Analysis of the genetic diversity and phylogenetic relationships of putative human papillomavirus types

The impact of HPV infection on human glycogen and lipid metabolism - a review

Reinterpretation of the Wartburg effect leads to understanding aerobic glycolysis as a process that provides considerable amount of molecular precursors for the production of lipids, nucleotides and amino acids that are necessary for continuous growth and rapid proliferation characteristic for cancer cells. Human papilloma virus (HPV) is a number one cause of cervical carcinoma with 99% of the cervical cancer patients being HPV positive. This tight link between HPV and cancer raises the question if and how HPV impact cells to reprogram their metabolism? Focusing on early phase proteins E1, E2, E5, E6 and E7 we demonstrate that HPV activates plethora of metabolic pathways and directly influences enzymes of the glycolysis pathway to promote the Warburg effect by increasing glucose uptake, activating glycolysis and pentose phosphate pathway, increasing the level of lactate dehydrogenase A synthesis and inhibiting β-oxidation. Our considerations lead to conclusion that HPV is substantially involved in metabolic cell reprogramming toward neoplastic phenotype and its metabolic activity is the fundamental reason of its oncogenicity.

Human Papillomavirus Oral Infection: Review of Methodological Aspects and Epidemiology

Oral infection by Human Papillomavirus (HPV) has recently gained great attention because of its involvement in the development of a subset of head and neck squamous cell carcinoma. The role of specific Alpha-HPVs in this regard has been well established, whereas the contribution of other genera is under investigation. Despite their traditional classification as “cutaneous” types, Beta and Gamma HPVs are frequently detected in oral samples. Due to the lack of a standardized protocol, a large variety of methodologies have been used for oral sample collection, DNA extraction, HPV detection and genotyping. Laboratory procedures influence the evaluation of oral HPV prevalence, which largely varies also according to the population characteristics, e.g., age, gender, sexual behavior, Human Immunodeficiency Virus (HIV) status. Nevertheless, oral infection by Beta and Gamma HPVs seems to be even more common than Alpha-HPVs. The latter is 5–7% in the general population, and increases up to 30% approximately in HIV-infected men who have sex with men. Despite major advances in the evaluation of oral HPV prevalence, its natural history is still little understood, especially for Beta and Gamma HPVs. The latest technologies, such as Next Generation Sequencing (NGS), can be exploited to gain new insights into oral HPV, and to improve the identification of novel HPV types.

Impact of COVID-19 and other viruses on reproductive health

Male infertility is linked to some viral infections including human papillomavirus (HPV), herpes simplex viruses (HSV) and human immunodeficiency viruses (HIVs). Almost nothing is known about severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) effect on fertility. The possible risk factors of coronavirus disease 2019 (COVID‐19) infection on fertility comes from the abundance of angiotensin‐Converting Enzyme‐2 (ACE2), receptor entry of the virus, on testes, a reduction in important sex hormone ratios and COVID‐19‐associated fever. Recent studies have shown a gender difference for COVID‐19 rates and comorbidity. In this review, we will discuss the potential effect of COVID‐19 on male fertility and talk about what needs to be done by the scientific community to tackle our limited understanding of the disease. On the other side, we will focus on what is known so far about the risk of COVID‐19 on pregnancy, neonatal health and the vertical transfer of the virus between mothers and their neonates. Finally, because reproduction is a human right and infertility is considered a health disease, we will discuss how assisted reproductive clinics can cope with the pandemic and what guidelines they should follow to minimise the risk of viral transmission.

Prevalence and Correlates of β- and γ-Human Papillomavirus Detection in Oral Samples From Mid-Adult Women

BACKGROUND

Little is known about the epidemiology of β and γ human papillomaviruses (HPVs) in oral cavities of healthy women.

METHODS

We performed multiplex polymerase chain reaction analysis for detection of 46 β-HPVs and 51 γ-HPVs in stored oral rinse samples from healthy mid-adult women (age, 30-50 years). A total of 407 women were tested for β-HPVs, and 310 were tested for γ-HPVs. We used log-binomial regression to identify determinants of β-HPV and γ-HPV in separate models. Using paired fingernail data from a subset of 184 women, we also evaluated whether fingernail β-HPV detection was associated with concurrent detection of the same type in the oral cavity.

