Modelling patterns of clearance of HPV-16 infection and vaccination efficacy

Modelling the impact of perfect and imperfect vaccination strategy against SARS CoV-2 by assuming varied vaccine efficacy over India

Background

The outbreak of Coronavirus disease (COVID-19) has swiftly spread globally and caused public health and socio-economic disruption in many countries. An epidemiological modelling studies in the susceptible-infectious-removed (SIR) has played an important role for making effective public health policy to mitigate the spread of COVID-19. The aim of the present study is to investigate the optimal vaccination strategy to control the COVID-19 pandemic in India.

Methods

We have applied compartment mathematical model susceptible-vaccination-infectious-removed (SVIR) with different range of vaccine efficacy scenarios and predicted the population to be covered for vaccination per day in India as well as state level was performed.

Results

The model assumed that a vaccine has 100% efficacy, predicted that >5 million populace to be vaccinated per day to flatten the epidemic curve in India. Similarly, different vaccination mechanisms such as ‘all-or-nothing’ (AoN) and leaky vaccines does not have potential discordance in their effectiveness at higher efficacies (>70%). However, AoN vaccine was found to be marginally effective than leaky at lower efficacies (<70%) when administered at the higher coverage strategies. Further state level analyses were performed and it was found that 0.3, 0.3, 0.2 and 1 million vaccinations required per day in Andhra Pradesh, Gujarat, Kerala and Maharashtra as it assumes that the vaccine efficacy is 70%.

Conclusion

The proposed modelling approach shows a range of assumptions on the efficacy of vaccine which helps the health authorities to prioritize the vaccination strategies to prevent the transmission as well as disease.

The confounding effect of multi-type human papillomavirus infections on type-specific natural history parameter identification

The natural history of human papillomavirus (HPV) from infection to cervical cancer differs between HPV types. Accordingly, type-specific natural history parameters are crucial for the mathematical models used to optimize the nearly life-long series of disease prevention measures. These parameters are estimated from genotyped data from trials and population level screening programs, typically one type at a time, which requires projecting the multiple-type data to the single type. To analyze impacts of such projection methods on the estimates, we compared estimating one type at a time using different projection methods with estimating all types together. We simulated genotyped data with chosen parameter values for two HPV types and analyzed the identifiability of the chosen values using the different estimation methods. We found the success of estimating one type at a time to be excessively sensitive to the data projection method, with potential to falsely identify the parameters at wrong values. Estimating all types together identified the parameters well. Our results were consistent both when trial and population level data were used. In conclusion, the potential confounding by multi-type infections has to be considered when choosing an estimation method for type-specific natural history parameters.

Impact of Human Papillomavirus Vaccination, Rwanda and Bhutan

Rwanda and Bhutan, 2 low- and middle-income countries, implemented primarily school-based national human papillomavirus (HPV) vaccination in 2011 (Rwanda) and 2010 (Bhutan). We estimated vaccination effectiveness through urine-based HPV prevalence surveys in schools in 2013–2014 and 2017. In Rwanda, 912 participants from baseline surveys and 1,087 from repeat surveys were included, and in Bhutan, 973 participants from baseline surveys and 909 from repeat surveys were included. The overall effectiveness against vaccine-targeted HPV types (i.e., HPV-6/11/16/18) was 78% (95% CI 51%–90%) in Rwanda, and 88% (6%–99%) in Bhutan and against other α-9 types was 58% (21–78) in Rwanda and 63% (27–82) in Bhutan. No effect against other HPV types was detectable. Prevalence of vaccine-targeted HPV types decreased significantly, as well as that of other α-9 types, suggesting cross-protection. These findings provide direct evidence from low- and middle-income countries of the marked effectiveness of high-coverage school-based, national HPV vaccination programs.

