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 - Funding Information:
We thank the HPTN Modelling Centre, which is funded by the U.S. National Institutes of Health (NIH UM1 AI068617) through HPTN, for partial funding of this work. Funding for this work was also provided by a supplement grant to the Johns Hopkins University Center for AIDS Research, an NIH-funded programme (P30AI094189) with support specifically from the Office of AIDS Research (OAR). The programme also received support from Linkages across the Continuum of HIV Services for Key Populations Affected by HIV project (LINKAGES, Cooperative Agreement AID-OAA-A-14-00,045) and HIV Prevention 2.0 (HP2): Achieving an AIDS-Free Generation in Senegal (AID-OAA-A-13-00,089). We acknowledge joint Centre funding from the UK Medical Research Council and Department for International Development. The content is solely the responsibility of the authors and does not necessarily represent the official views of any of the funding agencies.
Funding Information:
We thank the HPTN Modelling Centre, which is funded by the U.S. National Institutes of Health ( NIH UM1 AI068617 ) through HPTN, for partial funding of this work. Funding for this work was also provided by a supplement grant to the Johns Hopkins University Center for AIDS Research , an NIH-funded programme ( P30AI094189 ) with support specifically from the Office of AIDS Research (OAR). The programme also received support from Linkages across the Continuum of HIV Services for Key Populations Affected by HIV project (LINKAGES, Cooperative Agreement AID-OAA-A-14-00,045 ) and HIV Prevention 2.0 (HP2): Achieving an AIDS-Free Generation in Senegal ( AID-OAA-A-13-00,089 ). We acknowledge joint Centre funding from the UK Medical Research Council and Department for International Development . The content is solely the responsibility of the authors and does not necessarily represent the official views of any of the funding agencies.
Publisher Copyright:
© 2019 The Authors
PY - 2020/3
Y1 - 2020/3
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.
KW - Coalescent
KW - HIV
KW - Key populations
KW - Phylodynamics
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U2 - 10.1016/j.epidem.2019.100376
DO - 10.1016/j.epidem.2019.100376
M3 - Article
C2 - 31767497
AN - SCOPUS:85081579467
SN - 1755-4365
VL - 30
JO - Epidemics
JF - Epidemics
M1 - 100376
ER -