ArticleVirology2022
Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic.
Article in Virology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
14 citing papers in PubMed.
- Temporal and gene-specific dynamics of codon usage evolution in SARS-CoV-2 genomes.BMC genomics · 2026Article
- What Has SARS-CoV-2 Taught Us About Evolution?Cureus · 2025Review
- Is SARS-CoV-2 facing constraints in its adaptive evolution?Biomolecules & biomedicine · 2025Review
- The differential effect of SARS-CoV-2 NSP1 on mRNA translation and stability reveals new insights linking ribosome recruitment, codon usage, and virus evolution.Nucleic acids research · 2025Article
- SARS-CoV-2 CoCoPUTs: analyzing GISAID and NCBI data to obtain codon statistics, mutations, and free energy over a multiyear period.Virus evolution · 2025Article
- The RdRp genotyping of SARS-CoV-2 isolated from patients with different clinical spectrum of COVID-19.BMC infectious diseases · 2024Article
- A study on the codon usage bias of arenavirus common genes.Frontiers in microbiology · 2024Article
- 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
- Single cell phototransfection of mRNAs encoding SARS-CoV2 spike and nucleocapsid into human astrocytes results in RNA dependent translation interference.Frontiers in drug delivery · 2024Article
- An Integrated Research-Clinical BSL-2 Platform for a Live SARS-CoV-2 Neutralization Assay.Viruses · 2023Article
- Optimization and Deoptimization of Codons in SARS-CoV-2 and Related Implications for Vaccine Development.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- Analysis of 3.5 million SARS-CoV-2 sequences reveals unique mutational trends with consistent nucleotide and codon frequencies.Virology journal · 2023Article
- Review
- Utilizing the codon adaptation index to evaluate the susceptibility to HIV-1 and SARS-CoV-2 related coronaviruses in possible target cells in humans.Frontiers in cellular and infection microbiology · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
SARS-CoV-2, the seventh coronavirus known to infect humans, can cause severe life-threatening respiratory pathologies. To better understand SARS-CoV-2 evolution, genome-wide analyses have been made, including the general characterization of its codons usage profile. Here we present a bioinformatic analysis of the evolution of SARS-CoV-2 codon usage over time using complete genomes collected since December 2019. Our results show that SARS-CoV-2 codon usage pattern is antagonistic to, and it is getting farther away from that of the human host. Further, a selection of deoptimized codons over time, which was accompanied by a decrease in both the codon adaptation index and the effective number of codons, was observed. All together, these findings suggest that SARS-CoV-2 could be evolving, at least from the perspective of the synonymous codon usage, to become less pathogenic.
Indexed as
Identifiers
What OpenQuestion holds
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.