ArticleMolecular biology and evolution2022
The Emergence of SARS-CoV-2 Variants of Concern Is Driven by Acceleration of the Substitution Rate.
Article in Molecular biology and evolution, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers.
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Who cites it
75 citing papers in PubMed.
- Characterization of Treatment Resistance and Viral Kinetics in the Setting of Single-Active Versus Dual-Active Monoclonal Antibodies Against Severe Acute Respiratory Syndrome Coronavirus 2.The Journal of infectious diseases · 2024Trial
- Why Andes hantavirus is not the next SARS-CoV-2: contrasting viral shedding, transmissibility and genomic patterns.Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2026Article
- Slowdown of synonymous substitution rate preceding the emergence of multiple SARS-CoV-2 variants.Virus evolution · 2026Article
- Beyond traditional outbreak investigation: Using genomic data for enhanced detection of COVID-19 disease clusters in Utah.PloS one · 2026Article
- Review
- Genomic and epidemiologic characteristics of SARS-CoV-2 persistent infections in California, January 2021 - July 2023.PLoS pathogens · 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
- Long-term serial passaging of SARS-CoV-2 reveals signatures of convergent evolution.Journal of virology · 2025Article
- On Rooting and Dating Viral Trees With a Changing Evolutionary Rate Following Host-Switching.Genome biology and evolution · 2025Article
- Variable rates of SARS-CoV-2 evolution in chronic infections.PLoS pathogens · 2025Article
- JUNIPER: Reconstructing Transmission Events from Next-Generation Sequencing Data at Scale.Research square · 2025Article
- JUNIPER: Reconstructing Transmission Events from Next-Generation Sequencing Data at Scale.medRxiv : the preprint server for health sciences · 2025Article
- Diverse patterns of intra-host genetic diversity in chronically infected SARS-CoV-2 patients.Virus evolution · 2025Article
- Reflective Evaluation of Next-Generation Sequencing Data during Early Phase Detection of the Delta Variant.OBM genetics · 2025Article
- Investigating the evolutionary dynamics and mutational pattern of SARS-CoV-2 spike gene on selected SARS-CoV-2 variants.PloS one · 2025Article
- Routes of importation and spatial dynamics of SARS-CoV-2 variants during localized interventions in Chile.PNAS nexus · 2024Article
- SARS-CoV-2 Evolution: Immune Dynamics, Omicron Specificity, and Predictive Modeling in Vaccinated Populations.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Clockor2: Inferring Global and Local Strict Molecular Clocks Using Root-to-Tip Regression.Systematic biology · 2024Article
- Combining Molecular, Macroevolutionary, and Macroecological Perspectives on the Generation of Diversity.Cold Spring Harbor perspectives in biology · 2024Review
- High-resolution epidemiological landscape from ~290,000 SARS-CoV-2 genomes from Denmark.Nature communications · 2024Article
15 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
The ongoing SARS-CoV-2 pandemic has seen an unprecedented amount of rapidly generated genome data. These data have revealed the emergence of lineages with mutations associated to transmissibility and antigenicity, known as variants of concern (VOCs). A striking aspect of VOCs is that many of them involve an unusually large number of defining mutations. Current phylogenetic estimates of the substitution rate of SARS-CoV-2 suggest that its genome accrues around two mutations per month. However, VOCs can have 15 or more defining mutations and it is hypothesized that they emerged over the course of a few months, implying that they must have evolved faster for a period of time. We analyzed genome sequence data from the GISAID database to assess whether the emergence of VOCs can be attributed to changes in the substitution rate of the virus and whether this pattern can be detected at a phylogenetic level using genome data. We fit a range of molecular clock models and assessed their statistical performance. Our analyses indicate that the emergence of VOCs is driven by an episodic increase in the substitution rate of around 4-fold the background phylogenetic rate estimate that may have lasted several weeks or months. These results underscore the importance of monitoring the molecular evolution of the virus as a means of understanding the circumstances under which VOCs may emerge.
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