An exclusive 42 amino acid signature in pp1ab protein provides insights into the evolutive history of the 2019 novel human-pathogenic coronavirus (SARS-CoV-2).
Identifieur interne : 000637 ( PubMed/Corpus ); précédent : 000636; suivant : 000638An exclusive 42 amino acid signature in pp1ab protein provides insights into the evolutive history of the 2019 novel human-pathogenic coronavirus (SARS-CoV-2).
Auteurs : Yair Cárdenas-Conejo ; Andr Meda Li An-Rico ; Daniel Alejandro García-Rodríguez ; Sara Centeno-Leija ; Hugo Serrano-PosadaSource :
- Journal of medical virology [ 1096-9071 ] ; 2020.
Abstract
The city of Wuhan, Hubei province, China, was the origin of a severe pneumonia outbreak in December 2019, attributed to a novel coronavirus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]), causing a total of 2761 deaths and 81109 cases (25 February 2020). SARS-CoV-2 belongs to genus Betacoronavirus, subgenus Sarbecovirus. The polyprotein 1ab (pp1ab) remains unstudied thoroughly since it is similar to other sarbecoviruses. In this short communication, we performed phylogenetic-structural sequence analysis of pp1ab protein of SARS-CoV-2. The analysis showed that the viral pp1ab has not changed in most isolates throughout the outbreak time, but interestingly a deletion of 8 aa in the virulence factor nonstructural protein 1 was found in a virus isolated from a Japanese patient that did not display critical symptoms. While comparing pp1ab protein with other betacoronaviruses, we found a 42 amino acid signature that is only present in SARS-CoV-2 (AS-SCoV2). Members from clade 2 of sarbecoviruses have traces of this signature. The AS-SCoV2 located in the acidic-domain of papain-like protein of SARS-CoV-2 and bat-SL-CoV-RatG13 guided us to suggest that the novel 2019 coronavirus probably emerged by genetic drift from bat-SL-CoV-RaTG13. The implication of this amino acid signature in papain-like protein structure arrangement and function is something worth to be explored.
DOI: 10.1002/jmv.25758
PubMed: 32167166
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">An exclusive 42 amino acid signature in pp1ab protein provides insights into the evolutive history of the 2019 novel human-pathogenic coronavirus (SARS-CoV-2).</title><author><name sortKey="Cardenas Conejo, Yair" sort="Cardenas Conejo, Yair" uniqKey="Cardenas Conejo Y" first="Yair" last="Cárdenas-Conejo">Yair Cárdenas-Conejo</name><affiliation><nlm:affiliation>Laboratory of Agrobiotechnology, National Council of Science and Technology (CONACYT)-University of Colima, Colima, Colima, Mexico.</nlm:affiliation></affiliation></author><author><name sortKey="Li An Rico, Andr Meda" sort="Li An Rico, Andr Meda" uniqKey="Li An Rico A" first="Andr Meda" last="Li An-Rico">Andr Meda Li An-Rico</name><affiliation><nlm:affiliation>University Center for Biomedical Research, National Council of Science and Technology (CONACYT)-University of Colima, Colima, Colima, Mexico.</nlm:affiliation></affiliation></author><author><name sortKey="Garcia Rodriguez, Daniel Alejandro" sort="Garcia Rodriguez, Daniel Alejandro" uniqKey="Garcia Rodriguez D" first="Daniel Alejandro" last="García-Rodríguez">Daniel Alejandro García-Rodríguez</name><affiliation><nlm:affiliation>Laboratory of Agrobiotechnology, University of Colima, Colima, Colima, Mexico.</nlm:affiliation></affiliation></author><author><name sortKey="Centeno Leija, Sara" sort="Centeno Leija, Sara" uniqKey="Centeno Leija S" first="Sara" last="Centeno-Leija">Sara Centeno-Leija</name><affiliation><nlm:affiliation>Laboratory of Agrobiotechnology, National Council of Science and Technology (CONACYT)-University of Colima, Colima, Colima, Mexico.</nlm:affiliation></affiliation></author><author><name sortKey="Serrano Posada, Hugo" sort="Serrano Posada, Hugo" uniqKey="Serrano Posada H" first="Hugo" last="Serrano-Posada">Hugo Serrano-Posada</name><affiliation><nlm:affiliation>Laboratory of Agrobiotechnology, National Council of Science and Technology (CONACYT)-University of Colima, Colima, Colima, Mexico.