Variants of human papillomaviruses 16 and 18 and their natural history in human immunodeficiency virus-positive women

HPV16 Phylogenetic Variants in Anogenital and Head and Neck Cancers: State of the Art and Perspectives

HPV16 is responsible for approximately 60% and 90% of global HPV-induced cervical and oropharyngeal cancers, respectively. HPV16 intratype variants have been identified by HPV genome sequencing and classified into four phylogenetic lineages (A-D). Our understanding of HPV16 variants mostly derives from epidemiological studies on cervical cancer (CC) in which HPV16 B, C, and D lineages (previously named "non-European" variants) were mainly associated with high-grade cervical lesions and cancer. Although a predominance of HPV16 lineage A (previously named "European variants") has been observed in head and neck squamous cell carcinoma (HNSCC), epidemiological and in vitro biological studies are still limited for this tumor site. Next Generation Sequencing (NGS) of the entire HPV genome has deepened our knowledge of the prevalence and distribution of HPV variants in CC and HNSCC. Research on cervical cancer has shown that certain HPV16 sublineages, such as D2, D3, A3, and A4, are associated with an increased risk of cervical cancer, and sublineages A4, D2, and D3 are linked to a higher risk of developing adenocarcinomas. Additionally, lineage C and sublineages D2 or D3 of HPV16 show an elevated risk of developing premalignant cervical lesions. However, it is still crucial to conduct large-scale studies on HPV16 variants in different HPV-related tumor sites to deeply evaluate their association with disease development and outcomes. This review discusses the current knowledge and updates on HPV16 phylogenetic variants distribution in HPV-driven anogenital and head and neck cancers.

Fifteen new nucleotide substitutions in variants of human papillomavirus 18 in Korea : Korean HPV18 variants and clinical manifestation

High-risk human papillomavirus (HPV) infection is an essential factor for the development of cervical cancer. HPV18 is the second most common carcinogenic HPV type following HPV16, but the lineages of HPV18 have been less well studied than those of HPV 16. The purpose of this study was to analyze the nucleotide variants in the E6, E7, and L1 genes of HPV18, to assess the prevalence of HPV18 variants in Korea and to explore the relationship between HPV18 genetic variants and the risk for cervical cancer.

A total of 170 DNA samples from HPV18-positive cervical specimens were collected from women admitted to a secondary referral hospital located in Seoul. Among them, the lineages of the 97 samples could be successfully determined by historical nomenclature.

All the studied HPV 18 variants were lineage A. Sublineages A1 and A4 comprised 91.7% (89/97) and 1.0% (1/97), respectively. Sublineages other than A1 or A4 comprised 7.2% (7/97). We identified 15 new nucleotide substitutions among 44 nucleotide substitutions: C158T, T317G, T443G, A560G, A5467G, A5560C, A5678C, A6155G, G6462A, T6650G, G6701A, T6809C, A6823G, T6941C and T6953C. Among them, 6 substitutions at positions 317, 443, 5467, 5560, 6462, and 6823 resulted in amino acid changes (E6: F71L and N113K; L1: H13R, H44P, A345T, and N465S, respectively). The pathologic results were classified as normal in 25.8% (25/97) of the women, atypical squamous cells of undermined significance (ASCUS) in 7.2% (7/97), cervical intraepithelial neoplasia (CIN) 1 in 36.1% (35/97), CIN2/3 in 19.6% (18/97), and carcinoma in 12.4% (12/97). There was no significant association between the HPV18 sublineages and the severity of pathologic lesion or the disease progression.

This study is the first to analyze the distribution of HPV18 variants in Korean and to associate the results with pathologic findings. Although the HPV18 variants had no significant effect on the degree and progression of the disease, the newly discovered nonsynonymous mutation in L1 might serve as a database to determine vaccine efficacy in Korean women.

High prevalence of human papillomavirus and European variants of HPV 16 infecting concomitantly to cervix and oral cavity in HIV positive women

OBJECTIVE

Identify the prevalence of HPV infections in the uterine cervix and oral cavity and HPV16 variants in HIV+ women.

METHODS

A total of 174 HIV+ women attended an HIV+ specialized clinic in Mexico City. Cells were obtained from the oral cavity and cervix to extract DNA. Polymerase chain reaction (PCR) was used to amplify the HPV sequence with generic primers. We detected specific HPV types using the INNO-LiPA HPV Genotyping Extra II Kit (INNOGENETICS). The identification of variants was studied by sequencing the E6 gene with a Big Dye Terminator Kit and an Applied Biosystems 3500/3500xL genetic analyzer.

RESULTS

HPV infection was very high in the uterine cervix (168/174, 96.6%) and oral cavity (161/174, 92.5%). The prevalence of HPV concurrent infections in the cervix and oral cavity was 155/174 (89.1%). We found hrHPVs to be more prevalent than low-risk HPVs (lrHPVs) in the oral cavity (90.2% versus 45.4%) and that infections simultaneously affected the cervix (94.3% versus 36.2%) and oral cavity (85.1% versus 20.1%). Surprisingly, only European variants of HPV type 16 were found in the uterine cervix of women and the oral cavity of all tested samples (52 oral cavity samples and 52 uterine cervix samples).

CONCLUSIONS

The high prevalence of HPV, multiple infections and presence of the EP350G intravariant in both anatomical regions are strongly related to the persistence of the virus, which is fundamental for the development of cancer. Therefore, it is very important to control and monitor this high-risk population as well as implement programs for the early detection of HPV and vaccination.

Molecular characterisation of genital human papillomavirus among women in Southwestern, Nigeria

Background

Persistent infections with high-risk genital Human papillomavirus (HPV) especially types 16 and 18, are associated with cervical cancer. However, distribution of HPV types varies greatly across geographical regions and the available vaccines target only few types. This study was designed to determine the HPV types circulating in Southwestern Nigeria, thereby providing necessary information for effective control of the virus.

Methods

Endocervical swab samples were collected from a total of 295 consenting women attending routine cervical cancer screening, STI clinics and community-based outreach programme. Viral DNA was extracted from the samples and the consensus region of the HPV DNA was amplified by PCR using GP-E6/E7 primers. Type-specific nested multiplex PCR and Sanger sequencing were used to genotype the HPV isolates.

