Evolutionary analysis of SARS-CoV-2: how mutation of Non-Structural Protein 6 (NSP6) could affect viral autophagy.
Identifieur interne : 000194 ( PubMed/Corpus ); précédent : 000193; suivant : 000195Evolutionary analysis of SARS-CoV-2: how mutation of Non-Structural Protein 6 (NSP6) could affect viral autophagy.
Auteurs : Domenico Benvenuto ; Silvia Angeletti ; Marta Giovanetti ; Martina Bianchi ; Stefano Pascarella ; Roberto Cauda ; Massimo Ciccozzi ; Antonio CassoneSource :
- The Journal of infection [ 1532-2742 ] ; 2020.
Abstract
SARS-CoV-2 is a new coronavirus that has spread globally, infecting more than 150000 people, and being declared pandemic by the WHO. We provide here bio-informatic, evolutionary analysis of 351 available sequences of its genome with the aim of mapping genome structural variations and the patterns of selection.
DOI: 10.1016/j.jinf.2020.03.058
PubMed: 32283146
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Evolutionary analysis of SARS-CoV-2: how mutation of Non-Structural Protein 6 (NSP6) could affect viral autophagy.</title><author><name sortKey="Benvenuto, Domenico" sort="Benvenuto, Domenico" uniqKey="Benvenuto D" first="Domenico" last="Benvenuto">Domenico Benvenuto</name><affiliation><nlm:affiliation>Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Via Álvaro del Portillo, 21, Rome 00128, Italy. Electronic address: domenicobenvenuto95@gmail.com.</nlm:affiliation></affiliation></author><author><name sortKey="Angeletti, Silvia" sort="Angeletti, Silvia" uniqKey="Angeletti S" first="Silvia" last="Angeletti">Silvia Angeletti</name><affiliation><nlm:affiliation>Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Via Álvaro del Portillo, 21, Rome 00128, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Giovanetti, Marta" sort="Giovanetti, Marta" uniqKey="Giovanetti M" first="Marta" last="Giovanetti">Marta Giovanetti</name><affiliation><nlm:affiliation>Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil, 4365 - Manguinhos, Rio de Janeiro - RJ 21040-900, Brasil.</nlm:affiliation></affiliation></author><author><name sortKey="Bianchi, Martina" sort="Bianchi, Martina" uniqKey="Bianchi M" first="Martina" last="Bianchi">Martina Bianchi</name><affiliation><nlm:affiliation>Department of Biochemical Sciences "A. Rossi Fanelli", University of Rome "La Sapienza", Viale Regina Elena, 332, Rome 00185, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Pascarella, Stefano" sort="Pascarella, Stefano" uniqKey="Pascarella S" first="Stefano" last="Pascarella">Stefano Pascarella</name><affiliation><nlm:affiliation>Department of Biochemical Sciences "A. Rossi Fanelli", University of Rome "La Sapienza", Viale Regina Elena, 332, Rome 00185, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Cauda, Roberto" sort="Cauda, Roberto" uniqKey="Cauda R" first="Roberto" last="Cauda">Roberto Cauda</name><affiliation><nlm:affiliation>UOC Malattie Infettive - Fondazione Policlinico Universitario "A.Gemelli" IRCCS, Largo Agostino Gemelli, 8, Rome 00168, Italy; Department of Healthcare Surveillance and Bioethics, Catholic University of Sacred Heart, Largo Francesco Vito, 1, Rome 00168, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Ciccozzi, Massimo" sort="Ciccozzi, Massimo" uniqKey="Ciccozzi M" first="Massimo" last="Ciccozzi">Massimo Ciccozzi</name><affiliation><nlm:affiliation>Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Via Álvaro del Portillo, 21, Rome 00128, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Cassone, Antonio" sort="Cassone, Antonio" uniqKey="Cassone A" first="Antonio" last="Cassone">Antonio Cassone</name><affiliation><nlm:affiliation>Center of genomics, genetics and biology, University of Siena, Petriccio e Belriguardo, 35, Siena 53100, Italy.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2020">2020</date><idno type="RBID">pubmed:32283146</idno><idno type="pmid">32283146</idno><idno type="doi">10.1016/j.jinf.2020.03.058</idno><idno type="wicri:Area/PubMed/Corpus">000194</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000194</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Evolutionary analysis of SARS-CoV-2: how mutation of Non-Structural Protein 6 (NSP6) could affect viral autophagy.