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2020">2020</date><idno type="RBID">pubmed:32167166</idno><idno type="pmid">32167166</idno><idno type="doi">10.1002/jmv.25758</idno><idno type="wicri:Area/PubMed/Corpus">000637</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000637</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">An exclusive 42 amino acid signature in pp1ab protein provides insights into the evolutive history of the 2019 novel human-pathogenic coronavirus (SARS-CoV-2).</title><author><name sortKey="Cardenas Conejo, Yair" sort="Cardenas Conejo, Yair" uniqKey="Cardenas Conejo Y" first="Yair" last="Cárdenas-Conejo">Yair Cárdenas-Conejo</name><affiliation><nlm:affiliation>Laboratory of Agrobiotechnology, National Council of Science and Technology (CONACYT)-University of Colima, Colima, Colima, Mexico.</nlm:affiliation></affiliation></author><author><name sortKey="Li An Rico, Andr Meda" sort="Li An Rico, Andr Meda" uniqKey="Li An Rico A" first="Andr Meda" last="Li An-Rico">Andr Meda Li An-Rico</name><affiliation><nlm:affiliation>University Center for Biomedical Research, National Council of Science and Technology (CONACYT)-University of Colima, Colima, Colima, Mexico.</nlm:affiliation></affiliation></author><author><name sortKey="Garcia Rodriguez, Daniel Alejandro" sort="Garcia Rodriguez, Daniel Alejandro" uniqKey="Garcia Rodriguez D" first="Daniel Alejandro" last="García-Rodríguez">Daniel Alejandro García-Rodríguez</name><affiliation><nlm:affiliation>Laboratory of Agrobiotechnology, University of Colima, Colima, Colima, Mexico.</nlm:affiliation></affiliation></author><author><name sortKey="Centeno Leija, Sara" sort="Centeno Leija, Sara" uniqKey="Centeno Leija S" first="Sara" last="Centeno-Leija">Sara Centeno-Leija</name><affiliation><nlm:affiliation>Laboratory of Agrobiotechnology, National Council of Science and Technology (CONACYT)-University of Colima, Colima, Colima, Mexico.</nlm:affiliation></affiliation></author><author><name sortKey="Serrano Posada, Hugo" sort="Serrano Posada, Hugo" uniqKey="Serrano Posada H" first="Hugo" last="Serrano-Posada">Hugo Serrano-Posada</name><affiliation><nlm:affiliation>Laboratory of Agrobiotechnology, National Council of Science and Technology (CONACYT)-University of Colima, Colima, Colima, Mexico.</nlm:affiliation></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">The city of Wuhan, Hubei province, China, was the origin of a severe pneumonia outbreak in December 2019, attributed to a novel coronavirus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]), causing a total of 2761 deaths and 81109 cases (25 February 2020). SARS-CoV-2 belongs to genus Betacoronavirus, subgenus Sarbecovirus. The polyprotein 1ab (pp1ab) remains unstudied thoroughly since it is similar to other sarbecoviruses. In this short communication, we performed phylogenetic-structural sequence analysis of pp1ab protein of SARS-CoV-2. The analysis showed that the viral pp1ab has not changed in most isolates throughout the outbreak time, but interestingly a deletion of 8 aa in the virulence factor nonstructural protein 1 was found in a virus isolated from a Japanese patient that did not display critical symptoms. While comparing pp1ab protein with other betacoronaviruses, we found a 42 amino acid signature that is only present in SARS-CoV-2 (AS-SCoV2). Members from clade 2 of sarbecoviruses have traces of this signature. The AS-SCoV2 located in the acidic-domain of papain-like protein of SARS-CoV-2 and bat-SL-CoV-RatG13 guided us to suggest that the novel 2019 coronavirus probably emerged by genetic drift from bat-SL-CoV-RaTG13. The implication of this amino acid signature in papain-like protein structure arrangement and function is something worth to be explored.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">32167166</PMID><DateRevised><Year>2020</Year><Month>03</Month><Day>20</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1096-9071</ISSN><JournalIssue CitedMedium="Internet"><PubDate><Year>2020</Year><Month>Mar</Month><Day>13</Day></PubDate></JournalIssue><Title>Journal of medical virology</Title><ISOAbbreviation>J. Med. Virol.</ISOAbbreviation></Journal><ArticleTitle>An exclusive 42 amino acid signature in pp1ab protein provides insights into the evolutive history of the 2019 novel human-pathogenic coronavirus (SARS-CoV-2).