ArticleThe Journal of infectious diseases2019
Phylogenetic Methods Inconsistently Predict the Direction of HIV Transmission Among Heterosexual Pairs in the HPTN 052 Cohort.
Article in The Journal of infectious diseases, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 24 citations in OpenAlex.
- Genomic surveillance uncovers regional variation in HCV transmission networks in rural United States.Nature communications · 2025Article
- Power and sample size calculations for testing the ratio of reproductive values in phylogenetic samples.American journal of epidemiology · 2025Article
- The first-to-test bias: Impact of testing order on assigning responsibility for contagion.PloS one · 2024Article
- Phylogenetic inference of pneumococcal transmission from cross-sectional data, a pilot study.Wellcome open research · 2023Article
- Molecular source attribution.PLoS computational biology · 2022Article
- Using phylogenetics to infer HIV-1 transmission direction between known transmission pairs.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Integrated molecular and affiliation network analysis: Core-periphery social clustering is associated with HIV transmission patterns.Social networks · 2022Article
- Methodological synthesis of Bayesian phylodynamics, HIV-TRACE, and GEE: HIV-1 transmission epidemiology in a racially/ethnically diverse Southern U.S. context.Scientific reports · 2021Article
- Evaluation of Phylogenetic Methods for Inferring the Direction of Human Immunodeficiency Virus (HIV) Transmission: HIV Prevention Trials Network (HPTN) 052.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2021Article
- Number of HIV-1 founder variants is determined by the recency of the source partner infection.Science (New York, N.Y.) · 2020Article
- Evaluation of A Phylogenetic Pipeline to Examine Transmission Networks in A Canadian HIV Cohort.Microorganisms · 2020Article
- Phylogenetics in HIV transmission: taking within-host diversity into account.Current opinion in HIV and AIDS · 2019Review
- Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis.Nature communications · 2019Article
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Authors and funding
27 authors at 16 institutions in 9 countries.
Funding
Abstract
backgroundWe evaluated use of phylogenetic methods to predict the direction of human immunodeficiency virus (HIV) transmission.
methodsFor 33 pairs of HIV-infected patients (hereafter, "index patients") and their partners who acquired genetically linked HIV infection during the study, samples were collected from partners and index patients close to the time when the partner seroconverted (hereafter, "SC samples"); for 31 pairs, samples collected from the index patient at an earlier time point (hereafter, "early index samples") were also available. Phylogenies were inferred using env next-generation sequences (1 tree per pair/subtype). The direction of transmission (DoT) predicted from each tree was classified as correct or incorrect on the basis of which sequences (those from the index patient or the partner) were closest to the root. DoT was also assessed using maximum parsimony to infer ancestral node states for 100 bootstrap trees.
resultsDoT was predicted correctly for both single-pair and subtype-specific trees in 22 pairs (67%) by using SC samples and in 23 pairs (74%) by using early index samples. DoT was predicted incorrectly for 4 pairs (15%) by using SC or early index samples. In the bootstrap analysis, DoT was predicted correctly for 18 pairs (55%) by using SC samples and for 24 pairs (73%) by using early index samples. DoT was predicted incorrectly for 7 pairs (21%) by using SC samples and for 4 pairs (13%) by using early index samples.
conclusionsPhylogenetic methods based solely on the tree topology of HIV env sequences, particularly without consideration of phylogenetic uncertainty, may be insufficient for determining DoT.
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