Recurring infection with ecologically distinct HPV types can explain high prevalence and diversity

The evolutionary cost of homophily: social stratification facilitates stable variant coexistence and increased rates of evolution in host-associated pathogens

Coexistence of multiple strains of a pathogen in a host population can present significant challenges to vaccine development or treatment efficacy. Here we discuss a novel mechanism that can increase rates of long-lived strain polymorphism, rooted in the presence of social structure in a host population. We show that social preference of interaction, in conjunction with differences in immunity between host subgroups, can exert varying selection pressure on pathogen strains, creating a balancing mechanism that supports stable viral coexistence, independent of other known mechanisms. We use population genetic models to study rates of pathogen heterozygosity as a function of population size, host population composition, mutant strain fitness differences and host social preferences of interaction. We also show that even small periodic epochs of host population stratification can lead to elevated strain coexistence. These results are robust to varying social preferences of interaction, overall differences in strain fitnesses, and spatial heterogeneity in host population composition. Our results highlight the role of host population social stratification in increasing rates of pathogen strain diversity, with effects that should be considered when designing policies or treatments with a long-term view of curbing pathogen evolution.

Association of naturally acquired type-specific HPV antibodies and subsequent HPV re-detection: systematic review and meta-analysis

BACKGROUND

Understanding the role of naturally acquired (i.e., infection-induced) human papillomavirus (HPV) antibodies against reinfection is important given the high incidence of this sexually transmitted infection. However, the protective effect of naturally acquired antibodies in terms of the level of protection, duration, and differential effect by sex remains incompletely understood. We conducted a systematic review and a meta-analysis to (1) strengthen the evidence on the association between HPV antibodies acquired through past infection and subsequent type-specific HPV detection, (2) investigate the potential influence of type-specific HPV antibody levels, and (3) assess differential effects by HIV status.

METHODS

We searched Embase and Medline databases to identify studies which prospectively assessed the risk of type-specific HPV detection by baseline homologous HPV serostatus among unvaccinated individuals. Random-effect models were used to pool the measures of association of naturally acquired HPV antibodies against subsequent incident detection and persistent HPV positivity. Sources of heterogeneity for each type were assessed through subgroup analyses stratified by sex, anatomical site of infection, male sexual orientation, age group, and length of follow-up period. Evidence of a dose-response relationship of the association between levels of baseline HPV antibodies and type-specific HPV detection was assessed. Finally, we pooled estimates from publications reporting associations between HPV serostatus and type-specific HPV detection by baseline HIV status.

RESULTS

We identified 26 publications (16 independent studies, with 62,363 participants) reporting associations between baseline HPV serostatus and incident HPV detection, mainly for HPV-16 and HPV-18, the most detected HPV type. We found evidence of protective effects of baseline HPV seropositivity and subsequent detection of HPV DNA (0.70, 95% CI 0.61-0.80, NE = 11) and persistent HPV positivity (0.65, 95% CI 0.42-1.01, NE = 5) mainly for HPV-16 among females, but not among males, nor for HPV-18. Estimates from 8 studies suggested a negative dose-response relationship between HPV antibody level and subsequent detection among females. Finally, we did not observe any differential effect by baseline HIV status due to the limited number of studies available.

CONCLUSION

We did not find evidence that naturally acquired HPV antibodies protect against subsequent HPV positivity in males and provide only modest protection among females for HPV-16. One potential limitation to the interpretation of these findings is potential misclassification biases due to different causes.

HPV co-infections with other pathogens in cancer development: A comprehensive review

High-risk human papillomaviruses (HR-HPVs) cause various malignancies in the anogenital and oropharyngeal regions. About 70% of cervical and oropharyngeal cancers are caused by HPV types 16 and 18. Notably, some viruses including herpes simplex virus, Epstein-Barr virus, and human immunodeficiency virus along with various bacteria often interact with HPV, potentially impacting its replication, persistence, and cancer progression. Thus, HPV infection can be significantly influenced by co-infecting agents that influence infection dynamics and disease progression. Bacterial co-infections (e.g., Chlamydia trachomatis) along with bacterial vaginosis-related species also interact with HPV in genital tract leading to viral persistence and disease outcomes. Co-infections involving HPV and diverse infectious agents have significant implications for disease transmission and clinical progression. This review explores multiple facets of HPV infection encompassing the co-infection dynamics with other pathogens, interaction with the human microbiome, and its role in disease development.

Prevalence and Genetype Distribution of Human Papillomavirus in Women with Condyloma Acuminatum in Henan Province, Central China

Purpose

This study aims to analyze the distribution of human papillomavirus (HPV) genotypes and the associations of demographic characteristics with HPV infection among women with condyloma acuminatum (CA) in Henan Province of China.

Methods

From January 2019 to October 2022, 702 women with CA were sampled for HPV subtypes and surveyed by questionnaire at Henan Provincial People's Hospital. The HPV genotype was tested by flow-through hybridization after polymerase chain reaction (PCR).

Results

The location of warts was mainly vulva. The age of the subjects was mainly distributed in the 20-29-year-old, followed by 30-39-year-old. The most common subtypes were HPV 6 (43.59%), 11 (24.93%), 16 (11.82%), 52 (7.83%), 58 (7.55%), 51 (7.26%), 61 (5.70%), 39 (5.56%), 18 (5.13%), and 54 (4.70%), our results also suggested that HPV 6 and 11 were the dominant genotypes in each age group. The infection of low-risk HPV (LR-HPV) (74.50%) and single HPV (47.01%) were the main categories. In terms of educational level, women with senior high school or above were inclined to infect single and pure-LR HPV. Unmarried status, sometimes or never condom use increased the chances of multiple, pure high-risk (HR) and mixed HPV infections. Women with multiple sex partners were more likely to cause multiple and mixed HPV infections.

Conclusion

Our experimental data on the prevalence and subtype distribution of HPV in women with CA could provide valuable reference for preventing CA in Henan Province. The application of the nine-valent vaccine provides a broad prospect for female CA prevention.

Diversity of Anal HPV and Non-HPV Sexually Transmitted Infections and Concordance with Genital Infections in HIV-Infected and HIV-Uninfected Women in the Tapajós Region, Amazon, Brazil

The aim of this study was to classify the diversity of anal HPV and non-HPV sexually transmitted infections (STIs) and compare the concordance between anal and genital infections in HIV-infected and uninfected women living in the Tapajós region, Amazon, Brazil. A cross-sectional study was performed with 112 HIV-uninfected and 41 HIV-infected nonindigenous women. Anal and cervical scrapings were collected and analyzed for HPV, Chlamydia trachomatis (CT), Neisseria gonorrheae (NG), Trichomonas vaginalis (TV), Mycoplasma genitalium (MG), and Human alphaherpesvirus 2 (HSV-2). The Kappa test evaluated the concordance between anal and genital infections. The overall prevalence of anal HPV infection was 31.3% in HIV-uninfected and 97.6% in HIV-infected women. The most frequent anal high-risk HPV (hrHPV) types were HPV18 and HPV16 in HIV-uninfected women and HPV51, HPV59, HPV31, and HPV58 in HIV-infected women. Anal HPV75 Betapapillomavirus was also identified. Anal non-HPV STIs were identified in 13.0% of all participants. The concordance analysis was fair for CT, MG, and HSV-2, almost perfect agreement for NG, moderate for HPV, and variable for the most frequent anal hrHPV types. Thus, a high prevalence of anal HPV infection with moderate and fair concordance between anal and genital HPV and non-HPV STIs was observed in our study.

Vaccinating women previously treated for human papillomavirus-related cervical precancerous lesions is highly cost-effective in China

Background

The 2021 Chinese Expert Consensus on the Clinical Application of the Human Papillomavirus (HPV) Vaccine recommended vaccination for women who previously received ablative or excisional treatment for high-grade squamous intraepithelial lesion (HSIL). This study evaluates the cost-effectiveness of HPV vaccination in women previously treated for cervical precancerous lesions.