RESULTS

Oral HPV prevalence was 20.6% for β-HPV and 10.7% for γ-HPV. In multivariate analysis, oral β-HPV detection was associated with increasing age (adjusted prevalence ratio [aPR] per 5-year difference, 1.37; 95% confidence interval [CI], 1.01-1.86) and a greater lifetime number of oral sex partners (aPR for reporting ≥6 vs 0-5 partners, 2.06; 95% CI, 1.01-4.20). In a separate model, concurrent detection of the same β-HPV type in fingernails was strongly associated with oral β-HPV detection (aPR, 31.44; 95% CI, 19.81-49.49). No significant determinants of γ-HPV detection were identified.

CONCLUSIONS

Our results suggest a sexual transmission route for β-HPVs and support the hypothesis that fingers may serve as a source of transmission or autoinoculation of β-HPVs to the oral cavity.

Application of an entropy-based computational strategy to identify genomic markers for molecular detection and typing of human papillomavirus

Human papillomavirus (HPV) is a diverse group of double-stranded DNA viruses that present high tropism for the epithelium and infect keratinocytes. Currently, over 200 viral types have been identified, and almost 40 types preferentially infect the epithelial cells of the genital tract. Infections caused by HPV are the most prevalent viral infections that are sexually transmitted in the world. Given how HPV infection is one of the key factors in the development of cervical cancer, we need to develop more effective diagnostic methods to correctly diagnose patients. The significance of our research is that we have developed and applied a novel computational approach based on entropy to identify phylogenetically informative genomic regions that could be used as markers for the detection and typing of HPV. We have demonstrated that our strategy is capable of finding phylogenetically informative L1 regions to design a primer set that can be used to accurately detect and genotype HPV isolates.

The Host-Microbe Interplay in Human Papillomavirus-Induced Carcinogenesis

Every year nearly half a million new cases of cervix cancer are diagnosed worldwide, making this malignancy the fourth commonest cancer in women. In 2018, more than 270,000 women died of cervix cancer globally with 85% of them being from developing countries. The majority of these cancers are caused by the infection with carcinogenic strains of human papillomavirus (HPV), which is also causally implicated in the development of other malignancies, including cancer of the anus, penis cancer and head and neck cancer. HPV is by far the most common sexually transmitted infection worldwide, however, most infected people do not develop cancer and do not even have a persistent infection. The development of highly effective HPV vaccines against most common high-risk HPV strains is a great medical achievement of the 21st century that could prevent up to 90% of cervix cancers. In this article, we review the current understanding of the balanced virus-host interaction that can lead to either virus elimination or the establishment of persistent infection and ultimately malignant transformation. We also highlight the influence of certain factors inherent to the host, including the immune status, genetic variants and the coexistence of other microbe infections and microbiome composition in the dynamic of HPV infection induced carcinogenesis.

Beta Human Papillomavirus and Associated Diseases

The cutaneous human papillomavirus (HPV), mostly from β- and γ-HPV genus, is ubiquitously distributed throughout the human body and may be part of the commensal flora. The association of β-HPVs and cutaneous squamous cell carcinoma (cSCC) development was initially reported in patients with the rare genetic disorder Epidermodysplasia verruciformis. Likewise, immunosuppressed organ transplant recipients have an increased susceptibility to β-HPV infections in the skin as well as to cSCC development. Although ultraviolet radiation (UVR) is the main risk factor of cSCC, experimental data points toward β-HPVs as co-carcinogens, which appear to be required solely at early stages of skin carcinogenesis by facilitating the accumulation of UVR-induced DNA mutations. Several epidemiological studies relying on different biomarkers of β-HPV infections have also been conducted in immunocompetent individuals to access their association with cSCC development. Additionally, in vivo and in vitro studies are presenting cumulative evidence that E6 and E7 proteins from specific β-HPVs exhibit transforming activities and may collaborate with different environmental factors in promoting carcinogenesis. Nevertheless, further research is crucial to better understand the pathological implications of the broad distribution of these HPVs.

High prevalence of Gammapapillomaviruses (Gamma-PVs) in pre-malignant cutaneous lesions of immunocompetent individuals using a new broad-spectrum primer system, and identification of HPV210, a novel Gamma-PV type

Genus Gammapapillomavirus (Gamma-PV) is the most diverse and largest clade within the Papillomaviridae family. A novel set of degenerate primers targeting the E1 gene was designed and further used in combination with the well-known CUT PCR assay to assess HPV prevalence and genus distribution in a variety of cutaneous samples from 448 immunocompetent individuals. General HPV, Gamma-PV and mixed infections prevalence were significantly higher in actinic keratosis with respect to benign and malignant neoplasms, respectively (p = 0.0047, p = 0.0172, p = 0.00001). Gamma-PVs were significantly more common in actinic keratosis biopsies than Beta- and Alpha-PVs (p = 0.002). The full-length genome sequence of a novel putative Gamma-PV type was amplified by 'hanging droplet' long-range PCR and cloned. The novel virus, designated HPV210, clustered within species Gamma-12. This study provides an additional tool enabling detection of HPV infections in skin and adds new insights about possible early roles of Gamma-PVs in the development of cutaneous malignant lesions.

