Genomic variance of the 2019-nCoV coronavirus.
Identifieur interne : 000670 ( PubMed/Checkpoint ); précédent : 000669; suivant : 000671Genomic variance of the 2019-nCoV coronavirus.
Auteurs : Carmine Ceraolo [Italie] ; Federico M. Giorgi [Italie]Source :
- Journal of medical virology [ 1096-9071 ] ; 2020.
Descripteurs français
- KwdFr :
- MESH :
- génétique : ARN viral.
- virologie : Chiroptera.
- Animaux, Génome viral, Humains, Infections à coronavirus, Modèles génétiques, Phylogénie, Pneumopathie virale, Protéome, Séquence d'acides aminés, Séquence nucléotidique, Variation génétique.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : RNA, Viral.
- chemical : Proteome.
- classification : Betacoronavirus.
- genetics : Betacoronavirus.
- virology : Chiroptera.
- Amino Acid Sequence, Animals, Base Sequence, Coronavirus Infections, Genetic Variation, Genome, Viral, Humans, Models, Genetic, Phylogeny, Pneumonia, Viral.
Abstract
There is a rising global concern for the recently emerged novel coronavirus (2019-nCoV). Full genomic sequences have been released by the worldwide scientific community in the last few weeks to understand the evolutionary origin and molecular characteristics of this virus. Taking advantage of all the genomic information currently available, we constructed a phylogenetic tree including also representatives of other coronaviridae, such as Bat coronavirus (BCoV) and severe acute respiratory syndrome. We confirm high sequence similarity (>99%) between all sequenced 2019-nCoVs genomes available, with the closest BCoV sequence sharing 96.2% sequence identity, confirming the notion of a zoonotic origin of 2019-nCoV. Despite the low heterogeneity of the 2019-nCoV genomes, we could identify at least two hypervariable genomic hotspots, one of which is responsible for a Serine/Leucine variation in the viral ORF8-encoded protein. Finally, we perform a full proteomic comparison with other coronaviridae, identifying key aminoacidic differences to be considered for antiviral strategies deriving from previous anti-coronavirus approaches.
DOI: 10.1002/jmv.25700
PubMed: 32027036
Affiliations:
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Giorgi</name><affiliation wicri:level="1"><nlm:affiliation>Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Pharmacy and Biotechnology, University of Bologna, Bologna</wicri:regionArea><wicri:noRegion>Bologna</wicri:noRegion></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><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Sequence</term><term>Animals</term><term>Base Sequence</term><term>Betacoronavirus (classification)</term><term>Betacoronavirus (genetics)</term><term>Chiroptera (virology)</term><term>Coronavirus Infections</term><term>Genetic Variation</term><term>Genome, Viral</term><term>Humans</term><term>Models, Genetic</term><term>Phylogeny</term><term>Pneumonia, Viral</term><term>Proteome</term><term>RNA, Viral (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN viral (génétique)</term><term>Animaux</term><term>Chiroptera (virologie)</term><term>Génome viral</term><term>Humains</term><term>Infections à coronavirus</term><term>Modèles génétiques</term><term>Phylogénie</term><term>Pneumopathie virale</term><term>Protéome</term><term>Séquence d'acides aminés</term><term>Séquence nucléotidique</term><term>Variation génétique</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>RNA, Viral</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>Proteome</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Betacoronavirus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Betacoronavirus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN viral</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Chiroptera</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Chiroptera</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term><term>Animals</term><term>Base Sequence</term><term>Coronavirus Infections</term><term>Genetic Variation</term><term>Genome, Viral</term><term>Humans</term><term>Models, Genetic</term><term>Phylogeny</term><term>Pneumonia, Viral</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Animaux</term><term>Génome viral</term><term>Humains</term><term>Infections à coronavirus</term><term>Modèles génétiques</term><term>Phylogénie</term><term>Pneumopathie virale</term><term>Protéome</term><term>Séquence d'acides aminés</term><term>Séquence