From SARS and MERS CoVs to SARS-CoV-2: Moving toward more biased codon usage in viral structural and nonstructural genes.
Identifieur interne : 000651 ( PubMed/Curation ); précédent : 000650; suivant : 000652From SARS and MERS CoVs to SARS-CoV-2: Moving toward more biased codon usage in viral structural and nonstructural genes.
Auteurs : Mahmoud Kandeel [Égypte] ; Abdelazim Ibrahim [Arabie saoudite] ; Mahmoud Fayez ; Mohammed Al-Nazawi [Égypte]Source :
- Journal of medical virology [ 1096-9071 ] ; 2020.
Abstract
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.
DOI: 10.1002/jmv.25754
PubMed: 32159237
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Mahmoud Fayez<affiliation><nlm:affiliation>Al Ahsa Veterinary Diagnostic Laboratory, Ministry of Agriculture, Al-Ahsa, Kingdom of Saudi Arabia.</nlm:affiliation><wicri:noCountry code="subField">Kingdom of Saudi Arabia</wicri:noCountry></affiliation>Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">From SARS and MERS CoVs to SARS-CoV-2: Moving toward more biased codon usage in viral structural and nonstructural genes.</title><author><name sortKey="Kandeel, Mahmoud" sort="Kandeel, Mahmoud" uniqKey="Kandeel M" first="Mahmoud" last="Kandeel">Mahmoud Kandeel</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-hofuf, Egypt.</nlm:affiliation><country xml:lang="fr">Égypte</country><wicri:regionArea>Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-hofuf</wicri:regionArea></affiliation></author><author><name sortKey="Ibrahim, Abdelazim" sort="Ibrahim, Abdelazim" uniqKey="Ibrahim A" first="Abdelazim" last="Ibrahim">Abdelazim Ibrahim</name><affiliation wicri:level="1"><nlm:affiliation>Department of Pathology, College of Veterinary Medicine, King Faisal University, Al-hofuf, Saudi Arabia.</nlm:affiliation><country xml:lang="fr">Arabie saoudite</country><wicri:regionArea>Department of Pathology, College of Veterinary Medicine, King Faisal University, Al-hofuf</wicri:regionArea></affiliation></author><author><name sortKey="Fayez, Mahmoud" sort="Fayez, Mahmoud" uniqKey="Fayez M" first="Mahmoud" last="Fayez">Mahmoud Fayez</name><affiliation><nlm:affiliation>Al Ahsa Veterinary Diagnostic Laboratory, Ministry of Agriculture, Al-Ahsa, Kingdom of Saudi Arabia.</nlm:affiliation><wicri:noCountry code="subField">Kingdom of Saudi Arabia</wicri:noCountry></affiliation></author><author><name sortKey="Al Nazawi, Mohammed" sort="Al Nazawi, Mohammed" uniqKey="Al Nazawi M" first="Mohammed" last="Al-Nazawi">Mohammed Al-Nazawi</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-hofuf, Egypt.</nlm:affiliation><country xml:lang="fr">Égypte</country><wicri:regionArea>Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-hofuf</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2020">2020</date><idno type="RBID">pubmed:32159237</idno><idno type="pmid">32159237</idno><idno type="doi">10.1002/jmv.25754</idno><idno type="wicri:Area/PubMed/Corpus">000651</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000651</idno><idno type="wicri:Area/PubMed/Curation">000651</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000651</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">From SARS and MERS CoVs to SARS-CoV-2: Moving toward more biased codon usage in viral structural and nonstructural genes.</title><author><name sortKey="Kandeel, Mahmoud" sort="Kandeel, Mahmoud" uniqKey="Kandeel M" first="Mahmoud" last="Kandeel">Mahmoud Kandeel</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-hofuf, Egypt.</nlm:affiliation><country xml:lang="fr">Égypte</country><wicri:regionArea>Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-hofuf</wicri:regionArea></affiliation></author><author><name sortKey="Ibrahim, Abdelazim" sort="Ibrahim, Abdelazim" uniqKey="Ibrahim A" first="Abdelazim" last="Ibrahim">Abdelazim Ibrahim</name><affiliation wicri:level="1"><nlm:affiliation>Department of Pathology, College of Veterinary Medicine, King Faisal University, Al-hofuf, Saudi Arabia.</nlm:affiliation><country xml:lang="fr">Arabie saoudite</country><wicri:regionArea>Department of Pathology, College of Veterinary Medicine, King Faisal University, Al-hofuf</wicri:regionArea></affiliation></author><author><name sortKey="Fayez, Mahmoud" sort="Fayez, Mahmoud" uniqKey="Fayez M" first="Mahmoud" last="Fayez">Mahmoud Fayez</name><affiliation><nlm:affiliation>Al Ahsa Veterinary Diagnostic Laboratory, Ministry of Agriculture, Al-Ahsa, Kingdom of Saudi Arabia.