Epidemiology and biology of cutaneous human papillomavirus

Cutaneous human papillomaviruses (HPVs) include β- and γ-HPVs, in addition to a small fraction of α-HPVs. β-HPVs were first isolated from patients with the rare genetic disorder Epidermodysplasia verruciformis, and they are associated with the development of nonmelanoma skin cancer at sun-exposed skin sites in these individuals. Organ transplant recipients also have greater susceptibility to β-HPV infection of the skin and an increased risk of developing nonmelanoma skin cancer. In both immunosuppressed and immunocompromised individuals, cutaneous HPVs are ubiquitously disseminated throughout healthy skin and may be an intrinsic part of the commensal flora. Functional analysis of E6 and E7 proteins of specific cutaneous HPVs has provided a mechanistic comprehension of how these viruses may induce carcinogenesis. Nevertheless, additional research is crucial to better understand the pathological implications of the broad distribution of these HPVs.

Prevalence and correlates of beta human papillomavirus detection in fingernail samples from mid-adult women

Cutaneous human papillomaviruses (HPVs) have not been evaluated in fingernails from healthy individuals. To determine prevalence and correlates of β-HPVs in fingernails from healthy mid-adult women, we tested archived samples collected from 2011 to 2012 using a multiplex PCR combined with Luminex technology for 46 β-HPV genotypes. One hundred thirteen (61.1%) of 185 fingernail samples were positive for β-HPV, and the median number of types detected in positive samples was 2 (interquartile range: 1–4). The most common genotypes detected were HPV-23 (β−2) (13.5%), HPV-38 (β−2) (13.0%), HPV-5 (β−1) (9.2%), HPV-107 (β−2) (8.7%), and HPV-120 (β−2) (8.7%). In multivariate analysis, β-HPV detection was associated with age (prevalence ratio [PR] for women 40–51 years versus 30–39 years = 1.30, 95% CI: 1.05–1.62) and race (PR for non-white versus white race = 0.65, 95% CI: 0.45–0.94). The prevalence of β-HPV in fingernail samples from healthy mid-adult women was similar to the prevalence of β-HPV reported at other cutaneous sites in prior studies. We did not identify any significant health or sexual behavior predictors of β-HPV detection in fingernails. Our results support the hypothesis that fingers may serve as a source of transmission or autoinoculation of cutaneous HPVs to other anatomic sites.

Detection of novel Betapapillomaviruses and Gammapapillomaviruses in eyebrow hair follicles using a single-tube 'hanging droplet' PCR assay with modified pan-PV CODEHOP primers

A modified pan-PV consensus-degenerate hybrid oligonucleotide primer (CODEHOP) PCR was developed for generic and sensitive detection of a broad-spectrum of human papillomaviruses (HPVs) infecting the cutaneous epithelium. To test the analytical sensitivity of the assay we examined 149 eyebrow hair follicle specimens from immunocompetent male patients. HPV DNA was detected in 60 % (89/149) of analysed eyebrow samples with a total of 48 different HPV sequences, representing 21 previously described HPVs and 27 putative novel HPV types. Evidence for ten novel HPV subtypes and seven viral variants, clustering to three out of five genera containing cutaneous HPVs, was also obtained. Thus, we have shown that the modified pan-PV CODEHOP PCR assay is able to identify multiple HPV types, even from different genera, in the same clinical sample. Overall, these results demonstrate that the pan-PV CODEHOP PCR is an excellent tool for screening and identification of novel cutaneous HPVs, even in samples with low viral loads.

