ArticleGenome biology and evolution2021
Mutation Rates and Selection on Synonymous Mutations in SARS-CoV-2.
Article in Genome biology and evolution, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 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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Who cites it
85 citing papers in PubMed, 131 citations in OpenAlex.
- A Viral Protein Antagonist for Both AID and APOBEC3.Viruses · 2026Review
- Rate variation and recurrent sequence errors in pandemic-scale phylogenetics.Nature methods · 2026Article
- Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny.Nature methods · 2026Article
- Article
- Highly Recurrent Multinucleotide Mutations in SARS-CoV-2.Molecular biology and evolution · 2025Article
- Is SARS-CoV-2 facing constraints in its adaptive evolution?Biomolecules & biomedicine · 2025Review
- 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
- Impact of an oxidative RNA lesion on in vitro replication catalyzed by SARS-CoV-2 RNA-dependent RNA polymerase.The Journal of biological chemistry · 2025Article
- Article
- Secondary structure of the SARS-CoV-2 genome is predictive of nucleotide substitution frequency.eLife · 2025Article
- The mutation rate of SARS-CoV-2 is highly variable between sites and is influenced by sequence context, genomic region, and RNA structure.bioRxiv : the preprint server for biology · 2025Article
- Recently reported SARS-CoV-2 genomes suggested to be intermediate between the two early main lineages are instead likely derived.Virus evolution · 2025Article
- Over time analysis of the codon usage of SARS-CoV-2 and its variants.Computational and structural biotechnology journal · 2025Article
- C→U transition biases in SARS-CoV-2: still rampant 4 years from the start of the COVID-19 pandemic.mBio · 2024Article
- Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny.bioRxiv : the preprint server for biology · 2024Article
- How Trustworthy Are the Genomic Sequences of SARS-CoV-2 in GenBank?Microorganisms · 2024Article
- The impact of host microRNAs on the development of conserved mutations of SARS-CoV-2.Scientific reports · 2024Article
- Understanding the biology of monkeypox virus to prevent future outbreaks.Nature microbiology · 2024Review
- Crykey: Rapid identification of SARS-CoV-2 cryptic mutations in wastewater.Nature communications · 2024Article
25 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors at 4 institutions in 3 countries.
Funding
Abstract
The COVID-19 pandemic has seen an unprecedented response from the sequencing community. Leveraging the sequence data from more than 140,000 SARS-CoV-2 genomes, we study mutation rates and selective pressures affecting the virus. Understanding the processes and effects of mutation and selection has profound implications for the study of viral evolution, for vaccine design, and for the tracking of viral spread. We highlight and address some common genome sequence analysis pitfalls that can lead to inaccurate inference of mutation rates and selection, such as ignoring skews in the genetic code, not accounting for recurrent mutations, and assuming evolutionary equilibrium. We find that two particular mutation rates, G →U and C →U, are similarly elevated and considerably higher than all other mutation rates, causing the majority of mutations in the SARS-CoV-2 genome, and are possibly the result of APOBEC and ROS activity. These mutations also tend to occur many times at the same genome positions along the global SARS-CoV-2 phylogeny (i.e., they are very homoplasic). We observe an effect of genomic context on mutation rates, but the effect of the context is overall limited. Although previous studies have suggested selection acting to decrease U content at synonymous sites, we bring forward evidence suggesting the opposite.
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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.