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Mathematical models are powerful tools in HIV epidemiology, producing quantitative projections of key indicators such as HIV incidence and prevalence. In order to improve the accuracy of predictions, such models need to incorporate a number of behavioural and biological heterogeneities, especially those related to the sexual network within which HIV transmission occurs. An individual-based model, which explicitly models sexual partnerships, is thus often the most natural type of model to choose. In this paper we present PopART-IBM, a computationally efficient individual-based model capable of simulating 50 years of an HIV epidemic in a large, high-prevalence community in under a minute. We show how the model calibrates within a Bayesian inference framework to detailed age- and sex-stratified data from multiple sources on HIV prevalence, awareness of HIV status, ART status, and viral suppression for an HPTN 071 (PopART) study community in Zambia, and present future projections of HIV prevalence and incidence for this community in the absence of trial intervention., Author summary In this paper we present PopART-IBM, an individual-based model used to simulate HIV transmission in communities in high prevalence settings. We show that PopART-IBM can simulate transmission over a span of decades in a large community in less than a minute. This computational efficiency allows us to calibrate the model within an inference framework, and we show an illustrative example of calibration using an adaptive population Monte Carlo Approximate Bayesian Computation algorithm for a community in Zambia that was part of the HPTN-071 (PopART) trial. We compare the detailed model output to real-world data collected during the trial from this community. Finally, we project how the HIV epidemic would have changed over time in this community if no intervention from the trial had occurred.

Chlamydia trachomatis is the most common sexually transmitted infection (STI) in England. Our objective was to perform a detailed survey of the molecular epidemiology of C. trachomatis in the population of Southampton UK attending the genitourinary medicine clinic (GUM) to seek evidence of sexual network activity. Our hypothesis was that certain genotypes can be associated with specific demographic determinants. 380 positive samples were collected from 375 C. trachomatis positive GUM attendees out of the 3118 who consented to be part of the survey. 302 of the positive samples were fully genotyped. All six of the predominant genotypes possessed ompA locus type E. One ward of Southampton known to contain a large proportion of students had a different profile of genotypes compared to other areas of the city. Some genotypes appeared embedded in the city population whilst others appeared transient. Predominant circulating genotypes remain stable within a city population whereas others are sporadic. Sexual networks could be inferred but not conclusively identified using the data from this survey.

ObjectivesWe examined the association between anogenital human papillomavirus (HPV) infection and sexual networks in men who have sex with men (MSM).MethodsA total of 253 MSM, 20 years of age and older, were recruited from the community in Southern Taiwan in 2015-2016. At baseline and at each follow-up visit, MSM were screened for HPV to identify 37 HPV genotypes. At the six-month follow-up, MSM were asked to fill out an egocentric network assessment and to report the last five persons with whom they had sex regarding the characteristics of sexual behavior with each network member.ResultsA total of 182 participants (71.9%) returned for the follow-up and one third had at least one HPV type detected. A higher level of bridging network position calculated by the level of constraints in the network was significantly less likely to have HPV detection at the anal site. A high level of concurrency was associated with penile HPV detection (AOR = 3.16, 95% CI = 1.01-9.86).ConclusionsIdentifying network-related characteristics can advance our understanding of high-risk populations and for prioritizing HPV vaccine recommendations.

Emerging sexually transmitted hepatitis C virus (HCV) epidemics among men who have sex with men (MSM) have been reported worldwide, with higher HCV infection rates among those who are HIV-infected. This study aims to determine prevalence of recent and chronic HCV infections among community-recruited MSM in New York City (NYC), map HCV infections by home, social, and sexual neighborhoods, and identify clusters of genetically linked HCV variants using phylogenetic analysis. The NYC M2M study recruited MSM via modified time-space, venue-based sampling and internet/mobile app-based recruitment during 2010–13. Participants completed a Google Earth map on neighborhoods of where they lived, socialized, and had sex in the last 3 months, an ACASI questionnaire, and a sexual network inventory about their sex partners. The men received HIV testing and provided serum samples. Testing on stored serum samples included HCV antibody and RNA viral load, HCV antibody avidity assay (avidity index 40 years, adjusted odds ratio (aOR) 3.56 (95% CI 1.57, 8.08), HIV-positive serostatus, aOR 3.18 (95% CI 1.40, 7.22), any sexually transmitted infection (STI) in the last 3 months, aOR 2.81 (95% CI 1.11, 7.13), and injection drug use (IDU) ever, aOR 4.34 (95% CI 1.69, 11.17). Mapping of HCV infections differed slightly by home, social, and sexual neighborhoods. Based on phylogenetic analysis from 12 HCV RNA-positive samples, no evidence of a clustered HCV epidemic was found. Overall HCV seroprevalence was 2.8% among community-recruited MSM in NYC, with higher prevalence among HIV-positive MSM compared to HIV-negative MSM. Only two participants were found to have recent HCV infection, with no evidence of a clustered HCV epidemic based on phylogenetic analysis. Our results support testing of HCV infection among HIV-negative MSM if they report having a recent STI and IDU in the past rather than universal HCV testing in all HIV-negative MSM.

