Human papillomavirus genotypes and phylogenetic analysis of HPV-16 variants in HIV-1 infected subjects in Italy

The Epidemiology of Anal Human Papillomavirus (HPV) in HIV-Positive and HIV-Negative Women and Men: A Ten-Year Retrospective Observational Study in Rome (Italy)

Human papillomaviruses (HPVs) commonly infect the anogenital mucosa; most infections are transient, but a fraction of those caused by high-risk (HR) types persist and may lead to anogenital cancer. The epidemiology of HPV genotypes in anal infections in groups at different risk for anal cancer has not been well described in Italy. This retrospective study reports the results of HPV DNA testing and complete genotyping performed on anal swabs from 691 female and male patients attending proctology clinics in Rome during 2012-2021; one-third had repeated testing. Cumulative HPV positivity in 1212 anal swabs was approximately 60%, was not age related, and showed an increasing trend over the study period. HPV rates differed significantly by sex and HIV status: HIV-negative women had the lowest (43.6%) and HIV-positive men the highest (83.5%) HPV prevalence. HIV-positive men had more oncogenic HPV genotypes detected, more multiple infections, and the highest frequency of persistent infections. Two-thirds of all infections were vaccine-preventable. This study found that anal HPV infection rates are still elevated and even increasing in groups at low and high risk of developing anal cancer. Prevention programs need to be improved to reduce rates of anal infection in young women and men.

Genetic variants of HPV-16 and their geographical and anatomical distribution in men: A systematic review with meta-analysis

BACKGROUND

The prevalence of Human Papillomavirus type 16 (HPV-16) variants in men and the association with tumor development has not been fully investigated. We estimated the prevalence of genital, anal, and oral HPV-16 infections in men through a systematic review and meta-analysis.

METHODS

Seven databases were searched and included studies that identified HPV-16 positive males, HPV-16 variants (lineages/sublineages), and indicated the sample's anatomical origin. This protocol is registered in PROSPERO (CRD42020178013).

RESULTS

The database searches yielded 14 studies including 445 HPV-16 positive samples classified as lineage A (n = 390), lineage D (n = 43), lineage B (n = 10), and lineage C (n = 2) variants. Lineage A variants predominated among the anatomical sites and the diverse geographical regions.

CONCLUSIONS

HPV-16 lineages vary according to anatomical and geographical region. According to this preliminary evaluation of the current literature, we hypothesize that, similar to women, specific HPV-16 variants may also be associated to increased cancer risk in men.

Analysis of Human Papillomavirus (HPV) 16 Variants Associated with Cervical Infection in Italian Women

This study aims to evaluate HPV16 variants distribution in a population of Italian women living in two different regions (Lombardy and Sardinia) by sequence analyses of HPV16-positive cervical samples, in order to reconstruct the phylogenetic relationship among variants to identify the currently circulating lineages. Analyses were conducted starting from DNA isolated from 67 HPV16-positive cervical samples collected from two different Italian centres (31 from Lombardy and 36 from Sardinia) of women with normal and abnormal cervical cytology. The entire long control region (LCR) and 300 nt of the E6 gene was sequenced to identify intra-type variants. Sequence comparison and phylogenetic analysis were made using a distance-based neighbour joining method (NJ) and Kimura two-parameter model. Data obtained reported that Italian sequences mainly belonged to the European lineage, in particular sublineage A2. Only five sequences clustered in non-European branches: two in North American lineage (sublineage D1), two in African-1 (sublineage B1) and one in African-2. A new 27 nucleotide duplication in the central segment of the LCR region was found in a sequence obtained from a sample isolated in Sardinia. A predominance of European variants was detected, with some degree of variability among the studied HPV16 strains. This study contributes to the implementation of data regarding the molecular epidemiology of HPV16 variants.

