Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan
Identifieur interne : 000C37 ( Pmc/Corpus ); précédent : 000C36; suivant : 000C38Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan
Auteurs : Jasper Fuk-Woo Chan ; Kin-Hang Kok ; Zheng Zhu ; Hin Chu ; Kelvin Kai-Wang To ; Shuofeng Yuan ; Kwok-Yung YuenSource :
- Emerging Microbes & Infections [ 2222-1751 ] ; 2020.
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
Url:
DOI: 10.1080/22221751.2020.1719902
PubMed: 31987001
PubMed Central: 7067204
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan</title><author><name sortKey="Chan, Jasper Fuk Woo" sort="Chan, Jasper Fuk Woo" uniqKey="Chan J" first="Jasper Fuk-Woo" last="Chan">Jasper Fuk-Woo Chan</name><affiliation><nlm:aff id="AF1"><institution>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong</institution>, Pokfulam, Hong Kong Special Administrative Region,<country>China</country></nlm:aff></affiliation><affiliation><nlm:aff id="AF2"><institution>Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital</institution>, Shenzhen, Guangdong,<country>People's Republic of China</country></nlm:aff></affiliation><affiliation><nlm:aff id="AF3"><institution>Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong</institution>, Pokfulam, Hong Kong Special Administrative Region,<country>China</country></nlm:aff></affiliation><affiliation><nlm:aff id="AF4"><institution>Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong</institution>, Pokfulam, Hong Kong Special Administrative Region,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Kok, Kin Hang" sort="Kok, Kin Hang" uniqKey="Kok K" first="Kin-Hang" last="Kok">Kin-Hang Kok</name><affiliation><nlm:aff id="AF1"><institution>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong</institution>, Pokfulam, Hong Kong Special Administrative Region,<country>China</country></nlm:aff></affiliation><affiliation><nlm:aff id="AF3"><institution>Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong</institution>, Pokfulam, Hong Kong Special Administrative Region,<country>China</country></nlm:aff></affiliation><affiliation><nlm:aff id="AF4"><institution>Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong</institution>, Pokfulam, Hong Kong Special Administrative Region,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Zhu, Zheng" sort="Zhu, Zheng" uniqKey="Zhu Z" first="Zheng" last="Zhu">Zheng Zhu</name><affiliation><nlm:aff id="AF3"><institution>Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong</institution>, Pokfulam, Hong Kong Special Administrative Region,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Chu, Hin" sort="Chu, Hin" uniqKey="Chu H" first="Hin" last="Chu">Hin Chu</name><affiliation><nlm:aff id="AF1"><institution>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong</institution>, Pokfulam, Hong Kong Special Administrative Region,<country>China</country></nlm:aff></affiliation><affiliation><nlm:aff id="AF3"><institution>Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong</institution>, Pokfulam, Hong Kong Special Administrative Region,<country>China</country></nlm:aff></affiliation><affiliation><nlm:aff id="AF4"><institution>Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong</institution>, Pokfulam, Hong Kong Special Administrative Region,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="To, Kelvin Kai Wang" sort="To, Kelvin Kai Wang" uniqKey="To K" first="Kelvin Kai-Wang" last="To">Kelvin Kai-Wang To</name><affiliation><nlm:aff id="AF1"><institution>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong</institution>, Pokfulam, Hong Kong Special Administrative Region,<country>China</country></nlm:aff></affiliation><affiliation><nlm:aff id="AF2"><institution>Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital</institution>, Shenzhen, Guangdong,<country>People's Republic of China</country></nlm:aff></affiliation><affiliation><nlm:aff id="AF3"><institution>Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong</institution>, Pokfulam, Hong Kong Special Administrative Region,<country>China</country></nlm:aff></affiliation><affiliation><nlm:aff id="AF4"><institution>Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong</institution>, Pokfulam, Hong Kong Special Administrative Region,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Yuan, Shuofeng" sort="Yuan, Shuofeng" uniqKey="Yuan S" first="Shuofeng" last="Yuan">Shuofeng Yuan</name><affiliation><nlm:aff id="AF1"><institution>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong</institution>, Pokfulam, Hong Kong Special Administrative Region,<country>China</country></nlm:aff></affiliation><affiliation><nlm:aff id="AF3"><institution>Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong</institution>, Pokfulam, Hong Kong Special Administrative Region,<country>China</country></nlm:aff></affiliation><affiliation><nlm:aff id="AF4"><institution>Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong</institution>, Pokfulam, Hong Kong