Analysis of preferred codon usage in the coronavirus N genes and their implications for genome evolution and vaccine design.
Identifieur interne : 000296 ( PubMed/Corpus ); précédent : 000295; suivant : 000297Analysis of preferred codon usage in the coronavirus N genes and their implications for genome evolution and vaccine design.
Auteurs : Abdullah Sheikh ; Abdulla Al-Taher ; Mohammed Al-Nazawi ; Abdullah I. Al-Mubarak ; Mahmoud KandeelSource :
- Journal of virological methods [ 1879-0984 ] ; 2020.
Abstract
The nucleocapsid (N) protein of a coronavirus plays a crucial role in virus assembly and in its RNA transcription. It is important to characterize a virus at the nucleotide level to discover the virus's genomic sequence variations and similarities relative to other viruses that could have an impact on the functions of its genes and proteins. This entails a comprehensive and comparative analysis of the viral genomes of interest for preferred nucleotides, codon bias, nucleotide changes at the 3rd position (NT3s), synonymous codon usage and relative synonymous codon usage. In this study, the variations in the N proteins among 13 different coronaviruses (CoVs) were analysed at the nucleotide and amino acid levels in an attempt to reveal how these viruses adapt to their hosts relative to their preferred codon usage in the N genes. The results revealed that, overall, eighteen amino acids had different preferred codons and eight of these were over-biased. The N genes had a higher AT% over GC% and the values of their effective number of codons ranged from 40.43 to 53.85, indicating a slight codon bias. Neutrality plots and correlation analyses showed a very high level of GC3s/GC correlation in porcine epidemic diarrhea CoV (pedCoV), followed by Middle East respiratory syndrome-CoV (MERS CoV), porcine delta CoV (dCoV), bat CoV (bCoV) and feline CoV (fCoV) with r values 0.81, 0.68, -0.47, 0.98 and 0.58, respectively. These data implied a high rate of evolution of the CoV genomes and a strong influence of mutation on evolutionary selection in the CoV N genes. This type of genetic analysis would be useful for evaluating a virus's host adaptation, evolution and is thus of value to vaccine design strategies.
DOI: 10.1016/j.jviromet.2019.113806
PubMed: 31911390
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Al-Mubarak</name><affiliation><nlm:affiliation>Department of Microbiology, College of Veterinary Medicine, King Faisal University, Alhofuf, Alahsa 31982, Saudi Arabia.</nlm:affiliation></affiliation></author><author><name sortKey="Kandeel, Mahmoud" sort="Kandeel, Mahmoud" uniqKey="Kandeel M" first="Mahmoud" last="Kandeel">Mahmoud Kandeel</name><affiliation><nlm:affiliation>Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Alhofuf, Alahsa 31982, Saudi Arabia; Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh 33516, Egypt.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2020">2020</date><idno type="RBID">pubmed:31911390</idno><idno type="pmid">31911390</idno><idno type="doi">10.1016/j.jviromet.2019.113806</idno><idno type="wicri:Area/PubMed/Corpus">000296</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000296</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Analysis of preferred codon usage in the coronavirus N genes and their implications for genome evolution and vaccine design.</title><author><name sortKey="Sheikh, Abdullah" sort="Sheikh, Abdullah" uniqKey="Sheikh A" first="Abdullah" last="Sheikh">Abdullah Sheikh</name><affiliation><nlm:affiliation>The Camel Research Center, King Faisal University, Alhofuf, Alahsa 31982, Saudi Arabia.</nlm:affiliation></affiliation></author><author><name sortKey="Al Taher, Abdulla" sort="Al Taher, Abdulla" uniqKey="Al Taher A" first="Abdulla" last="Al-Taher">Abdulla Al-Taher</name><affiliation><nlm:affiliation>Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Alhofuf, Alahsa 31982, Saudi Arabia.</nlm:affiliation></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><nlm:affiliation>Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Alhofuf, Alahsa 31982, Saudi Arabia.</nlm:affiliation></affiliation></author><author><name sortKey="Al Mubarak, Abdullah I" sort="Al Mubarak, Abdullah I" uniqKey="Al Mubarak A" first="Abdullah I" last="Al-Mubarak">Abdullah I. Al-Mubarak</name><affiliation><nlm:affiliation>Department of Microbiology, College of Veterinary Medicine, King Faisal University, Alhofuf, Alahsa 31982, Saudi Arabia.</nlm:affiliation></affiliation></author><author><name sortKey="Kandeel, Mahmoud" sort="Kandeel, Mahmoud" uniqKey="Kandeel M" first="Mahmoud" last="Kandeel">Mahmoud Kandeel</name><affiliation><nlm:affiliation>Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Alhofuf, Alahsa 31982, Saudi Arabia; Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh 33516, Egypt.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Journal of virological methods</title><idno type="eISSN">1879-0984</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">The nucleocapsid (N) protein of a coronavirus plays a crucial role in virus assembly and in its RNA transcription. It is important to characterize a virus at the nucleotide level to discover the virus's genomic sequence variations and similarities relative to other viruses that could have an impact on the functions of its genes and proteins. This entails a comprehensive and comparative analysis of the viral genomes of interest for preferred nucleotides, codon bias, nucleotide changes at the 3<sup>rd</sup> position (NT3s), synonymous codon usage and relative synonymous codon usage. In this study, the variations in the N proteins among 13 different coronaviruses (CoVs) were analysed at the nucleotide and amino acid levels in an attempt to reveal how these viruses adapt to their hosts relative to their preferred codon usage in the N genes. The results revealed that, overall, eighteen amino acids had different preferred codons and eight of these were over-biased. The N genes had a higher AT% over GC% and the values of their effective number of codons ranged from 40.43 to 53.85, indicating a slight codon bias. Neutrality plots and correlation analyses showed a very high level of GC3s/GC correlation in porcine epidemic diarrhea CoV (pedCoV), followed by Middle East respiratory syndrome-CoV (MERS CoV), porcine delta CoV (dCoV), bat CoV (bCoV) and feline CoV (fCoV) with r values 0.81, 0.68, -0.47, 0.98 and 0.58, respectively. These data implied a high rate of evolution of the CoV genomes and a strong influence of mutation on evolutionary selection in the CoV N genes. This type of genetic analysis would be useful for evaluating a virus's host adaptation, evolution and is thus of value to vaccine design strategies.