ArticleEpidemics2015
Phylodynamic analysis of HIV sub-epidemics in Mochudi, Botswana.
Article in Epidemics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers, 1 of them a synthesis that pooled it.
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Who cites it
17 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
- Phylogenetics and molecular evolution to understand and curb the HIV pandemic.Nature reviews. Microbiology · 2026Review
- Rapid circulation of HIV-1 CRF85_BC in Southwest China: its geographic origins and molecular transmission networks analysis.Frontiers in cellular and infection microbiology · 2025Article
- Evidence from HIV sequencing for blood-borne transmission in Africa.Journal of public health in Africa · 2025Review
- Scalable gradients enable Hamiltonian Monte Carlo sampling for phylodynamic inference under episodic birth-death-sampling models.PLoS computational biology · 2024Article
- Scalable gradients enable Hamiltonian Monte Carlo sampling for phylodynamic inference under episodic birth-death-sampling models.bioRxiv : the preprint server for biology · 2023Article
- The role of migration networks in the development of Botswana's generalized HIV epidemic.eLife · 2023Article
- Population mobility and the development of Botswana's generalized HIV epidemic: a network analysis.medRxiv : the preprint server for health sciences · 2023Article
- Human Immunodeficiency Virus Type 1 Phylodynamics to Detect and Characterize Active Transmission Clusters in North Carolina.The Journal of infectious diseases · 2020Article
- Dynamics of HIV-1 Molecular Networks Reveal Effective Control of Large Transmission Clusters in an Area Affected by an Epidemic of Multiple HIV Subtypes.Frontiers in microbiology · 2020Article
- PANGEA-HIV 2: Phylogenetics And Networks for Generalised Epidemics in Africa.Current opinion in HIV and AIDS · 2019Review
- The effect of interventions on the transmission and spread of HIV in South Africa: a phylodynamic analysis.Scientific reports · 2019Article
- Geographic variation in sexual behavior can explain geospatial heterogeneity in the severity of the HIV epidemic in Malawi.BMC medicine · 2018Article
- 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
- Transmission networks and risk of HIV infection in KwaZulu-Natal, South Africa: a community-wide phylogenetic study.The lancet. HIV · 2017Article
- Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison.Molecular biology and evolution · 2017Article
- Impacts and shortcomings of genetic clustering methods for infectious disease outbreaks.Virus evolution · 2016Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Southern Africa continues to be the epicenter of the HIV/AIDS epidemic. This HIV-1 subtype C epidemic has a predominantly heterosexual mode of virus transmission and high (>15%) HIV prevalence among adults. The epidemiological dynamics of the HIV-1C epidemic in southern Africa are still poorly understood. Here, we aim at a better understanding of HIV transmission dynamics by analyzing HIV-1 subtype C sequences from Mochudi, a peri-urban village in Botswana. HIV-1C env gene sequences (gp120 V1C5) were obtained through enhanced household-based HIV testing and counseling in Mochudi. More than 1200 sequences were generated and phylogenetically distinct sub-epidemics within Mochudi identified. The Bayesian birth-death skyline plot was used to estimate the effective reproductive number, R, and the timing of virus transmission, to classify sub-epidemics as "acute" (those with recent viral transmissions) or "historic" (those without recent viral transmissions). We identified two of the 15 sub-epidemics as "acute." The median estimates of R among the clusters ranged from 0.72 to 1.77. The majority of HIV lineages, 11 out of 15 clusters with 5+ members, appear to have been introduced to Mochudi between 1996 and 2002. The median peak duration of viral transmissions was 7.1 years (range 2.9-9.7 years). The median life span of identified HIV sub-epidemics, i.e., the time between the inferred epidemic origin and its most recent sample, was 13.1 years (range 10.2-22.1 years). Most viral transmissions within the sub-epidemics occurred between 1997 and 2007. The time period during which infected people are infectious appears to have decreased since the introduction of the national ART program in Botswana. Real-time HIV genotyping and breaking down local HIV epidemics into phylogenetically distinct sub-epidemics may help to reveal the structure and dynamics of HIV transmission networks in communities, and aid in the design of targeted interventions for members of the acute sub-epidemics that likely fuel local HIV/AIDS epidemics.
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