Genetic characterization of variants of HPV‑16, HPV‑18 and HPV‑52 circulating in Italy among general and high‑risk populations

Viral factors, such as high‑risk human papillomavirus variants, can increase the risk of viral persistence and influence the progression to cancer. In the present study, the long control region (LCR) of human papillomavirus (HPV)‑16 and HPV‑52, and the L1 region of HPV‑16 and HPV‑18, identified from subjects belonging to both general and high‑risk populations (migrants, HIV+ subjects and adolescent/young people) residing in Italy, were characterized using molecular and phylogenetic techniques. To the best of our knowledge, this is the first Italian study to analyze a large number of sequences (n=458) and report phylogenetic data on the HPV‑52 variants. The phylogenetic analysis showed that 90% of the LCR variants of HPV‑16 and HPV‑52 clustered within lineage A (European lineage) and only sequences identified from subjects belonging to high‑risk populations fell into the non‑European lineages. Analysis of the LCRs revealed a high genomic diversity with a large number of changes. Several mutations in the binding sites for viral and cellular transcription factors characterized the HPV‑16 LCR variants belonging to the African lineages B and C, were observed in subjects with cytological abnormalities (high squamous intraepithelial lesions). The HPV‑16 and HPV‑18 L1 molecular characterization identified 30% of changes in the immune‑dominant epitope loops. These data give a clear picture of the situation in Italy, and a starting point for understanding the molecular pathogenesis and developing molecular diagnostics for HPV, vaccines and other therapeutic approaches in order to control and/or eliminate virus‑induced diseases.

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.

Identification of human papillomavirus type 16 variants circulating in the Calabria region by sequencing and phylogenetic analysis of HPV16 from cervical smears

Sequence analysis of HPV16 isolates reveals the presence of genome variants with characteristic mutations. The HPV16 variants have different geographical distribution and diverge into four phylogenetic lineages (A, B, C and D) and 16 sub-lineages: A1, A2, A3 (previously known as European variants), A4 (Asian variant), B1, B2, B3, B4, C1, C2, C3, and C4 (African variants), D1 (North-American variant), D2, D3 (Asian-American variants) and D4. Population studies showed that infections with viruses belonging to specific HPV16 sublineages confer different risks of viral persistence and cancer. In this study, 39 HPV16-positive cervical smears from European women living in Calabria (Italy) were analyzed for the presence of HPV16 variants. Cervical DNA extracts were processed by PCR to amplify L1, the Long Control Region (LCR), E6 and E7, which were sequenced. The sequences were concatenated and the 3169 nucleotides long fragments were characterized by BLAST and phylogenetic analysis. A total of 96 Single Nucleotide Polymorphism (SNPs) were detected, 29 of which mapping in the L1, 45 in the LCR, 15 in the E6 and 7 in the E7. The most common SNP was the T350G (29/39 samples, 74.4%), causing the L83 V amino acid change in the E6. Most of the HPV16 isolates (89.7%) had 99% of nucleotide (nt) identity to members of the A1 and A2 sublineages, while 4 isolates had 99% nt identity to members of the B2, B4, C1 and D4 sublineages. In conclusion, viruses belonging to the A1, A2, B2, B4, C1 and D4 HPV16 sublineages were found to circulate in the Calabria region.

Niche adaptation and viral transmission of human papillomaviruses from archaic hominins to modern humans

Recent discoveries on the origins of modern humans from multiple archaic hominin populations and the diversity of human papillomaviruses (HPVs) suggest a complex scenario of virus-host evolution. To evaluate the origin of HPV pathogenesis, we estimated the phylogeny, timing, and dispersal of HPV16 variants using a Bayesian Markov Chain Monte Carlo framework. To increase precision, we identified and characterized non-human primate papillomaviruses from New and Old World monkeys to set molecular clock models. We demonstrate specific host niche adaptation of primate papillomaviruses with subsequent coevolution with their primate hosts for at least 40 million years. Analyses of 212 HPV16 complete genomes and 3582 partial sequences estimated ancient divergence of HPV16 variants (between A and BCD lineages) from their most recent common ancestors around half a million years ago, roughly coinciding with the timing of the split between archaic Neanderthals and modern Homo sapiens, and nearly three times longer than divergence times of modern Homo sapiens. HPV16 A lineage variants were significantly underrepresented in present African populations, whereas the A sublineages were highly prevalent in European (A1-3) and Asian (A4) populations, indicative of viral sexual transmission from Neanderthals to modern non-African humans through multiple interbreeding events in the past 80 thousand years. Remarkably, the human leukocyte antigen B*07:02 and C*07:02 alleles associated with increased risk in cervix cancer represent introgressed regions from Neanderthals in present-day Eurasians. The archaic hominin-host-switch model was also supported by other HPV variants. Niche adaptation and virus-host codivergence appear to influence the pathogenesis of papillomaviruses.

Redetection of human papillomavirus type 16 infections of the cervix in mid-adult life

PURPOSE

To assess whether HPV 16 originally detected in adolescent women can be redetected in adulthood.