Special Administrative Region,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Yuen, Kwok Yung" sort="Yuen, Kwok Yung" uniqKey="Yuen K" first="Kwok-Yung" last="Yuen">Kwok-Yung Yuen</name><affiliation><nlm:aff id="AF2"><institution>Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital</institution>, Shenzhen, Guangdong,<country>People's Republic of China</country></nlm:aff></affiliation><affiliation><nlm:aff id="AF3"><institution>Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong</institution>, Pokfulam, Hong Kong Special Administrative Region,<country>China</country></nlm:aff></affiliation><affiliation><nlm:aff id="AF4"><institution>Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong</institution>, Pokfulam, Hong Kong Special Administrative Region,<country>China</country></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">31987001</idno><idno type="pmc">7067204</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7067204</idno><idno type="RBID">PMC:7067204</idno><idno type="doi">10.1080/22221751.2020.1719902</idno><date when="2020">2020</date><idno type="wicri:Area/Pmc/Corpus">000C37</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000C37</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan</title><author><name sortKey="Chan, Jasper Fuk Woo" sort="Chan, Jasper Fuk Woo" uniqKey="Chan J" first="Jasper Fuk-Woo" last="Chan">Jasper Fuk-Woo Chan</name><affiliation><nlm:aff id="AF1"><institution>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong</institution>, Pokfulam, Hong Kong Special Administrative Region,<country>China</country></nlm:aff></affiliation><affiliation><nlm:aff id="AF2"><institution>Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital</institution>, Shenzhen, Guangdong,<country>People's Republic of China</country></nlm:aff></affiliation><affiliation><nlm:aff id="AF3"><institution>Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong</institution>, Pokfulam, Hong Kong Special Administrative Region,<country>China</country></nlm:aff></affiliation><affiliation><nlm:aff id="AF4"><institution>Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong</institution>, Pokfulam, Hong Kong Special Administrative Region,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Kok, Kin Hang" sort="Kok, Kin Hang" uniqKey="Kok K" first="Kin-Hang" last="Kok">Kin-Hang Kok</name><affiliation><nlm:aff id="AF1"><institution>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong</institution>, Pokfulam, Hong Kong Special Administrative Region,<country>China</country></nlm:aff></affiliation><affiliation><nlm:aff id="AF3"><institution>Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong</institution>, Pokfulam, Hong Kong Special Administrative Region,<country>China</country></nlm:aff></affiliation><affiliation><nlm:aff id="AF4"><institution>Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong</institution>, Pokfulam, Hong Kong Special Administrative Region,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Zhu, Zheng" sort="Zhu, Zheng" uniqKey="Zhu Z" first="Zheng" last="Zhu">Zheng Zhu</name><affiliation><nlm:aff id="AF3"><institution>Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong</institution>, Pokfulam, Hong Kong Special Administrative Region,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Chu, Hin" sort="Chu, Hin" uniqKey="Chu H" first="Hin" last="Chu">Hin Chu</name><affiliation><nlm:aff id="AF1"><institution>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong</institution>, Pokfulam, Hong Kong Special Administrative Region,<country>China</country></nlm:aff></affiliation><affiliation><nlm:aff id="AF3"><institution>Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong</institution>, Pokfulam, Hong Kong Special Administrative Region,<country>China</country></nlm:aff></affiliation><affiliation><nlm:aff id="AF4"><institution>Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong</institution>, Pokfulam, Hong Kong Special Administrative Region,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="To, Kelvin Kai Wang" sort="To, Kelvin Kai Wang" uniqKey="To K" first="Kelvin Kai-Wang" last="To">Kelvin Kai-Wang To</name><affiliation><nlm:aff id="AF1"><institution>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong</institution>, Pokfulam, Hong Kong Special Administrative Region,<country>China</country></nlm:aff></affiliation><affiliation><nlm:aff id="AF2"><institution>Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital</institution>, Shenzhen, Guangdong,<country>People's Republic of China</country></nlm:aff></affiliation><affiliation><nlm:aff id="AF3"><institution>Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong</institution>, Pokfulam, Hong Kong Special Administrative Region,<country>China</country></nlm:aff></affiliation><affiliation><nlm:aff id="AF4"><institution>Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong</institution>, Pokfulam, Hong Kong Special Administrative Region,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Yuan, Shuofeng" sort="Yuan, Shuofeng" uniqKey="Yuan