Developing effective vaccines: Cues from natural infection

The ultimate goal of any vaccine is to generate a heterogeneous and stable pool of memory lymphocytes. Vaccine are designed with the hope to generate antigen specific long-lived T cell responses, as it may be the case in natural infection; however, inducing such response by sub-unit vaccine has been a challenge. Although significant progress has been made, there is lot of scope for designing novel vaccine strategies by taking cues from the natural infection. This review focuses upon the roadblocks and the possible ways to overcome them leading to developing effective vaccines. Here we propose that mimicking the natural course of infection as well as the inclusion of non-target antigens in vaccine formulations might generate heterogeneous pool of memory T cells to ensure long-lived protection.

Decline of HPV infections in Scandinavian cervical screening populations after introduction of HPV vaccination programs

OBJECTIVE

To monitor the changes in prevalence of human papillomavirus (HPV) infections in women <50 years of age, participating in cervical screening programs of Denmark, Norway, and Sweden, before and after introduction of quadrivalent HPV (qHPV) vaccination.

METHODS

Liquid-based cytology samples were collected from 6538 women who attended cervical screening in Denmark, Norway, and Sweden in 2006-2008 and from 6332 similarly enrolled women in 2012-2013. Denmark started organized qHPV vaccination in 2008, Norway in 2009, and Sweden in 2012. All HPV testing and genotyping was performed using identical enrollment and analysis methods, by accredited general primer polymerase chain reaction methods with typing using the Luminex system.

RESULTS

Overall HPV positivity declined slightly from 36.5% in 2006-2008 to 34.5% in 2012-2013. The decline was most pronounced among women 18-26 years of age: from 54.4% to 48.1% (P < 0.001). The decline was substantial for vaccine HPV types (HPV6/11/16/18: decline from 22.3% to 16.6%; P < 0.001) and was seen for both low-risk vaccine types (HPV6/11 declined from 5.0% to 2.5%) and high-risk vaccine types (HPV16/18 declined from 18.9% to 14.9%). Among women 27-50 years of age, there was no change between the time periods (22.5% and 21.6%, respectively). The significant decline in the younger age group was different in the 3 countries.

CONCLUSION

This population-based study enrolling >12,000 women participating in cervical screening in the 3 Nordic countries before and after introduction of organized qHPV vaccination demonstrated a marked decline in HPV infection in the younger population in the 2 countries where qHPV vaccination programs started in 2008-2009, suggesting that organized HPV vaccination programs resulted in a decrease of HPV types circulating in the general population.

Estimating effectiveness of HPV vaccination against HPV infection from post-vaccination data in the absence of baseline data

BACKGROUND

HPV vaccination programs have been introduced in large parts of the world, but monitoring of effectiveness is not routinely performed. Many countries introduced vaccination programs without establishing the baseline of HPV prevalences. We developed and validated methods to estimate protective effectiveness (PE) of vaccination from the post-vaccination data alone using references, which are invariant under HPV vaccination.

METHODS

Type-specific HPV prevalence data for 15-39 year-old women were collected from the pre- and post-vaccination era in a region in southern Sweden. In a region in middle Sweden, where no baseline data had been collected, only post-vaccination data was collected. The age-specific baseline prevalence of vaccine HPV types (vtHPV, HPV 6, 11, 16, 18) were reconstructed as Beta distributions from post-vaccination data by applying the reference odds ratios between the target HPV type and non-vaccine-type HPV (nvtHPV) prevalences. Older non-vaccinated age cohorts and the southern Sweden region were used as the references. The methods for baseline reconstructions were validated by computing the Bhattacharyya coefficient (BC), a measure for divergence, between reconstructed and actual observed prevalences for vaccine HPV types in Southern Sweden, and in addition, for non-vaccine types in both regions. The PE estimates among 18-21 year-old women were validated by comparing the PE estimates that were based on the reconstructed baseline prevalences against the PE estimates based on the actual baseline prevalences.

RESULTS

In Southern Sweden the PEs against vtHPV were 52.2% (95% CI: 44.9-58.5) using the reconstructed baseline and 49.6% (43.2-55.5) using the actual baseline, with high BC 82.7% between the reconstructed and actual baseline. In the middle Sweden region where baseline data was missing, the PE was estimated at 40.5% (31.6-48.5).