nucléotidique</term><term>Variation génétique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">There is a rising global concern for the recently emerged novel coronavirus (2019-nCoV). Full genomic sequences have been released by the worldwide scientific community in the last few weeks to understand the evolutionary origin and molecular characteristics of this virus. Taking advantage of all the genomic information currently available, we constructed a phylogenetic tree including also representatives of other coronaviridae, such as Bat coronavirus (BCoV) and severe acute respiratory syndrome. We confirm high sequence similarity (>99%) between all sequenced 2019-nCoVs genomes available, with the closest BCoV sequence sharing 96.2% sequence identity, confirming the notion of a zoonotic origin of 2019-nCoV. Despite the low heterogeneity of the 2019-nCoV genomes, we could identify at least two hypervariable genomic hotspots, one of which is responsible for a Serine/Leucine variation in the viral ORF8-encoded protein. Finally, we perform a full proteomic comparison with other coronaviridae, identifying key aminoacidic differences to be considered for antiviral strategies deriving from previous anti-coronavirus approaches.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">32027036</PMID><DateCompleted><Year>2020</Year><Month>03</Month><Day>18</Day></DateCompleted><DateRevised><Year>2020</Year><Month>03</Month><Day>25</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1096-9071</ISSN><JournalIssue CitedMedium="Internet"><Volume>92</Volume><Issue>5</Issue><PubDate><Year>2020</Year><Month>05</Month></PubDate></JournalIssue><Title>Journal of medical virology</Title><ISOAbbreviation>J. Med. Virol.</ISOAbbreviation></Journal><ArticleTitle>Genomic variance of the 2019-nCoV coronavirus.</ArticleTitle><Pagination><MedlinePgn>522-528</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1002/jmv.25700</ELocationID><Abstract><AbstractText>There is a rising global concern for the recently emerged novel coronavirus (2019-nCoV). Full genomic sequences have been released by the worldwide scientific community in the last few weeks to understand the evolutionary origin and molecular characteristics of this virus. Taking advantage of all the genomic information currently available, we constructed a phylogenetic tree including also representatives of other coronaviridae, such as Bat coronavirus (BCoV) and severe acute respiratory syndrome. We confirm high sequence similarity (>99%) between all sequenced 2019-nCoVs genomes available, with the closest BCoV sequence sharing 96.2% sequence identity, confirming the notion of a zoonotic origin of 2019-nCoV. Despite the low heterogeneity of the 2019-nCoV genomes, we could identify at least two hypervariable genomic hotspots, one of which is responsible for a Serine/Leucine variation in the viral ORF8-encoded protein. Finally, we perform a full proteomic comparison with other coronaviridae, identifying key aminoacidic differences to be considered for antiviral strategies deriving from previous anti-coronavirus approaches.</AbstractText><CopyrightInformation>© 2020 Wiley Periodicals, Inc.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Ceraolo</LastName><ForeName>Carmine</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Giorgi</LastName><ForeName>Federico M</ForeName><Initials>FM</Initials><Identifier Source="ORCID">0000-0002-7325-9908</Identifier><AffiliationInfo><Affiliation>Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>Montalcini 2016</GrantID><Agency>Ministero dell'Istruzione, dell'Università e della Ricerca</Agency><Country>International</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>02</Month><Day>19</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>J Med Virol</MedlineTA><NlmUniqueID>7705876</NlmUniqueID><ISSNLinking>0146-6615</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D020543">Proteome</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012367">RNA, Viral</NameOfSubstance></Chemical></ChemicalList><SupplMeshList><SupplMeshName Type="Disease" UI="C000657245">COVID-19</SupplMeshName><SupplMeshName Type="Organism" 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IdType="pubmed">32027036</ArticleId><ArticleId IdType="doi">10.1002/jmv.25700</ArticleId></ArticleIdList><ReferenceList><Title>REFERENCES</Title><Reference><Citation>Cui J, Li F, Shi Z-L. Origin and evolution of pathogenic coronaviruses. Nat Rev Microbiol. 