Social and molecular epidemiology of HIV among key populations in Nigeria: linking transmission insights to targeted prevention

Nigeria has a mixed HIV epidemic in which key populations – female sex workers (FSW), men who have sex with men (MSM), people who inject drugs (PWID), and transgender people – bear a disproportionate burden of HIV, yet molecular evidence characterizing this remains scarce. This thesis, guided by a programme science approach, combined a narrative review and molecular epidemiological analyses to characterize HIV transmission among four Nigerian key populations and inform more effective programming. Objective 1 used the modified social ecological model to organize a narrative review of 36 studies conducted among Nigerian key populations, identifying determinants of HIV prevention, testing, and treatment outcomes across individual, network, community, and policy levels. Criminalization, stigma, and programme delivery emerged as recurring structural barriers operating across several ecological levels. Objective 2 applied phylogenetic clustering and Bayesian phylodynamic modelling to the 2020 Nigerian Integrated Biological and Behavioural Surveillance Survey (IBBSS) and evaluated associations using multivariable Poisson regression. HIV protease sequences derived from 547 IBBSS participants (n=185 FSW, n=176 MSM, n=51 PWID, and n=135 transgender people) formed 47 phylogenetic clusters. After adjustment, transgender people had 5.52 times [95% CI: 2.96-10.28, p < 0.001] and MSM had 5.38 times [95% CI: 2.87-10.07, p < 0.001] higher prevalence in phylogenetic clusters relative to FSW, and geopolitical zone remained a significant predictor. Growth phases in median number of effective infections for HIV subtypes CRF02_AG (n=364) and G (n=139) between 2000–2020 aligned with rises in national HIV case counts and persisted during early-stage treatment scale-up, consistent with interventions still building toward the intensity needed to reduce transmission among key populations. Structured coalescent models identified conserved ancestral migration events between MSM and transgender people for both subtypes, while ancestral migration events between northern and southern geopolitical zones differed in direction and magnitude across subtypes. Framing molecular findings with individual-, network-, community-, and policy-level contexts strengthened this study’s relevance to programme planning and the needs of IBBSS partners, while providing molecular evidence that HIV transmission is not siloed, but cuts across both key population groups and geopolitical zones and highlights a need for sustained, integrated programming in Nigeria.