Cervical Infection with Cutaneous Beta and Mucosal Alpha Papillomaviruses

Background: Alpha-human papillomavirus (α-HPV) plays a causal role in cervical cancer, but little is known about the epidemiology of genital Beta-human papillomavirus (β-HPV) infection.Methods: We used Luminex and PCR hybridization to detect β- and α-HPVs prevalence at enrollment and 12-month follow-up in cervical samples from 505 women enrolled in the Ludwig-McGill cohort study. We compared epidemiologic correlates of both β- and α-HPVs and compared genotypes between these genera with respect to co-occurrence and association with cervical cytologic abnormalities.Results: Infection with β-HPV types was more prevalent than that with α-HPV types at both visits (cumulative prevalences: 27.3% vs. 21.6%, respectively, P = 0.034). β-HPVs were mostly transient; however, only 1.98% women retained their original positivity at 12 months, whereas persistence was higher for α-HPVs (5.15%; P = 0.007). Age, parity, and sexual activity variables were predictors of α-HPV but not of β-HPV. α- and β-HPV types occurred independently. Increased risk of cervical abnormalities was restricted to women infected with α-9 or α-6 HPV types. We found no epidemiologic correlates for β-HPV infections.Conclusions: Detection of β-HPV types in the cervix tends to occur as random and transient episodes not explained via the sexual-transmission correlates that characterize infections by α-HPVs.Impact: Although it is plausible that β-HPVs may play a direct or indirect carcinogenic role, the lack of epidemiologic correlates for detection episodes of these viruses and lack of association with cervical lesions speak against their ancillary role as sexually transmitted agents in cervical carcinogenesis. Cancer Epidemiol Biomarkers Prev; 26(8); 1312-20. ©2017 AACR.

Natural history of human papillomavirus infection of sun-exposed healthy skin of immunocompetent individuals over three climatic seasons and identification of HPV209, a novel betapapillomavirus

We present the first longitudinal study reporting the natural history of human papillomavirus (HPV) infection in sun-exposed skin of healthy individuals living in a geographical area in which solar UV radiation is influenced by the ozone content of the atmosphere. During three climatic seasons, skin swab samples were obtained from 78 healthy individuals and the prevalence of cutaneous HPVs was assessed with broad-spectrum FAP and CUT primers and determined at 54, 45 and 47 % in spring, summer and winter, respectively. Frequencies of mixed HPV infections were significantly higher in spring with respect to summer and winter (P=0.02). Seventy-one different HPV types/putative types were identified. While 62 volunteers were HPV-infected in at least one season, 23 had persistent infections. β-PVs (β-1) were the most prevalent and persistent. Age was associated with both the infection status (P=0.01) and the type of HPV infection (no infection, indeterminate/transient, persistent P=0.02). The molecular/phylogenetic analysis of the newly identified β-PV, officially designated as HPV209, showed that the virus has a typical genomic organization of cutaneous HPVs with five early (E6, E7, E1, E2 and E4) and two late genes (L2 and L1), which clusters to the species β-2. This provides useful data on cutaneous HPV infections in high UV-exposed regions.

High diversity of alpha, beta and gamma human papillomaviruses in genital samples from HIV-negative and HIV-positive heterosexual South African men

BACKGROUND

This study investigated the prevalence of HPVs in heterosexual South African men and the impact of HIV co-infection.

METHODS

HPV was detected in penile swabs from 195 HIV-infected and 140 HIV-uninfected men using PCR with FAP59/64 primers and Roche Linear Array HPV genotyping (LA). Genotyping of FAP positive specimens was achieved by high-throughput sequencing of amplicons.

RESULTS

HPV was detected by FAP PCR and LA in 79% (266/335) of the men. Men with HIV co-infection and men with HIV infected sexual partners had a significantly (p<0.0001) higher HPV infection risk (adjusted odds ratio 4.0 (2.1-8.2) and 3.7 (2.1-6.7), respectively). LA genotyping and 454 sequencing of 218 FAP positive specimens detected 45 known α-HPV types, 45 β-HPV types (34 known, 10 putative and 1 novel putative), and 91 γ-HPV types (26 known, 51 putative and 14 novel putative). Alpha, beta and gamma types were detected in 89.8%, 51.4% and 62.4% of the 218 men with HPV-62, HPV-5 and HPV-121 most common in each genus, respectively.

CONCLUSION

A great diversity of known and novel alpha, beta and gamma HPV types were detected with higher prevalence in HIV co-infected men and unknown associations, if any, with genital lesions and cancers.

