Modelling changes in sexual behavior and multi-site transmission of HPV to assess their impact on past and future trends of HPV infections and diseases

Introduction: Lors de l'élaboration des modèles de dynamiques de transmission du virus du papillome humain (VPH), différentes hypothèses sont émises pour simplifier les aspects complexes et peu compris de la transmission. Dans cette thèse, on s'intéresse à deux limites de ces modèles: 1) la transmission du VPH entre différents sites n'est pas modélisée, 2) les changements dans l'activité sexuelle à travers le temps sont ignorés. Les changements dans l'activité sexuelle au cours du dernier siècle pourraient être l'une des causes de l'augmentation des cancers de l'oropharynx des quatre dernières décennies. Cependant, notre compréhension des tendances des cancers reliés au VPH est entravée par le manque de connaissance des patrons de contacts sexuels. Un tel type de patron, l'assortativité, pourrait produire de la confusion dans les études épidémiologiques portant sur les facteurs de risques du VPH. Les objectifs de cette thèse sont 1) d'évaluer l'impact d'inclure la transmission multi-site du VPH dans un modèle sur les prédictions d'efficacité populationnelle du vaccin VPH, 2) d'examiner comment les changements dans l'activité sexuelle ont pu influencer les tendances des cancers de l'oropharynx (CO) et du col de l'utérus (CU) depuis les années 1970, et de prédire les tendances futures de ces cancers, 3) déterminer les conditions sous lesquelles l'assortativité pourrait causer un biais dans les études évaluant la causalité des facteurs de risques des infections transmissibles sexuellement et quantifier la magnitude de ce biais. Méthodes : Pour le premier objectif, nous avons développé un modèle de transmission du VPH multi-site (sites génital et extra-génital) et uni-site (site génital). Avec ces modèles, nous avons estimé la réduction relative de la prévalence du VPH au site génital après la vaccination (RR[indice prev]). Nous avons considéré deux types d'immunité naturelle : site-spécifique et systémique. Pour le deuxième objectif, nous avons développé un modèle mathématique individus-centré simulant la transmission du VPH16, la progression du VPH16 vers le cancer (CO et CU) et les comportements sexuels des américains nés entre 1850 et 1999. Nous avons calibré ce modèle et réalisé des simulations de l'incidence de CO et CU entre 1915 et 2045. Pour le troisième objectif, nous avons développé un modèle de transmission du VPH avec stratification pour deux niveaux d'activité sexuelle (élevé et faible) et de tabagisme (fumeur et non-fumeur). On a supposé dans ce modèle que le tabagisme n'était pas une cause biologique d'infection au VPH, et que le choix du partenaire sexuel est assortatif au statut fumeur. Nous avons simulé une étude fictive dans laquelle nous avons estimé le rapport de cotes (RC) de la prévalence d'infection VPH entre fumeurs et non-fumeurs. La magnitude du biais se mesurait par l'écart entre le RC et la valeur nulle (1,00). Résultats : Pour l'objectif 1, le modèle multi-site prédisait un RR[indice prev] supérieur à celui estimé par le modèle uni-site quand l'immunité était site-spécifique, et inférieur quand l'immunité était systémique. La magnitude de la transmission entre les sites génital et extra-génital était un facteur expliquant la variance du RR[indice prev]. Pour l'objectif 2, notre modèle a prédit, en absence de dépistage du CU, une augmentation importante de l'incidence de CU d'au moins 120% entre 1975 et 2015. Pour le cancer de l'oropharynx relié au VPH16, le modèle a prédit une augmentation d'au moins 310% entre 1985 et 2015, et d'environ 50% entre 2015 et 2045. Pour l'objectif 3, nous avons obtenu un RC de 1,51 après ajustement parfait du niveau d'activité sexuel des sujets de l'étude. Une plus grande assortativité dans le choix du partenaire sexuel causait une augmentation de la magnitude du biais. Conclusion : Étant donné les connaissances actuelles dans le domaine du VPH, il semble peu probable que les prédictions d'efficacité populationnelle de la vaccination contre le VPH faites avec un modèle uni-site soient significativement biaisées. Cependant, l'utilisation d'un modèle multi-site nous a permis de reproduire les changements de comportements sexuels, d'expliquer les tendances de CO observées depuis les années 1980 et de prédire une augmentation future dans l'incidence de CO. Toutefois, cette augmentation future ne pourra pas être prévenue par la vaccination car elle touche surtout des hommes nés avant 1990, qui n'ont pas été vaccinés. Finalement, le rôle du tabagisme dans l'acquisition du VPH demeure incertain dû au biais d'assortativité que nous avons identifié.Introduction: Dynamic models of HPV transmission have been the main tool to estimate the effectiveness and cost-effectiveness of different vaccination strategies. We focus on two limitations of these models: transmission of HPV across different sites (e.g., oral and anal) and changes in sexual behavior across birth cohorts are not modelled. Firstly, including multi-site transmission of HPV could affect estimates of effectiveness against genital diseases. Secondly, changes in sexual behavior throughout the last century could be causally related to the increase in oropharyngeal and anal cancers in the past four decades. Understanding these trends is hindered by our poor knowledge of sexual mixing patterns. One such pattern, assortative mixing, could cause confounding in epidemiological studies of HPV risk factors. The objectives of this thesis are to 1) Assess the impact of including multi-site transmission to current uni-site HPV models on predictions of the population-level effectiveness of HPV vaccination. 