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Article: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan
Title | Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan |
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Authors | |
Keywords | Coronavirus Wuhan SARS emerging genome |
Issue Date | 2020 |
Publisher | Taylor & 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? |
Abstract | A 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 Identifier | http://hdl.handle.net/10722/285307 |
ISSN | 2023 Impact Factor: 8.4 2023 SCImago Journal Rankings: 2.316 |
PubMed Central ID | |
ISI Accession Number ID | |
Errata |
DC Field | Value | Language |
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dc.contributor.author | Chan, JFW | - |
dc.contributor.author | Kok, KH | - |
dc.contributor.author | ZHU, Z | - |
dc.contributor.author | Chu, H | - |
dc.contributor.author | To, KKW | - |
dc.contributor.author | Yuan, S | - |
dc.contributor.author | Yuen, KY | - |
dc.date.accessioned | 2020-08-18T03:52:15Z | - |
dc.date.available | 2020-08-18T03:52:15Z | - |
dc.date.issued | 2020 | - |
dc.identifier.citation | Emerging Microbes & Infections, 2020, v. 9 n. 1, p. 221-236 | - |
dc.identifier.issn | 2222-1751 | - |
dc.identifier.uri | http://hdl.handle.net/10722/285307 | - |
dc.description.abstract | A 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.language | eng | - |
dc.publisher | Taylor & 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.ispartof | Emerging Microbes & Infections | - |
dc.rights | This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. | - |
dc.subject | Coronavirus | - |
dc.subject | Wuhan | - |
dc.subject | SARS | - |
dc.subject | emerging | - |
dc.subject | genome | - |
dc.title | Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan | - |
dc.type | Article | - |
dc.identifier.email | Chan, JFW: jfwchan@hku.hk | - |
dc.identifier.email | Kok, KH: khkok@hku.hk | - |
dc.identifier.email | Chu, H: hinchu@hku.hk | - |
dc.identifier.email | To, KKW: kelvinto@hku.hk | - |
dc.identifier.email | Yuan, S: yuansf@hku.hk | - |
dc.identifier.email | Yuen, KY: kyyuen@hkucc.hku.hk | - |
dc.identifier.authority | Chan, JFW=rp01736 | - |
dc.identifier.authority | Kok, KH=rp01455 | - |
dc.identifier.authority | Chu, H=rp02125 | - |
dc.identifier.authority | To, KKW=rp01384 | - |
dc.identifier.authority | Yuan, S=rp02640 | - |
dc.identifier.authority | Yuen, KY=rp00366 | - |
dc.description.nature | published_or_final_version | - |
dc.identifier.doi | 10.1080/22221751.2020.1719902 | - |
dc.identifier.pmid | 31987001 | - |
dc.identifier.pmcid | PMC7067204 | - |
dc.identifier.scopus | eid_2-s2.0-85078500139 | - |
dc.identifier.hkuros | 312852 | - |
dc.identifier.volume | 9 | - |
dc.identifier.issue | 1 | - |
dc.identifier.spage | 221 | - |
dc.identifier.epage | 236 | - |
dc.identifier.isi | WOS:000510381600001 | - |
dc.publisher.place | United Kingdom | - |
dc.relation.erratum | doi:10.1080/22221751.2020.1737364 | - |
dc.identifier.issnl | 2222-1751 | - |