Methods

We used a Markov model to simulate the disease progression of both low- and high-risk HPV subtypes. We followed a cohort of 100,000 women aged 18-45 years who received treatment for cervical precancerous lesions for a lifetime (80 years). We used the Incremental Cost-Effectiveness Ratios (ICER) with a 5% discount rate to measure the cost-effectiveness of nine vaccination strategies, including a combination of HPV bivalent (HPV-2), quadrivalent (HPV-4) and nonavalent vaccine (HPV-9), each with three vaccination doses (one-, two- and three-dose). We conducted one-way sensitivity analysis and probabilistic sensitivity analysis. We followed the CHEERS 2022 guidelines.

Results

Compared to the status quo, the nine vaccination strategies would result in $3.057-33.124 million incremental cost and 94-1,211 incremental quality-adjusted life-years (QALYs) in 100,000 women previously treated for cervical precancerous lesions. Three vaccination strategies were identified on the cost-effectiveness frontier. In particular, ICER for one-dose HPV-4 vaccination was US$10,025/QALY compared to the status quo (no vaccination); ICER for two-dose HPV-4 vaccination was US$17,641//QALY gained compared to one-dose HPV-4 vaccination; ICER for three-dose HPV-4 vaccination was US$27,785/QALY gained compared with two-dose HPV-4 vaccination. With a willingness-to-pay of three times gross domestic product per capita (US$37655), three-dose HPV-4 vaccination was the most cost-effective vaccination strategy compared with the lower-cost non-dominated strategy on the cost-effectiveness frontier. A probabilistic sensitivity analysis confirmed a 99.1% probability of being cost-effective. If the cost of the HPV-9 is reduced to 50% of the current price, three-dose HPV-9 vaccination would become the most cost-effective strategy.

Discussion

Three-dose HPV-4 vaccination is the most cost-effective vaccination strategy for women treated for precancerous cervical lesions in the Chinese setting.

An Update on Human Papillomavirus Vaccination in the United States

Cervical cancer remains a significant disease in the United States. Although the human papillomavirus (HPV) vaccine has been approved for those aged 9-26 years and for some individuals up to age 45 years, there are many circumstances in which health care professionals may not know whether the vaccine should be recommended, such as for patients with previous infection, health care workers, and those older than age 26 years. This article highlights the evidence that the HPV vaccine is a safe and highly effective way to prevent cervical cancer, with the strongest predictor of vaccine uptake being practitioner recommendation.

Factors affecting HPV infection in U.S. and Beijing females: A modeling study

Background

Human papillomavirus (HPV) infection is an important carcinogenic infection highly prevalent among many populations. However, independent influencing factors and predictive models for HPV infection in both U.S. and Beijing females are rarely confirmed. In this study, our first objective was to explore the overlapping HPV infection-related factors in U.S. and Beijing females. Secondly, we aimed to develop an R package for identifying the top-performing prediction models and build the predictive models for HPV infection using this R package.

Methods

This cross-sectional study used data from the 2009-2016 NHANES (a national population-based study) and the 2019 data on Beijing female union workers from various industries. Prevalence, potential influencing factors, and predictive models for HPV infection in both cohorts were explored.

Results

There were 2,259 (NHANES cohort, age: 20-59 years) and 1,593 (Beijing female cohort, age: 20-70 years) participants included in analyses. The HPV infection rate of U.S. NHANES and Beijing females were, respectively 45.73 and 8.22%. The number of male sex partners, marital status, and history of HPV infection were the predominant factors that influenced HPV infection in both NHANES and Beijing female cohorts. However, condom application was not an independent influencing factor for HPV infection in both cohorts. R package Modelbest was established. The nomogram developed based on Modelbest package showed better performance than the nomogram which only included significant factors in multivariate regression analysis.

Conclusion

Collectively, despite the widespread availability of HPV vaccines, HPV infection is still prevalent. Compared with condom promotion, avoidance of multiple sexual partners seems to be more effective for preventing HPV infection. Nomograms developed based on Modelbest can provide improved personalized risk assessment for HPV infection. Our R package Modelbest has potential to be a powerful tool for future predictive model studies.

Concomitant immunity to M. tuberculosis infection

Some persistent infections provide a level of immunity that protects against reinfection with the same pathogen, a process referred to as concomitant immunity. To explore the phenomenon of concomitant immunity during Mycobacterium tuberculosis infection, we utilized HostSim, a previously published virtual host model of the immune response following Mtb infection. By simulating reinfection scenarios and comparing with data from non-human primate studies, we propose a hypothesis that the durability of a concomitant immune response against Mtb is intrinsically tied to levels of tissue resident memory T cells (Trms) during primary infection, with a secondary but important role for circulating Mtb-specific T cells. Further, we compare HostSim reinfection experiments to observational TB studies from the pre-antibiotic era to predict that the upper bound of the lifespan of resident memory T cells in human lung tissue is likely 2-3 years. To the authors' knowledge, this is the first estimate of resident memory T-cell lifespan in humans. Our findings are a first step towards demonstrating the important role of Trms in preventing disease and suggest that the induction of lung Trms is likely critical for vaccine success.

Ecological and evolutionary dynamics of multi-strain RNA viruses

Potential interactions among co-circulating viral strains in host populations are often overlooked in the study of virus transmission. However, these interactions probably shape transmission dynamics by influencing host immune responses or altering the relative fitness among co-circulating strains. In this Review, we describe multi-strain dynamics from ecological and evolutionary perspectives, outline scales in which multi-strain dynamics occur and summarize important immunological, phylogenetic and mathematical modelling approaches used to quantify interactions among strains. We also discuss how host-pathogen interactions influence the co-circulation of pathogens. Finally, we highlight outstanding questions and knowledge gaps in the current theory and study of ecological and evolutionary dynamics of multi-strain viruses.

Reinfection of Nine-Valent Human Papillomavirus Vaccine Types Among HIV-Negative Men Who Have Sex With Men: A Prospective Cohort Study

Objectives

Reinfection of human papillomavirus (HPV) among men who have sex with men (MSM) after clearing the infection of HPV has not been well characterized. To understand the reinfection of HPV among human immunodeficiency virus (HIV) negative MSM without HPV vaccine, we analyzed the reinfection of nine-valent HPV vaccine (9v-HPV) types.

Methods

Data were acquired from a prospective cohort study among HIV-negative MSM in Urumqi of Xinjiang from 1 April 2016 to 14 July 2020. Participants were recruited through a local non-government organization using a website advertisement. Self-administered questionnaires and self-collected anal swabs were collected at baseline and every 6 months. The incidence rates of reinfection was calculated based on the number of events divided by person-months of observation of event risk. 95% confidence intervals (CIs) were calculated based on the Poisson distribution.

Results

A total of 515 HIV-negative unvaccinated MSM were included with a mean age of 30.93 years (SD 7.85), and 27.68% were reinfected with any 9v-HPV type after clearance. The reinfection incidence rate of any 9v-HPV was 14.47 per 1000 person-months (95% CI: 11.52–17.87). HPV52 was the most common type of reinfection, with a reinfection rate of 17.96 per 1,000 person months (95% CI: 11.58–26.33). Univariate analysis showed that MSM over the age of 30 had a slightly higher risk of reinfection with any 9v-HPV (Hazard ratio (HR): 1.57; 95% CI: 1.01–2.45), but no significant association was observed in multivariate analysis.

Conclusions

Our study showed MSM without HPV vaccine will become reinfected following the natural clearance of specific HPV types. It is also suggested that HPV vaccination is recommended not only prior to sexual debut but also after viral clearance for MSM to reduce HPV prevalence.