S" first="Shuofeng" last="Yuan">Shuofeng Yuan</name><affiliation><nlm:aff id="AF1"><institution>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong</institution>, Pokfulam, Hong Kong Special Administrative Region,<country>China</country></nlm:aff></affiliation><affiliation><nlm:aff id="AF3"><institution>Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong</institution>, Pokfulam, Hong Kong Special Administrative Region,<country>China</country></nlm:aff></affiliation><affiliation><nlm:aff id="AF4"><institution>Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong</institution>, Pokfulam, Hong Kong Special Administrative Region,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Yuen, Kwok Yung" sort="Yuen, Kwok Yung" uniqKey="Yuen K" first="Kwok-Yung" last="Yuen">Kwok-Yung Yuen</name><affiliation><nlm:aff id="AF2"><institution>Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital</institution>, Shenzhen, Guangdong,<country>People's Republic of China</country></nlm:aff></affiliation><affiliation><nlm:aff id="AF3"><institution>Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong</institution>, Pokfulam, Hong Kong Special Administrative Region,<country>China</country></nlm:aff></affiliation><affiliation><nlm:aff id="AF4"><institution>Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong</institution>, Pokfulam, Hong Kong Special Administrative Region,<country>China</country></nlm:aff></affiliation></author></analytic><series><title level="j">Emerging Microbes & Infections</title><idno type="eISSN">2222-1751</idno><imprint><date when="2020">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>ABSTRACT</title><p>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 <italic>betacoronavirus</italic>. 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.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Chan, Jf" uniqKey="Chan J">JF Chan</name></author><author><name sortKey="To, Kk" uniqKey="To K">KK To</name></author><author><name sortKey="Tse, H" uniqKey="Tse H">H Tse</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cheng, Vc" uniqKey="Cheng V">VC Cheng</name></author><author><name sortKey="Lau, Sk" uniqKey="Lau S">SK Lau</name></author><author><name sortKey="Woo, Pc" uniqKey="Woo P">PC Woo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chan, Jf" uniqKey="Chan J">JF Chan</name></author><author><name sortKey="Lau, Sk" uniqKey="Lau S">SK Lau</name></author><author><name sortKey="To, Kk" uniqKey="To K">KK To</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Woo, Pc" uniqKey="Woo P">PC Woo</name></author><author><name sortKey="Lau, Sk" uniqKey="Lau S">SK Lau</name></author><author><name sortKey="Chu, Cm" uniqKey="Chu C">CM Chu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Peiris, Js" uniqKey="Peiris J">JS Peiris</name></author><author><name sortKey="Lai, St" uniqKey="Lai S">ST Lai</name></author><author><name sortKey="Poon, Ll" uniqKey="Poon L">LL Poon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yeung, Ml" uniqKey="Yeung M">ML Yeung</name></author><author><name sortKey="Yao, Y" uniqKey="Yao Y">Y Yao</name></author><author><name sortKey="Jia, L" uniqKey="Jia L">L Jia</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Huang, C" uniqKey="Huang C">C Huang</name></author><author><name sortKey="Wang, Y" uniqKey="Wang Y">Y Wang</name></author><author><name sortKey="Li, X" uniqKey="Li X">X Li</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chan, Jf" uniqKey="Chan J">JF Chan</name></author><author><name sortKey="Yuan, S" uniqKey="Yuan S">S Yuan</name></author><author><name sortKey="Kok, Kh" uniqKey="Kok K">KH Kok</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Saitou, N" uniqKey="Saitou N">N Saitou</name></author><author><name sortKey="Nei, M" uniqKey="Nei M">M. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Emerg Microbes Infect</journal-id><journal-id journal-id-type="iso-abbrev">Emerg Microbes Infect</journal-id><journal-id journal-id-type="publisher-id">TEMI</journal-id><journal-id journal-id-type="publisher-id">temi20</journal-id><journal-title-group><journal-title>Emerging Microbes & Infections</journal-title></journal-title-group><issn pub-type="epub">2222-1751</issn><publisher><publisher-name>Taylor & Francis</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">31987001</article-id><article-id pub-id-type="pmc">7067204</article-id><article-id pub-id-type="publisher-id">1719902</article-id><article-id pub-id-type="doi">10.1080/22221751.2020.1719902</article-id><article-categories><subj-group subj-group-type="heading"><subject>Original Articles</subject></subj-group></article-categories><title-group><article-title>Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan</article-title><alt-title alt-title-type="running-title">EMERGING MICROBES AND INFECTIONS</alt-title><alt-title alt-title-type="running-authors">J. F-W. CHAN ET AL.