ArticleMolecular biology and evolution2017
Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison.
Article in Molecular biology and evolution, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers, 2 of them syntheses that pooled it.
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Who cites it
42 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Challenges in Elucidating HIV-1 Genetic Diversity in the Middle East and North Africa: A Review Based on a Systematic Search.Viruses · 2025Pooled it
- Prevention of Viral Hepatitis and HIV Infection among People Who Inject Drugs: A Systematic Review and Meta-Analysis.Viruses · 2024Pooled it
- Trial
- Viral Simulation Reveals Overestimation Bias in Within-Host Phylodynamic Migration Rate Estimates Under Selection.Molecular biology and evolution · 2026Article
- Phylogenetics and molecular evolution to understand and curb the HIV pandemic.Nature reviews. Microbiology · 2026Review
- Bayesian estimation of transmission networks for infectious diseases.Journal of mathematical biology · 2025Article
- Epidemiological inference for emerging viruses using segregating sites.Nature communications · 2023Article
- The need for linked genomic surveillance of SARS-CoV-2.Canada communicable disease report = Releve des maladies transmissibles au Canada · 2022Article
- A scalable model for simulating multi-round antibody evolution and benchmarking of clonal tree reconstruction methods.Frontiers in immunology · 2022Article
- Effective Human Immunodeficiency Virus Molecular Surveillance Requires Identification of Incident Cases of Infection.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2021Article
- PopART-IBM, a highly efficient stochastic individual-based simulation model of generalised HIV epidemics developed in the context of the HPTN 071 (PopART) trial.PLoS computational biology · 2021Article
- SEPIA: simulation-based evaluation of prioritization algorithms.BMC medical informatics and decision making · 2021Article
- Timing the SARS-CoV-2 index case in Hubei province.Science (New York, N.Y.) · 2021Article
- HIV Care Prioritization Using Phylogenetic Branch Length.Journal of acquired immune deficiency syndromes (1999) · 2021Article
- Genomic Epidemiology Analysis of Infectious Disease Outbreaks Using TransPhylo.Current protocols · 2021Article
- The probability distribution of the ancestral population size conditioned on the reconstructed phylogenetic tree with occurrence data.Journal of theoretical biology · 2021Article
- Empirical comparison of analytical approaches for identifying molecular HIV-1 clusters.Scientific reports · 2020Article
- Article
- Validation of Variant Assembly Using HAPHPIPE with Next-Generation Sequence Data from Viruses.Viruses · 2020Article
- Number of HIV-1 founder variants is determined by the recency of the source partner infection.Science (New York, N.Y.) · 2020Article
Corrections and comments
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Authors and funding
25 authors.
Funding
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.
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