A central region in the minor capsid protein of papillomaviruses facilitates viral genome tethering and membrane penetration for mitotic nuclear entry

Incoming papillomaviruses (PVs) depend on mitotic nuclear envelope breakdown to gain initial access to the nucleus for viral transcription and replication. In our previous work, we hypothesized that the minor capsid protein L2 of PVs tethers the incoming vDNA to mitotic chromosomes to direct them into the nascent nuclei. To re-evaluate how dynamic L2 recruitment to cellular chromosomes occurs specifically during prometaphase, we developed a quantitative, microscopy-based assay for measuring the degree of chromosome recruitment of L2-EGFP. Analyzing various HPV16 L2 truncation-mutants revealed a central chromosome-binding region (CBR) of 147 amino acids that confers binding to mitotic chromosomes. Specific mutations of conserved motifs (IVAL286AAAA, RR302/5AA, and RTR313EEE) within the CBR interfered with chromosomal binding. Moreover, assembly-competent HPV16 containing the chromosome-binding deficient L2(RTR313EEE) or L2(IVAL286AAAA) were inhibited for infection despite their ability to be transported to intracellular compartments. Since vDNA and L2 were not associated with mitotic chromosomes either, the infectivity was likely impaired by a defect in tethering of the vDNA to mitotic chromosomes. However, L2 mutations that abrogated chromatin association also compromised translocation of L2 across membranes of intracellular organelles. Thus, chromatin recruitment of L2 may in itself be a requirement for successful penetration of the limiting membrane thereby linking both processes mechanistically. Furthermore, we demonstrate that the association of L2 with mitotic chromosomes is conserved among the alpha, beta, gamma, and iota genera of Papillomaviridae. However, different binding patterns point to a certain variance amongst the different genera. Overall, our data suggest a common strategy among various PVs, in which a central region of L2 mediates tethering of vDNA to mitotic chromosomes during cell division thereby coordinating membrane translocation and delivery to daughter nuclei.

Papillomaviruses can cause carcinogenic malignancies such as cervical cancer. Like most DNA viruses, papillomaviruses must deliver their genome to the cell nucleus during initial infection, where it is expressed and replicated. However, papillomaviruses make use of unconventional mechanisms for genome delivery. They reside on the cell surface for protracted, hour-long times, before they are taken up by a novel endocytic mechanism. Moreover, they are delivered to the trans-Golgi-network by non-canonical endosomal trafficking prior to nuclear delivery. For entry into the nucleus, papillomaviruses access the nuclear space after nuclear envelope breakdown during mitosis unlike most other intranuclear viruses. The detailed mechanism how the viral genome is directed to nascent nuclei during mitosis remains elusive. Our previous work suggested that the minor capsid protein L2 may tether the incoming viral genome to mitotic chromosomes to direct it to the nascent nuclei. This work identifies a conserved central region in L2 protein to be necessary and sufficient for tethering. Moreover, it demonstrates that this mechanism is conserved across different papillomavirus genera. Importantly, this report also provides evidence that the processes of nuclear import by tethering and membrane penetration are mechanistically linked.

Seroprevalence of Cutaneous Human Papillomaviruses and the Risk of External Genital Lesions in Men: A Nested Case-Control Study

Background

A variety of cutaneous human papillomaviruses (HPV) are detectable in genital epithelial lesions in men and non-melanoma skin cancer patients. It remains unclear whether these viruses are associated causally with skin lesions. To date, no study has prospectively examined the association between cutaneous HPV seropositivity and development of external genital lesions (EGLs) in men.

Objectives

To examine the association between seropositivity to cutaneous HPV types and the risk of subsequent development of EGLs.

Methods

A nested case-control study including 163 incident EGL cases and 352 EGL-free controls in the HPV Infection in Men (HIM) Study cohort was conducted. Cases were ascertained at each of up to 10 biannual clinical visits and verified through biopsy and pathological diagnoses. EGLs were categorized as condyloma, suggestive of condyloma, penile intraepithelial neoplasia (PeIN), and other EGLs. Archived serum specimens collected at baseline were tested for antibodies against 14 cutaneous HPV types (β types (5, 8, 12, 14, 17, 22, 23, 24, 38, and 47), α type 27, γ type 4, μ type 1, and ν type 41) using a GST L1-based multiplex serology assay. Socio-demographic and sexual behavior data were collected through a questionnaire. Using logistic regression, adjusted odds ratios (AOR) and 95% confidence intervals (CI) were estimated.

Results

Overall, seropositivity to ≥1 cutaneous HPV type (any-HPV) and ≥1 β types (any-β) was 58.3% and 37.5% among other EGL cases, 71.6% and 46.8% among condyloma, 66.8% and 50.0% among PeIN, and 71.9% and 38.4% among controls, respectively. Type-specific seropositivity was most common for ɤ-HPV 4, μ-HPV 1, and β-HPV 8. No statistically significant association was observed between any-HPV, any-β, and type-specific HPV seropositivity and subsequent development of EGLs across all pathological diagnoses.