2) Examine how changes in specific aspects of sexual behavior such as mixing, rates of new partner acquisition, sexual practices, age of sexual debut, may have impacted trends in HPV-related oropharyngeal and cervical cancer incidence since the 1970s, and predict future trends in these cancers. 3) Determine conditions under which assortative mixing could cause bias in studies examining the causal role of risk factors of STIs and quantify the magnitude of this potential bias. Methods: For the first objective, we developed a multi-site (genital and extragenital sites) and a uni-site (genital site) model of HPV transmission. We estimated the reduction in genital HPV prevalence at equilibrium post-vaccination and compared the estimates of the two models. We considered two types of natural immunity: local (i.e., protects against subsequent infection at the same site) and systemic. For the second objective, we developed an individual-based model of HPV transmission at the genital and oral sites. We reproduced in this model the changes in sexual behavior from 1900 to 2015 in the US population, and simulated the incidence of HPV16-related oropharyngeal and cervical cancers between 1915 and 2045. We performed these simulations according to different scenarios regarding the practice of oral sex, the inclusion of oral infections, and the reporting bias in the number of sexual partners in surveys. Results of the simulations were compared with empirical data on HPV-related cancers. For the third objective, we developed a model of HPV transmission with stratifications for two levels of sexual activity and of smoking habits (smokers and non-smokers). In our simulation, smoking was not a biological cause of HPV infection. We then estimated the odds ratio of prevalent HPV infection between smokers and non-smokers. Deviation from the null value could only be due to a bias we termed assortativity bias. Results: For objective 1, multi-site model predicted higher vaccination effectiveness when natural immunity was local, and lower or equal effectiveness when natural immunity was systemic. Three important factors were identified to increase effectiveness predicted with the multi-site model: 1) higher proportion of genital infections caused by an extragenital infection, 2) lower proportion of extragenital infections caused by a genital infection, 3) higher proportion of susceptibles to extragenital infection. For objective 2, we predicted a sharp increase (IRR=[220%-380%]) between 1975 and 2015 in the simulations of cervical cancer incidence without cervical screening. The increase was lowest when assuming women under-report their number of sexual partners in surveys. In simulations of oropharyngeal cancer incidence, including past changes in the practice of oral sex produced a sharp increase between 1985 and 2015 similar to the observed US trends. Future incidence of oropharyngeal cancer was predicted to increase by 50% between 2015 and 2045. For objective 3, we obtained an OR of 1.51 after perfect adjustment for subjects' level of sexual activity. The non-biased OR for this simulation was 1.00. The magnitude of the bias, as measured by the deviation from the null value, increased with stronger association between sexual activity and smoking habits and with greater degree of assortativity with respect to smoking habits. Conclusion: The assumptions of natural immunity being local and of extragenital infections being an important reservoir for genital infections are not currently supported by evidences. Hence, a significant bias in estimates of vaccination effectiveness against genital infections and diseases from the use of uni-site models appears unlikely. However, using a multi-site model and including the practice of oral sex is necessary to reproduce trends in oropharyngeal cancer since the 1980s. Furthermore, the increase in oropharyngeal cancer is predicted to continue over the next three decades, affecting mainly unvaccinated men born before 1990. In addition, we predict that cervical screening prevented a sharp increase in cervical cancer in the past decades. Finally, the role of smoking in the acquisition and duration of HPV infection remains uncertain due to biases such as the assortativity bias

