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Updated: Jun 8, 2025
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Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3
Published on: December 27, 2010
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Phylodynamic Structure in the Botswana HIV Epidemic.
Kenanao Kotokwe1, Fabrícia F Nascimento1, Sikhulile Moyo2
1MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London.
Research Square
|November 1, 2024
Summary
Understanding HIV-1 transmission in Botswana reveals ongoing sub-epidemics with recent infections in areas of lower treatment coverage. Public health interventions should target these high-growth regions, considering population mobility.
Area of Science:
- Epidemiology
- Virology
- Public Health
Background:
- Viral sequences offer insights into host contact networks and HIV-1 transmission dynamics.
- Understanding the HIV-1 epidemic's population structure in Botswana is crucial for optimizing interventions and identifying hidden sub-epidemics.
Purpose of the Study:
- To determine the phylodynamic structure of the Botswana HIV-1 epidemic using viral genetic sequence data.
Main Methods:
- Reconstructed time-resolved phylogenies (gag and pol) from over 4,000 HIV-1 sequences from the Botswana Combination Prevention Project (BCPP).
- Inferred infection stage using a machine learning model and analyzed phylogenies for partitions indicating sub-epidemics.
- Estimated viral effective population size and compared demographic, clinical, and geographic characteristics across partitions.
Main Results:
- Identified three distinct partitions in HIV-1 phylogenies, showing divergent transmission patterns.
- Fast-growing partitions were associated with lower antiretroviral treatment (ART) coverage and more recent infections.
- The Southern and South East regions of Botswana were over-represented in rapidly expanding sub-epidemics.
Conclusions:
- HIV-1 transmission is slowing in populations with high ART coverage, but ongoing sub-epidemics persist with recent infections.
- Phylodynamic analysis highlights specific districts with higher growth, suggesting targeted public health interventions.
- Population mobility in Botswana is a key factor to consider for effective HIV-1 control strategies.
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