The impact of vaccination on human papillomavirus infection with disassortative geographical mixing: a two-patch modeling study

Human papillomavirus (HPV) infection can spread between regions. What is the impact of disassortative geographical mixing on the dynamics of HPV transmission? Vaccination is effective in preventing HPV infection. How to allocate HPV vaccines between genders within each region and between regions to reduce the total infection? Here we develop a two-patch two-sex model to address these questions. The control reproduction number [Formula: see text] under vaccination is obtained and shown to provide a critical threshold for disease elimination. Both analytical and numerical results reveal that disassortative geographical mixing does not affect [Formula: see text] and only has a minor impact on the disease prevalence in the total population given the vaccine uptake proportional to the population size for each gender in the two patches. When the vaccine uptake is not proportional to the population size, sexual mixing between the two patches can reduce [Formula: see text] and mitigate the consequence of disproportionate vaccine coverage. Using parameters calibrated from the data of a case study, we find that if the two patches have the same or similar sex ratios, allocating vaccines proportionally according to the new recruits in two patches and giving priority to the gender with a smaller recruit rate within each patch will bring the maximum benefit in reducing the total prevalence. We also show that a time-variable vaccination strategy between the two patches can further reduce the disease prevalence. This study provides some quantitative information that may help to develop vaccine distribution strategies in multiple regions with disassortative mixing.

Human Papillomavirus Infection and the Risk of Erectile Dysfunction: A Nationwide Population-Based Matched Cohort Study

BACKGROUND

Male patients with genital warts are known for higher rates of sexual dysfunction. This study was conducted to investigate whether human papillomaviruses (HPV) infection is associated with an increased risk of erectile dysfunction (ED).

METHODS

Patients aged over 18 with HPV infection (n = 13,296) and propensity score-matched controls (n = 53,184) were recruited from the Longitudinal Health Insurance Database (LHID). The primary endpoint was the diagnosis of ED. Chi-square tests were used to analyze the distribution of demographic characteristics. The Cox proportional hazards regression was used to estimate the hazard ratios (HRs) and 95% confidence intervals (CIs) for the development of ED in both groups, after adjusting for sex, age, relevant comorbidities, co-medication, and surgery.

RESULTS

ED developed in 181 patients of the study group. The incidence density of ED was 2.53 per 1000 person-years for the HPV group and 1.51 per 1000 person-years for the non-HPV group, with an adjusted HR (95% CI) of 1.63 (1.37-1.94). In stratification analysis, adjusted HR of diabetes-, chronic obstructive pulmonary disease (COPD-), and stroke-subgroup were 2.39, 2.51, and 4.82, with significant p values for interaction, respectively. Sensitivity analysis yields consistent findings.

CONCLUSIONS

The patients with HPV infection had a higher risk of subsequent ED in comparison to the non-HPV controls. The mechanism behind such association and its possible role in ED prevention deserves further study in the future.

HPV Vaccination after Primary Treatment of HPV-Related Disease across Different Organ Sites: A Multidisciplinary Comprehensive Review and Meta-Analysis

Objective: To assess evidence on the efficacy of adjuvant human papillomavirus (HPV) vaccination in patients treated for HPV-related disease across different susceptible organ sites. Methods: A systematic review was conducted to identify studies addressing the efficacy of adjuvant HPV vaccination on reducing the risk of recurrence of HPV-related preinvasive diseases. Results were reported as mean differences or pooled odds ratios (OR) with 95% confidence intervals (95% CI). Results: Sixteen studies were identified for the final analysis. Overall, 21,472 patients with cervical dysplasia were included: 4132 (19.2%) received the peri-operative HPV vaccine, while 17,340 (80.8%) underwent surgical treatment alone. The recurrences of CIN 1+ (OR 0.45, 95% CI 0.27 to 0.73; p = 0.001), CIN 2+ (OR 0.33, 95% CI 0.20 to 0.52; p < 0.0001), and CIN 3 (OR 0.28, 95% CI 0.13 to 0.59; p = 0.0009) were lower in the vaccinated than in unvaccinated group. Similarly, adjuvant vaccination reduced the risk of developing anal intraepithelial neoplasia (p = 0.005) and recurrent respiratory papillomatosis (p = 0.004). No differences in anogenital warts and vulvar intraepithelial neoplasia recurrence rate were observed comparing vaccinated and unvaccinated individuals. Conclusions: Adjuvant HPV vaccination is associated with a reduced risk of CIN recurrence, although there are limited data regarding its role in other HPV-related diseases. Further research is warranted to shed more light on the role of HPV vaccination as adjuvant therapy after primary treatment.

Approximate likelihood-based estimation method of multiple-type pathogen interactions: An application to longitudinal pneumococcal carriage data

While the serotypes of Streptococcus pneumoniae are known to compete during colonization in human hosts, our knowledge of how competition occurs is still incomplete. New insights of pneumococcal between‐type competition could be generated from carriage data obtained by molecular‐based detection methods, which record more complete sets of serotypes involved in co‐carriage than when detection is done by culture. Here, we develop a Bayesian estimation method for inferring between‐type interactions from longitudinal data recording the presence/absence of the types at discrete observation times. It allows inference from data containing co‐carriage of two or more serotypes, which is often the case when pneumococcal presence is determined by molecular‐based methods. The computational burden posed by the increased number of types detected in co‐carriage is addressed by approximating the likelihood under a multi‐state model with the likelihood of only those trajectories with minimum number of acquisition and clearance events between observation times. The proposed method's performance was validated on simulated data. The estimates of the interaction parameters of acquisition and clearance were unbiased in settings with short sampling intervals between observation times. With less frequent sampling, the estimates of the interaction parameters became more biased, but their ratio, which summarizes the total interaction, remained unbiased. Confounding due to unobserved heterogeneity in exposure could be corrected by including individual‐level random effects. In an application to empirical data about pneumococcal carriage in infants, we found new evidence for between‐serotype competition in clearance, although the effect size was small.

A two-sex model of human papillomavirus infection: Vaccination strategies and a case study

Vaccination is effective in preventing human papillomavirus (HPV) infection. It still remains debatable whether males should be included in a vaccination program and unclear how to allocate the vaccine in genders to achieve the maximum benefits. In this paper, we use a two-sex model to assess HPV vaccination strategies and use the data from Guangxi Province in China as a case study. Both mathematical analysis and numerical simulations show that the basic reproduction number, an important indicator of the transmission potential of the infection, achieves its minimum when the priority of vaccination is given to the gender with a smaller recruit rate. Given a fixed amount of vaccine, splitting the vaccine evenly usually leads to a larger basic reproduction number and a higher prevalence of infection. Vaccination becomes less effective in reducing the infection once the vaccine amount exceeds the smaller recruit rate of the two genders. In the case study, we estimate the basic reproduction number is 1.0333 for HPV 16/18 in people aged 15-55. The minimal bivalent HPV vaccine needed for the disease prevalence to be below 0.05% is 24050 per year, which should be given to females. However, with this vaccination strategy it would require a very long time and a large amount of vaccine to achieve the goal. In contrast with allocating the same vaccine amount every year, we find that a variable vaccination strategy with more vaccine given in the beginning followed by less vaccine in later years can save time and total vaccine amount. The variable vaccination strategy illustrated in this study can help to better distribute the vaccine to reduce the HPV prevalence. Although this work is for HPV infection and the case study is for a province in China, the model, analysis and conclusions may be applicable to other sexually transmitted diseases in other regions or countries.

Incidence and clearance of oral and cervicogenital HPV infection: longitudinal analysis of the MHOC cohort study

OBJECTIVES

The Michigan HPV and Oropharyngeal Cancer study aimed to evaluate patterns of oral and cervicogenital human papillomavirus (HPV) infection prevalence, incidence, and clearance as well as their relationship to sexual behaviours.

DESIGN

Cohort SETTING: General public in and around Ann Arbor, Michigan.

PARTICIPANTS

394 college-age and older-adult participants of both sexes provided oral samples, and 325 completed at least 2 visits. 130 who provided a cervicogenital samples, and 127 completed at least 2 visits.

