age 29.0 years, range 17 to 52), CIN II in 31 cases (mean age 30.8 years, 18 to 54), and CIN III in 34 cases (mean age 31.1 years, 16 to 57). The non-radioactive PCR-EIA showed an overall agreement rate of 90% (kappa value 0.75) when compared with conventional general primer PCR followed by radioactive Southern blot hybridisation. High risk HPVs were detected in 47% of CIN I, 77% of CIN II, and 97% of CIN III (p < or = 0.02). HPV types 39, 51, 56, and 58 were found in CIN I exclusively (between 2% and 8%). HPV 16 and HPV 31 were detected in 12% and 2% of CIN I, 35% and 21% of CIN II, and 74% and 13% of CIN III, respectively (p < or = 0.03 and p < or = 0.04). The virus load estimated by the semiquantitative PCR-EIA of HPV 16 was similar in CIN I, CIN II, and CIN III. CONCLUSIONS: The PCR-EIA has high clinical sensitivity for detecting CIN II/III (90%). There was a significantly higher prevalence rate of HPV 16 and 31 in CIN III than in CIN I and II.     

Prevalence of HPV cervical infection in a family planning clinic determined by polymerase chain reaction and dot blot hybridisation

The overall prevalence of human papillomavirus (HPV) cervical infection in 131 women attending a family planning clinic was 7% (HPV 6/11, 16, 18, 31) by dot blot hybridisation, 53% (HPV 11, 16, 31) by polymerase chain reaction (PCR), and 56% by the two methods combined. HPV 16 and 18 were the commonest types (4% each) by dot blot, HPV 16 (39%) by PCR. Fifteen percent of subjects had mildly abnormal cervical cytology (grades 1A, 2A, or 3). There was no significant correlation between cytological abnormality and HPV positivity, or between cytological or HPV status and other postulated risk factors for cervical neoplasia. It is concluded that PCR is considerably more sensitive than dot blot DNA hybridisation in detecting HPV cervical infection in such a "low risk" setting, where HPV copy number may be low. Firm conclusions cannot be drawn from our results regarding a causal role for HPV or other factors in the development of cervical neoplasia.     

Testing for human papillomavirus and measurement of viral load of HPV 16 and 18 in self‐collected vaginal swabs of women who do not undergo cervical cytological screening in Southern France

Self‐sampling using vaginal swabs could be a valuable alternative to screen for cervical cancer for women who do not attend regular cytological screening. The aim of this study was to determine the prevalence of high and low‐risk HPV types and of HPV type 16 and 18 DNA load in self‐collected vaginal swabs from 35‐ to 69‐year‐old Southern French women of low socioeconomic level or migrant populations who do not attend regular cervical screening. A good concordance (93.1%) was found between cervical brush and vaginal swabs in 29 samples. Self‐collected vaginal swabs were examined from 120 women. HPV infection was found in 28 women (23.3%; median age 48 years), 17 (14.1%) of whom harbored high‐risk HPV types. HPV type 16 was the high risk type found most frequently, followed by types 53, 31, 18, 58, and 66. The low‐risk type detected most frequently was HPV type 6, followed by types 61, 70, and 81. The mean HPV 16 and 18 load was 6.3 log₁₀ copies/10⁶ cells and 2.4 log₁₀ copies/10⁶ cells, respectively. These results suggest that vaginal self‐swabs can be a reliable tool for cervical cancer screening in non‐attending and inadequately screened elderly women. J. Med. Virol. 82:1431–1437, 2010. © 2010 Wiley‐Liss, Inc.     

Multiple HPV genotypes in cervical carcinomas: improved DNA detection and typing in archival tissues.

BACKGROUND: Human papillomaviruses (HPV) have been considered to be the necessary and central agents of cervical carcinoma. OBJECTIVE: The aim of this study was to determine the prevalence and genotypes of HPV in archival cervical carcinomas. STUDY DESIGN: The study included 152 paraffin-embedded, formaldehyde-fixed cervical carcinoma specimens. To improve the detection and typing of HPV in archival tissues, we conducted a comprehensive study in which, polymerase chain reaction (PCR)-based methods using E7 type-specific (TS) and L1 modified general primers (MY11/GP6+ and GP5+/GP6+) were employed. RESULTS: Overall HPV prevalence was 98% in the cervical carcinomas. HPV 16 was detected in 66% of the tumors, HPV 18 in 22%, HPV 31 in 13%, HPV 33 in 9%, and HPV 58 in 9%. Notably, multiple HPV types were present in 44 (28.9%) of the 152 cervical carcinomas. The most common co-infections were HPV types 16/18 (12 cases), followed by HPV types 16/31 (7 cases). Additionally, HPV 18 was more frequent in adenocarcinomas and adenosquamous carcinomas (86%) than in squamous cell carcinomas (15.8%) (P = 0.0002). CONCLUSIONS: The combination of L1 general primers and E7 type-specific primers can be of use in detecting HPV DNA in archival tissues. The present study showed a high frequency of multiple HPV infections in cervical carcinomas. Hence, relevant HPV typing information in cervical carcinoma is very important for further HPV vaccine design and application.     