</nlm:affiliation><wicri:noCountry code="subField">Kingdom of Saudi Arabia</wicri:noCountry></affiliation></author><author><name sortKey="Al Nazawi, Mohammed" sort="Al Nazawi, Mohammed" uniqKey="Al Nazawi M" first="Mohammed" last="Al-Nazawi">Mohammed Al-Nazawi</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-hofuf, Egypt.</nlm:affiliation><country xml:lang="fr">Égypte</country><wicri:regionArea>Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-hofuf</wicri:regionArea></affiliation></author></analytic><series><title level="j">Journal of medical virology</title><idno type="eISSN">1096-9071</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">32159237</PMID><DateRevised><Year>2020</Year><Month>03</Month><Day>16</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1096-9071</ISSN><JournalIssue CitedMedium="Internet"><PubDate><Year>2020</Year><Month>Mar</Month><Day>11</Day></PubDate></JournalIssue><Title>Journal of medical virology</Title><ISOAbbreviation>J. Med. Virol.</ISOAbbreviation></Journal><ArticleTitle>From SARS and MERS CoVs to SARS-CoV-2: Moving toward more biased codon usage in viral structural and nonstructural genes.</ArticleTitle><ELocationID EIdType="doi" ValidYN="Y">10.1002/jmv.25754</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="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.</AbstractText><AbstractText Label="METHODS" NlmCategory="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.</AbstractText><AbstractText Label="RESULTS" NlmCategory="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.</AbstractText><AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">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.</AbstractText><CopyrightInformation>© 2020 Wiley Periodicals, Inc.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Kandeel</LastName><ForeName>Mahmoud</ForeName><Initials>M</Initials><Identifier Source="ORCID">http://orcid.org/0000-0003-3668-5147</Identifier><AffiliationInfo><Affiliation>Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-hofuf, Egypt.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelshikh University, Kafrelshikh, Egypt.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ibrahim</LastName><ForeName>Abdelazim</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Pathology, College of Veterinary Medicine, King Faisal University, Al-hofuf, Saudi Arabia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Pathology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fayez</LastName><ForeName>Mahmoud</ForeName><Initials>M</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-2145-2714</Identifier><AffiliationInfo><Affiliation>Al Ahsa Veterinary Diagnostic Laboratory, Ministry of Agriculture, Al-Ahsa, Kingdom of Saudi Arabia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Veterinary Serum and Vaccine Institute, Cairo, Egypt.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Al-Nazawi</LastName><ForeName>Mohammed</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-hofuf, Egypt.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>1811016</GrantID><Agency>Deanship of Scientific Research, King Faisal University, Research Groups Track9</Agency><Country></Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>03</Month><Day>11</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>J Med Virol</MedlineTA><NlmUniqueID>7705876</NlmUniqueID><ISSNLinking>0146-6615</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">COVID-19</Keyword><Keyword MajorTopicYN="N">MERS CoV</Keyword><Keyword MajorTopicYN="N">SARS-CoV-2</Keyword><Keyword MajorTopicYN="N">codon bias</Keyword><Keyword MajorTopicYN="N">nonstructural protein</Keyword><Keyword MajorTopicYN="N">preferred codons</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>02</Month><Day>26</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>03</Month><Day>09</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>3</Month><Day>12</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>3</Month><Day>12</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>3</Month><Day>12</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>aheadofprint</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32159237</ArticleId><ArticleId IdType="doi">10.1002/jmv.25754</ArticleId></ArticleIdList><ReferenceList><Title>REFERENCES</Title><Reference><Citation>Velavan TP, Meyer CG. 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