OUTCOMES

Incidence and clearance rates as well as HRs for oral and cervicogenital HPV.

RESULTS

Oral HPV infections were transient, with only 16% of genotypes persisting to the next visit. The mean time to clearance of a genotype was 46 days (95% CI 37 to 58). In contrast, cervicogenital infections were more persistent, with 56% of genotypes persisting to the next visit. The mean time to clearance of a genotype was 87 days (95% CI 74 to 102). HPV vaccination was associated with reduced incidence of cervicogenital HPV infection (HR 0.63; 95% CI 0.47 to 0.83) but not oral HPV infection. Incidence of oral HPV infection was associated with 2+ recent deep kissing partners (HR 2.00; 95% CI 1.13 to 3.56). Incidence of both oral (HR: 1.70; 95% CI 1.08 to 2.68) and cervicogenital (HR 2.46; 95% CI 1.69 to 3.59) was associated with 2+ recent sexual partners.

CONCLUSIONS

Detection of oral HPV was highly transient, but incidence was associated with recent deep kissing and sexual partners. Detection of cervicogenital HPV was more persistent, and incidence was positively associated with recent sexual partners and negatively associated with HPV vaccination.

Reconstructing contact network structure and cross-immunity patterns from multiple infection histories

Interactions within a population shape the spread of infectious diseases but contact patterns between individuals are difficult to access. We hypothesised that key properties of these patterns can be inferred from multiple infection data in longitudinal follow-ups. We developed a simulator for epidemics with multiple infections on networks and analysed the resulting individual infection time series by introducing similarity metrics between hosts based on their multiple infection histories. We find that, depending on infection multiplicity and network sampling, multiple infection summary statistics can recover network properties such as degree distribution. Furthermore, we show that by mining simulation outputs for multiple infection patterns, one can detect immunological interference between pathogens (i.e. the fact that past infections in a host condition future probability of infection). The combination of individual-based simulations and analysis of multiple infection histories opens promising perspectives to infer and validate transmission networks and immunological interference for infectious diseases from longitudinal cohort data.

Longitudinal assessment of nonavalent vaccine HPV types in a sample of sexually active African American women from ten U.S. Cities

BACKGROUND

Chronic infection with high-risk human papillomavirus is a necessary cause for cervical carcinogenesis. This study examined prevalence of nonavalent vaccine preventable HPV types over four months among sexually active women in the United States.

METHODS

This sub-study obtained meta-data for 80 of the 1,365 women (18-25 years), enrolled in the BRAVO study, a randomized, open-label trial of home screening and treatment of asymptomatic bacterial vaginosis at high-risk for sexually transmitted infections conducted between 2008 and 2013. Participants were randomized to treatment or standard-of-care, and followed every 2-months for 12 months. Stored vaginal swabs from the first three visits were tested for the nine vaccine preventable HPV types using quantitative PCR. Prevalence and associated 95% confidence intervals for the HPV types were assessed using R (version 3.6.1).

RESULTS

The average age of the participants was 21.5 (SD ± 2.11) years, with 60% having ever been pregnant and all were African-American. Majority (71%) reported ≥ two sex partners in the prior year with 89% having unprotected vaginal sex and 45% having a new sex partner in the prior year. About 30% had ≥ one of the nine nonavalent vaccine HPV types at all three time points over a period of four months, 15% at two of any three visits, 19% at one of the three visits and 36% were negative for all nine vaccine HPV types at all time points. The most frequently detected HPV vaccine types were 52, 58, 16, and 18. The prevalence of any vaccine HPV types, and high-risk HPV types was 63.8% and 58.8%, respectively.

CONCLUSIONS

Our findings suggest that HPV vaccination which is currently recommended for all unvaccinated persons through age 26 years, is likely to be more beneficial than previously thought as nonavalent HPV vaccine was not available during the time these data were collected.

Prevalence and Risk Factors of Infection with High Risk Human Papilloma Viruses among HIV-Positive Women with Clinical Manifestations of Tuberculosis in a Middle-Income Country

Women living with HIV-1 are at high risk of infection with human papillomavirus of high carcinogenic risk (HR HPVs). M. tuberculosis (TB) promotes HPV infection and increases the risk to develop HPV-associated cancer. Our knowledge of persisting HR HPVs genotypes, and of the factors promoting HR HPV infection in people living with HIV-1 with clinical TB manifestations is sparse. Here, we analyzed 58 women living with HIV-1 with clinical TB manifestations (WLWH with TB) followed up in specialized centers in Russia, a middle income country endemic for HIV-1 and TB, for the presence in cervical smears of DNA of twelve HR HPV genotypes. DNA encoding HPV16 E5, E6/E7 was sequenced. Sociodemographic data of patients was collected by questionnaire. All women were at C2-C3 stages of HIV-infection (by CDC). The majority were over 30 years old, had secondary education, were unemployed, had sexual partners, experienced 2–3 pregnancies and at least one abortion, and were smokers. The most prevalent was HPV16 detected in the cervical smears of 38% of study participants. Altogether 34.5% of study participants were positive for HR HPV types other than HPV16; however, but none of these types was seen in more than 7% of tested samples. Altogether, 20.7% of study participants were positive for several HR HPV types. Infections with HPVs other than HPV16 were common among WLWH with generalized TB receiving combined ART/TB-therapy, and associated with their ability to work, indirectly reflecting both their health and lifestyle. The overall prevalence of HR HPVs was associated with sexual activity of women reflected by the number of pregnancies, and of HPV 16, with young age; none was associated to CD4+-counts, route of HIV-infection, duration of life with HIV, forms of TB-infection, or duration of ART, characterizing the immune status. Thus, WLWH with TB—especially young—were predisposed to infection with HPV16, advancing it as a basis for a therapeutic HPV vaccine. Phylogenetic analysis of HPV16 E5, E6/E7 DNA revealed no common ancestry; sequences were similar to those of the European and American HPV16 strains, indicating that HPV vaccine for WLWH could be the same as HPV16 vaccines developed for the general population. Sociodemographic and health correlates of HR HPV prevalence in WLWH deserve further analysis to develop criteria/recommendations for prophylactic catch-up and therapeutic HPV vaccination of this highly susceptible and vulnerable population group.

Type 2 human papillomavirus E7 attenuates E-cadherin expression in human keratinocytes

Human papillomaviruses (HPVs) are known to utilize the down-regulation of epithelial (E)-cadherin, a major component of adherens junctions of keratinocytes, to evade host immune surveillance in high-risk group. However, the effects of HPV on the function of E-cadherin in low-risk groups remain unknown. We investigated whether type 2 HPV (HPV-2) E7 could induce alterations in E-cadherin expression in transiently transfected keratinocytes and cell lines expressing HPV-2 E7. To examine the expression pattern of E-cadherin in cutaneous warts and normal skin samples, immunohistochemical analysis was performed. Quantitative real-time polymerase chain reactions, luciferase assays, western blot, immunocytochemistry, and electron microscopy were used to evaluate the mRNA and protein expression levels of E-cadherin in normal human epidermal keratinocytes transfected with HPV-2 E7 plasmid DNA or E7-specific siRNA and in E7-expressing cell lines. E-cadherin expression levels in HPV-2 positive cutaneous warts were significantly decreased compared to those in normal skin (p < 0.05). Similarly, the mRNA and protein expression levels of E-cadherin in E7 transiently transfected cells were significantly decreased compared to those in empty vector-transfected cells. The decreases were restored by transfection with E7-specific siRNA (p < 0.05). Likewise, cell lines expressing E7 showed a decreased expression of E-cadherin. When the cells were cultured in low attachment plates, cell-to-cell aggregation was inhibited. Taken together, our data suggest that HPV-2 E7, the causative agent of cutaneous warts, could mediate the transcriptional repression of E-cadherin.

