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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.
J Med Virol. 2020 06; 92(6):660-666.JM

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.

Links

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Authors+Show Affiliations

Kandeel M
Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-hofuf, Egypt. Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelshikh University, Kafrelshikh, Egypt.
Ibrahim A
Department of Pathology, College of Veterinary Medicine, King Faisal University, Al-hofuf, Saudi Arabia. Department of Pathology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt.
Fayez M
Al Ahsa Veterinary Diagnostic Laboratory, Ministry of Agriculture, Al-Ahsa, Kingdom of Saudi Arabia. Veterinary Serum and Vaccine Institute, Cairo, Egypt.
Al-Nazawi M
Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-hofuf, Egypt.

MeSH

AnimalsBase SequenceBetacoronavirusCOVID-19ChiropteraCodon UsageComputational BiologyCoronavirus 3C ProteasesCoronavirus Envelope ProteinsCoronavirus InfectionsCoronavirus Nucleocapsid ProteinsCysteine EndopeptidasesEutheriaGene ExpressionHumansMiddle East Respiratory Syndrome CoronavirusNucleocapsid ProteinsPandemicsPhosphoproteinsPneumonia, ViralRNA-Dependent RNA PolymeraseSevere acute respiratory syndrome-related coronavirusSARS-CoV-2Sequence Homology, Nucleic AcidSevere Acute Respiratory SyndromeSpike Glycoprotein, CoronavirusViral Envelope ProteinsViral Nonstructural Proteins

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

32159237

Citation

Kandeel, Mahmoud, et al. "From SARS and MERS CoVs to SARS-CoV-2: Moving Toward More Biased Codon Usage in Viral Structural and Nonstructural Genes." Journal of Medical Virology, vol. 92, no. 6, 2020, pp. 660-666.
Kandeel M, Ibrahim A, Fayez M, et al. From SARS and MERS CoVs to SARS-CoV-2: Moving toward more biased codon usage in viral structural and nonstructural genes. J Med Virol. 2020;92(6):660-666.
Kandeel, M., Ibrahim, A., Fayez, M., & Al-Nazawi, M. (2020). From SARS and MERS CoVs to SARS-CoV-2: Moving toward more biased codon usage in viral structural and nonstructural genes. Journal of Medical Virology, 92(6), 660-666. https://doi.org/10.1002/jmv.25754
Kandeel M, et al. From SARS and MERS CoVs to SARS-CoV-2: Moving Toward More Biased Codon Usage in Viral Structural and Nonstructural Genes. J Med Virol. 2020;92(6):660-666. PubMed PMID: 32159237.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - From SARS and MERS CoVs to SARS-CoV-2: Moving toward more biased codon usage in viral structural and nonstructural genes. AU - Kandeel,Mahmoud, AU - Ibrahim,Abdelazim, AU - Fayez,Mahmoud, AU - Al-Nazawi,Mohammed, Y1 - 2020/03/16/ PY - 2020/02/26/received PY - 2020/03/09/accepted PY - 2020/3/12/pubmed PY - 2020/7/1/medline PY - 2020/3/12/entrez KW - COVID-19 KW - MERS CoV KW - SARS-CoV-2 KW - codon bias KW - nonstructural protein KW - preferred codons SP - 660 EP - 666 JF - Journal of medical virology JO - J Med Virol VL - 92 IS - 6 N2 - 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. SN - 1096-9071 UR - https://www.unboundmedicine.com/medline/citation/32159237/From_SARS_and_MERS_CoVs_to_SARS_CoV_2:_Moving_toward_more_biased_codon_usage_in_viral_structural_and_nonstructural_genes_ DB - PRIME DP - Unbound Medicine ER -