Results

In this study, 51 (17.3%) individuals were positive for HPV DNA using consensus primers that target the E6/E7 genes but only 48 (16.3%) were genotyped. A total of 15 HPV types (HPV-6, 16, 18, 31, 33, 35, 42, 43, 44, 52, 58, 66, 74, 81, 86) were detected, with HPV-31 being the most predominant (32.8%), followed by HPV-35 (17.2%) and HPV-16 (15.5%). Two rare HPV types; 74 and 86 were also detected. The HPV-74 isolate had three nucleotide (CCT) insertions at E7 gene that translated into amino acid proline. Highest nucleotide substitutions (n = 32) were found in HPV-44 genotype. Among positive individuals, 20.8% had dual infections and 86.2% had High-risk HPV types.

Conclusions

Multiple Human papillomavirus types co-circulated in the study. Most of the circulating Human papillomavirus are high-risk type with type 31 being the most predominant. Although the implication of HPV-74 with proline insertion detected for the first time is unknown, it may have effect on the transformation potential of the virus. Polyvalent HPV vaccine will be more effective for the infection control in Nigeria.

Pre-vaccination prevalence of anogenital and oral human papillomavirus in young HIV-infected men who have sex with men

The aims of this study were to: 1) determine prevalence of anogenital and oral HPV, 2) determine concordance between HPV at anal, perianal, scrotal/penile, and oral sites; and 3) describe factors associated with anogenital HPV types targeted by the 9-valent vaccine. Data were collected from 2012 to 2015 among men who have sex with men 18-26 years of age enrolled in a vaccine trial (N = 145). Penile/scrotal, perianal, anal, and oral samples were tested for 61 HPV types. Logistic regression was used to identify factors associated with types in the 9-valent vaccine. Participants' mean age was 23.0 years, 55.2% were African-American, and 26.2% were Hispanic; 93% had anal, 40% penile, and 6% oral HPV. Among those with anogenital infection, 18% had HPV16. Concordance was low between anogenital and oral sites. Factors independently associated with a 9-valent vaccine-type HPV were: race (African-American vs. White, OR=2.67, 95% CI=1.11-6.42), current smoking (yes vs. no, OR=2.37, 95% CI=1.03-5.48), and number of recent receptive anal sex partners (2+ vs. 0, OR=3.47, 95% CI=1.16-10.4). Most MSM were not infected with HPV16 or HPV18, suggesting that they may still benefit from HPV vaccination, but anogenital HPV was very common, highlighting the importance of vaccinating men before sexual initiation. CLINICAL TRIAL NUMBER: NCT01209325.

Human papillomavirus (HPV) 18 genetic variants and cervical cancer risk in Taizhou area, China

Human papillomavirus (HPV) type 18 is predominantly associated with the development of cervical adenocarcinomas, whereas data on HPV18 genetic variability in China are limited. HPV18 genetic variants were formed phylogenetic tree, including lineages A, B, and C. We aimed to evaluate the diversity of HPV18 genetic variants by sequencing the entire E6, E7 and L1 genes. Between 2012 and 2015, a total of 138 (0.8%, 138/17669) women with single HPV18 infection were selected in this study. Finally, we observed 122 HPV18 isolates of the complete E6-E7-L1 sequences, and obtained 36 distinct variation patterns which the accession GenBank numbers as KY457805-KY457840. Except KY457805, KY457813, KY457819, KY457827, KY457829, the rest of HPV18 isolates (81.1%, 31/36) are novel variants. All of HPV18 variants belong to lineage A, while no lineage B, and C was found in our population of Taizhou region, Southeast China. Sublineage A1 was the most common variants (85.2%, 104/122), followed by sublineage A4, A3 and A5, while no sublineage A2 was obtained. Based on the tree topologies, there were three newly identified candidates' sublineages A6-A8. Out of 122 women, 67 (54.9%) had diagnosed by biopsy, including 49 women who diagnosed with cervicitis, 12 with cervical intraepithelial neoplasia (CIN)1, 4 with CIN2/3, and 2 with adenocarcinomas, respectively. Nevertheless, there was no association between HPV18 (sub) lineages and CIN1 or worse (CIN1+) lesions comparing with normal biopsies (P = .469). In conclusion, knowledge of the distribution of geographic/ethnical HPV18 genetic diversity provides critical information for developing diagnostic probes, epidemiologic correlate of cervical cancer risk and design of HPV vaccines for targeted populations.

Prevalence of Human Papilloma Virus Infection in Young Primiparous Women During Postpartum Period: Study from a Tertiary Care Center in Northern India

INTRODUCTION

Assessment of high-risk Human Papilloma Virus (HPV) prevalence is important for monitoring long-term decrease in cervical cancer after implementation of the prophylactic HPV vaccination.

AIM

To determine the prevalence of high-risk HPV infection and cytological abnormalities in young primiparous women in the age group of 16-26years.

MATERIALS AND METHODS

In this cross-sectional study, 214 primiparous women aged 16-26years were recruited from a public tertiary health care center postpartum clinic between June 2013 and May 2014. Cytological analysis was performed by Pap smear test and patients underwent sampling with cervical brushes for HPV-DNA detection and typing by a PCR-based assay for HPV types 16, 18, 33 and 45.

RESULTS

High-risk HPV was detected in 41 (19.2%) women. HPV 16 was found to be most prevalent with 17 (7.9%) samples testing positive, followed by HPV 18 in nine (4.2%), HPV 45 in six (2.8%) and HPV 31 in four (1.8%) women. Five women tested positive for more than one HPV types. There were no cases of intraepithelial lesions or cervical cancer. One patient who had Atypical Cells of Undetermined Significance (ASCUS) on cytology tested negative for all four HPV genotypes.

CONCLUSION

This study provides a geographic baseline data of high-risk HPV prevalence in young Indian women before implementation of a vaccination program. The results are important for comparison with other global regions and monitoring the effect of HPV vaccination.