Sexually transmitted infections (STIs) comprise a significant portion of the infectious-disease burden among rural people in the Global South. Particular characteristics of ruralness—low-density settlements and poor infrastructure—make healthcare provision difficult, and remoteness, typically a characteristic of ruralness, often compounds the difficultly. Remoteness may also accelerate STI transmission, particularly that of viral STIs, through formation of small, highly connected sexual networks through which pathogens can spread rapidly, especially when partner concurrency is broadly accepted. Herein, we explored the effect of remoteness on herpes simplex virus type-2 (HSV-2) epidemiology among semi-nomadic pastoralists in northwestern (Kaokoveld) Namibia, where, in 2009 we collected HSV-2-specific antibody status, demographic, sexual network, and travel data from 446 subjects (women = 213, men = 233) in a cross-sectional study design. HSV-2 prevalence was high overall in Kaokoveld (>35%), but was heterogeneously distributed across locally defined residential regions: some regions had significantly higher HSV-2 prevalence (39–48%) than others (21–33%). Using log-linear models, we asked the following questions: 1) Are sexual contacts among people in high HSV-2-prevalence regions more likely to be homophilous (i.e., from the same region) than those among people from low-prevalence regions? 2) Are high-prevalence regions more “functionally” remote, in that people from those regions are more likely to travel within their own region than outside, compared to people from other regions? We found that high-prevalence regions were more sexually homophilous than low-prevalence regions and that those regions also had higher rates of within-region travel than the other regions. These findings indicate that remoteness can create contact structures for accelerated STI transmission among people who are already disproportionately vulnerable to consequences of untreated STIs.

Background Generalized heterosexual epidemics are responsible for the largest share of the global burden of HIV. These occur in populations that do not have high rates of partner acquisition, and research suggests that a pattern of fewer, but concurrent, partnerships may be the mechanism that provides the connectivity necessary for sustained transmission. We examine how network size affects the impact of concurrency on network connectivity. Methodology/Principal Findings We use a stochastic network model to generate a sample of networks, varying the size of the network and the level of concurrency, and compare the largest components for each scenario to the asymptotic expected values. While the threshold for the growth of a giant component does not change, the transition is more gradual in the smaller networks. As a result, low levels of concurrency generate more connectivity in small networks. Conclusions/Significance Generalized HIV epidemics are by definition those that spread to a larger fraction of the population, but the mechanism may rely in part on the dynamics of transmission in a set of linked small networks. Examples include rural populations in sub-Saharan Africa and segregated minority populations in the US, where the effective size of the sexual network may well be in the hundreds, rather than thousands. Connectivity emerges at lower levels of concurrency in smaller networks, but these networks can still be disconnected with small changes in behavior. Concurrency remains a strategic target for HIV combination prevention programs in this context.

