COVID-2019: The role of the nsp2 and nsp3 in its pathogenesis.
Identifieur interne : 000A83 ( PubMed/Curation ); précédent : 000A82; suivant : 000A84COVID-2019: The role of the nsp2 and nsp3 in its pathogenesis.
Auteurs : Silvia Angeletti [Italie] ; Domenico Benvenuto [Italie] ; Martina Bianchi [Italie] ; Marta Giovanetti [Brésil] ; Stefano Pascarella [Italie] ; Massimo Ciccozzi [Italie]Source :
- Journal of medical virology [ 1096-9071 ] ; 2020.
Abstract
Last December 2019, a new virus, named novel Coronavirus (COVID-2019) causing many cases of severe pneumonia was reported in Wuhan, China. The virus knowledge is limited and especially about COVID-2019 pathogenesis. The Open Reading Frame 1ab (ORF1ab) of COVID-2019 has been analyzed to evidence the presence of mutation caused by selective pressure on the virus. For selective pressure analysis fast-unconstrained Bayesian approximation (FUBAR) was used. Homology modelling has been performed by SwissModel and HHPred servers. The presence of transmembrane helical segments in Coronavirus ORF1ab non structural protein 2 (nsp2) and nsp3 was tested by TMHMM, MEMSAT, and MEMPACK tools. Three-dimensional structures have been analyzed and displayed using PyMOL. FUBAR analysis revealed the presence of potential sites under positive selective pressure (P < .05). Position 723 in the COVID-2019 has a serine instead a glycine residue, while at aminoacidic position 1010 a proline instead an isoleucine. Significant (P < .05) pervasive negative selection in 2416 sites (55%) was found. The positive selective pressure could account for some clinical features of this virus compared with severe acute respiratory syndrome (SARS) and Bat SARS-like CoV. The stabilizing mutation falling in the endosome-associated-protein-like domain of the nsp2 protein could account for COVID-2019 high ability of contagious, while the destabilizing mutation in nsp3 proteins could suggest a potential mechanism differentiating COVID-2019 from SARS. These data could be helpful for further investigation aimed to identify potential therapeutic targets or vaccine strategy, especially in the actual moment when the epidemic is ongoing and the scientific community is trying to enrich knowledge about this new viral pathogen.
DOI: 10.1002/jmv.25719
PubMed: 32083328
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Rossi Fanelli", University of Rome "La Sapienza", Rome, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Biochemical Sciences "A. Rossi Fanelli", University of Rome "La Sapienza", Rome</wicri:regionArea></affiliation></author><author><name sortKey="Giovanetti, Marta" sort="Giovanetti, Marta" uniqKey="Giovanetti M" first="Marta" last="Giovanetti">Marta Giovanetti</name><affiliation wicri:level="1"><nlm:affiliation>Flavivirus Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Flavivirus Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro</wicri:regionArea></affiliation></author><author><name sortKey="Pascarella, Stefano" sort="Pascarella, Stefano" uniqKey="Pascarella S" first="Stefano" last="Pascarella">Stefano Pascarella</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biochemical Sciences "A. Rossi Fanelli", University of Rome "La Sapienza", Rome, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Biochemical Sciences "A. Rossi Fanelli", University of Rome "La Sapienza", Rome</wicri:regionArea></affiliation></author><author><name sortKey="Ciccozzi, Massimo" sort="Ciccozzi, Massimo" uniqKey="Ciccozzi M" first="Massimo" last="Ciccozzi">Massimo Ciccozzi</name><affiliation wicri:level="1"><nlm:affiliation>Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome</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">Last December 2019, a new virus, named novel Coronavirus (COVID-2019) causing many cases of severe pneumonia was reported in Wuhan, China. The virus knowledge is limited and especially about COVID-2019 pathogenesis. The Open Reading Frame 1ab (ORF1ab) of COVID-2019 has been analyzed to evidence the presence of mutation caused by selective pressure on the virus. For selective pressure analysis fast-unconstrained Bayesian approximation (FUBAR) was used. Homology modelling has been performed by SwissModel and HHPred servers. The presence of transmembrane helical segments in Coronavirus ORF1ab non structural protein 2 (nsp2) and nsp3 was tested by TMHMM, MEMSAT, and MEMPACK tools. Three-dimensional structures have been analyzed and displayed using PyMOL. FUBAR analysis revealed the presence of potential sites under positive selective pressure (P < .05). Position 723 in the COVID-2019 has a serine instead a glycine residue, while at aminoacidic position 1010 a proline instead an isoleucine. Significant (P < .05) pervasive negative selection in 2416 sites (55%) was found. The positive selective pressure could account for some clinical features of this virus compared with severe acute respiratory syndrome (SARS) and Bat SARS-like CoV. The stabilizing mutation falling in the endosome-associated-protein-like domain of the nsp2 protein could account for COVID-2019 high ability of contagious, while the destabilizing mutation in nsp3 proteins could suggest a potential mechanism differentiating COVID-2019 from SARS. These data could be helpful for further investigation aimed to identify potential therapeutic targets or vaccine strategy, especially in the actual moment when the epidemic is ongoing and the scientific community is trying to enrich knowledge about this new viral pathogen.