CONCLUSIONS

Protective effectiveness of HPV vaccination can be estimated from post-vaccination data alone via reconstructing the baseline using non-vaccine HPV type data.

Human Papillomavirus Vaccination at a Time of Changing Sexual Behavior

Human papillomavirus (HPV) prevalence varies widely worldwide. We used a transmission model to show links between age-specific sexual patterns and HPV vaccination effectiveness. We considered rural India and the United States as examples of 2 heterosexual populations with traditional age-specific sexual behavior and gender-similar age-specific sexual behavior, respectively. We simulated these populations by using age-specific rates of sexual activity and age differences between sexual partners and found that transitions from traditional to gender-similar sexual behavior in women <35 years of age can result in increased (2.6-fold in our study) HPV16 prevalence. Our model shows that reductions in HPV16 prevalence are larger if vaccination occurs in populations before transitions in sexual behavior and that increased risk for HPV infection attributable to transition is preventable by early vaccination. Our study highlights the importance of using time-limited opportunities to introduce HPV vaccination in traditional populations before changes in age-specific sexual patterns occur.

Vaccination Programs for Endemic Infections: Modelling Real versus Apparent Impacts of Vaccine and Infection Characteristics

Vaccine effect, as measured in clinical trials, may not accurately reflect population-level impact. Furthermore, little is known about how sensitive apparent or real vaccine impacts are to factors such as the risk of re-infection or the mechanism of protection. We present a dynamic compartmental model to simulate vaccination for endemic infections. Several measures of effectiveness are calculated to compare the real and apparent impact of vaccination, and assess the effect of a range of infection and vaccine characteristics on these measures. Although broadly correlated, measures of real and apparent vaccine effectiveness can differ widely. Vaccine impact is markedly underestimated when primary infection provides partial natural immunity, when coverage is high and when post-vaccination infectiousness is reduced. Despite equivalent efficacy, 'all or nothing' vaccines are more effective than 'leaky' vaccines, particularly in settings with high risk of re-infection and transmissibility. Latent periods result in greater real impacts when risk of re-infection is high, but this effect diminishes if partial natural immunity is assumed. Assessments of population-level vaccine effects against endemic infections from clinical trials may be significantly biased, and vaccine and infection characteristics should be considered when modelling outcomes of vaccination programs, as their impact may be dramatic.

Regional variations in HPV vaccination among 9-17 year old adolescent females from the BRFSS, 2008-2010

Human papillomavirus (HPV) vaccine uptake among 18-26 y old women varies by geographic region in the US. However, little is known about regional variations in vaccination among girls who are in the vaccine's targeted age groups. Regional variation in HPV vaccination among female adolescents (9-17 y old) was examined using cross-sectional data from the Behavioral Risk Factor Surveillance System (BRFSS) between 2008 and 2010. Multivariable logistic regression estimated the association of region of residence (10 states included questions about adolescent HPV vaccination) with uptake and completion of the 3-shot HPV vaccine series. Among 7,849 adolescents, 26.9% initiated, and 55.2% of initiators completed the series. Adolescents from Northeast/Midwest/West states were 1.74 (95% CI: 1.45-2.10) times more likely to have initiated HPV vaccination compared to the South/Southwestern states. Among initiators, vaccine series completion did not vary significantly between the South/Southwestern and Northeast/Midwest/West states. Flu vaccination was associated with increased odds of initiation in both regions and completion of the HPV vaccine series in the South/Southwestern states only. Girls 9-10 and 11-12 y old were less likely to have initiated and 11-12 y olds were less likely to have completed the HPV vaccine series compared to 13-17 y olds. The observed regional variations in vaccination could cause rates of cervical cancer to remain higher in the South/Southwest and widen currently observed regional disparities in cervical cancer rates.