Prevalence of human papillomavirus, Epstein-Barr virus, and cytomegalovirus in fine needle aspirates from lung carcinoma: A case-control study with review of literature

BACKGROUND

Oncogenic viruses have recently been allied with lung carcinoma, however, the causal association has not been established till date. The study was conducted to determine the prevalence of high-risk Human papillomavirus (HPV; subtypes 16, 18, 31, 33 and 45), Epstein-Barr virus (EBV) and cytomegalovirus (CMV) in lung carcinoma using polymerase chain reaction (PCR) on fine needle aspirates.

METHODS

Fine needle aspirates of patients with lung carcinoma were included as cases. The control samples included normal lung tissue, collected at the time of medico legal autopsies. DNA was extracted from samples of both cases and controls and analysed by PCR for the presence of HPV, EBV and CMV.

RESULTS

A total of 5/73 (6.8%) cases demonstrated the presence of HPV. Of these, 3 were positive for HPV-16 and one each for HPV-18 and HPV-45. A significant association of HPV with squamous cell carcinoma (SCC) (P = 0.01) was observed. Two cases were positive for EBV; however, the difference was not statistically significant for EBV (P = 0.5) as well as CMV. None of the controls were positive for HPV, EBV or CMV.

CONCLUSION

We conclude that fine needle aspirates can serve as reliable sample for PCR based detection of viruses. A significantly higher prevalence of HPV in lung cancer and a significant association with SCC was observed, thereby, indicating a positive link between HPV and etiopathogenesis of lung carcinoma. Diagn. Cytopathol. 2016;44:987-993. © 2016 Wiley Periodicals, Inc.

Characterization of Intra-Type Variants of Oncogenic Human Papillomaviruses by Next-Generation Deep Sequencing of the E6/E7 Region

Different human papillomavirus (HPV) types are characterized by differences in tissue tropism and ability to promote cell proliferation and transformation. In addition, clinical and experimental studies have shown that some genetic variants/lineages of high-risk HPV (HR-HPV) types are characterized by increased oncogenic activity and probability to induce cancer. In this study, we designed and validated a new method based on multiplex PCR-deep sequencing of the E6/E7 region of HR-HPV types to characterize HPV intra-type variants in clinical specimens. Validation experiments demonstrated that this method allowed reliable identification of the different lineages of oncogenic HPV types. Advantages of this method over other published methods were represented by its ability to detect variants of all HR-HPV types in a single reaction, to detect variants of HR-HPV types in clinical specimens with multiple infections, and, being based on sequencing of the full E6/E7 region, to detect amino acid changes in these oncogenes potentially associated with increased transforming activity.

Human Papillomavirus 18 Genetic Variation and Cervical Cancer Risk Worldwide

Human papillomavirus 18 (HPV18) is the second most carcinogenic HPV type, after HPV16, and it accounts for approximately 12% of squamous cell carcinoma (SCC) as well as 37% of adenocarcinoma (ADC) of the cervix worldwide. We aimed to evaluate the worldwide diversity and carcinogenicity of HPV18 genetic variants by sequencing the entire long control region (LCR) and the E6 open reading frame of 711 HPV18-positive cervical samples from 39 countries, taking advantage of the International Agency for Research on Cancer biobank. A total of 209 unique HPV18 sequence variants were identified that formed three phylogenetic lineages (A, B, and C). A and B lineages each divided into four sublineages, including a newly identified candidate B4 sublineage. The distribution of lineages varied by geographical region, with B and C lineages found principally in Africa. HPV18 (sub)lineages were compared between 453 cancer cases and 236 controls, as well as between 81 ADC and 160 matched SCC cases. In region-stratified analyses, there were no significant differences in the distribution of HPV18 variant lineages between cervical cancer cases and controls or between ADC and SCC. In conclusion, our findings do not support the role of HPV18 (sub)lineages for discriminating cancer risk or explaining why HPV18 is more strongly linked with ADC than SCC.

IMPORTANCE

This is the largest and most geographically/ethnically diverse study of the genetic variation of HPV18 to date, providing a comprehensive reference for phylogenetic classification of HPV18 sublineages for epidemiological and biological studies.

Lineages of oncogenic human papillomavirus types other than type 16 and 18 and risk for cervical intraepithelial neoplasia

BACKGROUND

Data on clinical outcomes of infection with variants of oncogenic human papillomavirus (HPV) types other than HPV16 and HPV18 are rare. We investigated intratypic variations in non-HPV16/18 oncogenic types and their corresponding relationships with cervical intraepithelial neoplasia grades 2-3 (CIN2/3).

METHODS

Study subjects were women who were positive for one or more of 11 non-HPV16/18 oncogenic types. Subjects were followed every six months for two years for detection of HPV and cervical lesions. Variant lineages were defined by sequencing the 3' part of the long control region and the entire E6/E7 region of HPV genome. Lineage-associated risk of CIN2/3 was assessed using logistic regression with generalized estimating equations.

RESULTS

A total of 4591 type-specific HPV infections among 2667 women were included in the analysis. The increase in risk of CIN2/3 was statistically significant for women with HPV31 A or B compared with C variants, HPV33 A1 compared with B variants, HPV45 A3 or B2 compared with B1 variants, HPV56 B compared with A2 variants, and HPV58 A1 or A3 compared with C variants. For these five types, the adjusted odds ratio associated with CIN2/3 was 2.0 (95% confidence interval [CI] = 1.5 to 2.6) for infections with single-type high-risk (HR) variants, 1.7 (95% CI = 1.0 to 2.7) for infections with two or more types but only one HR variant, and 5.3 (95% CI = 3.1 to 8.4) for infections with HR variants of two or more types as compared with those with single-type non-HR variants. The likelihood of CIN2/3 was similar for women with HPV16 infection and for those with HPV58 A1 variant infection.

CONCLUSIONS

These findings suggest that for a given HPV type, intratypic nucleotide changes may alter phenotypic traits that affect the probability of neoplasia.