Importance of Lifetime Sexual History on the Prevalence of Genital Human Papillomavirus (HPV) Among Unvaccinated Adults in the National Health and Nutrition Examination Surveys: Implications for Adult HPV Vaccination

BACKGROUND

Although the United States Food and Drug Administration recently approved the human papillomavirus (HPV) vaccine for individuals aged 27-45 years, the Centers for Disease Control and Prevention did not change its guidelines for routine HPV vaccination. Since recommendations for adult vaccination emphasize shared clinical decision-making based on risk of new infections, we examined the relationship between HPV prevalence and sexual behavior.

METHODS

This study was conducted among 5093 HPV-unvaccinated, sexually experienced adults aged 18-59 years in the National Health and Nutrition Examination Surveys (2013-2016). For each sex and age group, adjusted prevalences of 9-valent vaccine-specific, high-risk, and any HPV infection were estimated by number of lifetime sexual partners (LTSPs) using logistic regression. An analysis restricted to persons who did not have a new sexual partner in the past year (ie, removing those at highest risk of newly acquired HPV) was also conducted.

RESULTS

In each age group, genital HPV prevalence was higher among persons with >5 LTSPs compared with 1-5 LTSPs in both males and females. There were only slight reductions in HPV prevalence after removing participants who reported a new sexual partner in the past year. For example, among females aged 27-45 years with >5 LTSPs, the adjusted prevalence of 9-valent vaccine-type HPV infection was 13.4% (95% confidence interval [CI], 9.9%-17.0%) in the full population compared to 12.1% (95% CI, 8.8%-15.4%) among those with no new sexual partners.

CONCLUSIONS

Prevalent HPV infection was primarily reflective of cumulative exposures over time (higher LTSPs). New exposures had limited impact, emphasizing the need to consider sexual history in the decision-making process for adult HPV vaccination.

A Dynamic Model to Assess Human Papillomavirus Vaccination Strategies in a Heterosexual Population Combined with Men Who have Sex with Men

Vaccination is effective in preventing human papillomavirus (HPV) infection. It is imperative to investigate who should be vaccinated and what the best vaccine distribution strategy is. In this paper, we use a dynamic model to assess HPV vaccination strategies in a heterosexual population combined with gay, bisexual, and other men who have sex with men (MSM). The basic reproduction numbers for heterosexual females, heterosexual males and MSM as well as their average for the total population are obtained. We also derive a threshold parameter, based on basic reproduction numbers, for model analysis. From the analysis and numerical investigations, we have several conclusions. (1) To eliminate HPV infection, the priority of vaccination should be given to MSM, especially in countries that have already achieved high coverage in females. The heterosexual population gets great benefit but MSM only get minor benefit from vaccinating heterosexual females or males. (2) The best vaccination strategy is to vaccinate MSM firstly as many as possible, then heterosexual females, lastly heterosexual males. (3) Given a fixed vaccination coverage of MSM, distributing the remaining vaccines to only heterosexual females or males leads to a similar prevalence in the total population. This prevalence is lower than that when vaccines are distributed to both genders. The evener the distribution, the higher the prevalence in the total population. (4) Vaccination becomes less effective in reducing the prevalence as more vaccines are given. It is more effective to allocate vaccines to a region with lower vaccination coverage. This study provides information that may help policymakers formulate guidelines for vaccine distribution to reduce HPV prevalence on the basis of vaccine availability and prior vaccination coverage. Whether these guidelines are affected when the objective is to reduce HPV-associated cancer incidence remains to be further studied.

Prevalence and genotype distribution of human papillomavirus in women with cervical cancer or cervical intraepithelial neoplasia in Henan province, central China

To evaluate the prevalence of human papillomavirus (HPV) infection and its genotype among women with cervical lesions in Henan Province, central China. A total of 1317     cervical scrapes from patients with cervical intraepithelial neoplasia 1 (CIN1) (n = 91), CIN2/3 (n = 466), and cervical cancer (CC; n = 760) were collected from 2013 to 2018, and then tested for HPV genotypes using polymerase chain reaction followed by flow-through hybridization assay. The prevalence of HPV was 62.64% for patients with CIN1, 86.91% for patients with CIN2/3%, and 89.21% for patients with CC. In total, the HPV prevalence was 86.56%, and the most common HPV type was HPV16 (58.77%) followed by HPV58 (10.33%), 18 (7.67%), 52 (6.61%), and 33 (5.54%). In this study, the high-risk HPV cumulative attribution rate of nine-valent vaccine coverage was markedly higher than that of bivalent or quadrivalent vaccine coverage in each histopathological category or overall (P < .001). Single HPV infection was the main infection category in each histopathological diagnosis, and the total infection rate was 65.83% (867/1317; P < .001). The prevalence of HPV16 or single HPV infection increased with the severity of cervical lesions (P < .001). HPV16, 58, 18, 52, and 33 may be predominant high-risk factors for cervical lesions in Henan Province. The nine-valent prophylactic HPV vaccine is more effective than a bivalent or quadrivalent vaccine for protecting women from CC in the region.

HPV+ oropharyngeal squamous cell carcinomas from patients with two tumors display synchrony of viral genomes yet discordant mutational profiles and signatures

Human papillomavirus (HPV) positive oropharyngeal squamous cell carcinoma (HPV + OPSCC) is increasing in prevalence in the USA, as are cases of patients with multiple HPV + OPSCCs (mHPV + OPSCC). mHPV + OPSCCs present a unique opportunity to examine HPV + OPSCC mutation acquisition and evolution. We performed sequencing of the viral genome, somatic exome and somatic transcriptome from 8 patients each with 2 spatially distinct HPV + OPSCCs, and 37 'traditional' HPV + OPSCCs to first address if paired tumors are caused by the same viral isolate and next, if acquired alterations, and the underlying processes driving mutagenesis, are shared within pairs. All tumor pairs contained viral genomes from the same HPV type 16 sublineage and differed by 0-2 clonal single nucleotide polymorphisms (SNPs), suggesting infection with the same viral isolate. Despite this, there was significant discordance in expression profiles, mutational burden and mutational profiles between tumors in a pair, with only two pairs sharing any overlapping mutations (3/3343 variants). Within tumor pairs there was a striking discrepancy of mutational signatures, exemplified by no paired tumors sharing high APOBEC mutational burden. Here, leveraging mHPV + OPSCCs as a model system to study mutation acquisition in virally mediated tumors, in which the germline, environmental exposures, immune surveillance and tissue/organ type were internally controlled, we demonstrate that despite infection by the same viral isolate, paired mHPV + OPSCCs develop drastically different somatic alterations and even more strikingly, appear to be driven by disparate underlying mutational processes. Thus, despite a common starting point, HPV + OPSCCs evolve through variable mutational processes with resultant stochastic mutational profiles.

Rates of New Human Papillomavirus Detection and Loss of Detection in Middle-aged Women by Recent and Past Sexual Behavior

BACKGROUND

Understanding the source of newly detected human papillomavirus (HPV) in middle-aged women is important to inform preventive strategies, such as screening and HPV vaccination.

METHODS

We conducted a prospective cohort study in Baltimore, Maryland. Women aged 35-60 years underwent HPV testing and completed health and sexual behavior questionnaires every 6 months over a 2-year period. New detection/loss of detection rates were calculated and adjusted hazard ratios were used to identify risk factors for new detection.

RESULTS

The new and loss of detection analyses included 731 women, and 104 positive for high-risk HPV. The rate of new high-risk HPV detection was 5.0 per 1000 woman-months. Reporting a new sex partner was associated with higher detection rates (adjusted hazard ratio, 8.1; 95% confidence interval, 3.5-18.6), but accounted only for 19.4% of all new detections. Among monogamous and sexually abstinent women, new detection was higher in women reporting ≥5 lifetime sexual partners than in those reporting <5 (adjusted hazard ratio, 2.2; 95% confidence interval, 1.2-4.2).