The impact of HPV female immunization in Italy: model based predictions

The Human Papillomavirus (HPV) is a sexually transmitted virus that causes cervical cancer. Since 2008 a vaccination program targeting 12-year-old girls has been initiated in Italy, backing up the cervical screening program already active since 1996. We propose a mathematical model of HPV transmission dynamics with the aim of evaluating the impact of these prevention strategies. The model considers heterosexual transmission of HPV types 16 and 18, structured by sex, age and sexual activity level, where transition to sexual activity is explicitly modeled from recent survey data. The epidemiological structure is a hybrid SIS/SIR, where a fraction of individuals recovering from infection develops permanent immunity against reinfection. Infections may progress to cervical lesions and cancer and heal spontaneously or upon treatment. Women undergoing hysterectomy (either after treatment of HPV lesions or by other causes) also transmit HPV infection. The model fits well both the age-specific prevalence of HPV infections and the incidence of cervical cancers in Italy, and accurately reproduces the decreasing trend in cancer incidence due to the introduction of the screening program. The model predicts that if the screening coverage is maintained at current levels, even in the absence of vaccination, such trend will continue in the next few decades, eventually plateauing at 25% below the current level. The additional initiation of routine vaccination targeting 12-year-old girls will further reduce cervical cancer incidence by two thirds at equilibrium, under realistic assumptions of 70% coverage and a duration of protective immunity of 50 years. If catch-up immunization of 25-year-old women at first cervical screening is also introduced, about 3,000 cervical cancer cases overall can be averted, corresponding to 9.6% of all cases expected in the scenario without catch-up. We conclude that HPV vaccination in addition to cervical screening will significantly reduce the burden of cervical cancer in Italy.

Randomized controlled trial of two dosing schedules for human papillomavirus vaccination among college age males

BACKGROUND

Quadrivalent human papillomavirus (HPV) vaccine, for protection against sexually transmitted HPV infection, is licensed for females and males 9-26 years on a 3-dose schedule (0, 2, and 6 months; Standard schedule). Vaccine uptake has been low and catch-up vaccination of older adolescents using an alternate dosing schedule may increase coverage. This study tested the non-inferiority of the immunogenicity of an alternate dosing schedule (0, 2, 12 months) among college age males.

METHODS

220 18-25 year old males were randomly assigned to Standard or Alternate schedules. Blood samples were drawn immediately before Dose 1 and 2-6 weeks after Dose 3 and analyzed for antibody titers using a Luminex immunoassay. A value <1.5 for the upper 95% confidence interval (CI) bound of the Standard to Alternate schedule geometric mean titer (GMT) ratio was deemed non-inferior.

RESULTS

Participants averaged 21.3 years old; 19.1% were non-white; completion rate was 93%. The anti-HPV titers for the Alternate schedule group were non-inferior to those of Standard schedule group for all four HPV vaccine virus types. Our results also demonstrated superiority of the Alternate schedule group for all four HPV vaccine virus types.

CONCLUSION

A delayed third dose at 12 months is immunologically non-inferior and superior for four HPV virus types. Using an alternate dosing schedule offers more flexibility to receive the 3-dose HPV vaccine and may result in higher vaccination rates among college-age males.

Type-specific human papillomavirus biological features: validated model-based estimates

Infection with high-risk (hr) human papillomavirus (HPV) is considered the necessary cause of cervical cancer. Vaccination against HPV16 and 18 types, which are responsible of about 75% of cervical cancer worldwide, is expected to have a major global impact on cervical cancer occurrence. Valid estimates of the parameters that regulate the natural history of hrHPV infections are crucial to draw reliable projections of the impact of vaccination. We devised a mathematical model to estimate the probability of infection transmission, the rate of clearance, and the patterns of immune response following the clearance of infection of 13 hrHPV types. To test the validity of our estimates, we fitted the same transmission model to two large independent datasets from Italy and Sweden and assessed finding consistency. The two populations, both unvaccinated, differed substantially by sexual behaviour, age distribution, and study setting (screening for cervical cancer or Chlamydia trachomatis infection). Estimated transmission probability of hrHPV types (80% for HPV16, 73%-82% for HPV18, and above 50% for most other types); clearance rates decreasing as a function of time since infection; and partial protection against re-infection with the same hrHPV type (approximately 20% for HPV16 and 50% for the other types) were similar in the two countries. The model could accurately predict the HPV16 prevalence observed in Italy among women who were not infected three years before. In conclusion, our models inform on biological parameters that cannot at the moment be measured directly from any empirical data but are essential to forecast the impact of HPV vaccination programmes.