Detection of HPV 52, 58 and 87 in cervicovaginal intraepithelial lesions of HIV infected women

HIV positive or otherwise immunosuppressed patients are susceptible to cervicovaginal infections with a wide spectrum of HPV types. The aim of our study was to investigate the distribution of HPV in squamous intraepithelial lesions (SIL) with regard to HIV infection. We evaluated the HPV status in 20 HIV positive women with cytologically assessed SIL (11 high grade, 9 low grade) in relation to clinical and histological/cytological findings. Twenty HIV negative patients (15 high grade, 5 low grade SIL) served as a control. HPV typing was performed by polymerase chain reaction followed by PCR-ELISA (HPV 6/11, 16/18, 31/33, 40, 45, 52, 58) or sequence analysis of the amplicon (HPV 73, 87). HPV 52 was the most common type in the HIV positive group (8 HIV positive cases vs. 1 HIV negative case). HPV 16/18 was found in 6 HIV positive and 11 HIV negative patients. Further types detected in HIV positive patients were HPV 40, 58, 73 and 87 (one case each). No correlation was found between the HPV status and the CD4+ count or the grading of SIL. Persisting HPV infection with recurrence of SIL was documented in 5 cases after initial therapy of HPV positive lesions (HPV 87, 73, 58, 31/33, 16/18). HIV infected patients reveal a wider spectrum of HPV types in cervicovaginal SIL than HIV negative women. Especially HPV 87 and its relation with HIV infection and development and persistence of SIL needs further investigation. Our results indicate the inclusion of otherwise rare HPV types in screening programs for HIV positive and immunosuppressed patients.     

An ELISA capture assay for the E7 transforming proteins of HPV16 and HPV18.

ELISA capture assays were established for the E7 transforming proteins of HPV16 and HPV18, based on a range of previously characterised polyclonal and monoclonal antibodies. No cross-reactivity was observed in the ELISAs between HPV18 E7 and HPV16 E7. Immunoreactive E7 protein (iE7) was measured in a series of HPV-transformed cell lines, and ranged from 0.6 to 17.7 ng iE7/mg cell protein. iE7 was labile at 22 degrees C (t1/2 = 37 min) but relatively more stable at 4 degrees C (t1/2 = 210 min). HPV16 E7 protein at concentrations from 0.10 to 0.69 ng iE7/mg cell protein was detected in 5 of 13 smears from women with abnormal cervical cytology. Assay of E7 protein may play a role in the detection of HPV-induced cervical lesions with malignant potential.     

Comparison of real-time multiplex human papillomavirus (HPV) PCR assays with INNO-LiPA HPV genotyping extra assay

Real-time type-specific multiplex human papillomavirus (HPV) PCR assays were developed to detect HPV DNA in samples collected for the efficacy determination of the quadrivalent HPV (type 6, 11, 16, and 18) L1 virus-like particle (VLP) vaccine (Gardasil). Additional multiplex (L1, E6, and E7 open reading frame [ORF]) or duplex (E6 and E7 ORF) HPV PCR assays were developed to detect high-risk HPV types, including HPV type 31 (HPV31), HPV33, HPV35, HPV39, HPV45, HPV51, HPV52, HPV56, HPV58, and HPV59. Here, we evaluated clinical specimen concordance and compared the limits of detection (LODs) between multiplex HPV PCR assays and the INNO-LiPA HPV Genotyping Extra assay, which detects 28 types, for the 14 HPV types common to both of these methods. Overall HPV detection agreement rates were >90% for swabs and >95% for thin sections. Statistically significant differences in detection were observed for HPV6, HPV16, HPV18, HPV35, HPV39, HPV45, HPV56, HPV58, and HPV59 in swabs and for HPV45, HPV58, and HPV59 in thin sections. Where P was <0.05, discordance was due to detection of more HPV-positive samples by the multiplex HPV PCR assays. LODs were similar for eight HPV types, significantly lower in multiplex assays for five HPV types, and lower in INNO-LiPA for HPV6 only. LODs were under 50 copies for all HPV types, with the exception of HPV39, HPV58, and HPV59 in the INNO-LiPA assay. The overall percent agreement for detection of 14 HPV types between the type-specific multiplex HPV PCR and INNO-LiPA genotyping assays was good. The differences in positive sample detection favored multiplex HPV PCR, suggesting increased sensitivity of HPV DNA detection by type-specific multiplex HPV PCR assays.     

