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

Epidemics. 2020 Mar:30:100376. doi: 10.1016/j.epidem.2019.100376. Epub 2019 Nov 14.

Abstract

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: Coalescent; HIV; Key populations; Phylodynamics.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Epidemics
  • Female
  • HIV Infections / epidemiology
  • HIV Infections / virology*
  • HIV-1 / classification*
  • Homosexuality, Male
  • Humans
  • Male
  • Middle Aged
  • Models, Theoretical*
  • Phylogeny*
  • Senegal / epidemiology
  • Sexual and Gender Minorities
  • Young Adult