</alt-title></title-group><contrib-group><contrib contrib-type="author"><contrib-id contrib-id-type="orcid">http://orcid.org/0000-0001-6336-6657</contrib-id><name><surname>Chan</surname><given-names>Jasper Fuk-Woo</given-names></name><xref ref-type="aff" rid="AF1"><sup>a</sup></xref><xref ref-type="aff" rid="AF2"><sup>b</sup></xref><xref ref-type="aff" rid="AF3"><sup>c</sup></xref><xref ref-type="aff" rid="AF4"><sup>d</sup></xref><xref ref-type="author-notes" rid="an1"><sup>*</sup></xref></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid">http://orcid.org/0000-0003-3426-332X</contrib-id><name><surname>Kok</surname><given-names>Kin-Hang</given-names></name><xref ref-type="aff" rid="AF1"><sup>a</sup></xref><xref ref-type="aff" rid="AF3"><sup>c</sup></xref><xref ref-type="aff" rid="AF4"><sup>d</sup></xref><xref ref-type="author-notes" rid="an1"><sup>*</sup></xref><xref ref-type="corresp" rid="cor1"><sup>CONTACT</sup></xref></contrib><contrib contrib-type="author"><name><surname>Zhu</surname><given-names>Zheng</given-names></name><xref ref-type="aff" rid="AF3"><sup>c</sup></xref><xref ref-type="author-notes" rid="an1"><sup>*</sup></xref></contrib><contrib contrib-type="author"><name><surname>Chu</surname><given-names>Hin</given-names></name><xref ref-type="aff" rid="AF1"><sup>a</sup></xref><xref ref-type="aff" rid="AF3"><sup>c</sup></xref><xref ref-type="aff" rid="AF4"><sup>d</sup></xref><xref ref-type="author-notes" rid="an1"><sup>*</sup></xref></contrib><contrib contrib-type="author"><name><surname>To</surname><given-names>Kelvin Kai-Wang</given-names></name><xref ref-type="aff" rid="AF1"><sup>a</sup></xref><xref ref-type="aff" rid="AF2"><sup>b</sup></xref><xref ref-type="aff" rid="AF3"><sup>c</sup></xref><xref ref-type="aff" rid="AF4"><sup>d</sup></xref></contrib><contrib contrib-type="author"><name><surname>Yuan</surname><given-names>Shuofeng</given-names></name><xref ref-type="aff" rid="AF1"><sup>a</sup></xref><xref ref-type="aff" rid="AF3"><sup>c</sup></xref><xref ref-type="aff" rid="AF4"><sup>d</sup></xref></contrib><contrib contrib-type="author"><name><surname>Yuen</surname><given-names>Kwok-Yung</given-names></name><xref ref-type="aff" rid="AF2"><sup>b</sup></xref><xref ref-type="aff" rid="AF3"><sup>c</sup></xref><xref ref-type="aff" rid="AF4"><sup>d</sup></xref><xref ref-type="corresp" rid="cor1"><sup>CONTACT</sup></xref><xref ref-type="corresp" rid="cor2"></xref></contrib><aff id="AF1"><label>a</label><institution>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong</institution>, Pokfulam, Hong Kong Special Administrative Region,<country>China</country></aff><aff id="AF2"><label>b</label><institution>Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital</institution>, Shenzhen, Guangdong,<country>People's Republic of China</country></aff><aff id="AF3"><label>c</label><institution>Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong</institution>, Pokfulam, Hong Kong Special Administrative Region,<country>China</country></aff><aff id="AF4"><label>d</label><institution>Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong</institution>, Pokfulam, Hong Kong Special Administrative Region,<country>China</country></aff></contrib-group><author-notes><corresp id="cor1"><label>CONTACT</label> Kin-Hang Kok <email xlink:href="khkok@hku.hk">khkok@hku.hk</email></corresp><corresp id="cor2">Kwok-Yung Yuen <email xlink:href="kyyuen@hku.hk">kyyuen@hku.hk</email></corresp><fn id="an1"><label>*</label><p>Co-first authors.</p></fn><fn><p>This article was originally published with errors, which have now been corrected in the online version. Please see Correction (<ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.1080/22221751.2020.1737364">http://dx.doi.org/10.1080/22221751.2020.1737364</ext-link>)</p></fn></author-notes><pub-date pub-type="collection"><year>2020</year></pub-date><pub-date pub-type="epub"><day>28</day><month>1</month><year>2020</year></pub-date><volume>9</volume><issue>1</issue><fpage seq="23">221</fpage><lpage>236</lpage><history><date date-type="received"><day>16</day><month>1</month><year>2020</year></date><date date-type="accepted"><day>17</day><month>1</month><year>2020</year></date></history><permissions><copyright-statement>© 2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group, on behalf of Shanghai Shangyixun Cultural Communication Co., Ltd</copyright-statement><copyright-year>2020</copyright-year><copyright-holder>The Author(s)</copyright-holder><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link>), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><self-uri content-type="pdf" xlink:href="TEMI_9_1719902.pdf"></self-uri><abstract><title>ABSTRACT</title><p>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 <italic>betacoronavirus</italic>. 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.