Long-term follow-up of HPV16-positive women: persistence of the same genetic variant and low prevalence of variant co-infections

HPV16 variants correlate with geographic origin and ethnicity. The association between infection with a specific variant and the cervical disease risk remains unclear. We studied the prevalence, persistence and association with cervical intraepithelial neoplasia (CIN) of different HPV16 variants, using cervical swabs and whole tissue sections (WTS) of biopsies from 548 women in the placebo group of a HPV16/18 vaccine trial. In HPV16-positive samples, HPV16 variants were identified by a reverse hybridization assay (RHA). Laser-capture micro-dissection (LCM) was performed for localized detection of HPV. HPV16 variants were determined in 47 women. Frequency of mixed HPV16 variant infections was lower (8.5%) than for multiple HPV genotypes (39.1%). Among 35 women having consecutive HPV16 variant-positive swabs, 32 (91.4%) had the same variant while in three (8.6%) women a change in variant(s) was observed. HPV16-positive WTS were obtained from 12 women having consecutive HPV16 variant-positive swabs. The same variant was present in WTS of 10 women, while two were negative. WTS of five women were histologically normal. A single HPV16 variant was detected in four women having CIN1-3, while additional HPV genotypes were found in three other women having CIN2 and CIN3. In the WTS of one woman with mixed genotypes, the HPV16 variant was assigned to a CIN2 lesion by LCM. HPV16 variant infections can be effectively studied in cervical swabs and tissue specimens by the HPV16 variant RHA. Multiple HPV16 variants in one woman are rare. The HPV16 genotype consistently detected in follow-up samples usually involves a persistent infection with the same variant.

Latent papillomavirus infections and their regulation

Model systems show that papillomavirus DNA can persist after lesion-regression, and be maintained in a subset of epithelial basal cells. These are very likely long-lived 'stem-cells' or 'stem-like cells', with latency arising via at least two distinct mechanisms. The first involves low-titre virus infection and the retention of viral DNA at levels that are too low to allow life-cycle completion. The second involves lesion-formation, and clearance by the adaptive immune system, followed by persistence with low-level viral gene expression, and possible reactivation upon immune depletion. Mechanical irritation, inflammation and other extracellular influences affect viral copy number in the latently infected cell, and may predispose to lesion-reappearance. Reactivation may account for the recurrence of 'apparently cleared' cervical lesions caused by high-risk types, the appearance of Beta HPV-lesions following immunosuppression, and the development of recurrent respiratory papillomatosis in afflicted children.

High-risk human papillomavirus infection in HIV-positive African women living in Europe

Introduction

Cervical infection with high-risk human papillomavirus (HRHPV) induces cervical cancer and is present in 14% of women in Europe. We assessed the prevalence and incidence of cervical HRHPV in a cohort of HIV-positive women living in Belgium.

Methods

Prospective observational program of screening and follow up of HRHPV cervical infection performed by Hybrid Capture in 825 HIV-positive women between 2002 and 2011. Women without normal cervix at baseline were excluded.

Results

The final analysis included 652 women: median age 38 years, African origin (81%), median HIV follow-up (66 months), median CD4 count (426 cells/μL) and 79% on antiretroviral therapy (cART). At baseline, HRHPV prevalence was 43% and decreased significantly as both age and CD4 cell count increased: highest prevalence (100%) in women <30 years and <200 CD4/μL and lowest (19%) in women >40 years and >500 CD4/μL (p<0.0001, multivariate analysis). The relative risk (RR) to carry HRHPV at baseline decreases proportionally by 11% for each 5 years-age increase and by 11% for each 100 CD4 cells/μL rise (RR=0.89, 95% CI: 0.85-0.93; p<0.0001, Poisson regression for both). During follow-up, incidence rate of HRHPV was 13.4 per 100 women-years.

Conclusions

We found a high HRHPV prevalence of 43% and an incidence rate of 13 per 100 women-years in this cohort of HIV-positive women living in Europe and on cART. Women under 40 years-age had the highest prevalence even with CD4 count >350 cells/μL. The magnitude of HRHPV epidemiology should prompt to evaluate the clinical efficacy of vaccines against HPV in HIV-infected women.

Variant lineages of human papillomavirus type 18 in Northeast China populations characterized by sequence analysis of E6, E7, and L1 regions

INTRODUCTION

In cervical cancer, human papillomavirus (HPV) 18 is predominantly related to adenocarcinomas. Variant lineages of HPV type 16 have been well characterized, whereas the knowledge about HPV 18 variants is limited in Northeast China.

METHODS

To identify prevalent and novel HPV 18 variants in Northeast China, the E6, E7, and L1 genes of HPV 18 from patients with cervical lesion were amplified and sequenced, and intratypic variants were analyzed by comparing to the known phylogenetic branches.

RESULTS

The HPV-18 E6 variants of our studied strains belong to 2 main branches: Asian-American (AA) variants in 81.5% and European (E) variants in 18.5%. Strains with variations of C287G, T482C, and C519A in E6 and C751T in E7 were novel variants. All the L1 genes of the analyzed HPV 18 strains had 4 C-G transversions at nucleotide positions of 5701, 6460, 6625, and 6842 and one G-A transition at position 5503. Moreover, strains with L1 nucleotide variations of A5920T, A6431T, and G6987A leading to amino acid substitutions of A164V, Q334P/H, and D520N are novel variants.

CONCLUSIONS

Based on the E6 gene, the prevalent HPV 18 in Northeast China was AA and E variants. Besides some common variations reported before, some new variations in the E6, E7, and L1 genes were found. Data about the novel variations found in the L1 gene of HPV 18 variants may be helpful to design the diagnostic reagents and vaccine for naturally infected HPV 18 in Northeast China.

Differential presence of Papillomavirus variants in cervical cancer: an analysis for HPV33, HPV45 and HPV58

BACKGROUND

Certain human papillomaviruses (HPVs) are the causative agents of cervical carcinomas in humans. The identification of the link between infection and cancer has resulted in the successful establishment of clinical strategies such as screening or vaccination programs, aiming to prevent this pathology. More than 150 different HPVs have been described and classified and the large majority of them are not related to cancer. The genus Alphapapillomavirus encompasses many PVs, some of which are identified in humans as oncogenic, according to the epidemiological connection between infection and cervical cancer. Variants of some of these "high-risk" HPVs may have an increased involvement in cervical cancer, although definitive data are still wanting. The aim of the present work was to analyze the presence of HPV33, HPV45 and HPV58 variants in cases of cervical cancer.

