ArticleViruses2021
Prediction and Evolution of the Molecular Fitness of SARS-CoV-2 Variants: Introducing SpikePro.
Article in Viruses, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- A protocol for computational design of mRNA vaccines with high functionality and specificity.Biology direct · 2026Article
- Quantifying and combating zoonotic viruses poised for emergence: Using multiplex receptor screening and decoy engineering technologies.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- AbAgym: a well-curated dataset for the mutational analysis of antibody-antigen complexes.mAbs · 2025Article
- Clinical Manifestations and Cytokine Profiles of the Th1, Th2, and Th17 Response Associated with SARS-CoV-2 Omicron Subvariants.Biomedicines · 2025Article
- In silico genomic surveillance by CoVerage predicts and characterizes SARS-CoV-2 variants of interest.Nature communications · 2025Article
- Integrating genomic epidemiology and deep mutational scanning data for prevalence forecasting of SARS-CoV-2 Omicron lineages.PloS one · 2025Article
- Identification and biophysical characterization of epitope atlas of Porcine Reproductive and Respiratory Syndrome Virus.Computational and structural biotechnology journal · 2024Article
- The biophysical landscape of viral evolution.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Biophysical principles predict fitness of SARS-CoV-2 variants.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Ensemble-Based Mutational Profiling and Network Analysis of the SARS-CoV-2 Spike Omicron XBB Lineages for Interactions with the ACE2 Receptor and Antibodies: Cooperation of Binding Hotspots in Mediating Epistatic Couplings Underlies Binding Mechanism and Immune Escape.International journal of molecular sciences · 2024Article
- AlphaFold2-Enabled Atomistic Modeling of Structure, Conformational Ensembles, and Binding Energetics of the SARS-CoV-2 Omicron BA.2.86 Spike Protein with ACE2 Host Receptor and Antibodies: Compensatory Functional Effects of Binding Hotspots in Modulating Mechanisms of Receptor Binding and Immune Escape.Journal of chemical information and modeling · 2024Article
- Biophysical principles predict fitness of SARS-CoV-2 variants.bioRxiv : the preprint server for biology · 2024Article
- Article
- Risk Assessment of the Possible Intermediate Host Role of Pigs for Coronaviruses with a Deep Learning Predictor.Viruses · 2023Article
- Early warning of emerging infectious diseases based on multimodal data.Biosafety and health · 2023Review
- Impact of mAb-induced A475V substitution on viral fitness and antibody neutralization of SARS-CoV-2 omicron variants in the presence of monoclonal antibodies and human convalescent sera.Frontiers in immunology · 2023Article
- An integrated understanding of the evolutionary and structural features of the SARS-CoV-2 spike receptor binding domain (RBD).International journal of biological macromolecules · 2022Article
- Deep learning based on biologically interpretable genome representation predicts two types of human adaptation of SARS-CoV-2 variants.Briefings in bioinformatics · 2022Article
- Article
- Analysis of the Neutralizing Activity of Antibodies Targeting Open or Closed SARS-CoV-2 Spike Protein Conformations.International journal of molecular sciences · 2022Article
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2 authors.
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Abstract
The understanding of the molecular mechanisms driving the fitness of the SARS-CoV-2 virus and its mutational evolution is still a critical issue. We built a simplified computational model, called SpikePro, to predict the SARS-CoV-2 fitness from the amino acid sequence and structure of the spike protein. It contains three contributions: the inter-human transmissibility of the virus predicted from the stability of the spike protein, the infectivity computed in terms of the affinity of the spike protein for the ACE2 receptor, and the ability of the virus to escape from the human immune response based on the binding affinity of the spike protein for a set of neutralizing antibodies. Our model reproduces well the available experimental, epidemiological and clinical data on the impact of variants on the biophysical characteristics of the virus. For example, it is able to identify circulating viral strains that, by increasing their fitness, recently became dominant at the population level. SpikePro is a useful, freely available instrument which predicts rapidly and with good accuracy the dangerousness of new viral strains. It can be integrated and play a fundamental role in the genomic surveillance programs of the SARS-CoV-2 virus that, despite all the efforts, remain time-consuming and expensive.
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