CONCLUSION

Although women remain at risk of HPV acquisition from new sex partners as they age, our results suggest that most new detections in middle-aged women reflect recurrence of previously acquired HPV.

Inference on high-dimensional implicit dynamic models using a guided intermediate resampling filter

We propose a method for inference on moderately high-dimensional, nonlinear, non-Gaussian, partially observed Markov process models for which the transition density is not analytically tractable. Markov processes with intractable transition densities arise in models defined implicitly by simulation algorithms. Widely used particle filter methods are applicable to nonlinear, non-Gaussian models but suffer from the curse of dimensionality. Improved scalability is provided by ensemble Kalman filter methods, but these are inappropriate for highly nonlinear and non-Gaussian models. We propose a particle filter method having improved practical and theoretical scalability with respect to the model dimension. This method is applicable to implicitly defined models having analytically intractable transition densities. Our method is developed based on the assumption that the latent process is defined in continuous time and that a simulator of this latent process is available. In this method, particles are propagated at intermediate time intervals between observations and are resampled based on a forecast likelihood of future observations. We combine this particle filter with parameter estimation methodology to enable likelihood-based inference for highly nonlinear spatiotemporal systems. We demonstrate our methodology on a stochastic Lorenz 96 model and a model for the population dynamics of infectious diseases in a network of linked regions.

Incidence and Clearance of Anal High-risk Human Papillomavirus Infections and Their Determinants Over 5 Years Among Human Immunodeficiency Virus-negative Men Who Have Sex With Men

BACKGROUND

We aimed to assess the incidence and clearance of anal high-risk human papillomavirus (hrHPV) infections and determinants thereof among human immunodeficiency virus (HIV)-negative men who have sex with men (MSM) over a period of up to 5 years.

METHODS

From 2010 to 2015, HIV-negative MSM were followed every 6 months. Anal self-swabs were collected at inclusion and every 6 months thereafter, and were HPV genotyped using the SPF10-PCR DEIA/LiPA25-system-v1. Incidence rates (IRs) and clearance rates (CRs) of incident anal hrHPV infections were assessed by hrHPV type (types 16, 18, 31, 33, 45, 52, and 58). Determinants of transitions between uninfected and infected states were assessed by hrHPV type using a time-homogenous multi-state Markov model.

RESULTS

This study included 713 HIV-negative MSM, with a median age of 37 years (interquartile range [IQR] 31-43) and a median number of study visits of 6 (IQR 2-7). The IRs of anal infections had a median of 5.2 per 100 person-years (range: 2.2-7.9) across types, with HPV16 having the highest IR. The CRs of incident anal hrHPV infections had a median of 53.7 per 100 person-years (range: 33.4-65.3) across types, with HPV16 having the lowest CR. Having had over 100 lifetime sex partners was significantly associated with incident anal hrHPV infections in multivariable analyses.

CONCLUSIONS

The high incidence and low clearance rates of anal HPV16 infection, compared to other hrHPV types, is consistent with HPV16 being implicated in the large majority of anal cancer cases.

Capturing multiple-type interactions into practical predictors of type replacement following human papillomavirus vaccination

Current HPV vaccines target a subset of the oncogenic human papillomavirus (HPV) types. If HPV types compete during infection, vaccination may trigger replacement by the non-targeted types. Existing approaches to assess the risk of type replacement have focused on detecting competitive interactions between pairs of vaccine and non-vaccine types. However, methods to translate any inferred pairwise interactions into predictors of replacement have been lacking. In this paper, we develop practical predictors of type replacement in a multi-type setting, readily estimable from pre-vaccination longitudinal or cross-sectional prevalence data. The predictors we propose for replacement by individual non-targeted types take the form of weighted cross-hazard ratios of acquisition versus clearance, or aggregate odds ratios of coinfection with the vaccine types. We elucidate how the hazard-based predictors incorporate potentially heterogeneous direct and indirect type interactions by appropriately weighting type-specific hazards and show when they are equivalent to the odds-based predictors. Additionally, pooling type-specific predictors proves to be useful for predicting increase in the overall non-vaccine-type prevalence. Using simulations, we demonstrate good performance of the predictors under different interaction structures. We discuss potential applications and limitations of the proposed methodology in predicting type replacement, as compared to existing approaches. This article is part of the theme issue 'Silent cancer agents: multi-disciplinary modelling of human DNA oncoviruses'.

Integrating measures of viral prevalence and seroprevalence: a mechanistic modelling approach to explaining cohort patterns of human papillomavirus in women in the USA

Incidence of human papillomavirus (HPV) related cancers is increasing, generating substantial interest in understanding how trends in population prevalence of HPV infection are changing. However, there are no direct, population-scale measurements of HPV prevalence prior to 2003. Previous work using models to reconstruct historical trends have focused only on genital infection or seroprevalence (prevalence of antibodies) separately, and the results of these single-measure studies have been hard to reconcile. Here, we develop a mechanistic disease model fit jointly to cervicogential prevalence and seroprevalence in unvaccinated women in the USA using National Health and Nutrition Examination Survey data (2003-2010) and compare it to fits of statistical age-cohort models. We find that including a latent HPV state in our model significantly improves model fit and that antibody waning may be an important contributor to observed patterns of seroprevalence. Moreover, we find that the mechanistic model outperforms the statistical model and that the joint analysis prevents the inconsistencies that arise when estimating historical cohort trends in infection from genital prevalence and seroprevalence separately. Our analysis suggests that while there is substantial uncertainty associated with the estimation of historic HPV trends, there has likely been an increase in the force of infection for more recent birth cohorts. This article is part of the theme issue 'Silent cancer agents: multi-disciplinary modelling of human DNA oncoviruses'.

HPV infections among young MSM visiting sexual health centers in the Netherlands: Opportunities for targeted HPV vaccination

INTRODUCTION

In 2009, girls-only HPV16/18 vaccination was introduced in the Netherlands which has achieved 46-61% uptake. Heterosexual men have benefitted from herd protection, but it is unknown whether men who have sex with men (MSM) also benefit from herd effects of the girls-only HPV16/18 vaccination program. Because MSM bear a high HPV-related disease burden, countries might consider targeted vaccination for MSM. To study possible herd effects and prior HPV exposure at a potential moment of vaccination, we assessed trends in the HPV prevalence and proportions (sero)negative for the various vaccine types among young MSM visiting sexual health centers (SHCs).

METHODS

We used data from MSM included in PASSYON study years 2009-2017. In this biennial cross-sectional study among visitors of SHCs aged 16-24 years, MSM provided a penile and anal swab for HPV DNA testing (including vaccine types HPV6/11/16/18/31/33/45/52/58) and blood for HPV antibody testing (HPV16/18/31/33/45/52/58).

RESULTS

In total 575 MSM were included, with a median of 22 years of age and 15 lifetime sex partners and 3.5% HIV positive. Trends in penile or anal HPV prevalence during 2009-2017 were statistically non-significant for all vaccine types. Of the 455 MSM with a penile and anal swab, 360 (79%), 283 (62%) and 242 (53%) were HPV DNA negative at both anatomical sites for HPV16/18, HPV6/11/16/18 and HPV6/11/16/18/31/33/45/52/58 respectively. Among MSM who were HPV16/18 and HPV16/18/31/33/45/52/58 DNA negative and were tested for serology (n = 335 and 279 respectively), 82% and 71% were also seronegative for the respective types.

DISCUSSION

There were no significant declines in the HPV prevalence among MSM up to eight years after introduction of girls-only HPV16/18 vaccination, indicating that MSM are unlikely to benefit largely from herd effects from girls-only vaccination. Most MSM were vaccine-type DNA negative and seronegative, suggesting that vaccination of young MSM visiting SHCs could still be beneficial.

Human Papillomavirus Genotype Replacement: Still Too Early to Tell?

