ArticleNature communications2019
Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis.
Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers, 1 of them a synthesis that pooled it.
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Who cites it
46 citing papers in PubMed, 1 synthesis or guideline 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
- Detection of HIV-1 Transmission Clusters from Dried Blood Spots within a Universal Test-and-Treat Trial in East Africa.Viruses · 2022Trial
- Trial
- Integrating haplotype-enhanced HIV surveillance with national databases improves the resolution of transmission networks, drug resistance, and risk assessment.Emerging microbes & infections · 2026Article
- Phylogenetic Evidence of Local HIV-1 Transmission and Antiretroviral Drug Resistance in the Middle East and North Africa.Viruses · 2026Article
- Unpacking sources of transmission in HIV prevention trials with deep-sequence pathogen data.Nature communications · 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
- Bloodborne HIV infections in sub-Saharan Africa: evidence of clusters and response options.Frontiers in public health · 2026Article
- Genomic surveillance uncovers regional variation in HCV transmission networks in rural United States.Nature communications · 2025Article
- A graph homomorphism approach for unraveling histories of metastatic cancers and viral outbreaks under evolutionary constraints.Nature communications · 2025Article
- Article
- Integrating Partner Services and Molecular Epidemiology Data to Enhance HIV Transmission Disruption in Rhode Island.Open forum infectious diseases · 2025Article
- Quantifying prevalence and risk factors of HIV multiple infection in Uganda from population-based deep-sequence data.PLoS pathogens · 2025Article
- Article
- Bayesian mixture models for phylogenetic source attribution from consensus sequences and time since infection estimates.Statistical methods in medical research · 2025Article
- Evidence from HIV sequencing for blood-borne transmission in Africa.Journal of public health in Africa · 2025Review
- Comparative Evaluation of Open-Source Bioinformatics Pipelines for Full-Length Viral Genome Assembly.Viruses · 2024Article
- Molecular epidemiology of the HIV-1 epidemic in Fiji.Npj viruses · 2024Article
- 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
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Authors and funding
22 authors.
Funding
Abstract
To prevent new infections with human immunodeficiency virus type 1 (HIV-1) in sub-Saharan Africa, UNAIDS recommends targeting interventions to populations that are at high risk of acquiring and passing on the virus. Yet it is often unclear who and where these 'source' populations are. Here we demonstrate how viral deep-sequencing can be used to reconstruct HIV-1 transmission networks and to infer the direction of transmission in these networks. We are able to deep-sequence virus from a large population-based sample of infected individuals in Rakai District, Uganda, reconstruct partial transmission networks, and infer the direction of transmission within them at an estimated error rate of 16.3% [8.8-28.3%]. With this error rate, deep-sequence phylogenetics cannot be used against individuals in legal contexts, but is sufficiently low for population-level inferences into the sources of epidemic spread. The technique presents new opportunities for characterizing source populations and for targeting of HIV-1 prevention interventions in Africa.
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