SARS-CoV-2 Evolution in an HIV-Endemic Setting: A Genomic Epidemiology Study from Botswana
Xuhua Geng1, Ivan Barilar2, Monamodi Kesamang3
1Boston University School of Public Health, Boston, MA, USA.
Medrxiv : the Preprint Server for Health Sciences
|December 3, 2025
Summary
In Botswana, HIV infection did not significantly alter SARS-CoV-2 evolution during the Omicron period. However, subtle clustering in HIV-positive individuals suggests potential host-specific impacts, highlighting the need for ongoing genomic surveillance.
Area of Science:
- Genomic epidemiology
- Viral evolution
- Immunology
Background:
- HIV infection can impact SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) infection dynamics.
- Limited population-level genomic data exists from HIV-endemic settings.
- Botswana's high HIV prevalence and genomic infrastructure offer a unique setting to study host variation's influence on SARS-CoV-2 evolution during the Omicron period.
Purpose of the Study:
- To investigate the influence of host immune variation, specifically HIV status, on SARS-CoV-2 evolution.
- To analyze population-level genomic evidence of SARS-CoV-2 during the Omicron period in an HIV-endemic setting.
Main Methods:
- A population-based genomic epidemiology study was conducted in Botswana.
- 404 SARS-CoV-2 positive samples were collected, yielding 387 high-quality genomes.
- Phylogenetic trees were reconstructed and visualized, incorporating participant HIV status and vaccination history.
Main Results:
- Six successive Omicron sublineage waves were detected, indicating repeated viral introductions.
- SARS-CoV-2 genomes from HIV-positive and HIV-negative individuals were interspersed, showing no population-level separation by HIV status.
- Small clusters of HIV-positive hosts were observed within specific SARS-CoV-2 sublineages (BA, JN, KP).
Conclusions:
- In a highly treated and vaccinated population, HIV infection did not fundamentally alter population-level SARS-CoV-2 evolutionary trajectories.
- Subtle clustering among HIV-positive hosts suggests potential host-specific effects on viral adaptation.
- Continued genomic surveillance integrating host data is crucial for detecting early signals of viral adaptation.
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