METHODS

A convenience sample of 27 adult women with known HPV 16 detection during adolescence was assessed for HPV 16 redetection. A comparison of the long control region (LCR) DNA sequences was performed on some of the original and redetected HPV 16 isolates.

RESULTS

Median age at reenrollment was 27.5 years (interquartile range of 26.7-29.6). Reenrollment occurred six years on average after the original HPV 16 detection. Eleven of 27 women had HPV 16 redetected. Some of these HPV 16 infections had apparently cleared during adolescence. LCR sequencing was successful in paired isolates from 6 women; in 5 of 6 cases the redetected HPV 16 isolates were identical to those detected during adolescence, CONCLUSIONS: HPV 16 may be episodically detected in young women, even over long time periods. HPV 16 redetection with identical LCR sequences suggests low-level persistent infection rather than true clearance, although newly acquired infection with an identical HPV 16 isolate cannot be excluded. However, this study suggests that a new HPV 16-positive test in a clinical setting may not indicate a new infection.

Cervical Human Papillomavirus genotypes in HIV-infected women: a cross-sectional analysis of the VALHIDATE study

Introduction

Primary-prevention by prophylactic vaccination against HPV-related cancers and HPV-based screening programs are based on HPV-type distribution in immunocompetent individuals. HIV-infected women are at high risk of invasive HPV-disease sustained by a broader range of HPV-types and have higher multi-type infection rates than immunocompetent hosts.

Methods

This is a cross-sectional analysis of High Risk HPV (HR HPV) type distribution in 805 HIV+ women (HIW) compared with a control group of 1402 immunocompetent HIV- women (SPW) enrolled in the VALHIDATE study in order to define HPV type-specific distribution according to cytology.

Results

HIW had a 3.8, 3.6, and 2.7 times higher risk of atypical squamous cells of undetermined significance (ASCUS), low-grade squamous intraepithelial lesion (LSIL) and high grade squamous intraepithelial lesion (HSIL) than SPW respectively. HPV-DNA prevalence was 28.4% in HIW and 11.81% in SPW (p<0.0001). The prevalence of infection increased from normal cytology to HSIL both in HIW (from 21.45% to 90.91%) and SPW (from 9.54% to 75%). The OR for women with normal cytology of having a positive HPV-DNA test result of was 2.6 times higher in HIW than in SPW. The cumulative prevalence of HPV-16/18 in HSIL is much lower in HIW (36.4±28.4) than SPW (62.5±33.5).

Conclusions

A higher prevalence of infection and broader HPV type distribution were observed in HIV+ women compared to the general population. More than 60% of HSIL lesions of HIW patients are caused by single or multi-type infections from non-HPV16/18 HPVs. The potential 9v-HPV vaccine coverage could be even higher than that expected for the general population given the wide panel of HPV-types observed in the HSIL of HIV+ women.

Dating the origin and dispersal of Human Papillomavirus type 16 on the basis of ancestral human migrations

A major limitation when reconstructing the origin and evolution of HPV-16 is the lack of reliable substitution rate estimates for the viral genes. On the basis of the hypothesis of human HPV-16 co-divergence, we estimated a mean evolutionary rate of 1.47×10(-7) (95% HPD=0.64-2.47×10(-7)) subs/site/year for the viral LCR region. The results of a Bayesian phylogeographical analysis suggest that the currently circulating HPV-16 most probably originated in Africa about 110 thousand years ago (Kya), before giving rise to four known geographical lineages: the Asian/European lineage, which most probably originated in Asia a mean 38 Kya, and the Asian/American and two African lineages, which probably respectively originated about 33 and 27 Kya. These data closely reflect current hypotheses concerning modern human expansion based on studies of mitochondrial DNA phylogeny. The correlation between ancient human migration and the present HPV phylogeny may be explained by the co-existence of modes of transmission other than sexual transmission.

Rome Consensus Conference - statement; human papilloma virus diseases in males

BACKGROUND

Human Papillomavirus (HPV) is a very resistant, ubiquitous virus that can survive in the environment without a host. The decision to analyse HPV-related diseases in males was due to the broad dissemination of the virus, and, above all, by the need to stress the importance of primary and secondary prevention measures (currently available for women exclusively). The objective of the Consensus Conference was to make evidence-based recommendations that were designed to facilitate the adoption of a standard approach in clinical practice in Italy.