</p></abstract><kwd-group kwd-group-type="author"><title>KEYWORDS</title><kwd>Coronavirus</kwd><kwd>Wuhan</kwd><kwd>SARS</kwd><kwd>emerging</kwd><kwd>genome</kwd><kwd>respiratory</kwd><kwd>virus</kwd><kwd>bioinformatics</kwd></kwd-group><funding-group><award-group><funding-source><named-content content-type="funder-name">Respiratory Viral Research Foundation Limited</named-content></funding-source></award-group><award-group><funding-source><named-content content-type="funder-name">Hui Ming, Hui Hoy and Chow Sin Lan Charity Fund Limited</named-content></funding-source></award-group><award-group><funding-source><named-content content-type="funder-name">Chan Yin Chuen Memorial Charitable Foundation</named-content></funding-source></award-group><award-group><funding-source><named-content content-type="funder-name">Marina Man-Wai Lee</named-content></funding-source></award-group><award-group><funding-source><named-content content-type="funder-name">Research Grants Council</named-content></funding-source></award-group><award-group><funding-source><named-content content-type="funder-name">Sanming Project of Medicine in Shenzhen, China</named-content><named-content content-type="funder-identifier">10.13039/501100012151</named-content></funding-source><award-id>SZSM201911014</award-id></award-group><award-group><funding-source><named-content content-type="funder-name">Health Commission of Guangdong Province, China</named-content><named-content content-type="funder-identifier">10.13039/501100004509</named-content></funding-source></award-group><award-group><funding-source><named-content content-type="funder-name">Michael Seak-Kan Tong</named-content></funding-source></award-group><award-group><funding-source><named-content content-type="funder-name">Consultancy Service for Enhancing Laboratory Surveillance of Emerging Infectious Diseases and Research Capability on Antimicrobial Resistance for Department of Health of the Hong Kong Special Administrative Region Government</named-content></funding-source></award-group><award-group><funding-source><named-content content-type="funder-name">Hong Kong Hainan Commercial Association South China Microbiology Research Fund</named-content></funding-source></award-group><funding-statement>This study was partly supported by the donations of Michael Seak-Kan Tong, Respiratory Viral Research Foundation Limited, Hui Ming, Hui Hoy and Chow Sin Lan Charity Fund Limited, Chan Yin Chuen Memorial Charitable Foundation, Marina Man-Wai Lee, and the Hong Kong Hainan Commercial Association South China Microbiology Research Fund; and funding from the Consultancy Service for Enhancing Laboratory Surveillance of Emerging Infectious Diseases and Research Capability on Antimicrobial Resistance for Department of Health of the Hong Kong Special Administrative Region Government; the Theme-Based Research Scheme (T11/707/15) of the Research Grants Council, Hong Kong Special Administrative Region; Sanming Project of Medicine in Shenzhen, China (No. SZSM201911014); and the High Level-Hospital Program, Health Commission of Guangdong Province, China.</funding-statement></funding-group><counts><fig-count count="13"></fig-count><table-count count="3"></table-count><equation-count count="0"></equation-count><ref-count count="27"></ref-count><page-count count="16"></page-count></counts></article-meta></front><body><sec id="S001"><title>Introduction</title><p>Coronaviruses (CoVs) are enveloped, positive-sense, single-stranded RNA viruses that belong to the subfamily <italic>Coronavirinae</italic>, family <italic>Coronavirdiae</italic>, order <italic>Nidovirales</italic>. There are four genera of CoVs, namely, <italic>Alphacoronavirus</italic> (αCoV), <italic>Betacoronavirus</italic> (βCoV), <italic>Deltacoronavirus</italic> (δCoV), and <italic>Gammacoronavirus</italic> (γCoV) [<xref rid="CIT0001" ref-type="bibr">1</xref>]. Evolutionary analyses have shown that bats and rodents are the gene sources of most αCoVs and βCoVs, while avian species are the gene sources of most δCoVs and γCoVs. CoVs have repeatedly crossed species barriers and some have emerged as important human pathogens. The best-known examples include severe acute respiratory syndrome CoV (SARS-CoV) which emerged in China in 2002–2003 to cause a large-scale epidemic with about 8000 infections and 800 deaths, and Middle East respiratory syndrome CoV (MERS-CoV) which has caused a persistent epidemic in the Arabian Peninsula since 2012 [<xref rid="CIT0002" ref-type="bibr">2</xref>,<xref rid="CIT0003" ref-type="bibr">3</xref>]. In both of these epidemics, these viruses have likely originated from bats and then jumped into another amplification mammalian host [the Himalayan palm civet (<italic>Paguma larvata</italic>) for SARS-CoV and the dromedary camel (<italic>Camelus dromedarius</italic>) for MERS-CoV] before crossing species barriers to infect humans.