METHODS

Samples from cervical lesions in the context of different cervical cancer surveys were analyzed for presence of HPV DNA. Samples positive for HPV33, HPV45 or HPV58 DNA were selected and the E6/E7 genes were amplified and sequenced. The phylogenetic relationships of these sequences were inferred using an evolutionary placement algorithm and accordingly classified at the variant level.

RESULTS

All viral E6/E7 sequences were successfully placed in the classification schemes of the corresponding viruses. For HPV33 (n=23), 45 (n=61) or 58 (n=29), the distribution of variants found in cases of cervical cancer is not a random sample of the corresponding diversity. In all three HPVs, the respective A variants were more prevalent in the viral DNA-positive cases of cervical cancer analyzed. This is the first study trying to discern the phylogenetic connection between variants of the oncogenic HPV33, 45 and 58, and squamous cell carcinoma of the cervix.

Persistence of newly detected human papillomavirus type 31 infection, stratified by variant lineage

Variants of human papillomavirus (HPV) type 31 have been shown to be related both to risk of cervical lesions and racial composition of a population. It is largely undetermined whether variants differ in their likelihood of persistence. Study subjects were women who participated in the ASCUS-LSIL Triage Study and who had a newly detected HPV31 infection during a two-year follow-up with six-month intervals. HPV31 isolates were characterized by sequencing and assigned to one of three variant lineages. Loss of the newly detected HPV31 infection was detected in 76 (47.5%) of the 160 women (32/67 with A variants, 16/27 with B variants and 28/66 with C variants). The adjusted hazard ratio associating loss of the infection was 1.2 (95% CI, 0.7-2.1) for women with A variants and 2.1 (95% CI, 1.2-3.5) for women with B variants when compared with those with C variants. Infections with A and C variants were detected in 50 and 41 Caucasian women and in 15 and 23 African-American women, respectively. The likelihood of clearance of the infection was significantly lower in African-American women with C variants than in African-American women with A variants (p = 0.05). There was no difference in the likelihood of clearance between A and C variants among Caucasian women. Our data indicated that infections with B variants were more likely to resolve than those with C variants. The difference in clearance of A vs. C variants in African-Americans, but not in Caucasians, suggests a possibility of the race-related influence in retaining the variant-specific infection.

Association of human papillomavirus type 31 variants with risk of cervical intraepithelial neoplasia grades 2-3

Although the lineages of human papillomavirus type 31 (HPV31) variants are recognized, their clinical relevance is unknown. The purpose of our study was to examine risk of cervical intraepithelial neoplasia Grades 2-3 (CIN2/3) by HPV31 variants. Study subjects were women who participated in the atypical squamous cells of undetermined significance and low-grade squamous intraepithelial lesion Triage Study and who had HPV31 infections detected at one or more visits. They were followed semi-annually over 2 years for detection of HPV DNA and cervical lesion. HPV31 isolates were characterized by DNA sequencing and assigned into 1 of 3 variant lineages. CIN2/3 was histologically confirmed in 127 (27.0%) of the 470 HPV31-positive women, 83 diagnosed at the first HPV31-positive visit and 44 thereafter. The odds ratio for the association of 2-year cumulative risk of CIN2/3 was 1.7 (95% CI: 1.0-2.9) for infections with A variants and 2.2 (95% CI: 1.2-3.9) for infections with B variants as compared to those with C variants. Among women without CIN2/3 at the first HPV31-positive visit, the risk of subsequent CIN2/3 was 2.2-fold greater for those with A variants (95% CI: 1.0-4.8) and 2.0-fold greater for those with B variants (95% CI: 0.9-4.9) as compared to those with C variants. Similar associations were observed when CIN3 was used as the endpoint. The findings from our study help to tag HPV31 variants that differ in risk of CIN2/3 and to explain in part why some HPV31 infections regress spontaneously and others lead to disease progression.

Genetic variability and phylogeny of high risk HPV type 16, 18, 31, 33 and 45 L1 gene in Greek women

The present study explores nucleotide variability, phylogeny and association with cervical neoplasia in high risk HPV types 16, 18, 31, 33 and 45 collected from Greek women. Of the 1894 women undergoing routine cervical cytology examination, 160 samples test positive for single infections of HPV type 16 (n = 104), HPV 31 (n = 40), HPV 33 (n = 7), HPV 18 (n = 5), and HPV 45 (n = 4) were typed by microarrays method, amplified by PCR then sequenced and phylogenetically analyzed. For HPV 16, 9 variants with nucleotide variations were included into the study. For HPV 31, 33, 18 and 45, nucleotide variations were identified in 6, 4, 2 and 3 variants, respectively. The Bayesian inference and Maximum Parsimony methods were used in order to construct the phylogenetic trees. When types were analyzed independently HPV 16 (European and non-European) and HPV 18 (African and non-African) formed distinct clades. The genomic characterization of HPV variants will be important for illuminating the geographical relatedness and biological differences and for the determination of their risk.

Human papillomavirus 16 variants from Zambian women with normal pap smears

Human papillomavirus (HPV) type 16 is the most prevalent high-risk viral genotype associated with cervical cancer. Six distinct phylogenetic clusters of HPVs have been identified and are distributed differently across five continents. HPV16 DNA was extracted from cervicolavage samples from women with normal pap smears. The LCR regions were amplified in triplicate, cloned, sequenced, and analyzed from a total of 11 recovered HPV16 positive samples [Ng'andwe et al. (2007): BMC Infect Dis 7:77] were analyzed for sequence variation. The HPV16 LCR variants were assessed for promoter activity by use of a luciferase reporter gene. Six novel HPV16 variants with nucleotide exchanges in the LCR region were identified. Five clones were classified as European group HPV16 variants and one as an African group variant. Two of these variants had relatively lower promoter activity, 30% of that of the wild-type strain. The decreased promoter activity of some HPV16 variants may decrease expression of viral oncogenes and may be linked with the development, phenotype and severity of the cervical lesions in women infected with these across HPV16 variants.

Clinical evaluation of polymerase chain reaction reverse hybridization assay for detection and identification of human papillomavirus type 16 variants

BACKGROUND

Isolates of HPV16 comprise six variants: European (Eu), Asian (As), Asian-American (AA), North American (NA), African-1 (AF1), and African-2 (AF2) with different carcinogenic potentials. Highly reliable automatable techniques for HPV variant genotyping would be helpful to confirm the role of variants in cervical cancer in large epidemiological studies.