METHODS

The Sponsoring Panel put a series of questions to the members of the Scientific Committee who prepared a summary of the currently available information, relevant for each question, after the review and grading of the existing scientific literature. The summaries were presented to a Jury, also called multidisciplinary Consensus Panel, who drafted a series of recommendations.

RESULTS

The prevalence of HPV in males ranges between 1.3-72.9%;. The prevalence curve in males is much higher than that in females and does not tend to decline with age. Women appear to have a higher probability of acquiring HPV genotypes associated with a high oncogenic risk, whereas in males the probability of acquiring low- or high-risk genotypes is similar. The HPV-related diseases that affect males are anogenital warts and cancers of the penis, anus and oropharynx. The quadrivalent vaccine against HPV has proved to be effective in preventing external genital lesions in males aged 16-26 years in 90.4%; (95%; CI: 69.2-98.1) of cases. It has also proved to be effective in preventing precancerous anal lesions in 77.5%; (95%; CI: 39.6-93.3) of cases in a per-protocol analysis and in 91.7%; (95%; CI: 44.6-99.8) of cases in a post-hoc analysis. Early ecological studies demonstrate reduction of genital warts in vaccinated females and some herd immunity in males when vaccine coverage is high, although males who have sex with males gained no benefit at all. Males with an immunodeficiency disease are at greater risk of developing disease. Infertility seems to be caused by HPV in some cases. Studies demonstrate vaccination to both genders can be more efficacious and social equity matters are to be taken into consideration.

CONCLUSIONS

The Jury made Recommendations based on the scientific evidence presented by the Scientific Committee. Accordingly, for prevention purposes and social fairness and equality, as both sexes are affected by the disease, the vaccination of 12-year-old males against HPV should be recommended in order to guaranty protection to everyone. Aspects related to healthcare policy and economic sustainability, are to be discussed by respective public system representatives. More campaigns to raise awareness through all institutional channels are needed, not only regarding anogenital warts, but for HPV-related diseases in general in males in accordance to new scientific evidences.

Anal cytological abnormalities and epidemiological correlates among men who have sex with men at risk for HIV-1 infection

Background

The incidence of anal cancer, a Human Papillomavirus (HPV)-related neoplasia, has been increasing in recent decades, mainly in men who have sex with men (MSM). Cytological changes of the anal epithelium induced by HPV can be detected through an anal pap smear. This study aimed to evaluate the prevalence and epidemiological correlates of anal cytological abnormalities among relatively young MSM at risk for HIV-1 infection, to help clarify whether or not this population deserves further investigation to assess the presence of anal cancer precursor lesions.

Methods

MSM were recruited among attendees of a large STI clinic for a HIV-1 screening program. Anal samples, collected with a Dracon swab in PreservCyt, were used both for liquid-based cytology and HPV testing by the Linear Array HPV Genotyping Test. Data regarding socio-demographic characteristics and sexual behavior were collected in face-to-face interviews.

Results

A total of 346 MSM were recruited (median age 32 years). Overall, 72.5% of the individuals had an anal HPV infection, with 56.1% of them being infected by oncogenic HPV genotypes. Anal cytological abnormalities were found in 29.8% of the cases (16.7% ASC-US and 13.1% L-SIL). Presence of ASC-US+ was strongly associated with infection by any HPV type (OR=4.21, 95% CI: 1.97-9.23), and particularly by HPV 16 and/or 18 (OR=5.62, 95% CI: 2.33-13.81). A higher proportion of ASC-US+ was found in older MSM, in those with a higher number of lifetime partners and in those with a history of ano-genital warts. However, none of these variables or the others analyzed showed any significant association with abnormal cytological findings.

Conclusions

The presence of anal cytological abnormalities in about one third of the recruited MSM and their strong association with HPV infection, in particular that caused by HPV 16 and/or 18, might provide a further complement to the data that now support the introduction of HPV vaccination among MSM to protect them from the development of HPV-associated diseases. Additional studies are needed to determine whether and how screening for anal cancer precursor lesions should be performed in younger MSM.

Rationale and design of a multicenter prospective cohort study for the eVALuation and monitoring of HPV infections and relATEd cervical diseases in high-risk women (VALHIDATE study)

Background

Pap screening, an effective method for cervical cancer prevention, is now supported by molecular human papillomavirus (HPV) testing. Recently commercialised preventive vaccines also provide new tools for the primary prevention of cervical cancer. To determine appropriate prevention strategies, the Health General Direction, Lombardy Region, funded a project that aims to characterize and monitor HPV infections and related cervical diseases in high-risk women.

