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Phylogenetic tools for generalized HIV-1 epidemics : findings from the PANGEA-HIV methods comparison

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Ratmann, Oliver, Hodcroft, Emma B., Pickles, Michael, Cori, Anne, Hall, Matthew, Lycett, Samantha, Colijn, Caroline, Dearlove, Bethany, Didelot, Xavier, Frost, Simon et al.
(2017) Phylogenetic tools for generalized HIV-1 epidemics : findings from the PANGEA-HIV methods comparison. Molecular Biology and Evolution, 34 (1). pp. 185-203. doi:10.1093/molbev/msw217

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Official URL: http://dx.doi.org/10.1093/molbev/msw217

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Abstract

iral 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.

Item Type: Journal Article
Divisions: Faculty of Science > Life Sciences (2010- )
Journal or Publication Title: Molecular Biology and Evolution
Publisher: Oxford University Press
ISSN: 0737-4038
Official Date: January 2017
Dates:
DateEvent
January 2017Published
7 October 2016Available
Volume: 34
Number: 1
Page Range: pp. 185-203
DOI: 10.1093/molbev/msw217
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Open Access
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