ArticlePLoS pathogens2011
Assessing predicted HIV-1 replicative capacity in a clinical setting.
Article in PLoS pathogens, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Persistence of transmitted HIV-1 drug resistance mutations associated with fitness costs and viral genetic backgrounds.PLoS pathogens · 2015Trial
- Phylogenetics and molecular evolution to understand and curb the HIV pandemic.Nature reviews. Microbiology · 2026Review
- Attenuation of HIV severity by slightly deleterious mutations can explain the long-term trajectory of virulence evolution.PLoS computational biology · 2025Article
- Article
- Multiple-model machine learning identifies potential functional genes in dilated cardiomyopathy.Frontiers in cardiovascular medicine · 2022Article
- The within-host evolution of antimicrobial resistance in Mycobacterium tuberculosis.FEMS microbiology reviews · 2021Review
- Article
- Minimum epistasis interpolation for sequence-function relationships.Nature communications · 2020Article
- Accumulated mutations by 6 months of infection collectively render transmitted/founder HIV-1 significantly less fit.The Journal of infection · 2020Article
- Short-Sighted Virus Evolution and a Germline Hypothesis for Chronic Viral Infections.Trends in microbiology · 2017Review
- Effect of the Latent Reservoir on the Evolution of HIV at the Within- and Between-Host Levels.PLoS computational biology · 2017Article
- Article
- A transmission-virulence evolutionary trade-off explains attenuation of HIV-1 in Uganda.eLife · 2016Article
- Large Variations in HIV-1 Viral Load Explained by Shifting-Mosaic Metapopulation Dynamics.PLoS biology · 2016Article
- Prognostic Value of HIV-1 RNA on CD4 Trajectories and Disease Progression Among Antiretroviral-Naive HIV-Infected Adults in Botswana: A Joint Modeling Analysis.AIDS research and human retroviruses · 2016Article
- Observational
- Within-host stochastic emergence dynamics of immune-escape mutants.PLoS computational biology · 2015Article
- High heritability is compatible with the broad distribution of set point viral load in HIV carriers.PLoS pathogens · 2015Article
- Estimating HIV-1 fitness characteristics from cross-sectional genotype data.PLoS computational biology · 2014Article
- Virulence and pathogenesis of HIV-1 infection: an evolutionary perspective.Science (New York, N.Y.) · 2014Review
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Authors and funding
13 authors.
Funding
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Abstract
HIV-1 replicative capacity (RC) provides a measure of within-host fitness and is determined in the context of phenotypic drug resistance testing. However it is unclear how these in-vitro measurements relate to in-vivo processes. Here we assess RCs in a clinical setting by combining a previously published machine-learning tool, which predicts RC values from partial pol sequences with genotypic and clinical data from the Swiss HIV Cohort Study. The machine-learning tool is based on a training set consisting of 65000 RC measurements paired with their corresponding partial pol sequences. We find that predicted RC values (pRCs) correlate significantly with the virus load measured in 2073 infected but drug naïve individuals. Furthermore, we find that, for 53 pairs of sequences, each pair sampled in the same infected individual, the pRC was significantly higher for the sequence sampled later in the infection and that the increase in pRC was also significantly correlated with the increase in plasma viral load and with the length of the time-interval between the sampling points. These findings indicate that selection within a patient favors the evolution of higher replicative capacities and that these in-vitro fitness measures are indicative of in-vivo HIV virus load.
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