Groupes d'homotopie des sphères

Tableau d'honneur de la Faculté des études supérieures et postdoctorales, 2011-2012Ce mémoire porte sur les groupes d'homotopie des sphères Sn. Plus précisément, on s'intéresse à la méthode des suites spectrales développée d'abord par Jean-Pierre Serre puis rafinée par la suite par d'autres mathématiciens tels que Frank Adams. On expose dans un premier temps les concepts inhérents aux suites spectrales et on introduit ensuite celles-ci pour enfin démontrer certains résultats classiques. Le premier théorème d'importance est que πk(Sn) est fini sauf si k = n ou si n paire et k = 2n — 1. Dans ce dernier cas, on a que π 4n-i(S2n) sont des groupes de type fini avec une seule composante Z. On obtient ensuite un contrôle modeste sur la p-torsion : le premier élément de p-torsion des groupes d'homotopie de Sn apparaissent en dimension n + 2p — 3 où la p-composante est Zp. On utilise enfin l'algèbre de Steenrod pour reproduire certains calculs explicites de groupes d'homotopie effectués par Jean-Pierre Serre : πn+1(Sn) = Z2, (n > 3), πn+2(Sn) = Z2 (n > 2), π6(S3) = Z12 et π7(S4) = Z 0 Z12

Comparing the cost-effectiveness of two- and three-dose schedules of human papillomavirus vaccination: a transmission-dynamic modelling study.

BACKGROUND: Recent evidence suggests that two doses of HPV vaccines may be as protective as three doses in the short-term. We estimated the incremental cost-effectiveness of two- and three-dose schedules of girls-only and girls & boys HPV vaccination programmes in Canada. METHODS: We used HPV-ADVISE, an individual-based transmission-dynamic model of multi-type HPV infection and diseases (anogenital warts, and cancers of the cervix, vulva, vagina, anus, penis and oropharynx). We conducted the analysis from the health payer perspective, with a 70-year time horizon and 3% discount rate, and performed extensive sensitivity analyses, including duration of vaccine protection and vaccine cost. FINDINGS: Assuming 80% coverage and a vaccine cost per dose of $85, two-dose girls-only vaccination (vs. no vaccination) produced cost/quality-adjusted life-year (QALY)-gained varying between$7900-24,300. The incremental cost-effectiveness ratio of giving the third dose to girls (vs. two doses) was below $40,000/QALY-gained when: (i) three doses provide longer protection than two doses and (ii) two-dose protection was shorter than 30 years. Vaccinating boys (with two or three doses) was not cost-effective (vs. girls-only vaccination) under most scenarios investigated. INTERPRETATION: Two-dose HPV vaccination is likely to be cost-effective if its duration of protection is at least 10 years. A third dose of HPV vaccine is unlikely to be cost-effective if two-dose duration of protection is longer than 30 years. Finally, two-dose girls & boys HPV vaccination is unlikely to be cost-effective unless the cost per dose for boys is substantially lower than the cost for girls

Human papillomavirus vaccine effectiveness by number of doses: Updated systematic review of data from national immunization programs.

