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From SARS and MERS CoVs to SARS-CoV-2: Moving toward more biased codon usage in viral structural and nonstructural genes.
Kandeel, Mahmoud; Ibrahim, Abdelazim; Fayez, Mahmoud; Al-Nazawi, Mohammed.
  • Kandeel M; Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-hofuf, Egypt.
  • Ibrahim A; Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelshikh University, Kafrelshikh, Egypt.
  • Fayez M; Department of Pathology, College of Veterinary Medicine, King Faisal University, Al-hofuf, Saudi Arabia.
  • Al-Nazawi M; Department of Pathology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt.
J Med Virol ; 92(6): 660-666, 2020 06.
Article in English | MEDLINE | ID: covidwho-7544
ABSTRACT

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.
Subject(s)
Betacoronavirus/genetics; Cysteine Endopeptidases/genetics; Middle East Respiratory Syndrome Coronavirus/genetics; Nucleocapsid Proteins/genetics; RNA-Dependent RNA Polymerase/genetics; Severe acute respiratory syndrome-related coronavirus/genetics; Spike Glycoprotein, Coronavirus/genetics; Viral Envelope Proteins/genetics; Viral Nonstructural Proteins/genetics; Animals; Base Sequence; Betacoronavirus/classification; Betacoronavirus/pathogenicity; COVID-19; Chiroptera/microbiology; Codon Usage; Computational Biology; Coronavirus 3C Proteases; Coronavirus Envelope Proteins; Coronavirus Infections/epidemiology; Coronavirus Infections/transmission; Coronavirus Infections/virology; Coronavirus Nucleocapsid Proteins; Cysteine Endopeptidases/metabolism; Eutheria/microbiology; Gene Expression; Humans; Middle East Respiratory Syndrome Coronavirus/classification; Middle East Respiratory Syndrome Coronavirus/pathogenicity; Nucleocapsid Proteins/metabolism; Pandemics; Phosphoproteins; Pneumonia, Viral/epidemiology; Pneumonia, Viral/transmission; Pneumonia, Viral/virology; RNA-Dependent RNA Polymerase/metabolism; Severe acute respiratory syndrome-related coronavirus/classification; Severe acute respiratory syndrome-related coronavirus/pathogenicity; SARS-CoV-2; Sequence Homology, Nucleic Acid; Severe Acute Respiratory Syndrome/epidemiology; Severe Acute Respiratory Syndrome/transmission; Severe Acute Respiratory Syndrome/virology; Spike Glycoprotein, Coronavirus/metabolism; Viral Envelope Proteins/metabolism; Viral Nonstructural Proteins/metabolism
Keywords

Full text: Available Collection: International databases Database: MEDLINE Main subject: RNA-Dependent RNA Polymerase / Cysteine Endopeptidases / Viral Envelope Proteins / Viral Nonstructural Proteins / Nucleocapsid Proteins / Severe acute respiratory syndrome-related coronavirus / Spike Glycoprotein, Coronavirus / Middle East Respiratory Syndrome Coronavirus / Betacoronavirus Type of study: Experimental Studies / Observational study Language: English Journal: J Med Virol Year: 2020 Document Type: Article Affiliation country: Jmv.25754

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Full text: Available Collection: International databases Database: MEDLINE Main subject: RNA-Dependent RNA Polymerase / Cysteine Endopeptidases / Viral Envelope Proteins / Viral Nonstructural Proteins / Nucleocapsid Proteins / Severe acute respiratory syndrome-related coronavirus / Spike Glycoprotein, Coronavirus / Middle East Respiratory Syndrome Coronavirus / Betacoronavirus Type of study: Experimental Studies / Observational study Language: English Journal: J Med Virol Year: 2020 Document Type: Article Affiliation country: Jmv.25754