ArticleVirology2007
Cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in coronaviruses.
Article in Virology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed.
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- C→U transition biases in SARS-CoV-2: still rampant 4 years from the start of the COVID-19 pandemic.mBio · 2024Article
- Synonymous codon usage influences the transmission of peste des petits ruminants (PPR) virus in camels.Veterinary research communications · 2024Article
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- Correlated substitutions reveal SARS-like coronaviruses recombine frequently with a diverse set of structured gene pools.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
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- 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
- Hydrophobic Alpha-Helical Short Peptides in Overlapping Reading Frames of the Coronavirus Genome.Pathogens (Basel, Switzerland) · 2022Article
- Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic.Virology · 2022Article
- The low abundance of CpG in the SARS-CoV-2 genome is not an evolutionarily signature of ZAP.Scientific reports · 2022Article
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- Large-scale analysis of SARS-CoV-2 synonymous mutations reveals the adaptation to the human codon usage during the virus evolution.Virus evolution · 2022Article
- Host proviral and antiviral factors for SARS-CoV-2.Virus genes · 2021Review
- The Rise of SARS-CoV-2 Variants and the Role of Convalescent Plasma Therapy for Management of Infections.Life (Basel, Switzerland) · 2021Review
- The Evolution of Severe Acute Respiratory Syndrome Coronavirus-2 during Pandemic and Adaptation to the Host.Journal of molecular evolution · 2021Article
- The Functional Consequences of the Novel Ribosomal Pausing Site in SARS-CoV-2 Spike Glycoprotein RNA.International journal of molecular sciences · 2021Article
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- Mutation Rates and Selection on Synonymous Mutations in SARS-CoV-2.Genome biology and evolution · 2021Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Using the complete genome sequences of 19 coronavirus genomes, we analyzed the codon usage bias, dinucleotide relative abundance and cytosine deamination in coronavirus genomes. Of the eight codons that contain CpG, six were markedly suppressed. The mean NNU/NNC ratio of the six amino acids using either NNC or NNU as codon is 3.262, suggesting cytosine deamination. Among the 16 dinucleotides, CpG was most markedly suppressed (mean relative abundance 0.509). No correlation was observed between CpG abundance and mean NNU/NNC ratio. Among the 19 coronaviruses, CoV-HKU1 showed the most extreme codon usage bias and extremely high NNU/NNC ratio of 8.835. Cytosine deamination and selection of CpG suppressed clones by the immune system are the two major independent biochemical and biological selective forces that shape codon usage bias in coronavirus genomes. The underlying mechanism for the extreme codon usage bias, cytosine deamination and G+C content in CoV-HKU1 warrants further studies.
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