ArticleVirus evolution2021
Synonymous mutations and the molecular evolution of SARS-CoV-2 origins.
Article in Virus evolution, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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Who cites it
54 citing papers in PubMed.
- Inference of Cytochrome P450 Evolutionary History Using Structural and Physicochemical Metrics.Genome biology and evolution · 2025Article
- SARS-CoV-2 genomic diversity and within-host evolution in individuals with persistent infection in the UK: an observational, longitudinal, population-based surveillance study.The Lancet. Microbe · 2025Observational
- On Rooting and Dating Viral Trees With a Changing Evolutionary Rate Following Host-Switching.Genome biology and evolution · 2025Article
- Paying attention to the SARS-CoV-2 dialect : a deep neural network approach to predicting novel protein mutations.Communications biology · 2025Article
- Recombination across distant coronavirid species and genera is a rare event with distinct genomic features.Journal of virology · 2024Article
- How Trustworthy Are the Genomic Sequences of SARS-CoV-2 in GenBank?Microorganisms · 2024Article
- COVID-19 mutations: An overview.World journal of methodology · 2024Review
- Population genetic considerations regarding the interpretation of within-patient SARS-CoV-2 polymorphism data.Nature communications · 2024Article
- Article
- Identification of Evolutionary Trajectories Shared across Human Betacoronaviruses.Genome biology and evolution · 2023Article
- Antitarget, Anti-SARS-CoV-2 Leads, Drugs, and the Drug Discovery-Genetics Alliance Perspective.Journal of medicinal chemistry · 2023Review
- Rooting and Dating Large SARS-CoV-2 Trees by Modeling Evolutionary Rate as a Function of Time.Viruses · 2023Article
- Variation in synonymous evolutionary rates in the SARS-CoV-2 genome.Frontiers in microbiology · 2023Article
- Review
- Optimising predictive models to prioritise viral discovery in zoonotic reservoirs.The Lancet. Microbe · 2022Review
- SARS-CoV-2 and Emerging Foodborne Pathogens: Intriguing Commonalities and Obvious Differences.Pathogens (Basel, Switzerland) · 2022Review
- Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2.Chemical reviews · 2022Review
- Unlocking capacities of genomics for the COVID-19 response and future pandemics.Nature methods · 2022Article
- Statistical modeling of SARS-CoV-2 substitution processes: predicting the next variant.Communications biology · 2022Article
- SARS-CoV-2: tracing the origin, tracking the evolution.BMC medical genomics · 2022Review
Corrections and comments
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3 authors.
Funding
Abstract
Human severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is most closely related, by average genetic distance, to two coronaviruses isolated from bats, RaTG13 and RmYN02. However, there is a segment of high amino acid similarity between human SARS-CoV-2 and a pangolin-isolated strain, GD410721, in the receptor-binding domain (RBD) of the spike protein, a pattern that can be caused by either recombination or by convergent amino acid evolution driven by natural selection. We perform a detailed analysis of the synonymous divergence, which is less likely to be affected by selection than amino acid divergence, between human SARS-CoV-2 and related strains. We show that the synonymous divergence between the bat-derived viruses and SARS-CoV-2 is larger than between GD410721 and SARS-CoV-2 in the RBD, providing strong additional support for the recombination hypothesis. However, the synonymous divergence between pangolin strain and SARS-CoV-2 is also relatively high, which is not consistent with a recent recombination between them, instead, it suggests a recombination into RaTG13. We also find a 14-fold increase in the
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