From SARS and MERS CoVs to SARS‐CoV‐2: Moving toward more biased codon usage in viral structural and nonstructural genes

• Autor: Kandeel, Mahmoud ; Ibrahim, Abdelazim ; Fayez, Mahmoud ; Al‐Nazawi, Mohammed
• Assuntos: Animals ; Base Sequence ; Betacoronavirus - classification ; Betacoronavirus - genetics ; Betacoronavirus - pathogenicity ; Bias ; Chiroptera - microbiology ; Codon bias ; Codon Usage ; Codons ; Computational Biology ; Coronaviridae ; Coronavirus 3C Proteases ; Coronavirus Envelope Proteins ; Coronavirus Infections - epidemiology ; Coronavirus Infections - transmission ; Coronavirus Infections - virology ; Coronavirus Nucleocapsid Proteins ; Coronaviruses ; COVID-19 ; Cysteine Endopeptidases - genetics ; Cysteine Endopeptidases - metabolism ; DNA-directed RNA polymerase ; Epidemics ; Eutheria - microbiology ; Gene Expression ; Genes ; Genomes ; Humans ; MERS CoV ; Middle East respiratory syndrome ; Middle East Respiratory Syndrome Coronavirus - classification ; Middle East Respiratory Syndrome Coronavirus - genetics ; Middle East Respiratory Syndrome Coronavirus - pathogenicity ; nonstructural protein ; Nucleocapsid Proteins - genetics ; Nucleocapsid Proteins - metabolism ; Nucleocapsids ; Nucleotides ; Pandemics ; Phosphoproteins ; Pneumonia, Viral - epidemiology ; Pneumonia, Viral - transmission ; Pneumonia, Viral - virology ; preferred codons ; Proteins ; Purines ; Respiratory diseases ; Ribonucleic acid ; RNA ; RNA polymerase ; RNA-Dependent RNA Polymerase - genetics ; RNA-Dependent RNA Polymerase - metabolism ; SARS Virus - classification ; SARS Virus - genetics ; SARS Virus - pathogenicity ; SARS-CoV-2 ; Sequence Homology, Nucleic Acid ; Severe acute respiratory syndrome ; Severe Acute Respiratory Syndrome - epidemiology ; Severe Acute Respiratory Syndrome - transmission ; Severe Acute Respiratory Syndrome - virology ; Severe acute respiratory syndrome coronavirus 2 ; Spike Glycoprotein, Coronavirus - genetics ; Spike Glycoprotein, Coronavirus - metabolism ; Spikes ; Structural proteins ; Viral diseases ; Viral Envelope Proteins - genetics ; Viral Envelope Proteins - metabolism ; Viral Nonstructural Proteins - genetics ; Viral Nonstructural Proteins - metabolism ; Virology
• É parte de: Journal of medical virology, 2020-06, Vol.92 (6), p.660-666
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• Descrição: Background Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) is an emerging disease with fatal outcomes. In this study, a fundamental knowledge gap question is to be resolved by evaluating the differences in biological and pathogenic aspects of SARS‐CoV‐2 and the changes in SARS‐CoV‐2 in comparison with the two prior major COV epidemics, SARS and Middle East respiratory syndrome (MERS) coronaviruses. Methods The genome composition, nucleotide analysis, codon usage indices, relative synonymous codons usage, and effective number of codons (ENc) were analyzed in the four structural genes; Spike (S), Envelope (E), membrane (M), and Nucleocapsid (N) genes, and two of the most important nonstructural genes comprising RNA‐dependent RNA polymerase and main protease (Mpro) of SARS‐CoV‐2, Beta‐CoV from pangolins, bat SARS, MERS, and SARS CoVs. Results SARS‐CoV‐2 prefers pyrimidine rich codons to purines. Most high‐frequency codons were ending with A or T, while the low frequency and rare codons were ending with G or C. SARS‐CoV‐2 structural proteins showed 5 to 20 lower ENc values, compared with SARS, bat SARS, and MERS CoVs. This implies higher codon bias and higher gene expression efficiency of SARS‐CoV‐2 structural proteins. SARS‐CoV‐2 encoded the highest number of over‐biased and negatively biased codons. Pangolin Beta‐CoV showed little differences with SARS‐CoV‐2 ENc values, compared with SARS, bat SARS, and MERS CoV. Conclusion Extreme bias and lower ENc values of SARS‐CoV‐2, especially in Spike, Envelope, and Mpro genes, are suggestive for higher gene expression efficiency, compared with SARS, bat SARS, and MERS CoVs.
  
• Editor: United States: Wiley Subscription Services, Inc
  
• Idioma: Inglês