</ArticleTitle><ELocationID EIdType="doi" ValidYN="Y">10.1002/jmv.25758</ELocationID><Abstract><AbstractText>The city of Wuhan, Hubei province, China, was the origin of a severe pneumonia outbreak in December 2019, attributed to a novel coronavirus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]), causing a total of 2761 deaths and 81109 cases (25 February 2020). SARS-CoV-2 belongs to genus Betacoronavirus, subgenus Sarbecovirus. The polyprotein 1ab (pp1ab) remains unstudied thoroughly since it is similar to other sarbecoviruses. In this short communication, we performed phylogenetic-structural sequence analysis of pp1ab protein of SARS-CoV-2. The analysis showed that the viral pp1ab has not changed in most isolates throughout the outbreak time, but interestingly a deletion of 8 aa in the virulence factor nonstructural protein 1 was found in a virus isolated from a Japanese patient that did not display critical symptoms. While comparing pp1ab protein with other betacoronaviruses, we found a 42 amino acid signature that is only present in SARS-CoV-2 (AS-SCoV2). Members from clade 2 of sarbecoviruses have traces of this signature. The AS-SCoV2 located in the acidic-domain of papain-like protein of SARS-CoV-2 and bat-SL-CoV-RatG13 guided us to suggest that the novel 2019 coronavirus probably emerged by genetic drift from bat-SL-CoV-RaTG13. The implication of this amino acid signature in papain-like protein structure arrangement and function is something worth to be explored.</AbstractText><CopyrightInformation>© 2020 Wiley Periodicals, Inc.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Cárdenas-Conejo</LastName><ForeName>Yair</ForeName><Initials>Y</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-0190-244X</Identifier><AffiliationInfo><Affiliation>Laboratory of Agrobiotechnology, National Council of Science and Technology (CONACYT)-University of Colima, Colima, Colima, Mexico.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liñan-Rico</LastName><ForeName>Andrómeda</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>University Center for Biomedical Research, National Council of Science and Technology (CONACYT)-University of Colima, Colima, Colima, Mexico.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>García-Rodríguez</LastName><ForeName>Daniel Alejandro</ForeName><Initials>DA</Initials><AffiliationInfo><Affiliation>Laboratory of Agrobiotechnology, University of Colima, Colima, Colima, Mexico.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Centeno-Leija</LastName><ForeName>Sara</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Laboratory of Agrobiotechnology, National Council of Science and Technology (CONACYT)-University of Colima, Colima, Colima, Mexico.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Serrano-Posada</LastName><ForeName>Hugo</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Laboratory of Agrobiotechnology, National Council of Science and Technology (CONACYT)-University of Colima, Colima, Colima, Mexico.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>APN-2015-01-741 to Yair Cárdenas-Conejo</GrantID><Agency>Consejo Nacional de Ciencia y Tecnología</Agency><Country></Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>03</Month><Day>13</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">SARS</Keyword><Keyword MajorTopicYN="N">SARS-CoV-2</Keyword><Keyword MajorTopicYN="N">Wuhan</Keyword><Keyword MajorTopicYN="N">coronavirus</Keyword><Keyword MajorTopicYN="N">pp1ab protein</Keyword><Keyword MajorTopicYN="N">virus</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>14</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>3</Month><Day>14</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>3</Month><Day>14</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>aheadofprint</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32167166</ArticleId><ArticleId IdType="doi">10.1002/jmv.25758</ArticleId></ArticleIdList><ReferenceList><Title>REFERENCES</Title><Reference><Citation>Wu F, Zhao S, Yu B, et al. 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