Background

Although human papillomavirus (HPV) vaccines are highly efficacious in protecting against HPV infections and related diseases, vaccination may trigger replacement by nontargeted genotypes if these compete with the vaccine-targeted types. HPV genotype replacement has been deemed unlikely, based on the lack of systematic increases in the prevalence of nonvaccine-type (NVT) infection in the first decade after vaccination, and on the presence of cross-protection for some NVTs.

Methods

To investigate whether type replacement can be inferred from early postvaccination surveillance, we constructed a transmission model in which a vaccine type and an NVT compete through infection-induced cross-immunity. We simulated scenarios of different levels of cross-immunity and vaccine-induced cross-protection to the NVT. We validated whether commonly used measures correctly indicate type replacement in the long run.

Results

Type replacement is a trade-off between cross-immunity and cross-protection; cross-immunity leads to type replacement unless cross-protection is strong enough. With weak cross-protection, NVT prevalence may initially decrease before rebounding into type replacement, exhibiting a honeymoon period. Importantly, vaccine effectiveness for NVTs is inadequate for indicating type replacement.

Conclusions

Although postvaccination surveillance thus far is reassuring, it is still too early to preclude type replacement. Monitoring of NVTs remains pivotal in gauging population-level impacts of HPV vaccination.

Untangling the dynamics of persistence and colonization in microbial communities

A central goal of community ecology is to infer biotic interactions from observed distributions of co-occurring species. Evidence for biotic interactions, however, can be obscured by shared environmental requirements, posing a challenge for statistical inference. Here, we introduce a dynamic statistical model, based on probit regression, that quantifies the effects of spatial and temporal covariance in longitudinal co-occurrence data. We separate the fixed pairwise effects of species occurrences on persistence and colonization rates, a potential signal of direct interactions, from latent pairwise correlations in occurrence, a potential signal of shared environmental responses. We first validate our modeling framework with several simulation studies. Then, we apply the approach to a pressing epidemiological question by examining how human papillomavirus (HPV) types coexist. Our results suggest that while HPV types respond similarly to common host traits, direct interactions are sparse and weak, so that HPV type diversity depends largely on shared environmental drivers. Our modeling approach is widely applicable to microbial communities and provides valuable insights that should lead to more directed hypothesis testing and mechanistic modeling.

Detection of Incident Anal High-Risk Human Papillomavirus DNA in Men Who Have Sex With Men: Incidence or Reactivation?

Background

We aimed to assess whether sexual exposure may explain all incident anal human papillomavirus (HPV) detections among men who have sex with men (MSM).

Methods

A longitudinal study among MSM was conducted between 2010 and 2013 with visits every 6 months and up to 24 months of follow-up. Risk-factor questionnaires, blood samples, and anal and penile self-swabs were collected at each visit. Self-swabs were used for detection and genotyping of HPV by the broad spectrum L1 based SPF10 PCR DNA/enzyme immunoassay LiPA25 system. Serum samples were tested for high-risk HPV (hrHPV) antibodies. Incident anal HPV detection rates among sexually non-, low, and highly exposed MSM were compared. Factors associated with incident anal hrHPV detection were assessed using multivariable Cox regression.

Results

Seven hundred fourteen men (median age, 40 years; 39% human immunodeficiency virus [HIV] infected) were included in the analysis. Incident anal detections of all hrHPV types were observed among both sexually nonexposed and exposed MSM. In multivariable analyses, being highly sexually exposed, being HIV infected, and having a penile HPV infection were positively associated with incident anal HPV detection; those reporting more sex partners had a nonsignificantly increased risk of HPV detection.

Conclusions

Incident anal hrHPV detection is common among recently nonexposed MSM, suggesting that a reactivated latent HPV infection instead of an incident infection may underlie incident HPV detection.

Panel Data Analysis via Mechanistic Models

Panel data, also known as longitudinal data, consist of a collection of time series. Each time series, which could itself be multivariate, comprises a sequence of measurements taken on a distinct unit. Mechanistic modeling involves writing down scientifically motivated equations describing the collection of dynamic systems giving rise to the observations on each unit. A defining characteristic of panel systems is that the dynamic interaction between units should be negligible. Panel models therefore consist of a collection of independent stochastic processes, generally linked through shared parameters while also having unit-specific parameters. To give the scientist flexibility in model specification, we are motivated to develop a framework for inference on panel data permitting the consideration of arbitrary nonlinear, partially observed panel models. We build on iterated filtering techniques that provide likelihood-based inference on nonlinear partially observed Markov process models for time series data. Our methodology depends on the latent Markov process only through simulation; this plug-and-play property ensures applicability to a large class of models. We demonstrate our methodology on a toy example and two epidemiological case studies. We address inferential and computational issues arising due to the combination of model complexity and dataset size. Supplementary materials for this article are available online.

Position statement for the diagnosis and management of anogenital warts

BACKGROUND

Anogenital warts (AGW) can cause economic burden on healthcare systems and are associated with emotional, psychological and physical issues.

OBJECTIVE

To provide guidance to physicians on the diagnosis and management of AGW.

METHODS

Fourteen global experts on AGW developed guidance on the diagnosis and management of AGW in an effort to unify international recommendations. Guidance was developed based on published international and national AGW guidelines and an evaluation of relevant literature published up to August 2016. Authors provided expert opinion based on their clinical experiences.

RESULTS

A checklist for a patient's initial consultation is provided to help physicians when diagnosing AGW to get the relevant information from the patient in order to manage and treat the AGW effectively. A number of frequently asked questions are also provided to aid physicians when communicating with patients about AGW. Treatment of AGW should be individualized and selected based on the number, size, morphology, location, and keratinization of warts, and whether they are new or recurrent. Different techniques can be used to treat AGW including ablation, immunotherapy and other topical therapies. Combinations of these techniques are thought to be more effective at reducing AGW recurrence than monotherapy. A simplified algorithm was created suggesting patients with 1-5 warts should be treated with ablation followed by immunotherapy. Patients with >5 warts should use immunotherapy for 2 months followed by ablation and a second 2-month course of immunotherapy. Guidance for daily practice situations and the subsequent action that can be taken, as well as an algorithm for treatment of large warts, were also created.

CONCLUSION

The guidance provided will help physicians with the diagnosis and management of AGW in order to improve the health and quality of life of patients with AGW.

Opportunities to improve immune-based prevention of HPV-associated cancers

Immunization of adolescent girls with VLP vaccines, made of L1 proteins from the most medically significant high risk HPV types, is a major strategy for prevention of cervical cancer plus other HPV-associated cancers. Maximal population impact, including through herd immunity, requires high vaccination coverage. However, protection of unvaccinated women requires secondary prevention through cytology screening. Unfortunately in countries with the highest incidence/mortality due to cervical cancer HPV vaccination (or cytology screening) is not sufficiently available. Vaccination programme costs and a lack of accessibility of the populations for immunization remain significant hurdles. Several approaches could increase effective implementation of HPV vaccination. 1) Use of a single immunization of the current VLP vaccines. 2) Vaccination bundled with other paediatric vaccines with lower dosage to facilitate delivery, improve coverage and reduce costs through established logistics. 3) Local manufacture with lower cost systems (e.g. bacteria) for VLP or capsomer based vaccine production and utilization of additional protective epitopes (e.g L2) for increasing breadth of protection. However, all the latter need appropriate clinical validation. Gender neutral vaccination and extending routine vaccination strategies to women up to age 30 years in combination with at least one HPV screening test can also hasten impact on cancer incidence.

