ArticleVirology journal2020
Characterization of codon usage pattern in SARS-CoV-2.
Article in Virology journal, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 43 citations in OpenAlex.
- Evolution and Functional Implications of Codon Usage Bias in Eukaryotes.Journal of molecular evolution · 2026Review
- EIOFX-DT: Leveraging graph centrality metrics for feature extraction and classification of viral genetic sequences.Biotechnology reports (Amsterdam, Netherlands) · 2026Article
- Article
- Codon usage bias of low-risk human papillomavirus types 6 and 11.Antonie van Leeuwenhoek · 2025Article
- Predicting viral host codon fitness and path shifting through tree-based learning on codon usage biases and genomic characteristics.Scientific reports · 2025Article
- Complete combinatorial mutational enumeration of a protein functional site enables sequence-landscape mapping and identifies highly-mutated variants that retain activity.Protein science : a publication of the Protein Society · 2024Article
- Analysis of codon usage bias of thioredoxin in apicomplexan protozoa.Parasites & vectors · 2023Article
- Vivid COVID-19 LAMP is an ultrasensitive, quadruplexed test using LNA-modified primers and a zinc ion and 5-Br-PAPS colorimetric detection system.Communications biology · 2023Article
- Application of codon usage and context analysis in genes up- or down-regulated in neurodegeneration and cancer to combat comorbidities.Frontiers in molecular neuroscience · 2023Article
- Comparative analysis of codon usage patterns ofFrontiers in microbiology · 2023Article
- Lycopene: a therapeutic strategy against coronavirus disease 19 (COVID- 19).Inflammopharmacology · 2022Review
- Host adaptation of codon usage in SARS-CoV-2 from mammals indicates potential natural selection and viral fitness.Archives of virology · 2022Article
- Dissecting Naturally Arising Amino Acid Substitutions at Position L452 of SARS-CoV-2 Spike.Journal of virology · 2022Article
- There is no "origin" to SARS-CoV-2.Environmental research · 2022Article
- Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic.Virology · 2022Article
- Covariance predicts conserved protein residue interactions important to the emergence and continued evolution of SARS-CoV-2 as a human pathogen.bioRxiv : the preprint server for biology · 2022Article
- SARS-CoV-2 competes with host mRNAs for efficient translation by maintaining the mutations favorable for translation initiation.Journal of applied genetics · 2022Article
- Plasma cell-free RNA characteristics in COVID-19 patients.Genome research · 2022Article
- MSH3 Homology and Potential Recombination Link to SARS-CoV-2 Furin Cleavage Site.Frontiers in virology (Lausanne, Switzerland) · 2022Article
- Article
Corrections and comments
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Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The outbreak of coronavirus disease 2019 (COVID-19) due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed significant threats to international health. The genetic traits as well as evolutionary processes in this novel coronavirus are not fully characterized, and their roles in viral pathogenesis are yet largely unknown. To get a better picture of the codon architecture of this newly emerging coronavirus, in this study we perform bioinformatic analysis, based on publicly available nucleotide sequences of SARS-CoV-2 along with those of other members of human coronaviruses as well as non-human coronaviruses in different hosts, to take a snapshot of the genome-wide codon usage pattern of SARS-CoV-2 and uncover that all over-represented codons end with A/U and this newly emerging coronavirus has a relatively low codon usage bias, which is shaped by both mutation pressure and natural selection. Additionally, there is slight variation in the codon usage pattern among the SARS-CoV-2 isolates from different geo-locations. Furthermore, the overall codon usage pattern of SARS-CoV-2 is generally similar to that of its phylogenetic relatives among non-human betacoronaviruses such as RaTG13. Taken together, we comprehensively analyze the characteristics of codon usage pattern in SARS-CoV-2 via bioinformatic approaches. The information from this research may not only be helpful to get new insights into the evolution of SARS-CoV-2, but also have potential value for developing coronavirus vaccines.
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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.