Sexual contact patterns, both in their temporal and network structure, can influence the spread of sexually transmitted infections (STI). Most previous literature has focused on effects of network topology; few studies have addressed the role of temporal structure. We simulate disease spread using SI and SIR models on an empirical temporal network of sexual contacts in high-end prostitution. We compare these results with several other approaches, including randomization of the data, classic mean-field approaches, and static network simulations. We observe that epidemic dynamics in this contact structure have well-defined, rather high epidemic thresholds. Temporal effects create a broad distribution of outbreak sizes, even if the per-contact transmission probability is taken to its hypothetical maximum of 100%. In general, we conclude that the temporal correlations of our network accelerate outbreaks, especially in the early phase of the epidemics, while the network topology (apart from the contact-rate distribution) slows them down. We find that the temporal correlations of sexual contacts can significantly change simulated outbreaks in a large empirical sexual network. Thus, temporal structures are needed alongside network topology to fully understand the spread of STIs. On a side note, our simulations further suggest that the specific type of commercial sex we investigate is not a reservoir of major importance for HIV., Author Summary Human sexual contacts form a spatiotemporal network—the underlying structure over which sexually transmitted infections (STI) spread. By understanding the structure of this system we can better understand the dynamics of STIs. So far, there has been much focus on the static network structure of sexual contacts. In this paper, we extend this approach and also address temporal effects in a special type of sexual network—that of Internet-mediated prostitution. We analyze reported sexual contacts, probably the largest record of such, from a Brazilian Internet community where sex buyers rate their encounters with escorts. First, we thoroughly investigated disease spread in this dynamic sexual network. We found that the temporal correlations in this system would accelerate disease spread, especially at shorter time scales, whereas geographical effects would slow down an outbreak. More specifically, we found that this contact structure could sustain more contagious diseases, like human papillomavirus, but not HIV. These results highlight the importance of prostitution in the global dynamics of STIs.

BACKGROUND: Population HIV prevalence across West Africa varies substantially. We assess the national epidemiological and behavioural factors associated with this. METHODS: National, urban and rural data on HIV prevalence, the percentage of younger (15-24) and older (25-49) women and men reporting multiple (2+) partners in the past year, HIV prevalence among female sex workers (FSWs), men who have bought sex in the past year (clients), and ART coverage, were compiled for 13 countries. An Ecological analysis using linear regression assessed which factors are associated with national variations in population female and male HIV prevalence, and with each other. FINDINGS: National population HIV prevalence varies between 0 4-2 9% for men and 0 4-5.6% for women. ART coverage ranges from 6-23%. National variations in HIV prevalence are not shown to be associated with variations in HIV prevalence among FSWs or clients. Instead they are associated with variations in the percentage of younger and older males and females reporting multiple partners. HIV prevalence is weakly negatively associated with ART coverage, implying it is not increased survival that is the cause of variations in HIV prevalence. FSWs and younger female HIV prevalence are associated with client population sizes, especially older men. Younger female HIV prevalence is strongly associated with older male and female HIV prevalence. INTERPRETATION: In West Africa, population HIV prevalence is not significantly higher in countries with high FSW HIV prevalence. Our analysis suggests, higher prevalence occurs where more men buy sex, and where a higher percentage of younger women, and older men and women have multiple partnerships. If a sexual network between clients and young females exists, clients may potentially bridge infection to younger females. HIV prevention should focus both on commercial sex and transmission between clients and younger females with multiple partners.

BACKGROUND: Three trials have demonstrated the prophylactic effect of male circumcision (MC) for HIV acquisition among heterosexuals and MC interventions are underway throughout sub-Saharan Africa. Similar efforts for men who have sex with men (MSM) are stymied by the potential for circumcised MSM to acquire HIV easily through receptive sex and transmit easily through insertive sex. Existing work suggests that MC for MSM should reach its maximum potential in settings where sexual role segregation is historically high and relatively stable across the lifecourse; HIV incidence among MSM is high; reported willingness for prophylactic circumcision is high; and pre-existing circumcision rates are low. We aim to identify the likely public health impact that MC interventions among MSM would have in one setting that fulfills these conditions-Peru-as a theoretical upper bound for their effectiveness among MSM generally. METHODS AND FINDINGS: We use a dynamic stochastic sexual network model based in exponential-family random graph modeling and parameterized from multiple behavioral surveys of Peruvian MSM. We consider three enrollment criteria (insertive during 100% >80% or >60% of UAI) and two levels of uptake (25% and 50% of eligible men); we explore sexual role proportions from two studies and different frequencies of switching among role categories. Each scenario is simulated 10 times. We estimate that efficiency could reach one case averted per 6 circumcisions. However the population-level impact of an optimistic MSM-MC intervention in this setting would likely be at most approximately 5-10% incidence and prevalence reductions over 25 years. CONCLUSIONS: Roll-out of MC for MSM in Peru would not result in a substantial reduction in new HIV infections despite characteristics in this population that could maximize such effects. Additional studies are needed to confirm these results for other MSM populations and providers may consider the individual health benefits of offering MC to their MSM patients.