OBJECTIVE

To validate the performance of a novel assay for identification of HPV16 variants.

STUDY DESIGN

The test is a multiplex PCR amplifying four small fragments from the E6 open reading frame (ORF). Variants are identified in a reverse hybridization assay with variant specific probes. The novel assay was compared to sequence analysis of the E6 ORF in 68 clinical samples. In addition, HPV16 variant distribution was studied in 218 cervical samples from women with normal cytology, squamous cell carcinoma (SCC) and adenocarcinoma of countries in Africa, Asia and South-America.

RESULTS

There was 95.6% agreement between the test and sequencing. Analysis of the clinical panel including 218 positive samples revealed worldwide distribution patterns of HPV16 variants. Finally, a threefold increased risk for SCC with grouped Eu and As variants in South-American countries as compared to controls was found, although the association was not statistically significant.

CONCLUSIONS

The novel assay is a reliable and simple technique, distribution patterns of HPV16 variants in different world regions and disease associations could be established and it may be useful in further epidemiological studies investigating the role of HPV16 variants in cervical carcinogenesis.

E6 molecular variants of human papillomavirus (HPV) type 16: an updated and unified criterion for clustering and nomenclature

Reports on taxonomic identification of E6/HPV 16 variants, don't have a worldwide, updated and unified criterion for clustering and nomenclature. Our aim was to update the existing criterion and propose a new one for clustering and nomenclature for E6/HPV 16 molecular variants based on the descriptive and comparative analyses of nucleotide sequences. A systematic search of the publications between 1991 and 2010 was carried out in PUBMED and manually. 240 E6/HPV 16 variants were identified. 157 were classified as European (E), 24 as Asian (As), 14 as Asian American (AA), 11 as North American 1 (NA 1), 19 as African 1 (Af 1) and 15 as African 2 (Af 2). Three classes were determined for the E, 3 each for the As, Af 2 and AA branches, 4 classes for the NA 1 and 6 for the Af 1 branch. This study reports our results and proposes an updated criterion for clustering and nomenclature that will be useful for E6 variant identification.

A population-based prospective study of carcinogenic human papillomavirus variant lineages, viral persistence, and cervical neoplasia

Human papillomavirus (HPV) types differ profoundly in cervical carcinogenicity. For the most carcinogenic type HPV16, variant lineages representing further evolutionary divergence also differ in cancer risk. Variants of the remaining 10 to 15 carcinogenic HPV types have not been well studied. In the first prospective, population-based study of HPV variants, we explored whether, on average, the oldest evolutionary branches within each carcinogenic type predicted different risks of >2-year viral persistence and/or precancer and cancer [cervical intraepithelial neoplasia grade 3+ (CIN3+)]. We examined the natural history of HPV variants in the 7-year, 10,049-woman Guanacaste Cohort Study, using a nested case-control design. Infections were assigned to a variant lineage determined by phylogenetic parsimony methods based on URR/E6 sequences. We used the Fisher's combination test to evaluate significance of the risk associations, cumulating evidence across types. Globally, for HPV types including HPV16, the P value was 0.01 for persistence and 0.07 for CIN3+. Excluding HPV16, the P values were 0.04 and 0.37, respectively. For HPV16, non-European viral variants were significantly more likely than European variants to cause persistence [odds ratio (OR), 2.6; P = 0.01] and CIN3+ (OR, 2.4; P = 0.004). HPV35 and HPV51 variant lineages also predicted CIN3+. HPV variants generally differ in risk of persistence. For some HPV types, especially HPV16, variant lineages differ in risk of CIN3+. The findings indicate that continued evolution of HPV types has led to even finer genetic discrimination linked to HPV natural history and cervical cancer risk. Larger viral genomic studies are warranted, especially to identify the genetic basis for HPV16's unique carcinogenicity.

Papillomavirus DNA complementation in vivo

Recent phylogenic studies indicate that DNA recombination could have occurred in ancient papillomavirus types. However, no experimental data are available to demonstrate this event because of the lack of human papillomavirus infection models. We have used the cottontail rabbit papillomavirus (CRPV)/rabbit model to study pathogenesis and immunogenicity of different mutant genomes in vivo. Although the domestic rabbit is not a natural host for CRPV infection, it is possible to initiate infection with naked CRPV DNA cloned into a plasmid and monitor papilloma outgrowth on these animals. Taking advantage of a large panel of mutants based on a CRPV strain (Hershey CRPV), we tested the hypothesis that two non-viable mutant genomes could induce papillomas by either recombination or complementation. We found that co-infection with a dysfunctional mutant with an E2 transactivation domain mutation and another mutant with an E7 ATG knock out generated papillomas in rabbits. DNA extracted from these papillomas contained genotypes from both parental genomes. Three additional pairs of dysfunctional mutants also showed similar results. Individual wild type genes were also shown to rescue the function of corresponding dysfunctional mutants. Therefore, we suggest that complementation occurred between these two non-viable mutant PV genomes in vivo.

Current understanding and potential immunotherapy for HIV-associated squamous cell carcinoma of the anus (SCCA)

Squamous cell carcinoma of the anus (SCCA) is a rare disease in the average population but is an increasing concern among immunocompromised individuals, such as the HIV-seropositive. Coinfection with human papillomavirus (HPV) in this population is common. HPV infection is difficult to clear with a compromised immune system, which results in a greater risk of tumor development and a more aggressive progression of the disease. The recent approval of a prophylactic HPV vaccine for cervical cancer has sparked an interest in a search for improved immunotherapeutic multimodality therapies to combat anogenital tumors associated with the virus. In this review, we discuss the known mechanisms of action of HIV-associated SCCA, examine the current treatments for the disease, and focus on the potential of an immunotherapeutic vaccine approach for both prophylactic and therapeutic application.

