ArticleClinical infectious diseases : an official publication of the Infectious Diseases Society of America2021
Evaluation of Phylogenetic Methods for Inferring the Direction of Human Immunodeficiency Virus (HIV) Transmission: HIV Prevention Trials Network (HPTN) 052.
Article in Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
- [Impact of HIV-1 genotypes and population mobility on HIV-1 transmission in Guangzhou: a molecular transmission network analysis].Nan fang yi ke da xue xue bao = Journal of Southern Medical University · 2026Article
- The age and sex dynamics of heterosexual HIV transmission in Zambia: an HPTN 071 (PopART) phylogenetic and modelling study.medRxiv : the preprint server for health sciences · 2026Article
- Ethical considerations and the social context of HIV phylogenetic research in uMkhanyakude district, KwaZulu-Natal, South Africa.Southern African journal of HIV medicine · 2026Article
- Genomic surveillance uncovers regional variation in HCV transmission networks in rural United States.Nature communications · 2025Article
- Ethics of Identifying Individuals Involved in HIV Transmission Events by Phylogenetics in Molecular Surveillance.Bioethics · 2025Article
- A graph homomorphism approach for unraveling histories of metastatic cancers and viral outbreaks under evolutionary constraints.Nature communications · 2025Article
- Inferring HIV transmission patterns from viral deep-sequence data via latent typed point processes.Biometrics · 2024Article
- Longitudinal population-level HIV epidemiologic and genomic surveillance highlights growing gender disparity of HIV transmission in Uganda.Nature microbiology · 2024Article
- Human immunodeficiency virus 1 5'-leader mutations in plasma viruses before and after the development of reverse transcriptase inhibitor-resistance mutations.The Journal of general virology · 2023Article
- Public health use of HIV phylogenetic data in sub-Saharan Africa: ethical issues.BMJ global health · 2023Review
- Phylogenetic inference of pneumococcal transmission from cross-sectional data, a pilot study.Wellcome open research · 2023Article
- Molecular source attribution.PLoS computational biology · 2022Article
- SOPHIE: Viral outbreak investigation and transmission history reconstruction in a joint phylogenetic and network theory framework.Cell systems · 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
- Identification of Genetically Related HCV Infections Among Self-Described Injecting Partnerships.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2022Article
- Integrated molecular and affiliation network analysis: Core-periphery social clustering is associated with HIV transmission patterns.Social networks · 2022Article
- Addressing Ethical Challenges in US-Based HIV Phylogenetic Research.The Journal of infectious diseases · 2020Article
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23 authors.
Funding
Abstract
backgroundPhylogenetic analysis can be used to assess human immunodeficiency virus (HIV) transmission in populations. We inferred the direction of HIV transmission using whole-genome HIV sequences from couples with known linked infection and known transmission direction.
methodsComplete next-generation sequencing (NGS) data were obtained for 105 unique index-partner sample pairs from 32 couples enrolled in the HIV Prevention Trials Network (HPTN) 052 study (up to 2 samples/person). Index samples were obtained up to 5.5 years before partner infection; partner samples were obtained near the time of seroconversion. The bioinformatics method, phyloscanner, was used to infer transmission direction. Analyses were performed using samples from individual sample pairs, samples from all couples (1 sample/person; group analysis), and all available samples (multisample group analysis). Analysis was also performed using NGS data from defined regions of the HIV genome (gag, pol, env).
resultsUsing whole-genome NGS data, transmission direction was inferred correctly (index to partner) for 98 of 105 (93.3%) of the individual sample pairs, 99 of 105 (94.3%) sample pairs using group analysis, and 31 of the 32 couples (96.9%) using multisample group analysis. There were no cases where the incorrect transmission direction (partner to index) was inferred. The accuracy of the method was higher with greater time between index and partner sample collection. Pol region sequences performed better than env or gag sequences for inferring transmission direction.
conclusionsWe demonstrate the potential of a phylogenetic method to infer the direction of HIV transmission between 2 individuals using whole-genome and pol NGS data.
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