2019;17(3):181-192. https://doi.org/10.1038/s41579-018-0118-9</Citation></Reference><Reference><Citation>Schoeman D, Fielding BC. Coronavirus envelope protein: current knowledge. Virol J. 2019;16(1):69. https://doi.org/10.1186/s12985-019-1182-0</Citation></Reference><Reference><Citation>Hu B, Ge X, Wang L-F, Shi Z. Bat origin of human coronaviruses. Virol J. 2015;12(1):221. https://doi.org/10.1186/s12985-015-0422-1</Citation></Reference><Reference><Citation>Benvenuto D, Giovannetti M, Ciccozzi A, Spoto S, Angeletti S, Ciccozzi M. The 2019-new coronavirus epidemic: evidence for virus evolution. J Med Virol. 2020. https://doi.org/10.1002/jmv.25688</Citation></Reference><Reference><Citation>Lu H, Stratton CW, Tang Y. Outbreak of pneumonia of unknown etiology in Wuhan China: the mystery and the miracle. J Med Virol. 2020. https://doi.org/10.1002/jmv.25678</Citation></Reference><Reference><Citation>Lu R, Zhao X, LI J, et al. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. The Lancet. 2020:S0140673620302518. https://doi.org/10.1016/S0140-6736(20)30251-8</Citation></Reference><Reference><Citation>Shu Y, McCauley J. GISAID: global initiative on sharing all influenza data-from vision to reality. Euro Surveill. Mar. 2017;22(13):1-3. https://doi.org/10.2807/1560-7917.ES.2017.22.13.30494</Citation></Reference><Reference><Citation>Sayers EW, Cavanaugh M, Clark K, Ostell J, Pruitt KD, Karsch-Mizrachi I. GenBank. Nucleic Acids Res. 2019;47(D1):D94-D99. https://doi.org/10.1093/nar/gky989</Citation></Reference><Reference><Citation>Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32(5):1792-1797. https://doi.org/10.1093/nar/gkh340</Citation></Reference><Reference><Citation>Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ. Jalview Version 2-a multiple sequence alignment editor and analysis workbench. Bioinformatics. 2009;25(9):1189-1191. https://doi.org/10.1093/bioinformatics/btp033</Citation></Reference><Reference><Citation>Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 2018;35(6):1547-1549. https://doi.org/10.1093/molbev/msy096</Citation></Reference><Reference><Citation>Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol. 1993;10(3):512-526. https://doi.org/10.1093/oxfordjournals.molbev.a040023</Citation></Reference><Reference><Citation>Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 1985;39(4):783-791. https://doi.org/10.1111/j.1558-5646.1985.tb00420.x</Citation></Reference><Reference><Citation>Le S, Joss J, Husson F. FactoMineR: an R package for multivariate analysis. J Stat Softw. 2008;25(1):1-18.</Citation></Reference><Reference><Citation>Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215(3):403-410. https://doi.org/10.1016/S0022-2836(05)80360-2</Citation></Reference><Reference><Citation>Linding R. GlobPlot: exploring protein sequences for globularity and disorder. Nucleic Acids Res. 2003;31(13):3701-3708. https://doi.org/10.1093/nar/gkg519</Citation></Reference><Reference><Citation>Narayanan K, Huang C, Makino S. SARS coronavirus accessory proteins. Virus Res. 2008;133(1):113-121. https://doi.org/10.1016/j.virusres.2007.10.009</Citation></Reference><Reference><Citation>Manaresi E, Conti I, Bua G, Bonvicini F, Gallinella G. A Parvovirus B19 synthetic genome: sequence features and functional competence. Virology. 2017;508:54-62. https://doi.org/10.1016/j.virol.2017.05.006</Citation></Reference><Reference><Citation>Burley SK, Berman HM, Kleywegt GJ, Markley JL, Nakamura H, Velankar S. Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive. In: Wlodawer A, Dauter Z, Jaskolski M, eds. Protein Crystallography. 1607. New York, NY: Springer New York; 2017:627-641.</Citation></Reference><Reference><Citation>Anand K. Coronavirus main proteinase (3CLpro) structure: basis for design of anti-SARS drugs. Science. 2003;300(5626):1763-1767. https://doi.org/10.1126/science.1085658</Citation></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>Italie</li></country></list><tree><country name="Italie"><noRegion><name sortKey="Ceraolo, Carmine" sort="Ceraolo, Carmine" uniqKey="Ceraolo C" first="Carmine" last="Ceraolo">Carmine Ceraolo</name></noRegion><name sortKey="Giorgi, Federico M" sort="Giorgi, Federico M" uniqKey="Giorgi F" first="Federico M" last="Giorgi">Federico M. Giorgi</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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