</p><p>Prior to December 2019, 6 CoVs were known to infect human, including 2 αCoV (HCoV-229E and HKU-NL63) and 4 βCoV (HCoV-OC43 [lineage A], HCoV-HKU1 [lineage A], SARS-CoV [lineage B] and MERS-CoV [lineage C]). The βCoV lineage A HCoV-OC43 and HCoV-HKU1 usually cause self-limiting upper respiratory infections in immunocompetent hosts and occasionally lower respiratory tract infections in immunocompromised hosts and elderly [<xref rid="CIT0004" ref-type="bibr">4</xref>]. In contrast, SARS-CoV (lineage B βCoV) and MERS-CoV (lineage C βCoV) may cause severe lower respiratory tract infection with acute respiratory distress syndrome and extrapulmonary manifestations, such as diarrhea, lymphopenia, deranged liver and renal function tests, and multiorgan dysfunction syndrome, among both immunocompetent and immunocompromised hosts with mortality rates of ∼10% and ∼35%, respectively [<xref rid="CIT0005" ref-type="bibr">5</xref>,<xref rid="CIT0006" ref-type="bibr">6</xref>]. On 31 December 2019, the World Health Organization (WHO) was informed of cases of pneumonia of unknown cause in Wuhan City, Hubei Province, China [<xref rid="CIT0007" ref-type="bibr">7</xref>]. Subsequent virological testing showed that a novel CoV was detected in these patients. As of 16 January 2020, 43 patients have been diagnosed to have infection with this novel CoV, including two exported cases of mild pneumonia in Thailand and Japan [<xref rid="CIT0008" ref-type="bibr">8</xref>,<xref rid="CIT0009" ref-type="bibr">9</xref>]. The earliest date of symptom onset was 1 December 2019 [<xref rid="CIT0010" ref-type="bibr">10</xref>]. The symptomatology of these patients included fever, malaise, dry cough, and dyspnea. Among 41 patients admitted to a designated hospital in Wuhan, 13 (32%) required intensive care and 6 (15%) died. All 41 patients had pneumonia with abnormal findings on chest computerized tomography scans [<xref rid="CIT0010" ref-type="bibr">10</xref>].</p><p>We recently reported a familial cluster of 2019-nCoV infection in a Shenzhen family with travel history to Wuhan [<xref rid="CIT0011" ref-type="bibr">11</xref>]. In the present study, we analyzed a 2019-nCoV complete genome from a patient in this familial cluster and compared it with the genomes of related β CoVs to provide insights into the potential source and control strategies.</p></sec><sec id="S002"><title>Materials and methods</title><sec id="S002-S2001"><title>Viral sequences</title><p>The complete genome sequence of 2019-nCoV HKU-SZ-005b was available at GenBank (accession no. MN975262) (<xref rid="T0001" ref-type="table">Table 1</xref>). The representative complete genomes of other related βCoVs strains collected from human or mammals were included for comparative analysis. These included strains collected from human, bats, and Himalayan palm civet between 2003 and 2018, with one 229E coronavirus strain as the outgroup.
<table-wrap id="T0001" orientation="portrait" position="float"><label>Table 1.</label><caption><title>List of coronaviruses used in this study.</title></caption><pmc-comment>OASIS TABLE HERE</pmc-comment><table frame="hsides" rules="groups"><colgroup><col width="1*"></col><col width="1*"></col><col width="1*"></col><col width="1*"></col></colgroup><thead valign="bottom"><tr><th align="left">Accession number</th><th align="center">Name displayed on the tree</th><th align="center">Name of full-length genome</th><th align="center">Year</th></tr></thead><tbody><tr><td align="left">AY274119</td><td align="left">Human SARS-CoV Tor2 2003</td><td align="left">SARS-related coronavirus isolate Tor2</td><td align="char" char=".">2003</td></tr><tr><td align="left">AY278488</td><td align="left">Human SARS-CoV BJ01 2003</td><td align="left">SARS coronavirus BJ01</td><td align="char" char=".">2003</td></tr><tr><td align="left">AY278491</td><td align="left">SARS coronavirus HKU-39849 2003</td><td align="left">SARS coronavirus HKU-39849 2003</td><td align="char" char=".">2003</td></tr><tr><td align="left">AY390556</td><td align="left">Human SARS-CoV GZ02 2003</td><td align="left">SARS coronavirus GZ02</td><td align="char" char=".">2003</td></tr><tr><td align="left">AY391777</td><td align="left">Human CoV OC43 2003</td><td align="left">Human coronavirus OC43</td><td align="char" char=".">2003</td></tr><tr><td align="left">AY515512</td><td align="left">Paguma SARS CoV HC/SZ/61/03 2003</td><td align="left">SARS coronavirus HC/SZ/61/03 (paguma SARS)</td><td align="char" char=".">2018</td></tr><tr><td align="left">EF065513</td><td align="left">Bat CoV HKU9-1 2006</td><td align="left">Bat coronavirus HKU9-1</td><td align="char" char=".">2006</td></tr><tr><td align="left">FJ588686</td><td align="left">Bat SL-CoV Rs672 2006</td><td align="left">Bat SARS CoV Rs672/2006</td><td align="char" char=".">2006</td></tr><tr><td align="left">KC881005</td><td align="left">Bat SL-CoV RsSHC014 2013</td><td align="left">Bat SARS-like coronavirus RsSHC014</td><td align="char" char=".">2013</td></tr><tr><td align="left">KC881006</td><td align="left">Bat SL-CoV Rs3367 2013</td><td align="left">Bat SARS-like coronavirus Rs3367</td><td align="char" char=".">2013</td></tr><tr><td align="left">KY417146</td><td align="left">Bat SL-CoV Rs4231 2016</td><td align="left">Bat SARS-like coronavirus isolate Rs4231</td><td