ArticleProceedings of the National Academy of Sciences of the United States of America2011
Estimate of effective recombination rate and average selection coefficient for HIV in chronic infection.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
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Who cites it
71 citing papers in PubMed, 112 citations in OpenAlex.
- Relationship between latent and rebound viruses in a clinical trial of anti-HIV-1 antibody 3BNC117.The Journal of experimental medicine · 2018Trial
- Single cell analysis of lymph node tissue from HIV-1 infected patients reveals that the majority of CD4+ T-cells contain one HIV-1 DNA molecule.PLoS pathogens · 2013Trial
- Keystone Epitope Theory: An Ecological Perspective on RNA Viruses, Tumor Immunoediting, and Vaccine Design.Pathogens & immunity · 2026Review
- Tradeoffs between proliferation and transmission in virus evolution- insights from evolutionary and functional analyses of SARS-CoV-2.Virology journal · 2025Article
- Review
- Estimates of HIV-1 within-host recombination rates across the whole genome.Virus evolution · 2025Article
- The Confluence of HIV-1 and HIV-2: Implications for Disease Progression and Insights for Therapy.International journal of microbiology · 2025Review
- Engineered deletions of HIV replicate conditionally to reduce disease in nonhuman primates.Science (New York, N.Y.) · 2024Article
- Incorporating Intracellular Processes in Virus Dynamics Models.Microorganisms · 2024Review
- Elevated HIV Viral Load is Associated with Higher Recombination Rate In Vivo.Molecular biology and evolution · 2024Article
- Elevated HIV viral load is associated with higher recombination ratebioRxiv : the preprint server for biology · 2023Article
- Long-range linkage effects in adapting sexual populations.Scientific reports · 2023Article
- Evolutionary implications of SARS-CoV-2 vaccination for the future design of vaccination strategies.Communications medicine · 2023Review
- Recombination smooths the time signal disrupted by latency in within-host HIV phylogenies.Virus evolution · 2023Article
- Review
- MPL resolves genetic linkage in fitness inference from complex evolutionary histories.Nature biotechnology · 2021Article
- HIV-1-Specific Immunodominant T-Cell Responses Drive the Dynamics of HIV-1 Recombination Following Superinfection.Frontiers in immunology · 2021Article
- An Evolutionary Model of Progression to AIDS.Microorganisms · 2020Article
- A de novo approach to inferring within-host fitness effects during untreated HIV-1 infection.PLoS pathogens · 2020Article
- Genetic characterization of HIV-1 epidemic in Anhui Province, China.Virology journal · 2020Article
11 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
HIV adaptation to a host in chronic infection is simulated by means of a Monte-Carlo algorithm that includes the evolutionary factors of mutation, positive selection with varying strength among sites, random genetic drift, linkage, and recombination. By comparing two sensitive measures of linkage disequilibrium (LD) and the number of diverse sites measured in simulation to patient data from one-time samples of pol gene obtained by single-genome sequencing from representative untreated patients, we estimate the effective recombination rate and the average selection coefficient to be on the order of 1% per genome per generation (10(-5) per base per generation) and 0.5%, respectively. The adaptation rate is twofold higher and fourfold lower than predicted in the absence of recombination and in the limit of very frequent recombination, respectively. The level of LD and the number of diverse sites observed in data also range between the values predicted in simulation for these two limiting cases. These results demonstrate the critical importance of finite population size, linkage, and recombination in HIV evolution.
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