ArticleEpidemics2018
Comparison of cluster-based and source-attribution methods for estimating transmission risk using large HIV sequence databases.
Article in Epidemics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Trial
- Robust phylodynamic inference and model specification for HIV transmission dynamics.Epidemics · 2025Article
- Lessons learned from community engagement regarding phylodynamic research with molecular HIV surveillance data.Journal of the International AIDS Society · 2023Article
- Predictors of HIV Molecular Cluster Membership and Implications for Partner Services.AIDS research and human retroviruses · 2023Article
- Application of Phylodynamic Tools to Inform the Public Health Response to COVID-19: Qualitative Analysis of Expert Opinions.JMIR formative research · 2023Article
- Characterization of HIV-1 Transmission Clusters Inferred from the Brazilian Nationwide Genotyping Service Database.Viruses · 2022Article
- Optimized phylogenetic clustering of HIV-1 sequence data for public health applications.PLoS computational biology · 2022Article
- Cluster Analysis Algorithm in the Analysis of College Students' Mental Health Education.Applied bionics and biomechanics · 2022Article
- Sorting by Race/Ethnicity Across HIV Genetic Transmission Networks in Three Major Metropolitan Areas in the United States.AIDS research and human retroviruses · 2021Article
- Persistence of HIV transmission clusters among people who inject drugs.AIDS (London, England) · 2020Article
- Incident infection in high-priority HIV molecular transmission clusters in the United States.AIDS (London, England) · 2020Article
- Natural selection favoring more transmissible HIV detected in United States molecular transmission network.Nature communications · 2019Article
- Phylogenetic Methods Inconsistently Predict the Direction of HIV Transmission Among Heterosexual Pairs in the HPTN 052 Cohort.The Journal of infectious diseases · 2019Article
- HIV-1 Transmission Patterns in Men Who Have Sex with Men: Insights from Genetic Source Attribution Analysis.AIDS research and human retroviruses · 2019Article
- Inferring putative transmission clusters with Phydelity.Virus evolution · 2019Article
- Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis.Nature communications · 2019Article
- Exploring Evolutionary and Transmission Dynamics of HIV Epidemic in Serbia: Bridging Socio-Demographic With Phylogenetic Approach.Frontiers in microbiology · 2019Article
- Growth of HIV-1 Molecular Transmission Clusters in New York City.The Journal of infectious diseases · 2018Article
- HIV-TRACE (TRAnsmission Cluster Engine): a Tool for Large Scale Molecular Epidemiology of HIV-1 and Other Rapidly Evolving Pathogens.Molecular biology and evolution · 2018Article
- Inferring the age difference in HIV transmission pairs by applying phylogenetic methods on the HIV transmission network of the Swiss HIV Cohort Study.Virus evolution · 2018Article
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8 authors.
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Abstract
Phylogenetic clustering of HIV sequences from a random sample of patients can reveal epidemiological transmission patterns, but interpretation is hampered by limited theoretical support and statistical properties of clustering analysis remain poorly understood. Alternatively, source attribution methods allow fitting of HIV transmission models and thereby quantify aspects of disease transmission. A simulation study was conducted to assess error rates of clustering methods for detecting transmission risk factors. We modeled HIV epidemics among men having sex with men and generated phylogenies comparable to those that can be obtained from HIV surveillance data in the UK. Clustering and source attribution approaches were applied to evaluate their ability to identify patient attributes as transmission risk factors. We find that commonly used methods show a misleading association between cluster size or odds of clustering and covariates that are correlated with time since infection, regardless of their influence on transmission. Clustering methods usually have higher error rates and lower sensitivity than source attribution method for identifying transmission risk factors. But neither methods provide robust estimates of transmission risk ratios. Source attribution method can alleviate drawbacks from phylogenetic clustering but formal population genetic modeling may be required to estimate quantitative transmission risk factors.
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