High-risk HPV detection and concurrent HPV 16 and 18 typing with Abbott RealTime High Risk HPV test

BackgroundHigh-risk human papillomavirus (HPV) is the causative agent of cervical cancer. Among the high-risk types, infection with HPV 16 and 18 is associated with significantly higher risk of disease progression, and consequently these two types together cause approximately 70% of invasive cervical cancer worldwide. Identification of HPV 16 and HPV 18 can provide valuable information for risk stratification and clinical management of patients infected with these two types in both ASC-US triage and primary screening in women over age 30. It may also be valuable in the assessment of HPV vaccine efficacy. Abbott RealTime High Risk (HR) HPV is a recently developed test for the detection of 14 high-risk HPV types with the ability to concurrently identify HPV 16 and 18.ObjectiveTo evaluate the clinical performance of Abbott RealTime HR HPV test. Study design: Abbott RealTime HR HPV was evaluated with 253 cervical specimens obtained from patients with CIN 3 and 340 specimens from patients with cervical cancer to determine clinical sensitivity of the test and the prevalence of types 16 and 18. Additionally, 757 cervical specimens obtained from women 30 years of age or older with normal cytology in a general screening population were tested to determine high-risk HPV positivity rate.ResultsThe Abbott RealTime HR HPV test detected 97.2% (246/253) of CIN 3 specimens and 98.5% (335/340) of cancer specimens. HPV 16 was the most prevalent type in both CIN 3 (72.8%) and cancer specimens (64.5%). HPV 16 and 18 combined were detected in 78.9% of high-risk HPV positive CIN 3 and 84.8% of high-risk HPV positive cancer specimens. In specimens from women 30 years of age or older with normal cytology in a screening population, the HPV positivity rate was 6.5% (49/757).ConclusionsAbbott RealTime HR HPV is a highly sensitive test for detection of high-grade cervical disease and cancer. The HPV 16 and HPV 18 typing capability of the test offers the advantage of stratifying patients at greater risk of progression and may thus aid in better patient care and management.     

Evolution of in vitro transformation and tumorigenesis of HPV16 and HPV18 immortalized primary cervical epithelial cells.

Cervical carcinoma develops through a progressive spectrum of premalignant intraepithelial lesions (CIN I-III), the majority of which are associated with human papillomavirus (HPV) types 16 and 18. We established HPV16 and HPV18 immortalized human cervical epithelial cell lines and used them as a model to investigate the genesis and progression of cervical malignancy. The cell lines when cultured in vitro in a system mimicking their in vivo environment exhibit cytologic atypia and a variety of defects in morphologic differentiation at early passage compared to their normal counterparts. With increased passage, these alterations progress to more severe grades, histologically similar to CIN III; however only a limited number of the cell lines are tumorigenic, mimicking the epidemiologic evidence on the rate of conversion from premalignant to invasive carcinoma. The observed changes are not associated with alterations of viral DNA integration or expression and may reflect specific cellular events or changes in virus-host interactions associated with malignant progression.     

HPV episomal copy number closely correlates with cell size in keratinocyte monolayer cultures

W12E keratinocytes maintaining episomal copies of HPV DNA were separated according to size by centrifugal elutriation. HPV DNA copy number was greatly increased in the largest, most differentiated cells of the population. The large cells with the highest HPV copy number also showed evidence of endoreduplication of host cell DNA. Other cell lines maintaining episomal copies of HPV18 and HPV31 were also tested with all lines showing similar results. The results demonstrate that increase in HPV DNA copy number correlates well with increased cell size, a fundamental marker of keratinocyte differentiation. The results also indicate that simple monolayer cultures may be useful for studying the relationship between differentiation, HPV DNA replication, and cell-cycle events.