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

Fabrícia F Nascimento, Stefan Baral, Lily Geidelberg, Christinah Mukandavire, Sheree R Schwartz, Gnilane Turpin, Nguissali Turpin, Daouda Diouf, Nafissatou Leye Diouf, Karleen Coly, Coumba Toure Kane, Cheikh Ndour, Peter Vickerman, Marie-Claude Boily, Erik M Volz

Research output: Contribution to journalArticle (Academic Journal)peer-review

2 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)100376
Early online date14 Nov 2019
Publication statusE-pub ahead of print - 14 Nov 2019

Bibliographical note

Copyright © 2019 The Authors. Published by Elsevier B.V. All rights reserved.

Structured keywords

  • Bristol Population Health Science Institute

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