ArticleProtein science : a publication of the Protein Society2016
Evolutionary dynamics of viral escape under antibodies stress: A biophysical model.
Article in Protein science : a publication of the Protein Society, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Phase diagrams for biophysical fitness landscape design.bioRxiv : the preprint server for biology · 2026Article
- Predicting high-fitness viral protein variants with Bayesian active learning and biophysics.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Few-Shot Viral Variant Detection via Bayesian Active Learning and Biophysics.bioRxiv : the preprint server for biology · 2025Article
- Bioengineering hybrid artificial life.Frontiers in bioinformatics · 2025Review
- Biophysical principles predict fitness of SARS-CoV-2 variants.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Biophysical principles predict fitness of SARS-CoV-2 variants.bioRxiv : the preprint server for biology · 2024Article
- A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics.Computers in biology and medicine · 2021Article
- Survival of the simplest in microbial evolution.Nature communications · 2019Article
- Using Antibodies and Mutants To Localize the Presumptive gH/gL Binding Site on Herpes Simplex Virus gD.Journal of virology · 2018Article
- Evolution on the Biophysical Fitness Landscape of an RNA Virus.Molecular biology and evolution · 2018Article
- Human dengue virus serotype 2 neutralizing antibodies target two distinct quaternary epitopes.PLoS pathogens · 2018Article
- Host proteostasis modulates influenza evolution.eLife · 2017Article
- Bridging the physical scales in evolutionary biology: from protein sequence space to fitness of organisms and populations.Current opinion in structural biology · 2017Review
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Authors and funding
4 authors.
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Abstract
Viruses constantly face the selection pressure of antibodies, either from innate immune response of the host or from administered antibodies for treatment. We explore the interplay between the biophysical properties of viral proteins and the population and demographic variables in the viral escape. The demographic and population genetics aspect of the viral escape have been explored before; however one important assumption was the a priori distribution of fitness effects (DFE). Here, we relax this assumption by instead considering a realistic biophysics-based genotype-phenotype relationship for RNA viruses escaping antibodies stress. In this model the DFE is itself an evolvable property that depends on the genetic background (epistasis) and the distribution of biophysical effects of mutations, which is informed by biochemical experiments and theoretical calculations in protein engineering. We quantitatively explore in silico the viability of viral populations under antibodies pressure and derive the phase diagram that defines the fate of the virus population (extinction or escape from stress) in a range of viral mutation rates and antibodies concentrations. We find that viruses are most resistant to stress at an optimal mutation rate (OMR) determined by the competition between supply of beneficial mutation to facilitate escape from stressors and lethal mutagenesis caused by excess of destabilizing mutations. We then show the quantitative dependence of the OMR on genome length and viral burst size. We also recapitulate the experimental observation that viruses with longer genomes have smaller mutation rate per nucleotide.
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