Evolutionary dynamics of variant genomes of human papillomavirus types 18, 45, and 97

Human papillomavirus type 18 (HPV18) and HPV45 account for approximately 20% of all cervix cancers. We show that HPV18, HPV45, and the recently discovered HPV97 comprise a clade sharing a most recent common ancestor within HPV alpha7 species. Variant lineages of these HPV types were classified by sequence analysis of the upstream regulatory region/E6 region among cervical samples from a population-based study in Costa Rica, and 27 representative genomes from each major variant lineage were sequenced. Nucleotide variation within HPV18 and HPV45 was 3.82% and 2.39%, respectively, and amino acid variation was 4.73% and 2.87%, respectively. Only 18 nucleotide variations, of which 10 were nonsynonymous, were identified among three HPV97 genomes. Full-genome comparisons revealed maximal diversity between HPV18 African and non-African variants (2.6% dissimilarity), whereas HPV18 Asian-American [E1 (AA)] and European (E2) variants were closely related (less than 0.5% dissimilarity); HPV45 genomes had a maximal difference of 1.6% nucleotides. Using a Bayesian Markov chain Monte Carlo (MCMC) method, the divergence times of HPV18, -45, and -97 from their most recent common ancestors indicated that HPV18 diverged approximately 7.7 million years (Myr) ago, whereas HPV45 and HPV97 split off around 5.7 Myr ago, in a period encompassing the divergence of the great ape species. Variants within the HPV18/45/97 lineages were estimated to have diverged from their common ancestors in the genus Homo within the last 1 Myr (<0.7 Myr). To investigate the molecular basis of HPV18, HPV45, and HPV97 evolution, regression models of codon substitution were used to identify lineages and amino acid sites under selective pressure. The E5 open reading frame (ORF) of HPV18 and the E4 ORFs of HPV18, HPV45, and HPV18/45/97 had nonsynonymous/synonymous substitution rate ratios (d(N)/d(S)) over 1 indicative of positive Darwinian selection. The L1 ORF of HPV18 genomes had an increased proportion of nonsynonymous substitutions (4.93%; average d(N)/d(S) ratio [M3] = 0.3356) compared to HPV45 (1.86%; M3 = 0.1268) and HPV16 (2.26%; M3 = 0.1330) L1 ORFs. In contrast, HPV18 and HPV16 genomes had similar amino acid substitution rates within the E1 ORF (2.89% and 3.24%, respectively), while HPV45 E1 was highly conserved (amino acid substitution rate was 0.77%). These data provide an evolutionary history of this medically important clade of HPVs and identify an unexpected divergence of the L1 gene of HPV18 that may have clinical implications for the long-term use of an L1-virus-like particle-based prophylactic vaccine.

Human papillomavirus (HPV) genotypes and HPV16 variants in human immunodeficiency virus-positive Italian women

Human immunodeficiency virus (HIV)-positive women have high rates of cervical squamous intraepithelial lesions (SIL) and concurrent human papillomavirus (HPV) infections with a variety of genotypes whose oncogenic risk is poorly documented. The prevalence and persistence of HPV genotypes and HPV16 variants were analysed in 112 HIV-positive and 115 HIV-negative Italian women. HIV-positive women were more likely than HIV-negative women to be infected by HPV at the initial examination (39.3 vs 13.9 %, P<0.001) and to have a higher period prevalence of HPV infection over a 3-year follow-up (43.8 % vs 17.4 %, P<0.001), regardless of CD4+ cell counts and anti-retroviral therapy. 'High-risk' and 'probable high-risk' HPVs (types 16, 18, 31, 33, 35, 45, 52, 58 and 66), among the 20 different viral genotypes identified, were predominant in HIV-positive (33.9 %) compared with HIV-negative (13.9 %) women. Among HIV-infected women, with normal cytology as well as with SIL of any grade, the most common genotypes were HPV16 followed by HPV81, -58, -72, -33 and -62. HPV16 isolates from 18 HIV-positive and eight HIV-negative women were classified into variant lineages based on sequencing analysis of E6 and E7 genes and the long control region. Whilst the HPV16 G350 European variant was prevalent in both HIV-positive (10.7 %) and -negative women (3.5 %), HPV16 African 2 variant was only detected in HIV-positive women (3.6 %), suggesting different sexual mixing behaviours. The increased prevalence of uncommon viral genotypes and HPV16 variants in HIV-positive Italian women underscores the need to target a wide range of HPV types in cervical screening of high-risk women.

Prevention, diagnosis, and treatment of cervical cancer

This article reviews the current data on human papillomavirus as the cause of most cervical cancer cases, data on the recently approved human papillomavirus vaccines, and updated information concerning the Bethesda System for interpretation of Papanicolaou test results. Current recommendations for surgical treatment, concurrent chemotherapy, and radiation therapy and recent advances in systemic therapy for advanced or metastatic cervical cancer are reviewed.

Risk for high-grade cervical intraepithelial neoplasia associated with variants of human papillomavirus types 16 and 18

BACKGROUND

Although the variant lineages of human papillomavirus (HPV) types 16 and 18 are well established, their individual associations with high-grade cervical intraepithelial neoplasia (CIN) have not been extensively evaluated.

METHODS

Study subjects were women participating in the Atypical Squamous Cells of Undetermined Significance/Low-Grade Squamous Intraepithelial Lesion Triage Study who were positive for HPV16 or HPV18 at enrollment. These women were followed every 6 months for 2 years. Viral isolates from enrollment samples were characterized by DNA sequencing and classified as variant lineages.

RESULTS

Over a 2-year study period, CIN3 was histologically diagnosed in 291 of the 779 HPV16-positive women and 47 of the 275 HPV18-positive women. Among women without CIN2-3 at enrollment, the risk of subsequent CIN3 was 2.7-fold greater for those with HPV16 African-2 [95% confidence interval (95% CI), 1.0-7.0] and 3.1-fold greater for those with HPV16 Asian American (95% CI, 1.6-6.0), compared with European variants. Relative to infection with HPV18 African variants, the risk associating subsequent CIN3 was 3.8 (95% CI, 0.9-17.2) for infection with HPV18 European variants and 4.8 (95% CI, 1.0-23.6) for infection with HPV18 Asian American variants. Similar associations were observed when the 2-year prevalence of CIN3 was used as the end point. Further, for those with HPV16 European variants, the 2-year prevalence of CIN3 was higher in White women than in African American women (P = 0.01); this trend was reversed for those with HPV16 African-1 variants (P = 0.22). A similar pattern was present for infections with HPV18 European versus African variants.