align="char" char=".">2016</td></tr><tr><td align="left">KY417149</td><td align="left">Bat SL-CoV Rs4255 2016</td><td align="left">Bat SARS-like coronavirus isolate Rs4255</td><td align="char" char=".">2016</td></tr><tr><td align="left">MG772933</td><td align="left">Bat SL-CoV ZC45 2018</td><td align="left">Bat SARS-like coronavirus isolate bat-SL-CoVZC45</td><td align="char" char=".">2018</td></tr><tr><td align="left">MG772934</td><td align="left">Bat SL-CoV ZXC21 2018</td><td align="left">Bat SARS-like coronavirus isolate bat-SL-CoVZXC21</td><td align="char" char=".">2018</td></tr><tr><td align="left">MK211377</td><td align="left">Bat CoV YN2018C 2018</td><td align="left">Coronavirus BtRs-BetaCoV/YN2018C</td><td align="char" char=".">2018</td></tr><tr><td align="left">MK211378</td><td align="left">Bat CoV YN2018D 2018</td><td align="left">Coronavirus BtRs-BetaCoV/YN2018D<sup>a</sup></td><td align="char" char=".">2018</td></tr><tr><td align="left">MN975262</td><td align="left">HKU-SZ-005b</td><td align="left">Human 2019-nCoV HKU-SZ-005b</td><td align="char" char=".">2020</td></tr><tr><td align="left">NC002645</td><td align="left">Human CoV 229E 2000</td><td align="left">Human coronavirus 229E</td><td align="char" char=".">2000</td></tr><tr><td align="left">NC006577</td><td align="left">Human CoV HKU1 2004</td><td align="left">Human coronavirus HKU1</td><td align="char" char=".">2004</td></tr><tr><td align="left">NC009019</td><td align="left">Bat CoV HKU4-1 2006</td><td align="left">Bat coronavirus HKU4-1</td><td align="char" char=".">2006</td></tr><tr><td align="left">NC009020</td><td align="left">Bat CoV HKU5-1 2006</td><td align="left">Bat coronavirus HKU5-1</td><td align="char" char=".">2006</td></tr><tr><td align="left">NC014470</td><td align="left">Bat SARS-related CoV BM48-31 2009</td><td align="left">Bat coronavirus BM48-31/BGR/2008</td><td align="char" char=".">2008</td></tr><tr><td align="left">NC019843</td><td align="left">Human MERS-CoV 2012</td><td align="left">Middle East respiratory syndrome coronavirus</td><td align="char" char=".">2012</td></tr></tbody></table><table-wrap-foot><p><sup>a</sup>One nucleotide was added within M gene to maintain the sequence in-frame.</p></table-wrap-foot></table-wrap></p></sec><sec id="S002-S2002"><title>Genome characterization and phylogenetic analysis</title><p>Phylogenetic tree construction by the neighbour joining method was performed using MEGA X software, with bootstrap values being calculated from 1000 trees [<xref rid="CIT0012" ref-type="bibr">12</xref>]. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) was shown next to the branches [<xref rid="CIT0013" ref-type="bibr">13</xref>]. The tree was drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Poisson correction method and were in the units of the number of amino acid substitutions per site [<xref rid="CIT0014" ref-type="bibr">14</xref>]. All ambiguous positions were removed for each sequence pair (pairwise deletion option). Evolutionary analyses were conducted in MEGA X [<xref rid="CIT0015" ref-type="bibr">15</xref>]. Multiple alignment was performed using CLUSTAL 2.1 and further visualized using BOXSHADE 3.21. Structural analysis of orf8 was performed using PSI-blast-based secondary structure PREDiction (PSIPRED) [<xref rid="CIT0016" ref-type="bibr">16</xref>]. For the prediction of protein secondary structure including beta sheet, alpha helix, and coil, initial amino acid sequences were input and analysed using neural networking and its own algorithm. Predicted structures were visualized and highlighted on the BOXSHADE alignment. Prediction of transmembrane domains was performed using the TMHMM 2.0 server (<ext-link ext-link-type="uri" xlink:href="http://www.cbs.dtu.dk/services/TMHMM/">http://www.cbs.dtu.dk/services/TMHMM/</ext-link>). Secondary structure prediction in the 5′-untranslated region (UTR) and 3′-UTR was performed using the RNAfold WebServer (<ext-link ext-link-type="uri" xlink:href="http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi">http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi</ext-link>) with minimum free energy (MFE) and partition function in Fold algorithms and basic options. The human SARS-CoV 5′- and 3′- UTR were used as references to adjust the prediction results.</p></sec></sec><sec id="S003"><title>Results and discussion</title><sec id="S003-S2001"><title>Genome organization</title><p>The single-stranded RNA genome of the 2019-nCoV was 29891 nucleotides in size, encoding 9860 amino acids. The G + C content was 38%. Similar to other βCoVs, the 2019-nCoV genome contains two flanking untranslated regions (UTRs) and a single long open reading frame encoding a polyprotein. The 2019-nCoV genome is arranged in the order of 5′-replicase (orf1/ab)-structural proteins [Spike (S)-Envelope (E)-Membrane (M)-Nucleocapsid (N)]−3′ and lacks the hemagglutinin-esterase gene which is characteristically found in lineage A β-CoVs (<xref rid="F0001" ref-type="fig">Figure 1</xref>).