HPV18 Utilizes Two Alternative Branch Sites for E6*I Splicing to Produce E7 Protein

Human papillomavirus 18 (HPV18) E6 and E7 oncogenes are transcribed as a single bicistronic E6E7 pre-mRNA. The E6 ORF region in the bicistronic E6E7 pre-mRNA contains an intron. Splicing of this intron disrupts the E6 ORF integrity and produces a spliced E6*I RNA for efficient E7 translation. Here we report that the E6 intron has two overlapped branch point sequences (BPS) upstream of its 3′ splice site, with an identical heptamer AACUAAC, for E6*I splicing. One heptamer has a branch site adenosine (underlined) at nt 384 and the other at nt 388. E6*I splicing efficiency correlates to the expression level of E6 and E7 proteins and depends on the selection of which branch site. In general, E6*I splicing prefers the 3′ss-proximal branch site at nt 388 over the distal branch site at nt 384. Inactivation of the nt 388 branch site was found to activate a cryptic acceptor site at nt 636 for aberrant RNA splicing. Together, these data suggest that HPV18 modulates its production ratio of E6 and E7 proteins by alternative selection of the two mapped branch sites for the E6*I splicing, which could be beneficial in its productive or oncogenic infection according to the host cell environment.

Human Papillomavirus and Genital Disease in Men: What We Have Learned from the HIM Study

It is currently recognized that in addition to the major impact of human papillomavirus (HPV) infection in females, HPV causes considerable disease in men at the genitals, anal canal, and oropharynx. Specifically, genital HPV infections may progress to genital warts and penile carcinoma. Although studies concerning the natural history of HPV infections and associated neoplasias have mainly focused on women, during the last 2 decades considerable attention has been given in further understanding these infections in men. The HIM (HPV infection in men) Study, the only prospective multicenter study of male HPV natural history, consisted of a large prospective international cohort study in which men from Brazil, the United States, and Mexico were enrolled. The design and protocols of this study allowed unraveling crucial information regarding the relationship between HPV infection and clinical consequences in men, and associated risk factors at each of the anatomic sites where HPV is known to cause cancer in men.

Dynamics and Determinants of HPV Infection: The Michigan HPV and Oropharyngeal Cancer (M-HOC) Study

INTRODUCTION

Human papillomavirus (HPV) is the primary cause of cervical and other anogenital cancers and is also associated with head and neck cancers. Incidence of HPV-related oropharyngeal squamous cell cancers (OPSCCs) is increasing, and HPV-related OPSCCs have surpassed cervical cancer as the most common HPV-related cancer in the USA. Given the multisite nature of HPV, there is strong interest in collecting data from both genital and oral sites, as well as associated data on social and sexual behaviours. The overarching goal of this study is to evaluate patterns of oral HPV infection incidence, clearance and persistence and their relationship to sexual behaviour history.

METHODS AND ANALYSIS

Participants are recruited from two populations: college students at a large public university and general population from the surrounding area. At the first study visit, participants complete a detailed sexual history, health and behaviour questionnaire. Follow-up visits occur every 3-4 months over 3 years, when participants complete an abbreviated questionnaire. All participants provide a saliva sample at each visit, and eligible participants may provide a cervicovaginal self-swab. Genetic material isolated from specimens is tested for 15 high-risk and 3 low-risk HPV types. Statistical analyses will examine outcome variables including HPV prevalence, incidence, persistence and clearance. Logistic regression models will be used to estimate odds ratios and 95% confidence intervals for associations between the outcomes of interest and demographic/behavioural variables collected in the questionnaires. The longitudinal HPV infection data and detailed sexual history data collected in the questionnaires will allow us to develop individual-based network models of HPV transmission and will be used to parameterise multiscale models of HPV-related OPSC carcinogenesis.

ETHICS AND DISSEMINATION

This study has been approved by the University of Michigan Institutional Review Board. All participants are consented in person by trained study staff. Study results will be disseminated through peer-reviewed publications.

Cervico-vaginal self-collection in HIV-infected and uninfected women from Tapajós region, Amazon, Brazil: High acceptability, hrHPV diversity and risk factors

OBJECTIVE

We evaluated acceptability of cervico-vaginal self-collection (CVSC) and prevalence of human papillomavirus (HPV) in Human immunodeficiency virus (HIV)-infected and HIV-uninfected women living in the Tapajós region, Amazon, Brazil.

METHODS

Cross-sectional study recruited 153 non-indigenous women (HIV-uninfected, n = 112 and HIV-infected, n = 41) who voluntarily sought assistance in health services. Peripheral blood for HIV screening and cervical scraping (CS) for HPV detection were collected. Women who accepted to perform CVSC received instructions and individual collection kits. Risk factors for high-risk HPV genotypes (hrHPV) were identified by uni- and multivariate analyses.

RESULTS

The overall acceptability of CVSC was 87%. Only HIV-infected women had cytological abnormalities (12.2%). Prevalence of any HPV and hrHPV infection was 42.9% and 47.9% for HIV-uninfected and 97.6% and 77.5% for HIV-infected women, respectively. There was significant agreement in the detection of HPV (88%, 0.76, 95% confidence interval [CI], 0.65-0.87) and hrHPV (79.7%, 0.56, 95% CI, 0.41-0.71) between self-collected and clinician-collected samples. The most prevalent hrHPV types were HPV16 and HPV18 in HIV-uninfected and HPV16, HPV51 and HPV59 in HIV-infected women. HIV-infected women with hrHPV infection had multiple hrHPV infections (p = 0.005) and lower CD4 count (p = 0.018). Risk factors for hrHPV infection included being HIV-infected and having five or more sexual partners.

CONCLUSIONS

CVSC had high acceptability and high prevalence of hrHPV types in women living in the Tapajós region, Amazon, Brazil.

Efficacy of sinecatechins 10% as proactive sequential therapy of external genital warts after laser CO2 ablative therapy: The PACT study (post-ablation immunomodulator treatment of condylomata with sinecatechins): a randomized, masked outcome assessment, multicenter trial

External genital warts (EGW) are the most common viral sexually transmitted infection. Ablative treatments like cryotherapy, curettage, and CO₂ laser therapies offer rapid onset of effect, fast clearance, and reduction of virus load. However, these procedures are associated with high recurrence rates (RRs) ranging from 20% to 77% in the short and medium terms and do not provide sustained clearance. After laser therapy removal of EGW, an RR up to 77% has been reported. Topical sinecatechins (TS) 10% is a patient-applied regimen for the treatment of EGW with a low RR (<6.5%) at three months after completion of the therapy in the pivotal trials conducted so far. Sinecatechins can be considered a suitable proactive sequential therapy (PST) after ablative strategies to obtain a low RR. So far, no prospective data are available regarding the efficacy of sinecatechins 10% as PST. We evaluated the efficacy and tolerability of TS 10% ointment applied twice daily in subjects with "difficult to treat" EGW after CO₂ laser ablative treatment in a prospective controlled trial. A total of 87 subjects (76 men and 11 women; mean age 42 years) were enrolled in this three-month masked outcome assessment parallel group trial with imbalanced randomization allocation (2:1). One week after a successful CO₂ laser treatment, 60 subjects were randomized to TS 10% treatment and 27 subjects to no treatment (control group: ConTRol (CTR); no sequential therapy). All patients had a history of an average of 4.5 previous ablative treatments in the last 12 months due to recurrent EGW. Mean (standard deviation) baseline number of treated lesions was 6.5 (2.7). One subject in the TS arm dropped out due to burning sensation after the application of the product. Therefore, 86 subjects completed the study. After three months, in the TS group, three subjects presented new EGW lesions (RR: 5%) on treated sites. In the CTR group, eight subjects presented new EGW lesions (RR: 29%) on treated sites (p = 0.0024; odds ratio: 0.16; 95% confidence interval: 0.04-0.68). In the TS group, 34 subjects (56%) reported mild to moderate erythema or burning sensation at the application site. In this prospective multicenter trial, the use of TS 10% as PST after ablative treatment with CO₂ laser was associated with a lower recurrence rate of new EGW lesions in the short term in comparison with the control group. Comparative larger trials are warranted to evaluate the role of this approach as PST (Trial Registration Number: ISRCTN44037479).