ArticleProceedings of the National Academy of Sciences of the United States of America2016
Phylogenetically resolving epidemiologic linkage.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers, 2 of them syntheses that pooled it.
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Who cites it
66 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
- Defining HIV-1 transmission clusters based on sequence data.AIDS (London, England) · 2017Pooled it
- The tree labeling polytope: A unified approach to ancestral reconstruction problems.Cell systems · 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
- Phylogenetics and molecular evolution to understand and curb the HIV pandemic.Nature reviews. Microbiology · 2026Review
- 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
- Bayesian mixture models for phylogenetic source attribution from consensus sequences and time since infection estimates.Statistical methods in medical research · 2025Article
- Looking back into the Hepatitis C Virus epidemic dynamics from Unnao, India through phylogenetic approach.PloS one · 2025Article
- Identifying impacts of contact tracing on HIV epidemiological inference from phylogenetic data.Virus evolution · 2025Article
- Higher HIV-1 evolutionary rate is associated with cytotoxic T lymphocyte escape mutations in infants.Journal of virology · 2024Article
- Inferring HIV transmission patterns from viral deep-sequence data via latent typed point processes.Biometrics · 2024Article
- Inferring Viral Transmission Time from Phylogenies for Known Transmission Pairs.Molecular biology and evolution · 2024Article
- Inference of Infectious Disease Transmission through a Relaxed Bottleneck Using Multiple Genomes Per Host.Molecular biology and evolution · 2024Article
- Inferring viral transmission time from phylogenies for known transmission pairs.bioRxiv : the preprint server for biology · 2023Article
- Public health use of HIV phylogenetic data in sub-Saharan Africa: ethical issues.BMJ global health · 2023Review
- Recombination smooths the time signal disrupted by latency in within-host HIV phylogenies.Virus evolution · 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
6 more citing papers are in PubMed but not listed here.
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3 authors.
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Abstract
Although the use of phylogenetic trees in epidemiological investigations has become commonplace, their epidemiological interpretation has not been systematically evaluated. Here, we use an HIV-1 within-host coalescent model to probabilistically evaluate transmission histories of two epidemiologically linked hosts. Previous critique of phylogenetic reconstruction has claimed that direction of transmission is difficult to infer, and that the existence of unsampled intermediary links or common sources can never be excluded. The phylogenetic relationship between the HIV populations of epidemiologically linked hosts can be classified into six types of trees, based on cladistic relationships and whether the reconstruction is consistent with the true transmission history or not. We show that the direction of transmission and whether unsampled intermediary links or common sources existed make very different predictions about expected phylogenetic relationships: (i) Direction of transmission can often be established when paraphyly exists, (ii) intermediary links can be excluded when multiple lineages were transmitted, and (iii) when the sampled individuals' HIV populations both are monophyletic a common source was likely the origin. Inconsistent results, suggesting the wrong transmission direction, were generally rare. In addition, the expected tree topology also depends on the number of transmitted lineages, the sample size, the time of the sample relative to transmission, and how fast the diversity increases after infection. Typically, 20 or more sequences per subject give robust results. We confirm our theoretical evaluations with analyses of real transmission histories and discuss how our findings should aid in interpreting phylogenetic results.
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