Abstract
Surveillance of HIV epidemics in key populations and in developing countries is often challenging due to sparse, incomplete, or low-quality data. Analysis of HIV sequence data can provide an alternative source of information about epidemic history, population structure, and transmission patterns. To understand HIV-1 dynamics and transmission patterns in Senegal, we carried out model-based phylodynamic analyses using the structured-coalescent approach using HIV-1 sequence data from three different subgroups: reproductive aged males and females from the adult Senegalese population and men who have sex with other men (MSM). We fitted these phylodynamic analyses to time-scaled phylogenetic trees individually for subtypes C and CRF 02_AG, and for the combined data for subtypes B, C and CRF 02_AG. In general, the combined analysis showed a decreasing proportion of effective number of infections among all reproductive aged adults relative to MSM. However, we observed a nearly time-invariant distribution for subtype CRF 02_AG and an increasing trend for subtype C on the proportion of effective number of infections. The population attributable fraction also differed between analyses: subtype CRF 02_AG showed little contribution from MSM, while for subtype C and combined analyses this contribution was much higher. Despite observed differences, results suggested that the combination of high assortativity among MSM and the unmet HIV prevention and treatment needs represent a significant component of the HIV epidemic in Senegal.
Highlights
There are an estimated 36.7 million people around the world living with HIV with approximately 1.8 million newly infected in 2016 equating to approximately 5000 new infections per day (UNAIDS, 2017)
We only reported results for population attributable fraction (PAF) and effective number of infections derived from the base model: phylodynamic analysis carried out using self-reported risk group and adding a term based on previously published HIV prevalence in gpm and msm in Dakar, Senegal
When only genetic data were considered (Models 1 to 3), our estimates were, in general, much lower than the ones reported by Mukandavire et al (2018) (Fig. 5). This analysis provides additional insights into HIV epidemiological dynamics in Senegal using model-based phylodynamic methods applied to hundreds of HIV sequences
Summary
There are an estimated 36.7 million people around the world living with HIV with approximately 1.8 million newly infected in 2016 equating to approximately 5000 new infections per day (UNAIDS, 2017). A more recent study showed a prevalence in Senegal MSM population of 23.5% (Lyons et al, 2017) While generalizability of these estimates is limited by the number of sample locations, they do suggest a concentration of HIV in MSM which is further reflected by genetic populations structure of the virus. These surveys have shown that in Senegal HIV-1 subtype C is the predominant subtype circulating among MSM, but HIV1 CRF 02_AG predominates among the broader population of people living with HIV by a large margin (Ndiaye et al, 2009, 2013; DiopNdiaye et al, 2010), which shows a high degree of compartmentalization of these risk groups
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