A critical review of cost-effectiveness analyses of vaccinating males against human papillomavirus

A critical review of cost-effectiveness analyses of HPV vaccination in males was conducted and nine studies were identified in different countries. Due to the heterogeneity among these studies in terms of modeling approach, vaccination strategies, health outcomes considered, assumptions and parameters, limited conclusions can be drawn with regard to the absolute cost-effectiveness. Nevertheless, key drivers were identified. More favorable cost-effectiveness appeared when all HPV-related diseases outcomes were considered, a suboptimal vaccine coverage among girls and/or lower vaccine prices were assumed. There was a general lack of transparency to fully describe the details of the methodological approach of modeling and calibration. Further research should be conducted to generate robust evidence-based data sets (HPV-related diseases epidemiology, costs and quality of life). The best modeling practice for HPV vaccination and how to better capture the true economic value of vaccination beyond cost-effectiveness in a broader policy context need to be investigated.

Exploring individual HPV coinfections is essential to predict HPV-vaccination impact on genotype distribution: a model-based approach

INTRODUCTION

As for other vaccines that only target a subset of circulating pathogen types, human papillomavirus (HPV) immunization raises the concern of a potential risk of genotype replacement. Potential interactions between HPV types may affect infection acquisition and clearance. However, the existence and the nature of these interactions are still largely unknown. Here, we assess how such interactions might affect the impact of HPV vaccination on genotype distribution in the long term.

METHODS

We develop two mathematical models of the transmission of oncogenic HPV infections that include interactions between vaccine and nonvaccine genotypes to examine the influence of different coinfection dynamics (simultaneous vs. sequential clearance of coinfections) on the evolution of nonvaccine prevalences postimmunization.

RESULTS

After introducing vaccination, the two models give contrasting genotype-replacement outcomes. When hypothesizing that coinfections clear sequentially, genotype replacement depends on whether vaccine and nonvaccine genotypes reduce or favor the acquisition by one or the other. Interestingly, the hypothesis that coinfections clear simultaneously always leads to genotype replacement, even when infections with vaccine types favor the acquisition of infections with nonvaccine types.

CONCLUSION

Our results suggest that predictions regarding HPV genotype replacement strongly depend on the assumptions describing the dynamics (acquisition and clearance) of coinfections. In particular, HPV genotype replacement could be compatible with synergistic interactions between types affecting infections acquisition, contrary to previous suggestions. Understanding better how concurrent infections with multiple types change the acquisition and time to clearance of type-specific infections is essential to be able to predict the impact of vaccination on genotype distribution. Longitudinal data collection in populations, particularly examining infection and coinfection acquisition and clearance, is needed to better predict HPV-vaccine impact.

Inference of type-specific HPV transmissibility, progression and clearance rates: a mathematical modelling approach

