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
Affiliations
Fabrícia F. Nascimento
Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place W2 1PG, UK
Stefan Baral
Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, MD, USA
Lily Geidelberg
Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place W2 1PG, UK
Christinah Mukandavire
Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place W2 1PG, UK
Sheree R. Schwartz
Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, MD, USA
Gnilane Turpin
Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, MD, USA
Nguissali Turpin
Enda Sante, Dakar, Senegal
Daouda Diouf
Enda Sante, Dakar, Senegal
Nafissatou Leye Diouf
Institut de Recherche en Santé, de Surveillance Epidemiologique et de Formations, Dakar, Senegal
Karleen Coly
Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, MD, USA
Coumba Toure Kane
Institut de Recherche en Santé, de Surveillance Epidemiologique et de Formations, Dakar, Senegal
Cheikh Ndour
Division de La Lutte Contre Le Sida et Les IST, Ministry of Health, Dakar, Senegal
Peter Vickerman
Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
Marie-Claude Boily
Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place W2 1PG, UK
Erik M. Volz
Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place W2 1PG, UK; MRC Centre for Global Infectious Disease Analysis, Imperial College London, UK; Corresponding author.
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. Keywords: HIV, Phylodynamics, Key populations, Coalescent