Methods/design

VALHIDATE is a 5-year multicentre open prospective cohort study. It will recruit 7000 consenting women aged 13–65 years to provide information about the local biomolecular epidemiology of HPV infection and cervical diseases in high-risk women recruited from nine clinical centres and one faith-based organisation. The study will estimate the overall and type-specific prevalence of HPV infection and cervical abnormalities. It also aims to compare standard Pap screening with biomolecular screening, and to assist in the design of targeted regional prevention programs directed specifically at high-risk groups. Three groups of high-risk women: 1000 HIV-infected women (aged 26–65 years), 1000 recent migrant women (aged 26–65 years) and 3000 young women (aged 13–26 years) and 1 control group: 2000 women (aged 26–45 years) attending a spontaneous screening program, will be recruited. Sample sizes will be revised after the first year. Adult participants will undergo conventional cervical cytology, HPV DNA screening and genotyping. Paediatric participants will undergo HPV DNA testing and genotyping of urine samples. HPV DNA, cytological abnormalities and HPV types will be analysed according to demographic, epidemiological, behavioural, and clinical data collected in an electronic case report form. Overall and stratified prevalences will be estimated to analyse the associations between HPV infection and selected characteristics. Logistic regression models will be used to estimate crude and adjusted odds ratios. Cox proportional hazard models will be used to estimate hazard ratios over time and between groups.

Discussion/main expected results

This study will provide substantial insight into HPV infections and related cervical diseases in high-risk groups and will help determine appropriate regional cervical cancer prevention strategies.

Diversity and uncommon HPV types in HIV seropositive and seronegative women attending an STI clinic

Given the causal relationship between specific types of HPV with cervical cancer and precursor lesions, it is important to identify the viral type involved. The aim of this study is to access the prevalence of HPV types in HIV seropositive and seronegative women. Accordingly, 77 HPV positive cervical samples were obtained from 284 women (seropositive (n=112) and seronegative (n=172) for HIV) who attended a Sexually Transmitted Infection clinic, in Vitoria, Southeastern Brazil. Viral DNA was amplified by PCR using MY09/MY11 degenerated primers and the genotyping was performed by Restriction Fragment Length Polymorphism. Seventy five out of the 77 HPV samples were genotyped: 6, 11, 13, 16, 18, 26, 31, 31b, 32, 33, 34, 35, 52, 53, 55, 56, 58, 59, 61, 62, 64, 66, 71, 81, 83, 84. The most prevalent type was HPV16 followed by HPV types 6, 11 and 53. Fifty five percent and 45% belonged to high and low risk types, respectively. High risk types corresponded to 59% and 54.5% of the HPV detected in HIV seronegative and seropositive women, respectively. The uncommon HPV 13 type in cervical samples was also observed in this study. The oncogenic types were more common in the HIV seronegative samples and the number of cases with multiple infections was similar for the two groups. HPV typing is not only important clinically for the establishment of monitoring and treatment of a patient, it also provides knowledge of the viral types circulating in a population, which is of interest in the development of prevention and treatment programs for this disease.

Prevalence and genotype characterization of human papillomaviruses among HIV-seropositive in Ouagadougou, Burkina Faso

BACKGROUND

Approximately, 15-20 of 40 HPVs that infect the female genital tract confer a high-risk of invasive cancer, thus HPVs account for 95% of cervix cancers. The objectives of this study were to: (i) estimate the prevalence of HPV infection in women infected with HIV in Ouagadougou, (ii) identify potential carcinogenic HPV strains and (iii) determine whether existing HPV vaccines match the isolated strains.

METHODS

From May 2009 to April 2010, 250 HIV-infected women were included in this study. Each woman was screened for the presence of HPV and for HPV genotype using PCR/hybridization technique.

RESULTS

Of the 250 HIV-infected women, 59.6% were infected with at least one type of HPV. High-risk HPVs were identified with the following prevalence: HPV-18 (25.0%); HPV-50'S (25.5%); HPV-30'S (20.8%); HPV-16 (4.7%); HPV-45 (3.7%). Low-risk HPVs were represented by HPV-6 (5.7%) and HPV-11 (0.9%).

CONCLUSION

The issue of the study showed that the existing vaccines: Gardasil and Cervarix may be used in the country although they match only HPV-16, HPV-18, HPV-6 and HPV-11. Further investigations should be continued for the establishment of vaccine that matches all genotypes circulating in the country.