Phylodynamic analysis of HIV-1 subtypes B, C and CRF 02_AG in Senegal

Nascimento, Fabrícia F; Baral, Stefan; Geidelberg, Lily; Mukandavire, ChristinahORCID logo; Schwartz, Sheree R; Turpin, Gnilane; Turpin, Nguissali; Diouf, Daouda; Diouf, Nafissatou Leye; Coly, Karleen; +5 more...Kane, Coumba Toure; Ndour, Cheikh; Vickerman, Peter; Boily, Marie-Claude; and Volz, Erik M (2020) Phylodynamic analysis of HIV-1 subtypes B, C and CRF 02_AG in Senegal. Epidemics, 30. p. 100376. ISSN 1755-4365 DOI: 10.1016/j.epidem.2019.100376
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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.


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