ArticleGenome biology and evolution2021
Causes and Consequences of Purifying Selection on 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 24 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.
The trial behind it
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Who cites it
24 citing papers in PubMed, 48 citations in OpenAlex.
- Study on the correlation between molecular characteristics of SARS-CoV-2 and its epidemiology and clinical manifestations in Lu'an city.World journal of virology · 2026Article
- Codon Usage Evolution in Viruses: Implications for Survival and Pathogenicity.Journal of molecular evolution · 2025Review
- Heterogeneous Evolution Among SARS-CoV-2 Genes and Variants of Concern.Journal of medical virology · 2025Article
- Codon Usage Bias: A Potential Factor Affecting VGLUT Developmental Expression and Protein Evolution.Molecular neurobiology · 2025Article
- SARS-CoV-2 introductions to the island of Ireland: a phylogenetic and geospatiotemporal study of infection dynamics.Genome medicine · 2024Article
- Wastewater-based surveillance as a tool for public health action: SARS-CoV-2 and beyond.Clinical microbiology reviews · 2024Review
- Genome analysis of SARS-CoV-2 isolates from a population reveals the rapid selective sweep of a haplotype carrying many pre-existing and new mutations.Virology journal · 2023Article
- Intra-Host Co-Existing Strains of SARS-CoV-2 Reference Genome Uncovered by Exhaustive Computational Search.Viruses · 2023Article
- Developing an appropriate evolutionary baseline model for the study of SARS-CoV-2 patient samples.PLoS pathogens · 2023Review
- Article
- Review
- Variation in synonymous evolutionary rates in the SARS-CoV-2 genome.Frontiers in microbiology · 2023Article
- Review
- Distinguishing COVID-19 from seasonal influenza in patients under age 65 years-a retrospective observational cohort study comparing the 2009 influenza A (H1N1) and 2022 SARS-CoV-2 pandemics.Frontiers in cellular and infection microbiology · 2023Observational
- Mutational Patterns Observed in SARS-CoV-2 Genomes Sampled From Successive Epochs Delimited by Major Public Health Events in Ontario, Canada: Genomic Surveillance Study.JMIR bioinformatics and biotechnology · 2022Article
- Identification of mutations in SARS-CoV-2 PCR primer regions.Scientific reports · 2022Article
- SARS-CoV-2 omicron variant: the black swan of microbiology.Archives of microbiology · 2022Article
- The current status of gene expression profilings in COVID-19 patients.Clinical and translational discovery · 2022Article
- Emergence of SARS-CoV-2 Variants in the World: How Could This Happen?Life (Basel, Switzerland) · 2022Review
- How to Deal With Vaccine Breakthrough Infection With SARS-CoV-2 Variants.Frontiers in public health · 2022Review
Corrections and comments
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Authors and funding
10 authors at 3 institutions in 2 countries.
Funding
Abstract
Owing to a lag between a deleterious mutation's appearance and its selective removal, gold-standard methods for mutation rate estimation assume no meaningful loss of mutations between parents and offspring. Indeed, from analysis of closely related lineages, in SARS-CoV-2, the Ka/Ks ratio was previously estimated as 1.008, suggesting no within-host selection. By contrast, we find a higher number of observed SNPs at 4-fold degenerate sites than elsewhere and, allowing for the virus's complex mutational and compositional biases, estimate that the mutation rate is at least 49-67% higher than would be estimated based on the rate of appearance of variants in sampled genomes. Given the high Ka/Ks one might assume that the majority of such intrahost selection is the purging of nonsense mutations. However, we estimate that selection against nonsense mutations accounts for only ∼10% of all the "missing" mutations. Instead, classical protein-level selective filters (against chemically disparate amino acids and those predicted to disrupt protein functionality) account for many missing mutations. It is less obvious why for an intracellular parasite, amino acid cost parameters, notably amino acid decay rate, is also significant. Perhaps most surprisingly, we also find evidence for real-time selection against synonymous mutations that move codon usage away from that of humans. We conclude that there is common intrahost selection on SARS-CoV-2 that acts on nonsense, missense, and possibly synonymous mutations. This has implications for methods of mutation rate estimation, for determining times to common ancestry and the potential for intrahost evolution including vaccine escape.
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Registered trials
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.