CONCLUSIONS

The lineages of HPV16 and HPV18 variants are associated with differing risks for high-grade CIN.

High grade cervical lesions are caused preferentially by non-European variants of HPVs 16 and 18

The intratypic variability of HPVs 16 and 18 has been extensively studied and has been used as an important tool in epidemiological studies of viral transmission, persistence and progression to clinically relevant cervical lesions. Infections by non-European variants of HPVs 16 and 18 are associated with an increased risk for the development of high grade squamous intraepithelial lesions (HSIL). Our aim was to correlate the intratypic molecular variability of both HPV types and risk of persistent infection and lesion outcome in a cohort study conducted in Brazil. We characterized molecular variants of HPV types 16 and 18 by sequencing a fragment of the LCR, and of the E6 and L1 genes, for HPV-16 variants only. For both types, European variants composed the most prevalent and diverse group. Persistent infections with HPV-18 were associated with continuous detection of European variants. However, risk for simultaneous detection of HSIL and HPV DNA was higher in women harboring non-European variants of HPV-16. The same trend was observed with HSIL detected during follow-up. Our study confirms the association between non-European variants and risk of cervical neoplasia, and highlights the importance of their geographic distribution for cervical cancer risk assessment.

Human papillomavirus infection and disease in the HIV+ individual

HPV infection of both the genital tract and oral cavity of HIV+ men and women is increased. HPV-related pathology is also increased in the HIV+ individuals, usually with further increases seen for those HIV+ individuals with lower CD4 cell counts. Fortunately, the rates of cervical cancer and anal cancer are relatively low and not related to CD4 cell count. Treatment of the HIV+ individual with HPV-related disease is challenging and requires close long-term follow-up to prevent recurrent disease. The mechanism of how HPV and HIV interact is still not known but is more likely to be linked to immune suppression rather than a direct interaction between viruses. The newly developed HPV vaccines will likely have a significant impact on HPV-related disease in immunocompetent individuals. It remains to be seen what impact these vaccine will have on the immune depressed.

Human papillomavirus: the burden of infection

Vaccines for preventing human papillomavirus (HPV) infection are far along in clinical development and testing, and hold great promise for reducing HPV infections and HPV-associated disease. HPV is the most common sexually transmitted infection in the United States, affecting an estimated 75% of the U.S. population. HPV infection is highly prevalent in sexually active adolescents and young adults. Sexual activity is the most important risk factor for infection, with 64% to 82% of sexually active adolescent girls testing positive for HPV. Clinical manifestations of HPV infection include genital warts, cervical intraepithelial neoplasia (CIN), and invasive cervical cancer, all of which cause significant morbidity and, in the case of cervical cancer, mortality. The majority of HPV-associated disease is caused by 4 HPV types: HPV 6 and 11 are responsible for low-grade genital lesions and more than 90% of genital warts, and HPV 16 and 18 both account for approximately 70% of all high-grade CIN or dysplasia and invasive cervical cancer. Although current screening methods have proven effective in reducing cervical cancer incidence and associated mortality, more than 10,000 women are diagnosed annually and 4000 U.S. women die from the disease each year.

HPV16 variants in squamous intraepithelial lesions in human immunodeficiency virus-negative and -positive Brazilian women

Emerging evidence supports the role of human papillomavirus (HPV) intratype variations in the development of cervical lesions in immunocompetent women, but few studies investigated HPV16 variants in human immunodeficiency virus (HIV)-positive women. This is the first study in Brazil evaluating HPV16 variants in women with (n = 19) and without (n = 22) HIV infection, as well as cervical lesions. Although non-European variants presented an almost 3-fold increase (13.6% vs. 36.8%) among HIV-positive women, associations between HPV16 variants and HIV infection did not reach statistical significance (Fisher's exact test, p = 0.15). No associations were found between non-European variants and HSIL (Fisher's exact test, p = 0.41), although a significant association was observed between European variants and HSIL among HIV-negative women (Fisher's exact test, p = 0.01). In conclusion, in HIV-negative women the HPV16 European variants seem to influence the occurrence of HSIL, whereas in HIV-positive women, similar roles are atributted to both variants.

Human Papillomavirus Type 16 and 18 Variants: Race-Related Distribution and Persistence

BACKGROUND

Analogous to the geographic distribution of variants of human papillomavirus (HPV) types, the distribution and persistence of these variants among infected individuals may be related to the racial composition of a population living in one geographic region.

METHODS

We studied 1114 women in the United States participating in the Atypical Squamous Cells of Undetermined Significance/Low-Grade Squamous Intraepithelial Lesion Triage Study who were positive for HPV16 and/or HPV18 at enrollment. Race was self-reported. HPV samples were characterized by sequencing the E6 gene and part of the long control region and classified as variants according to established lineages. Subjects were examined for HPV every 6 months for 2 years. All statistical tests were two-sided.

RESULTS

HPV18 African variants were predominant in the 97 HPV18-infected African American women (i.e., 62 women or 63.9%, 95% confidence interval [CI] = 53.5% to 73.4%), and European variants were common in the 168 HPV18-infected white women (i.e., 91 women or 54.2%, 95% CI = 46.3% to 61.9%). HPV16 African variants accounted for 43 (26.5%, 95% CI = 19.9% to 34.0%) of the infections in the 162 HPV16-infected African American women but for only 25 (4.3%, 95% CI = 2.8% to 6.3%) in the 584 HPV16-infected white women. The likelihood of remaining HPV18 positive was statistically significantly higher in white women infected with European than in white women infected with African variants (P = .04); the reverse was observed in African American women (P = .03). A similar pattern was observed for persistence of HPV16 variants, with the likelihood of remaining positive being higher for white women, but lower for African American women, infected with an European variant than with an African variant (P = .03 and P = .16, respectively).

CONCLUSIONS

Variants of HPV16 and HPV18 appear to persist longer in a host whose race indicates an ancestral geographic distribution that was once shared with that of the variant-i.e., European variants persist longer in white women, and African variants persist longer in African American women.