Quantifying rates governing the clearance of Human Papillomavirus (HPV) and its progression to clinical disease, together with viral transmissibility and the duration of naturally-acquired immunity, is essential in estimating the impact of vaccination programmes and screening or testing regimes. However, the complex natural history of HPV makes this difficult. We infer the viral transmissibility, rate of waning natural immunity and rates of progression and clearance of infection of 13 high-risk and 2 non-oncogenic HPV types, making use of a number of rich datasets from Sweden. Estimates of viral transmissibility, clearance of initial infection and waning immunity were derived in a Bayesian framework by fitting a susceptible-infectious-recovered-susceptible (SIRS) transmission model to age- and type-specific HPV prevalence data from both a cross-sectional study and a randomised controlled trial (RCT) of primary HPV screening. The models fitted well, but over-estimated the prevalence of four high-risk types with respect to the data. Three of these types (HPV-33, -35 and -58) are among the most closely related phylogenetically to the most prevalent HPV-16. The fourth (HPV-45) is the most closely related to HPV-18; the second most prevalent type. We suggest that this may be an indicator of cross-immunity. Rates of progression and clearance of clinical lesions were additionally estimated from longitudinal data gathered as part of the same RCT. Our estimates of progression and clearance rates are consistent with the findings of survival analysis studies and we extend the literature by estimating progression and clearance rates for non-16 and non-18 high-risk types. We anticipate that such type-specific estimates will be useful in the parameterisation of further models and in developing our understanding of HPV natural history.

Modeling preventative strategies against human papillomavirus-related disease in developed countries

Over the last 5 years, prophylactic vaccination against human papillomavirus (HPV) in pre-adolescent females has been introduced in most developed countries, supported by modeled evaluations that have almost universally found vaccination of pre-adolescent females to be cost-effective. Studies to date suggest that vaccination of pre-adolescent males may also be cost-effective at a cost per vaccinated individual of ~US$400-500 if vaccination coverage in females cannot be increased above ~50%; but if it is possible, increasing coverage in females appears to be a better return on investment. Comparative evaluation of the quadrivalent (HPV16,18,6,11) and bivalent (HPV16,18) vaccines centers around the potential trade-off between protection against anogenital warts and vaccine-specific levels of cross-protection against infections not targeted by the vaccines. Future evaluations will also need to consider the cost-effectiveness of a next generation nonavalent vaccine designed to protect against ~90% of cervical cancers. The timing of the effect of vaccination on cervical screening programs will be country-specific and will depend on vaccination catch-up age range and coverage and the age at which screening starts. Initial evaluations suggest that if screening remains unchanged, it will be less cost-effective in vaccinated compared to unvaccinated women but, in the context of current vaccines, will remain an important prevention method. Comprehensive evaluation of new approaches to screening will need to consider the population-level effects of vaccination over time. New screening strategies of particular interest include delaying the start age of screening, increasing the screening interval and switching to primary HPV screening. Future evaluations of screening will also need to focus on the effects of disparities in screening and vaccination uptake, the potential effects of vaccination on screening participation, and the effects of imperfect compliance with screening recommendations. This article forms part of a special supplement entitled "Comprehensive Control of HPV Infections and Related Diseases" Vaccine Volume 30, Supplement 5, 2012.

Causal diagrams in systems epidemiology

Methods of diagrammatic modelling have been greatly developed in the past two decades. Outside the context of infectious diseases, systematic use of diagrams in epidemiology has been mainly confined to the analysis of a single link: that between a disease outcome and its proximal determinant(s). Transmitted causes ("causes of causes") tend not to be systematically analysed.

The infectious disease epidemiology modelling tradition models the human population in its environment, typically with the exposure-health relationship and the determinants of exposure being considered at individual and group/ecological levels, respectively. Some properties of the resulting systems are quite general, and are seen in unrelated contexts such as biochemical pathways. Confining analysis to a single link misses the opportunity to discover such properties.

The structure of a causal diagram is derived from knowledge about how the world works, as well as from statistical evidence. A single diagram can be used to characterise a whole research area, not just a single analysis - although this depends on the degree of consistency of the causal relationships between different populations - and can therefore be used to integrate multiple datasets.

Additional advantages of system-wide models include: the use of instrumental variables - now emerging as an important technique in epidemiology in the context of mendelian randomisation, but under-used in the exploitation of "natural experiments"; the explicit use of change models, which have advantages with respect to inferring causation; and in the detection and elucidation of feedback.