ArticlePloS one2013
Phylogenetic relatedness of circulating HIV-1C variants in Mochudi, Botswana.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers, 2 of them syntheses that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
25 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Pooled it
- Defining HIV-1 transmission clusters based on sequence data.AIDS (London, England) · 2017Pooled it
- Demographics of sources of HIV-1 transmission in Zambia: a molecular epidemiology analysis in the HPTN 071 PopART study.The Lancet. Microbe · 2024Trial
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- Unpacking sources of transmission in HIV prevention trials with deep-sequence pathogen data.Nature communications · 2026Article
- Evidence from HIV sequencing for blood-borne transmission in Africa.Journal of public health in Africa · 2025Review
- High prevalence of pre-treatment and acquired HIV-1 drug resistance mutations among non-citizens living with HIV in Botswana.Frontiers in microbiology · 2024Article
- Human Immunodeficiency Virus (HIV) Genetic Diversity Informs Stage of HIV-1 Infection Among Patients Receiving Antiretroviral Therapy in Botswana.The Journal of infectious diseases · 2022Article
- Network science inspires novel tree shape statistics.PloS one · 2021Article
- Characteristics of HIV-1 molecular transmission networks and drug resistance among men who have sex with men in Tianjin, China (2014-2018).Virology journal · 2020Article
- PANGEA-HIV 2: Phylogenetics And Networks for Generalised Epidemics in Africa.Current opinion in HIV and AIDS · 2019Review
- Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis.Nature communications · 2019Article
- HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences.AIDS research and human retroviruses · 2017Article
- Reconstructing contact network parameters from viral phylogenies.Virus evolution · 2016Article
- Plasma Cytokine Levels in Chronic Asymptomatic HIV-1 Subtype C Infection as an Indicator of Disease Progression in Botswana: A Retrospective Case Control Study.AIDS research and human retroviruses · 2016Article
- HIV Infection and AIDS in Sub-Saharan Africa: Current Status, Challenges and Opportunities.The open AIDS journal · 2016Article
- Phylodynamic analysis of HIV sub-epidemics in Mochudi, Botswana.Epidemics · 2015Article
- Strengthening HIV surveillance in the antiretroviral therapy era: rationale and design of a longitudinal study to monitor HIV prevalence and incidence in the uMgungundlovu District, KwaZulu-Natal, South Africa.BMC public health · 2015Article
Corrections and comments
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Authors and funding
18 authors.
Funding
Abstract
backgroundDetermining patterns of HIV transmission is increasingly important for the most efficient use of modern prevention interventions. HIV phylogeny can provide a better understanding of the mechanisms underlying HIV transmission networks in communities.
methodsTo reconstruct the structure and dynamics of a local HIV/AIDS epidemic, the phylogenetic relatedness of HIV-1 subtype C env sequences obtained from 785 HIV-infected community residents in the northeastern sector of Mochudi, Botswana, during 2010-2013 was estimated. The genotyping coverage was estimated at 44%. Clusters were defined based on relatedness of HIV-1C env sequences and bootstrap support of splits.
resultsThe overall proportion of clustered HIV-1C env sequences was 19.1% (95% CI 17.5% to 20.8%). The proportion of clustered sequences from Mochudi was significantly higher than the proportion of non-Mochudi sequences that clustered, 27.0% vs. 14.7% (p = 5.8E-12; Fisher exact test). The majority of clustered Mochudi sequences (90.1%; 95% CI 85.1% to 93.6%) were found in the Mochudi-unique clusters. None of the sequences from Mochudi clustered with any of the 1,244 non-Botswana HIV-1C sequences. At least 83 distinct HIV-1C variants, or chains of HIV transmission, in Mochudi were enumerated, and their sequence signatures were reconstructed. Seven of 20 genotyped seroconverters were found in 7 distinct clusters.
conclusionsThe study provides essential characteristics of the HIV transmission network in a community in Botswana, suggests the importance of high sampling coverage, and highlights the need for broad HIV genotyping to determine the spread of community-unique and community-mixed viral variants circulating in local epidemics. The proposed methodology of cluster analysis enumerates circulating HIV variants and can work well for surveillance of HIV transmission networks. HIV genotyping at the community level can help to optimize and balance HIV prevention strategies in trials and combined intervention packages.
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