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">32083328</PMID><DateRevised><Year>2020</Year><Month>02</Month><Day>28</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1096-9071</ISSN><JournalIssue CitedMedium="Internet"><PubDate><Year>2020</Year><Month>Feb</Month><Day>21</Day></PubDate></JournalIssue><Title>Journal of medical virology</Title><ISOAbbreviation>J. Med. Virol.</ISOAbbreviation></Journal><ArticleTitle>COVID-2019: The role of the nsp2 and nsp3 in its pathogenesis.</ArticleTitle><ELocationID EIdType="doi" ValidYN="Y">10.1002/jmv.25719</ELocationID><Abstract><AbstractText>Last December 2019, a new virus, named novel Coronavirus (COVID-2019) causing many cases of severe pneumonia was reported in Wuhan, China. The virus knowledge is limited and especially about COVID-2019 pathogenesis. The Open Reading Frame 1ab (ORF1ab) of COVID-2019 has been analyzed to evidence the presence of mutation caused by selective pressure on the virus. For selective pressure analysis fast-unconstrained Bayesian approximation (FUBAR) was used. Homology modelling has been performed by SwissModel and HHPred servers. The presence of transmembrane helical segments in Coronavirus ORF1ab non structural protein 2 (nsp2) and nsp3 was tested by TMHMM, MEMSAT, and MEMPACK tools. Three-dimensional structures have been analyzed and displayed using PyMOL. FUBAR analysis revealed the presence of potential sites under positive selective pressure (P < .05). Position 723 in the COVID-2019 has a serine instead a glycine residue, while at aminoacidic position 1010 a proline instead an isoleucine. Significant (P < .05) pervasive negative selection in 2416 sites (55%) was found. The positive selective pressure could account for some clinical features of this virus compared with severe acute respiratory syndrome (SARS) and Bat SARS-like CoV. The stabilizing mutation falling in the endosome-associated-protein-like domain of the nsp2 protein could account for COVID-2019 high ability of contagious, while the destabilizing mutation in nsp3 proteins could suggest a potential mechanism differentiating COVID-2019 from SARS. These data could be helpful for further investigation aimed to identify potential therapeutic targets or vaccine strategy, especially in the actual moment when the epidemic is ongoing and the scientific community is trying to enrich knowledge about this new viral pathogen.</AbstractText><CopyrightInformation>© 2020 Wiley Periodicals, Inc.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Angeletti</LastName><ForeName>Silvia</ForeName><Initials>S</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-7393-8732</Identifier><AffiliationInfo><Affiliation>Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Rome, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Benvenuto</LastName><ForeName>Domenico</ForeName><Initials>D</Initials><Identifier Source="ORCID">http://orcid.org/0000-0003-3833-2927</Identifier><AffiliationInfo><Affiliation>Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy.</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", Rome, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Giovanetti</LastName><ForeName>Marta</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Flavivirus Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil.</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", Rome, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ciccozzi</LastName><ForeName>Massimo</ForeName><Initials>M</Initials><Identifier Source="ORCID">http://orcid.org/0000-0003-3866-9239</Identifier><AffiliationInfo><Affiliation>Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>02</Month><Day>21</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">epidemiology</Keyword><Keyword MajorTopicYN="N">infection</Keyword><Keyword MajorTopicYN="N">pandemics</Keyword><Keyword MajorTopicYN="N">pathogenesis</Keyword><Keyword MajorTopicYN="N">protein-protein interaction analysis</Keyword><Keyword MajorTopicYN="N">research and analysis methods</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>02</Month><Day>13</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>02</Month><Day>19</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>2</Month><Day>23</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>2</Month><Day>23</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>2</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>aheadofprint</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32083328</ArticleId><ArticleId IdType="doi">10.1002/jmv.25719</ArticleId></ArticleIdList><ReferenceList><Title>REFERENCES</Title><Reference><Citation>Hui DS, I Azhar E, Madani TA, et al. 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