ArticleViruses2020
Phylogenetic and Demographic Characterization of Directed HIV-1 Transmission Using Deep Sequences from High-Risk and General Population Cohorts/Groups in Uganda.
Article in Viruses, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Demographics of sources of HIV-1 transmission in Zambia: a molecular epidemiology analysis in the HPTN 071 PopART study.The Lancet. Microbe · 2024Trial
- Detection of HIV-1 Transmission Clusters from Dried Blood Spots within a Universal Test-and-Treat Trial in East Africa.Viruses · 2022Trial
- The "Porto Alegre HIV Charter": Confronting the HIV epidemic in Rio Grande do Sul, Southern Brazil.The Brazilian journal of infectious diseases : an official publication of the Brazilian Society of Infectious Diseases · 2026Article
- Local implementation of scalable malaria molecular surveillance in a low-resource setting: a North-South collaborative model.Malaria journal · 2026Article
- Pathways, outputs and impact of NIH-supported bioinformatics and genomics graduate trainees in Africa.Briefings in bioinformatics · 2026Review
- Evidence from HIV sequencing for blood-borne transmission in Africa.Journal of public health in Africa · 2025Review
- Geospatial and phylogenetic clustering of acute and recent HIV infections in Lilongwe, Malawi.PLOS global public health · 2025Article
- Inferring HIV transmission patterns from viral deep-sequence data via latent typed point processes.Biometrics · 2024Article
- Nonstudent Young Men Put Students at High Risk of HIV Acquisition in Guangxi, China: A Phylogenetic Analysis of Surveillance Data.Open forum infectious diseases · 2022Article
- Methods Combining Genomic and Epidemiological Data in the Reconstruction of Transmission Trees: A Systematic Review.Pathogens (Basel, Switzerland) · 2022Review
- Employing phylogenetic tree shape statistics to resolve the underlying host population structure.BMC bioinformatics · 2021Article
- MicrobeTrace: Retooling molecular epidemiology for rapid public health response.PLoS computational biology · 2021Article
- Article
- The Molecular Epidemiology and Transmission Dynamics of HIV Type 1 in a General Population Cohort in Uganda.Viruses · 2020Article
- Empirical comparison of analytical approaches for identifying molecular HIV-1 clusters.Scientific reports · 2020Article
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Authors and funding
13 authors.
Funding
Abstract
Across sub-Saharan Africa, key populations with elevated HIV-1 incidence and/or prevalence have been identified, but their contribution to disease spread remains unclear. We performed viral deep-sequence phylogenetic analyses to quantify transmission dynamics between the general population (GP), fisherfolk communities (FF), and women at high risk of infection and their clients (WHR) in central and southwestern Uganda. Between August 2014 and August 2017, 6185 HIV-1 positive individuals were enrolled in 3 GP and 10 FF communities, 3 WHR enrollment sites. A total of 2531 antiretroviral therapy (ART) naïve participants with plasma viral load >1000 copies/mL were deep-sequenced. One hundred and twenty-three transmission networks were reconstructed, including 105 phylogenetically highly supported source-recipient pairs. Only one pair involved a WHR and male participant, suggesting that improved population sampling is needed to assess empirically the role of WHR to the transmission dynamics. More transmissions were observed from the GP communities to FF communities than vice versa, with an estimated flow ratio of 1.56 (95% CrI 0.68-3.72), indicating that fishing communities on Lake Victoria are not a net source of transmission flow to neighboring communities further inland. Men contributed disproportionally to HIV-1 transmission flow regardless of age, suggesting that prevention efforts need to better aid men to engage with and stay in care.
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