ArticleMolecular biology and evolution2023
Evolution of the SARS-CoV-2 Mutational Spectrum.
Article in Molecular biology and evolution, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
56 citing papers in PubMed.
- Harnessing the central dogma: Enzyme-driven gene diversification strategies for in cellulo continuous directed evolution.Fundamental research · 2026Review
- From sites to structure to serology: a roadmap for structure-aware molecular evolution of antigenically evolving viruses.Journal of virology · 2026Review
- A Multiepitope Intranasal Adenoviral Vaccine Induces Robust Mucosal Immunity and Protection against SARS‑CoV‑2.Journal of nanobiotechnology · 2026Article
- Distinct Patterns of Clinical Features and Cardiac Biomarker Elevation in Community-Acquired Pneumonia and COVID-19 Pneumonia.Pathogens (Basel, Switzerland) · 2026Article
- Common respiratory virus spectrum and epidemiological trends among children in Northwest China during the post-COVID-19 era.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2026Article
- Compressive pangenomics using mutation-annotated networks.Nature genetics · 2026Article
- On the role of dcm and vsr in Escherichia coli adaptive mutation.Molecular genetics and genomics : MGG · 2025Article
- A Pandemic-Scale Ancestral Recombination Graph for SARS-CoV-2.bioRxiv : the preprint server for biology · 2025Article
- Functional and Structural Characterization of Treatment-Emergent Nirmatrelvir Resistance Mutations at Low Frequencies in the Main Protease (Mpro) Reveals a Unique Evolutionary Route for SARS-CoV-2 to Gain Resistance.The Journal of infectious diseases · 2025Article
- Organoids in respiratory virus research: advances and perspectives.Molecular biomedicine · 2025Review
- Intra-host diversity of SARS-CoV-2 in children with long-term and short-term excretion in nasopharyngeal samples.BMC infectious diseases · 2025Article
- Association between SARS-CoV-2 levels in urban wastewater and reported COVID-19 cases in Changsha, Central China.BMC infectious diseases · 2025Article
- A single mutation may contribute to accelerated evolution of SARS-CoV-2 toward Omicron.Nature communications · 2025Article
- The mutation rate of SARS-CoV-2 is highly variable between sites and is influenced by sequence context, genomic region, and RNA structure.Nucleic acids research · 2025Article
- A Critical Reexamination of Recovered SARS-CoV-2 Sequencing Data.Molecular biology and evolution · 2025Article
- Deciphering the Code of Viral-Host Adaptation Through Maximum-Entropy Nucleotide Bias Models.Molecular biology and evolution · 2025Article
- The Data are Insufficient to Confidently Root the SARS-CoV-2 Phylogenetic Tree.Molecular biology and evolution · 2025Article
- SARS-CoV-2 point mutations are over-represented in terminal loops of RNA stem-loop structures that can be resolved by Nsp13 helicase in a unique manner with respect to nucleotide dependence.Nucleic acids research · 2025Article
- SARS-CoV-2 biological clones are genetically heterogeneous and include clade-discordant residues.Journal of virology · 2025Article
- Genomic and spatial epidemiology: lessons learned from SARS-CoV-2 pandemic.Current opinion in HIV and AIDS · 2025Review
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4 authors.
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Abstract
SARS-CoV-2 evolves rapidly in part because of its high mutation rate. Here, we examine whether this mutational process itself has changed during viral evolution. To do this, we quantify the relative rates of different types of single-nucleotide mutations at 4-fold degenerate sites in the viral genome across millions of human SARS-CoV-2 sequences. We find clear shifts in the relative rates of several types of mutations during SARS-CoV-2 evolution. The most striking trend is a roughly 2-fold decrease in the relative rate of G→T mutations in Omicron versus early clades, as was recently noted by Ruis et al. (2022. Mutational spectra distinguish SARS-CoV-2 replication niches. bioRxiv, doi:10.1101/2022.09.27.509649). There is also a decrease in the relative rate of C→T mutations in Delta, and other subtle changes in the mutation spectrum along the phylogeny. We speculate that these changes in the mutation spectrum could arise from viral mutations that affect genome replication, packaging, and antagonization of host innate-immune factors, although environmental factors could also play a role. Interestingly, the mutation spectrum of Omicron is more similar than that of earlier SARS-CoV-2 clades to the spectrum that shaped the long-term evolution of sarbecoviruses. Overall, our work shows that the mutation process is itself a dynamic variable during SARS-CoV-2 evolution and suggests that human SARS-CoV-2 may be trending toward a mutation spectrum more similar to that of other animal sarbecoviruses.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.