Phylogenetic tools for generalized HIV-1 epidemics: findings from the PANGEA-HIV methods comparison
File(s)
Published version
Author(s)
Type
Journal Article
Abstract
Viral phylogenetic methods contribute to understanding how HIV spreads in populations, and thereby help guide the design of prevention interventions. So far, most analyses have been applied to well-sampled concentrated HIV-1 epidemics in wealthy countries. To direct the use of phylogenetic tools to where the impact of HIV-1 is greatest, the Phylogenetics And Networks for Generalized HIV Epidemics in Africa (PANGEA-HIV) consortium generates full-genome viral sequences from across sub-Saharan Africa. Analyzing these data presents new challenges, since epidemics are principally driven by heterosexual transmission and a smaller fraction of cases is sampled. Here, we show that viral phylogenetic tools can be adapted and used to estimate epidemiological quantities of central importance to HIV-1 prevention in sub-Saharan Africa. We used a community-wide methods comparison exercise on simulated data, where participants were blinded to the true dynamics they were inferring. Two distinct simulations captured generalized HIV-1 epidemics, before and after a large community-level intervention that reduced infection levels. Five research groups participated. Structured coalescent modeling approaches were most successful: phylogenetic estimates of HIV-1 incidence, incidence reductions, and the proportion of transmissions from individuals in their first 3 months of infection correlated with the true values (Pearson correlation > 90%), with small bias. However, on some simulations, true values were markedly outside reported confidence or credibility intervals. The blinded comparison revealed current limits and strengths in using HIV phylogenetics in challenging settings, provided benchmarks for future methods’ development, and supports using the latest generation of phylogenetic tools to advance HIV surveillance and prevention.
Date Issued
2017-01
Date Acceptance
2016-09-27
Citation
Molecular Biology and Evolution, 2017, 34 (1), pp.185-203
ISSN
1537-1719
Publisher
Oxford University Press
Start Page
185
End Page
203
Journal / Book Title
Molecular Biology and Evolution
Volume
34
Issue
1
Copyright Statement
© 2016 The Authors. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Sponsor
Engineering & Physical Science Research Council (EPSRC)
Medical Research Council (MRC)
Grant Number
EP/K026003/1
MR/K010174/1B
Subjects
HIV transmission and prevention
molecular epidemiology of infectious diseases
viral phylogenetic methods validation
Evolutionary Biology
0604 Genetics
0603 Evolutionary Biology
0601 Biochemistry And Cell Biology
Publication Status
Published
Article Number
msw217v2
Date Publish Online
2016-10-07