Phylogenetic and demographic characterization of directed HIV-1 transmission using deep sequences from high-risk and general population cohorts/groups in Uganda
File(s)
Published version
Author(s)
Type
Journal Article
Abstract
Across sub-Saharan Africa, key populations with elevated HIV-1 incidence and/or prevalence have been identified, but their contribution to disease spread remains unclear. We performed viral deep-sequence phylogenetic analyses to quantify transmission dynamics between the general population (GP), fisherfolk communities (FF), and women at high risk of infection and their clients (WHR) in central and southwestern Uganda. Between August 2014 and August 2017, 6185 HIV-1 positive individuals were enrolled in 3 GP and 10 FF communities, 3 WHR enrollment sites. A total of 2531 antiretroviral therapy (ART) naïve participants with plasma viral load >1000 copies/mL were deep-sequenced. One hundred and twenty-three transmission networks were reconstructed, including 105 phylogenetically highly supported source-recipient pairs. Only one pair involved a WHR and male participant, suggesting that improved population sampling is needed to assess empirically the role of WHR to the transmission dynamics. More transmissions were observed from the GP communities to FF communities than vice versa, with an estimated flow ratio of 1.56 (95% CrI 0.68-3.72), indicating that fishing communities on Lake Victoria are not a net source of transmission flow to neighboring communities further inland. Men contributed disproportionally to HIV-1 transmission flow regardless of age, suggesting that prevention efforts need to better aid men to engage with and stay in care.
Date Issued
2020-03-18
Date Acceptance
2020-03-16
Citation
Viruses, 2020, 12 (3)
ISSN
1999-4915
Publisher
MDPI AG
Journal / Book Title
Viruses
Volume
12
Issue
3
Copyright Statement
© 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
License URL
Sponsor
Bill & Melinda Gates Foundation
Identifier
https://www.ncbi.nlm.nih.gov/pubmed/32197553
PII: v12030331
Grant Number
1705CR001/LD1
Subjects
deep sequences
human immunodeficiency virus
key populations
phylogenetic analysis
transmission
Publication Status
Published
Coverage Spatial
Switzerland
Article Number
331