BACKGROUND: Human papillomavirus (HPV) vaccines were first licensed as a three-dose series. Two doses are now widely recommended in some age groups; there are data suggesting high efficacy with one dose. We updated a systematic literature review of HPV vaccine effectiveness by number of doses in observational studies. METHODS: We searched Medline and Embase databases from January 1, 2007, through September 29, 2021. Data were extracted and summarized in a narrative synthesis. We also conducted quality assessments for bias due to selection, information, and confounding. RESULTS: Overall, 35 studies were included; all except one were conducted within the context of a recommended three-dose schedule. Evaluations were in countries that used bivalent HPV vaccine (seven), quadrivalent HPV vaccine (27) or both (one). Nine evaluated effectiveness against HPV infection, ten anogenital warts, and 16 cervical abnormalities. All studies were judged to have moderate or serious risk of bias. The biases rated as serious would likely result in lower effectiveness with fewer doses. Investigators attempted to control for or stratify by potentially important variables, such as age at vaccination. Eight studies evaluated impact of buffer periods (lag time) for case counting and 10 evaluated different intervals between doses for two-dose vaccine recipients. Studies that stratified by vaccination age found higher effectiveness with younger age at vaccination, although differences were not all formally tested. Most studies found highest estimates of effectiveness with three doses; significant effectiveness was found among 28/29 studies that evaluated three doses, 19/29 that evaluated two doses, and 18/30 that evaluated one dose. Some studies that adjusted or stratified analyses by age at vaccination found similar effectiveness with three, two and one doses. CONCLUSION: Observational studies of HPV vaccine effectiveness have many biases. Studies examining persons vaccinated prior to sexual activity and using methods to reduce sources of bias are needed for valid effectiveness estimates

Population-level impact and herd effects following human papillomavirus vaccination programs : a systematic review and meta-analysis

Human papillomavirus (HPV) vaccination programs were first implemented in 2007. We conducted a systematic review and meta-analysis to examine the population-level impact and herd effects following female HPV vaccination programs, to verify whether the high efficacy measured in randomized controlled clinical trials are materialising under real-world conditions. We searched Medline and Embase databases (01/2007-02/2014), and conference abstracts for time- trend studies examining changes, between the pre- and post-vaccination periods, in the incidence/prevalence of at least one HPV-related endpoint: HPV infection, anogenital warts (AGW), and high-grade cervical lesions. We derived pooled relative risk (RR) estimates using random effect models. We stratified all analyses by age and gender. We performed subgroups analysis by comparing studies according to vaccine type, vaccination coverage and years since vaccination implementation. We assessed heterogeneity across studies using I2 and χ2 statistics. We performed trends analysis to examine dose-response between HPV vaccination coverage and each study effect measure. We identified 20 eligible studies, conducted in nine high-income countries, and representing >140 million person-years of follow-up. In countries with female vaccination coverage ≥50%, HPV-16/18 infections and AGW decreased significantly between the pre- and post-vaccination periods by 68% (RR=0·32, 95%CI[0·19;0·52]) and 61% (RR=0·39, 95%CI[0·22;0·71]), respectively, among females <20 years. Significant reductions in HPV-31/33/45 among females <20 years (RR=0·72, 95%CI[0·54;0·96]), and AGW among males <20 years (RR=0·66, 95%CI[0·47;0·91]) and older females (RR=0·68, 95CI[0·51;0·89]) were also observed, respectively suggesting cross-protection and herd effects. In countries with female vaccination coverage <50%, significant reductions were observed for HPV-16/18 infection (RR=0·50, 95%CI[0·34;0·74]) and AGW (RR=0·86, 95%CI[0·79;0·94]) among females <20 years, with no indication of cross-protection or herd effects. Our results are promising for the long-term population-level impact of HPV vaccination programs. However, continued monitoring is essential to identify any signals of potential waning efficacy or type-replacement