TY - JOUR
T1 - Phylodynamic analysis of HIV-1 subtypes B, C and CRF 02_AG in Senegal
AU - Nascimento, Fabrícia F
AU - Baral, Stefan
AU - Geidelberg, Lily
AU - Mukandavire, Christinah
AU - Schwartz, Sheree R
AU - Turpin, Gnilane
AU - Turpin, Nguissali
AU - Diouf, Daouda
AU - Diouf, Nafissatou Leye
AU - Coly, Karleen
AU - Kane, Coumba Toure
AU - Ndour, Cheikh
AU - Vickerman, Peter
AU - Boily, Marie-Claude
AU - Volz, Erik M
N1 - Copyright © 2019 The Authors. Published by Elsevier B.V. All rights reserved.
PY - 2019/11/14
Y1 - 2019/11/14
N2 - 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.
AB - 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.
U2 - 10.1016/j.epidem.2019.100376
DO - 10.1016/j.epidem.2019.100376
M3 - Article (Academic Journal)
C2 - 31767497
SP - 100376
JO - Epidemics
JF - Epidemics
SN - 1755-4365
ER -