</title><author><name sortKey="Benvenuto, Domenico" sort="Benvenuto, Domenico" uniqKey="Benvenuto D" first="Domenico" last="Benvenuto">Domenico Benvenuto</name><affiliation><nlm:affiliation>Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Via Álvaro del Portillo, 21, Rome 00128, Italy. Electronic address: domenicobenvenuto95@gmail.com.</nlm:affiliation></affiliation></author><author><name sortKey="Angeletti, Silvia" sort="Angeletti, Silvia" uniqKey="Angeletti S" first="Silvia" last="Angeletti">Silvia Angeletti</name><affiliation><nlm:affiliation>Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Via Álvaro del Portillo, 21, Rome 00128, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Giovanetti, Marta" sort="Giovanetti, Marta" uniqKey="Giovanetti M" first="Marta" last="Giovanetti">Marta Giovanetti</name><affiliation><nlm:affiliation>Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil, 4365 - Manguinhos, Rio de Janeiro - RJ 21040-900, Brasil.</nlm:affiliation></affiliation></author><author><name sortKey="Bianchi, Martina" sort="Bianchi, Martina" uniqKey="Bianchi M" first="Martina" last="Bianchi">Martina Bianchi</name><affiliation><nlm:affiliation>Department of Biochemical Sciences "A. Rossi Fanelli", University of Rome "La Sapienza", Viale Regina Elena, 332, Rome 00185, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Pascarella, Stefano" sort="Pascarella, Stefano" uniqKey="Pascarella S" first="Stefano" last="Pascarella">Stefano Pascarella</name><affiliation><nlm:affiliation>Department of Biochemical Sciences "A. Rossi Fanelli", University of Rome "La Sapienza", Viale Regina Elena, 332, Rome 00185, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Cauda, Roberto" sort="Cauda, Roberto" uniqKey="Cauda R" first="Roberto" last="Cauda">Roberto Cauda</name><affiliation><nlm:affiliation>UOC Malattie Infettive - Fondazione Policlinico Universitario "A.Gemelli" IRCCS, Largo Agostino Gemelli, 8, Rome 00168, Italy; Department of Healthcare Surveillance and Bioethics, Catholic University of Sacred Heart, Largo Francesco Vito, 1, Rome 00168, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Ciccozzi, Massimo" sort="Ciccozzi, Massimo" uniqKey="Ciccozzi M" first="Massimo" last="Ciccozzi">Massimo Ciccozzi</name><affiliation><nlm:affiliation>Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Via Álvaro del Portillo, 21, Rome 00128, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Cassone, Antonio" sort="Cassone, Antonio" uniqKey="Cassone A" first="Antonio" last="Cassone">Antonio Cassone</name><affiliation><nlm:affiliation>Center of genomics, genetics and biology, University of Siena, Petriccio e Belriguardo, 35, Siena 53100, Italy.</nlm:affiliation></affiliation></author></analytic><series><title level="j">The Journal of infection</title><idno type="eISSN">1532-2742</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">SARS-CoV-2 is a new coronavirus that has spread globally, infecting more than 150000 people, and being declared pandemic by the WHO. We provide here bio-informatic, evolutionary analysis of 351 available sequences of its genome with the aim of mapping genome structural variations and the patterns of selection.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">32283146</PMID><DateRevised><Year>2020</Year><Month>04</Month><Day>19</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1532-2742</ISSN><JournalIssue CitedMedium="Internet"><PubDate><Year>2020</Year><Month>Apr</Month><Day>10</Day></PubDate></JournalIssue><Title>The Journal of infection</Title><ISOAbbreviation>J. Infect.</ISOAbbreviation></Journal><ArticleTitle>Evolutionary analysis of SARS-CoV-2: how mutation of Non-Structural Protein 6 (NSP6) could affect viral autophagy.</ArticleTitle><ELocationID EIdType="pii" ValidYN="Y">S0163-4453(20)30186-9</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.jinf.2020.03.058</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">SARS-CoV-2 is a new coronavirus that has spread globally, infecting more than 150000 people, and being declared pandemic by the WHO. We provide here bio-informatic, evolutionary analysis of 351 available sequences of its genome with the aim of mapping genome structural variations and the patterns of selection.