ArticleVirus evolution2022
Large-scale analysis of SARS-CoV-2 synonymous mutations reveals the adaptation to the human codon usage during the virus evolution.
Article in Virus evolution, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 63 citations in OpenAlex.
- Transmission of mutated SARS-CoV-2 variants is favored by relatively prolonged infections due to delayed immunity.bioRxiv : the preprint server for biology · 2026Article
- Within-host SARS-CoV-2 diversity in immunocompromised patients during acute infection.Journal of virology · 2026Article
- Temporal and gene-specific dynamics of codon usage evolution in SARS-CoV-2 genomes.BMC genomics · 2026Article
- Geographic and cross-species transmission of Mamastroviruses from multiple hosts.Animal microbiome · 2026Article
- SARS-CoV-2 within-host population expansion, diversification and adaptation in zoo tigers, lions and hyenas.Nature communications · 2025Article
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- SARS-CoV-2 CoCoPUTs: analyzing GISAID and NCBI data to obtain codon statistics, mutations, and free energy over a multiyear period.Virus evolution · 2025Article
- Impact of Obesity-Associated SARS-CoV-2 Mutations on COVID-19 Severity and Clinical Outcomes.Viruses · 2024Article
- Retrospective Analysis of Omicron in Minas Gerais, Brazil: Emergence, Dissemination, and Diversification.Microorganisms · 2024Article
- The RdRp genotyping of SARS-CoV-2 isolated from patients with different clinical spectrum of COVID-19.BMC infectious diseases · 2024Article
- What Is life? Rethinking Biology in Light of Fundamental Parameters.Life (Basel, Switzerland) · 2024Review
- Enhanced detection and molecular modeling of adaptive mutations in SARS-CoV-2 coding and non-coding regions using the c/µ test.Virus evolution · 2024Article
- Optimization and Deoptimization of Codons in SARS-CoV-2 and Related Implications for Vaccine Development.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- Web Resources for SARS-CoV-2 Genomic Database, Annotation, Analysis and Variant Tracking.Viruses · 2023Review
- Article
- Analysis of 3.5 million SARS-CoV-2 sequences reveals unique mutational trends with consistent nucleotide and codon frequencies.Virology journal · 2023Article
- Review
- Molecular transition of SARS-CoV-2 from critical patients during the first year of the COVID-19 pandemic in Mexico City.Frontiers in cellular and infection microbiology · 2023Article
- Characterization of SARS-CoV-2 Mutational Signatures from 1.5+ Million Raw Sequencing Samples.Viruses · 2022Article
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Authors and funding
10 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Many large national and transnational studies have been dedicated to the analysis of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) genome, most of which focused on missense and nonsense mutations. However, approximately 30 per cent of the SARS-CoV-2 variants are synonymous, therefore changing the target codon without affecting the corresponding protein sequence. By performing a large-scale analysis of sequencing data generated from almost 400,000 SARS-CoV-2 samples, we show that silent mutations increasing the similarity of viral codons to the human ones tend to fixate in the viral genome overtime. This indicates that SARS-CoV-2 codon usage is adapting to the human host, likely improving its effectiveness in using the human aminoacyl-tRNA set through the accumulation of deceitfully neutral silent mutations. One-Sentence Summary. Synonymous SARS-CoV-2 mutations related to the activity of different mutational processes may positively impact viral evolution by increasing its adaptation to the human codon usage.
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