ArticlePLoS computational biology2015
Broad CTL Response in Early HIV Infection Drives Multiple Concurrent CTL Escapes.
Article in PLoS computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- A consensus mathematical model of vaccine-induced antibody dynamics for multiple vaccine platforms and pathogens.Frontiers in immunology · 2025Article
- Plasma Levels of Secreted Cytokines in Virologically Controlled HIV-Infected Aging Adult Individuals on Long-Term Antiretroviral Therapy.Viral immunology · 2024Article
- Intrahost evolution of the HIV-2 capsid correlates with progression to AIDS.Virus evolution · 2022Article
- MPL resolves genetic linkage in fitness inference from complex evolutionary histories.Nature biotechnology · 2021Article
- A de novo approach to inferring within-host fitness effects during untreated HIV-1 infection.PLoS pathogens · 2020Article
- Modeling the immune response to HIV infection.Current opinion in systems biology · 2018Article
- Insight into treatment of HIV infection from viral dynamics models.Immunological reviews · 2018Review
- Evolution of HIV-1 within untreated individuals and at the population scale in Uganda.PLoS pathogens · 2018Article
- Time Intervals in Sequence Sampling, Not Data Modifications, Have a Major Impact on Estimates of HIV Escape Rates.Viruses · 2018Article
- Immune Evasion of Enteroviruses Under Innate Immune Monitoring.Frontiers in microbiology · 2018Review
- Kinetics of HIV-Specific CTL Responses Plays a Minimal Role in Determining HIV Escape Dynamics.Frontiers in immunology · 2018Article
- Global properties of nested network model with application to multi-epitope HIV/CTL dynamics.Journal of mathematical biology · 2017Article
- A penalized regression approach to haplotype reconstruction of viral populations arising in early HIV/SIV infection.Bioinformatics (Oxford, England) · 2017Article
- Short-Sighted Virus Evolution and a Germline Hypothesis for Chronic Viral Infections.Trends in microbiology · 2017Review
- Within-Epitope Interactions Can Bias CTL Escape Estimation in Early HIV Infection.Frontiers in immunology · 2017Article
- Large Variations in HIV-1 Viral Load Explained by Shifting-Mosaic Metapopulation Dynamics.PLoS biology · 2016Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent studies have highlighted the ability of HIV to escape from cytotoxic T lymphocyte (CTL) responses that concurrently target multiple viral epitopes. Yet, the viral dynamics involved in such escape are incompletely understood. Previous analyses have made several strong assumptions regarding HIV escape from CTL responses such as independent or non-concurrent escape from individual CTL responses. Using experimental data from evolution of HIV half genomes in four patients we observe concurrent viral escape from multiple CTL responses during early infection (first 100 days of infection), providing confirmation of a recent result found in a study of one HIV-infected patient. We show that current methods of estimating CTL escape rates, based on the assumption of independent escapes, are biased and perform poorly when CTL escape proceeds concurrently at multiple epitopes. We propose a new method for analyzing longitudinal sequence data to estimate the rate of CTL escape across multiple epitopes; this method involves few parameters and performs well in simulation studies. By applying our novel method to experimental data, we find that concurrent multiple escapes occur at rates between 0.03 and 0.4 day(-1), a relatively broad range that reflects uncertainty due to sparse sampling and wide ranges of parameter values. However, we show that concurrent escape at rates 0.1-0.2 day(-1) across multiple epitopes is consistent with our patient datasets.
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