Conclusions

Overall, seropositivity to cutaneous HPV was common among men; however, it appears that cutaneous HPV is not associated with the development of genital lesions in men.

Diversity of beta-papillomavirus at anogenital and oral anatomic sites of men: The HIM Study

Our goal was to describe prevalence of β-HPVs at three anatomic sites among 717 men from Brazil, Mexico and US enrolled in the HPV Infection in Men (HIM) Study. β-HPVs were genotyped using Luminex technology. Overall, 77.7%, 54.3% and 29.3% men were positive for any β-HPV at the genitals, anal canal, and oral cavity, respectively. Men from US and Brazil were significantly less likely to have β-HPV at the anal canal than men from Mexico. Older men were more likely to have β-HPV at the anal canal compared to younger men. Prevalence of β-HPV at the oral cavity was significantly associated with country of origin and age. Current smokers were significantly less likely to have β-HPV in the oral cavity than men who never smoked. Lack of associations between β-HPV and sexual behaviors may suggest other routes of contact such as autoinoculation which need to be explored further.

Characterization of novel human papillomavirus types 157, 158 and 205 from healthy skin and recombination analysis in genus γ-Papillomavirus

Gammapapillomavirus (γ-PV) is a diverse and rapidly expanding genus, currently consisting of 79 fully characterized human PV (HPV) types. In this study, three novel types, HPV157, HPV158 and HPV205, obtained from healthy sun-exposed skin of two immunocompetent individuals, were amplified by the "Hanging droplet" long PCR technique, cloned, sequenced and characterized. HPV157, HPV158 and HPV205 genomes comprise 7154-bp, 7192-bp and 7298-bp, respectively, and contain four early (E1, E2, E6 and E7) and two late genes (L1 and L2). Phylogenetic analysis of the L1 ORF placed all novel types within the γ-PV genus: HPV157 was classified as a new member of species γ-12 while HPV158 and HPV205 belong to species γ-1. We then explored potential recombination events in genus γ-PV with the RDP4 program in a dataset of 74 viruses (71 HPV types with available full-length genomes and the 3 novel types). Two events, both located in the E1 ORF, met the inclusion criterion (p-values <0.05 with at least four methods) and persisted in different ORF combinations: an inter-species recombination in species γ-8 (major and minor parents: species γ-24 and γ-11, respectively), and an intra-species recombination in species γ-7 (recombinant strain: HPV170; major and minor parents: HPV-109 and HPV-149, respectively). These findings were confirmed by phylogenetic tree incongruence analysis. An additional incongruence was found in members of species γ-9 but it was not detected by the RDP4. This report expands our knowledge of the family Papillomaviridae and provides for the first time in silico evidence of recombination in genus γ-PV.

Recent Insights into the Control of Human Papillomavirus (HPV) Genome Stability, Loss, and Degradation

Most human papillomavirus (HPV) antiviral strategies have focused upon inhibiting viral DNA replication, but it is increasingly apparent that viral DNA levels can be chemically controlled by approaches that promote its instability. HPVs and other DNA viruses have a tenuous relationship with their hosts. They must replicate and hide from the DNA damage response (DDR) and innate immune systems, which serve to protect cells from foreign or “non-self” DNA, and yet they draft these same systems to support their life cycles. DNA binding antiviral agents promoting massive viral DNA instability and elimination are reviewed. Mechanistic studies of these agents have identified genetic antiviral enhancers and repressors, antiviral sensitizers, and host cell elements that protect and stabilize HPV genomes. Viral DNA degradation appears to be an important means of controlling HPV DNA levels in some cases, but the underlying mechanisms remain poorly understood. These findings may prove useful not only for understanding viral DNA persistence but only in devising future antiviral strategies.

Characterization of two novel gammapapillomaviruses, HPV179 and HPV184, isolated from common warts of a renal-transplant recipient