</div></front></TEI><pubmed><MedlineCitation Status="In-Data-Review" Owner="NLM"><PMID Version="1">31911390</PMID><DateRevised><Year>2020</Year><Month>04</Month><Day>19</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1879-0984</ISSN><JournalIssue CitedMedium="Internet"><Volume>277</Volume><PubDate><Year>2020</Year><Month>Mar</Month></PubDate></JournalIssue><Title>Journal of virological methods</Title><ISOAbbreviation>J. Virol. Methods</ISOAbbreviation></Journal><ArticleTitle>Analysis of preferred codon usage in the coronavirus N genes and their implications for genome evolution and vaccine design.</ArticleTitle><Pagination><MedlinePgn>113806</MedlinePgn></Pagination><ELocationID EIdType="pii" ValidYN="Y">S0166-0934(18)30580-9</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.jviromet.2019.113806</ELocationID><Abstract><AbstractText>The nucleocapsid (N) protein of a coronavirus plays a crucial role in virus assembly and in its RNA transcription. It is important to characterize a virus at the nucleotide level to discover the virus's genomic sequence variations and similarities relative to other viruses that could have an impact on the functions of its genes and proteins. This entails a comprehensive and comparative analysis of the viral genomes of interest for preferred nucleotides, codon bias, nucleotide changes at the 3<sup>rd</sup> position (NT3s), synonymous codon usage and relative synonymous codon usage. In this study, the variations in the N proteins among 13 different coronaviruses (CoVs) were analysed at the nucleotide and amino acid levels in an attempt to reveal how these viruses adapt to their hosts relative to their preferred codon usage in the N genes. The results revealed that, overall, eighteen amino acids had different preferred codons and eight of these were over-biased. The N genes had a higher AT% over GC% and the values of their effective number of codons ranged from 40.43 to 53.85, indicating a slight codon bias. Neutrality plots and correlation analyses showed a very high level of GC3s/GC correlation in porcine epidemic diarrhea CoV (pedCoV), followed by Middle East respiratory syndrome-CoV (MERS CoV), porcine delta CoV (dCoV), bat CoV (bCoV) and feline CoV (fCoV) with r values 0.81, 0.68, -0.47, 0.98 and 0.58, respectively. These data implied a high rate of evolution of the CoV genomes and a strong influence of mutation on evolutionary selection in the CoV N genes. This type of genetic analysis would be useful for evaluating a virus's host adaptation, evolution and is thus of value to vaccine design strategies.</AbstractText><CopyrightInformation>Copyright © 2019 Elsevier B.V. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Sheikh</LastName><ForeName>Abdullah</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>The Camel Research Center, King Faisal University, Alhofuf, Alahsa 31982, Saudi Arabia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Al-Taher</LastName><ForeName>Abdulla</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Alhofuf, Alahsa 31982, Saudi Arabia.</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, Alhofuf, Alahsa 31982, Saudi Arabia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Al-Mubarak</LastName><ForeName>Abdullah I</ForeName><Initials>AI</Initials><AffiliationInfo><Affiliation>Department of Microbiology, College of Veterinary Medicine, King Faisal University, Alhofuf, Alahsa 31982, Saudi Arabia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kandeel</LastName><ForeName>Mahmoud</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Alhofuf, Alahsa 31982, Saudi Arabia; Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh 33516, Egypt.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>01</Month><Day>05</Day></ArticleDate></Article><MedlineJournalInfo><Country>Netherlands</Country><MedlineTA>J Virol Methods</MedlineTA><NlmUniqueID>8005839</NlmUniqueID><ISSNLinking>0166-0934</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Amino acid</Keyword><Keyword MajorTopicYN="N">Codon bias</Keyword><Keyword MajorTopicYN="N">Coronavirus</Keyword><Keyword MajorTopicYN="N">Nucleocapsid protein</Keyword><Keyword MajorTopicYN="N">Preferred nucleotides</Keyword></KeywordList><CoiStatement>Declaration of Competing Interest None.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year><Month>11</Month><Day>27</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2019</Year><Month>11</Month><Day>24</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2019</Year><Month>12</Month><Day>20</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>1</Month><Day>9</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>1</Month><Day>9</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>1</Month><Day>9</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">31911390</ArticleId><ArticleId IdType="pii">S0166-0934(18)30580-9</ArticleId><ArticleId IdType="doi">10.1016/j.jviromet.2019.113806</ArticleId><ArticleId IdType="pmc">PMC7119019</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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