</AbstractText><AbstractText Label="METHODS" NlmCategory="METHODS">A Maximum likelihood tree has been built and selective pressure has been investigated in order to find any mutation developed during the SARS-CoV-2 epidemic that could potentially affect clinical evolution of the infection.</AbstractText><AbstractText Label="FINDING" NlmCategory="RESULTS">We have found in more recent isolates the presence of two mutations affecting the Non-Structural Protein 6 (NSP6) and the Open Reding Frame10 (ORF 10) adjacent regions. Amino acidic change stability analysis suggests both mutations could confer lower stability of the protein structures.</AbstractText><AbstractText Label="INTERPRETATION" NlmCategory="CONCLUSIONS">One of the two mutations, likely developed within the genome during virus spread, could affect virus intracellular survival. Genome follow-up of SARS-CoV-2 spread is urgently needed in order to identify mutations that could significantly modify virus pathogenicity.</AbstractText><CopyrightInformation>Copyright © 2020 Elsevier Ltd. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Benvenuto</LastName><ForeName>Domenico</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Via Álvaro del Portillo, 21, Rome 00128, Italy. Electronic address: domenicobenvenuto95@gmail.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Angeletti</LastName><ForeName>Silvia</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Via Álvaro del Portillo, 21, Rome 00128, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Giovanetti</LastName><ForeName>Marta</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil, 4365 - Manguinhos, Rio de Janeiro - RJ 21040-900, Brasil.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bianchi</LastName><ForeName>Martina</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Biochemical Sciences "A. Rossi Fanelli", University of Rome "La Sapienza", Viale Regina Elena, 332, Rome 00185, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pascarella</LastName><ForeName>Stefano</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Biochemical Sciences "A. Rossi Fanelli", University of Rome "La Sapienza", Viale Regina Elena, 332, Rome 00185, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cauda</LastName><ForeName>Roberto</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>UOC Malattie Infettive - Fondazione Policlinico Universitario "A.Gemelli" IRCCS, Largo Agostino Gemelli, 8, Rome 00168, Italy; Department of Healthcare Surveillance and Bioethics, Catholic University of Sacred Heart, Largo Francesco Vito, 1, Rome 00168, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ciccozzi</LastName><ForeName>Massimo</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Via Álvaro del Portillo, 21, Rome 00128, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cassone</LastName><ForeName>Antonio</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Center of genomics, genetics and biology, University of Siena, Petriccio e Belriguardo, 35, Siena 53100, Italy.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>04</Month><Day>10</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>J Infect</MedlineTA><NlmUniqueID>7908424</NlmUniqueID><ISSNLinking>0163-4453</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Autophagy</Keyword><Keyword MajorTopicYN="N">Bio-informatic</Keyword><Keyword MajorTopicYN="N">COVID-19</Keyword><Keyword MajorTopicYN="N">Coronavirus</Keyword><Keyword MajorTopicYN="N">Molecular evolution</Keyword><Keyword MajorTopicYN="N">SARS-CoV-2</Keyword></KeywordList><CoiStatement>Declaration of Competing Interest We declare no competing interests.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>03</Month><Day>27</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>03</Month><Day>28</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>4</Month><Day>14</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>4</Month><Day>14</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>4</Month><Day>14</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>aheadofprint</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32283146</ArticleId><ArticleId IdType="pii">S0163-4453(20)30186-9</ArticleId><ArticleId IdType="doi">10.1016/j.jinf.2020.03.058</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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