Gammapapillomavirus (Gamma-PV) is a diverse and rapidly expanding PV-genus, currently consisting of 76 fully characterized human papillomavirus (HPV) types. In this study, DNA genomes of two novel HPV types, HPV179 and HPV184, obtained from two distinct facial verrucae vulgares specimens of a 64 year-old renal-transplant recipient, were fully cloned, sequenced and characterized. HPV179 and HPV184 genomes comprise 7,228-bp and 7,324-bp, respectively, and contain four early (E1, E2, E6 and E7) and two late genes (L1 and L2); the non-coding region is typically positioned between L1 and E6 genes. Phylogenetic analysis of the L1 nucleotide sequence placed both novel types within the Gamma-PV genus: HPV179 was classified as a novel member of species Gamma-15, additionally containing HPV135 and HPV146, while HPV184 was classified as a single member of a novel species Gamma-25. HPV179 and HPV184 type-specific quantitative real-time PCRs were further developed and used in combination with human beta-globin gene quantitative real-time PCR to determine the prevalence and viral load of the novel types in the patient's facial warts and several follow-up skin specimens, and in a representative collection, a total of 569 samples, of HPV-associated benign and malignant neoplasms, hair follicles and anal and oral mucosa specimens obtained from immunocompetent individuals. HPV179 and HPV184 viral loads in patients' facial warts were estimated to be 2,463 and 3,200 genome copies per single cell, respectively, suggesting their active role in the development of common warts in organ-transplant recipients. In addition, in this particular patient, both novel types had established a persistent infection of the skin for more than four years. Among immunocompetent individuals, HPV179 was further detected in low-copy numbers in a few skin specimens, indicating its cutaneous tissue tropism, while HPV184 was further detected in low-copy numbers in one mucosal and a few skin specimens, suggesting its dual tissue tropism.

Diversity of human papillomavirus in the anal canal of men: the HIM Study

Human papillomavirus (HPV) infections are associated with the development of anogenital lesions in men. There are no reports describing the distribution of non-α HPV types in the anal canal of a sexually diverse group of men. The HPV Infection in Men (HIM) Study is a multicentre study on the natural history of HPV infection in Brazil, Mexico, and the USA. At baseline, 12% of anal canal PCR HPV-positive specimens were not typed by the Roche Linear Array, and were considered to be unclassified. Our goals were to characterize HPVs among these unclassified specimens at baseline, and to assess associations with participant socio-demographic and behavioural characteristics. Unclassified HPVs were typed by sequencing of amplified PGMY09/11 products or cloning of PGMY/GP + nested amplicons followed by sequencing. Further analysis was conducted with FAP primers. Of men with unclassified HPV in the anal canal, most (89.1%) were men who have sex with women. Readable sequences were produced for 62.8% of unclassified specimens, of which 75.2% were characterized HPV types. Eighteen, 26 and three different α-HPV, β-HPV and γ-HPV types were detected, respectively. α-HPVs were more commonly detected among young men (18-30 years) than among older men (45-70 years), whereas β-HPVs were more frequent among mid-adult men (31-44 years). β-HPVs were more common among heterosexual men (85.0%) than among non-heterosexual men. All β-HPVs detected among non-heterosexual men were β2-HPV types. The high prevalence of β-HPV in the anal canal of men who do not report receptive anal sex is suggestive of other forms of transmission that do not involve penile-anal intercourse.

High genital prevalence of cutaneous human papillomavirus DNA on male genital skin: the HPV Infection in Men Study

Background

The genital skin of males hosts a diversity of HPV genotypes and uncharacterized HPV genotypes. Previously we demonstrated that a specific viral genotype was not identified in 14% of all genital specimens (i.e., HPV unclassified specimens) using the Roche Linear Array method. Our goal was to identify and assess the prevalence of individual HPV types among genital HPV unclassified specimens collected in the HIM Study population, at enrollment, and examine associations with socio-demographic and behavioral characteristics.

Methods

Genital skin specimens of men that were considered unclassified (HPV PCR positive, no genotype specified) at enrollment were typed by sequencing amplified PGMY09/11 products or cloning of PGMY/GP+ nested amplicons followed by sequencing. PGMY/GP+ negative specimens were further analyzed using FAP primers. HPV type classification was conducted through comparisons with sequences in the GenBank database.

Results

Readable nucleotide sequences were generated for the majority of previously unclassified specimens (66%), including both characterized (77%) and yet uncharacterized (23%) HPV types. Of the characterized HPV types, most (73%) were Beta [β]-HPVs, primarily from β-1 and β-2 species, followed by Alpha [α]-HPVs (20%). Smokers (current and former) were significantly more likely to have an α-HPV infection, compared with any other genus; no other factors were associated with specific HPV genera or specific β-HPV species.

Conclusions

Male genital skin harbor a large number of β-HPV types. Knowledge concerning the prevalence of the diverse HPV types in the men genital is important to better understand the transmission of these viruses.

Electronic supplementary material

The online version of this article (doi:10.1186/s12879-014-0677-y) contains supplementary material, which is available to authorized users.

