Phylodynamic analysis of HIV-1 subtypes B, C and CRF 02_AG in Senegal
File(s)
Published version
Author(s)
Type
Journal Article
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.
Date Issued
2020-03-01
Date Acceptance
2019-11-04
Citation
Epidemics: the journal of infectious disease dynamics, 2020, 30, pp.1-11
ISSN
1755-4365
Publisher
Elsevier
Start Page
1
End Page
11
Journal / Book Title
Epidemics: the journal of infectious disease dynamics
Volume
30
Copyright Statement
© 2019 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license
(http://creativecommons.org/licenses/BY/4.0/).
(http://creativecommons.org/licenses/BY/4.0/).
License URL
Sponsor
National Institutes of Health
United States Agency for International Development (USAID)
Medical Research Council (MRC)
Identifier
http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000522664200010&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=1ba7043ffcc86c417c072aa74d649202
Grant Number
UM1AI068617 Sub#0001014222
PO: 2003388501
MR/R015600/1
Subjects
Science & Technology
Life Sciences & Biomedicine
Infectious Diseases
HIV
Phylodynamics
Key populations
Coalescent
ALIGNMENT
RISK
MEN
SEX
PREVALENCE
INFECTION
Publication Status
Published
Article Number
ARTN 100376
Date Publish Online
2019-11-14