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Article: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan

TitleGenomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan
Authors
KeywordsCoronavirus
Wuhan
SARS
emerging
genome
Issue Date2020
PublisherTaylor & Francis Group, on behalf of Shanghai ShangyixunCultural Communication Co., Ltd. The Journal's web site is located at https://www.tandfonline.com/toc/temi20/current
Citation
Emerging Microbes & Infections, 2020, v. 9 n. 1, p. 221-236 How to Cite?
AbstractA mysterious outbreak of atypical pneumonia in late 2019 was traced to a seafood wholesale market in Wuhan of China. Within a few weeks, a novel coronavirus tentatively named as 2019 novel coronavirus (2019-nCoV) was announced by the World Health Organization. We performed bioinformatics analysis on a virus genome from a patient with 2019-nCoV infection and compared it with other related coronavirus genomes. Overall, the genome of 2019-nCoV has 89% nucleotide identity with bat SARS-like-CoVZXC21 and 82% with that of human SARS-CoV. The phylogenetic trees of their orf1a/b, Spike, Envelope, Membrane and Nucleoprotein also clustered closely with those of the bat, civet and human SARS coronaviruses. However, the external subdomain of Spike’s receptor binding domain of 2019-nCoV shares only 40% amino acid identity with other SARS-related coronaviruses. Remarkably, its orf3b encodes a completely novel short protein. Furthermore, its new orf8 likely encodes a secreted protein with an alpha-helix, following with a beta-sheet(s) containing six strands. Learning from the roles of civet in SARS and camel in MERS, hunting for the animal source of 2019-nCoV and its more ancestral virus would be important for understanding the origin and evolution of this novel lineage B betacoronavirus. These findings provide the basis for starting further studies on the pathogenesis, and optimizing the design of diagnostic, antiviral and vaccination strategies for this emerging infection.
Persistent Identifierhttp://hdl.handle.net/10722/285307
ISSN
2018 Impact Factor: 6.212
2015 SCImago Journal Rankings: 1.774
PubMed Central ID
ISI Accession Number ID
Errata

 

DC FieldValueLanguage
dc.contributor.authorChan, JFW-
dc.contributor.authorKok, KH-
dc.contributor.authorZHU, Z-
dc.contributor.authorChu, H-
dc.contributor.authorTo, KKW-
dc.contributor.authorYuan, S-
dc.contributor.authorYuen, KY-
dc.date.accessioned2020-08-18T03:52:15Z-
dc.date.available2020-08-18T03:52:15Z-
dc.date.issued2020-
dc.identifier.citationEmerging Microbes & Infections, 2020, v. 9 n. 1, p. 221-236-
dc.identifier.issn2222-1751-
dc.identifier.urihttp://hdl.handle.net/10722/285307-
dc.description.abstractA mysterious outbreak of atypical pneumonia in late 2019 was traced to a seafood wholesale market in Wuhan of China. Within a few weeks, a novel coronavirus tentatively named as 2019 novel coronavirus (2019-nCoV) was announced by the World Health Organization. We performed bioinformatics analysis on a virus genome from a patient with 2019-nCoV infection and compared it with other related coronavirus genomes. Overall, the genome of 2019-nCoV has 89% nucleotide identity with bat SARS-like-CoVZXC21 and 82% with that of human SARS-CoV. The phylogenetic trees of their orf1a/b, Spike, Envelope, Membrane and Nucleoprotein also clustered closely with those of the bat, civet and human SARS coronaviruses. However, the external subdomain of Spike’s receptor binding domain of 2019-nCoV shares only 40% amino acid identity with other SARS-related coronaviruses. Remarkably, its orf3b encodes a completely novel short protein. Furthermore, its new orf8 likely encodes a secreted protein with an alpha-helix, following with a beta-sheet(s) containing six strands. Learning from the roles of civet in SARS and camel in MERS, hunting for the animal source of 2019-nCoV and its more ancestral virus would be important for understanding the origin and evolution of this novel lineage B betacoronavirus. These findings provide the basis for starting further studies on the pathogenesis, and optimizing the design of diagnostic, antiviral and vaccination strategies for this emerging infection.-
dc.languageeng-
dc.publisherTaylor & Francis Group, on behalf of Shanghai ShangyixunCultural Communication Co., Ltd. The Journal's web site is located at https://www.tandfonline.com/toc/temi20/current-
dc.relation.ispartofEmerging Microbes & Infections-
dc.rightsThis work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.-
dc.subjectCoronavirus-
dc.subjectWuhan-
dc.subjectSARS-
dc.subjectemerging-
dc.subjectgenome-
dc.titleGenomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan-
dc.typeArticle-
dc.identifier.emailChan, JFW: jfwchan@hku.hk-
dc.identifier.emailKok, KH: khkok@hku.hk-
dc.identifier.emailChu, H: hinchu@hku.hk-
dc.identifier.emailTo, KKW: kelvinto@hku.hk-
dc.identifier.emailYuan, S: yuansf@hku.hk-
dc.identifier.emailYuen, KY: kyyuen@hkucc.hku.hk-
dc.identifier.authorityChan, JFW=rp01736-
dc.identifier.authorityKok, KH=rp01455-
dc.identifier.authorityChu, H=rp02125-
dc.identifier.authorityTo, KKW=rp01384-
dc.identifier.authorityYuan, S=rp02640-
dc.identifier.authorityYuen, KY=rp00366-
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1080/22221751.2020.1719902-
dc.identifier.pmid31987001-
dc.identifier.pmcidPMC7067204-
dc.identifier.scopuseid_2-s2.0-85078500139-
dc.identifier.hkuros312852-
dc.identifier.volume9-
dc.identifier.issue1-
dc.identifier.spage221-
dc.identifier.epage236-
dc.identifier.isiWOS:000510381600001-
dc.publisher.placeUnited Kingdom-
dc.relation.erratumdoi:10.1080/22221751.2020.1737364-

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