A large spectrum of alpha and beta papillomaviruses are detected in human stool samples

Human papillomaviruses (HPVs) have been detected in urban wastewaters, demonstrating that epitheliotropic viruses can find their way into sewage through the washing of skin and mucous membranes. Papillomavirus shedding through faeces is still an unexplored issue. The objective of the present study was to investigate the presence of HPVs in stool samples. We analysed 103 faecal specimens collected from hospitalized patients with diarrhoea using validated primers able to detect α, β and γ HPVs. PCR products underwent sequencing analysis and sequences were aligned to reference genomes from the Papillomavirus Episteme database. A total of 15 sequences were characterized from the faecal samples. Thirteen samples (12.6 %) were positive for nine genotypes belonging to the α and β genera: HPV32 (LR, α1), HPV39 (HR, α7), HPV44 (LR, α10), HPV8 (β1), HPV9, HPV23, HPV37, HPV38 and HPV120 (β2). Two putative novel genotypes of the β genus, species 1 and 2, were also detected. The tissue(s) of origin is unknown, since faeces can collect HPVs originating from or passing through the entire digestive system. To our knowledge, this is the first investigation on the occurrence and diversity of HPVs in faecal samples. Results from this study demonstrate that HPVs can find their way into sewage as a consequence of shedding in the faeces. This highlights the need for further studies aimed at understanding the prevalence of HPV in different water environments and the potential for waterborne transmission.

The role of ubiquitin and ubiquitin-like modification systems in papillomavirus biology

Human papillomaviruses (HPVs) are small DNA viruses that are important etiological agents of a spectrum of human skin lesions from benign to malignant. Because of their limited genome coding capacity they express only a small number of proteins, only one of which has enzymatic activity. Additionally, the HPV productive life cycle is intimately tied to the epithelial differentiation program and they must replicate in what are normally non-replicative cells, thus, these viruses must reprogram the cellular environment to achieve viral reproduction. Because of these limitations and needs, the viral proteins have evolved to co-opt cellular processes primarily through protein-protein interactions with critical host proteins. The ubiquitin post-translational modification system and the related ubiquitin-like modifiers constitute a widespread cellular regulatory network that controls the levels and functions of thousands of proteins, making these systems an attractive target for viral manipulation. This review describes the interactions between HPVs and the ubiquitin family of modifiers, both to regulate the viral proteins themselves and to remodel the host cell to facilitate viral survival and reproduction.

No association between Birt-Hogg-Dubé syndrome skin fibrofolliculomas and the first 10 described human polyomaviruses or human papillomaviruses

The rare autosomal dominant condition Birt-Hogg-Dubé syndrome (BHD) is attributed to mutations on chromosome 17 in the folliculin (FLCN) gene, but not always diagnosed due to lack of, or a variety of symptoms such as fibrofolliculomas, lung cystic lesions, spontaneous pneumothorax and renal cancer. We hypothesized that the lack of or variability in symptoms could be due to BHD patients potentially being abnormally susceptible to infections with human papillomavirus (HPV) or human polyomavirus (HPyV), which can be associated with skin lesions or latency in the kidneys. Seven fibrofolliculoma skin lesions, one renal cancer and one lung cyst from nine patients with BHD treated at the Karolinska University Hospital were therefore analyzed for cutaneous and mucosal HPV types and 10 HPyVs by bead based multiplex assays or by PCR. All samples were negative for viral DNA. In conclusion, the data suggest that HPV and HPyVs do not contribute to BHD pathology.

Frequency and distribution of simple and compound microsatellites in forty-eight Human papillomavirus (HPV) genomes

Simple sequence repeats (SSRs) are tandem-repeated sequences ubiquitously present but differentially distributed across genomes. Present study is a systematic analysis for incidence, composition and complexity of different microsatellites in 48 representative Human papillomavirus (HPV) genomes. The analysis revealed a total of 1868 SSRs and 120 cSSRs. However, four genomes (HPV-60, HPV-92, HPV-112 and HPV-136) lacked any cSSR content; while HPV-31 accounted for a maximum of 10 cSSRs. An overall increase in cSSR% with higher dMAX was observed. The SSRs and cSSRs were prevalent in coding regions. Poly(A/T) repeats were significantly more abundant than poly(G/C) repeats possibly due to high (A/T) content of the HPV genomes. Further, higher prevalence of di-nucleotide repeats over tri-nucleotide repeats may be attributed to instability of former because of higher slippage rate. An in-depth study of the satellite sequences would provide an insight into the imperfections and evolution of microsatellites.