<fig id="F0001" orientation="portrait" position="float"><label>Figure 1.</label><caption><p>Betacoronavirus genome organization. The betacoronavirus genome comprises of the 5'-untranslated region (5'-UTR), open reading frame (orf) 1a/b (yellow box) encoding non-structural proteins (nsp) for replication, structural proteins including spike (blue box), envelop (orange box), membrane (red box), and nucleocapsid (cyan box) proteins, accessory proteins (purple boxes) such as orf 3, 6, 7a, 7b, 8 and 9b in the 2019-nCoV (HKU-SZ-005b) genome, and the 3'-untranslated region (3'-UTR). Examples of lineages A to D betacoronaviruses include human coronavirus (HCoV) HKU1 (lineage A), 2019-nCoV (HKU-SZ-005b) and SARS-CoV (lineage B), MERS-CoV and <italic>Tylonycteris</italic> bat CoV HKU4 (lineage C), and <italic>Rousettus</italic> bat CoV HKU9 (lineage D). The length of nsps and orfs are not drawn in scale.</p></caption><graphic xlink:href="TEMI_A_1719902_F0001_OC"></graphic></fig></p><p>There are 12 putative, functional open reading frames (orfs) expressed from a nested set of 9 subgenomic mRNAs carrying a conserved leader sequence in the genome, 9 transcription-regulatory sequences, and 2 terminal untranslated regions. The 5′- and 3′-UTRs are 265 and 358 nucleotides long, respectively. The 5′- and 3 ′-UTR sequences of 2019-nCoV are similar to those of other βCoVs with nucleotide identities of ⩾83.6%. The large replicase polyproteins pp1a and pp1ab encoded by the partially overlapping 5′-terminal orf1a/b within the 5′ two-thirds of the genome is proteolytic cleaved into 16 putative non-structural proteins (nsps). These putative nsps included two viral cysteine proteases, namely, nsp3 (papain-like protease) and nsp5 (chymotrypsin-like, 3C-like, or main protease), nsp12 (RNA-dependent RNA polymerase [RdRp]), nsp13 (helicase), and other nsps which are likely involved in the transcription and replication of the virus (<xref rid="T0002" ref-type="table">Table 2</xref>). There are no remarkable differences between the orfs and nsps of 2019-nCoV with those of SARS-CoV (<xref rid="T0003" ref-type="table">Table 3</xref>). The major distinction between SARSr-CoV and SARS-CoV is in orf3b, Spike and orf8 but especially variable in Spike S1 and orf8 which were previously shown to be recombination hot spots.
<table-wrap id="T0002" orientation="portrait" position="float"><label>Table 2.</label><caption><title>Putative functions and proteolytic cleavage sites of 16 nonstructural proteins in orf1a/b as predicted by bioinformatics.</title></caption><pmc-comment>OASIS TABLE HERE</pmc-comment><table frame="hsides" rules="groups"><colgroup><col width="1*"></col><col width="1*"></col><col width="1*"></col><col width="1*"></col></colgroup><thead valign="bottom"><tr><th align="left">NSP</th><th align="center">Putative function/domain</th><th align="center">Amino acid position</th><th align="center">Putative cleave site</th></tr></thead><tbody><tr><td align="left">nsp1</td><td align="left">suppress antiviral host response</td><td align="left">M1 – G180</td><td align="left">(LNGG'AYTR)</td></tr><tr><td align="left">nsp2</td><td align="left">unknown</td><td align="left">A181 – G818</td><td align="left">(LKGG'APTK)</td></tr><tr><td align="left">nsp3</td><td align="left">putative PL-pro domain</td><td align="left">A819 – G2763</td><td align="left">(LKGG'KIVN)</td></tr><tr><td align="left">nsp4</td><td align="left">complex with nsp3 and 6: DMV formation</td><td align="left">K2764 – Q3263</td><td align="left">(AVLQ'SGFR)</td></tr><tr><td align="left">nsp5</td><td align="left">3CL-pro domain</td><td align="left">S3264 – Q3569</td><td align="left">(VTFQ'SAVK)</td></tr><tr><td align="left">nsp6</td><td align="left">complex with nsp3 and 4: DMV formation</td><td align="left">S3570 – Q3859</td><td align="left">(ATVQ'SKMS)</td></tr><tr><td align="left">nsp7</td><td align="left">complex with nsp8: primase</td><td align="left">S3860 – Q3942</td><td align="left">(ATLQ'AIAS)</td></tr><tr><td align="left">nsp8</td><td align="left">complex with nsp7: primase</td><td align="left">A3943 – Q4140</td><td align="left">(VKLQ'NNEL)</td></tr><tr><td align="left">nsp9</td><td align="left">RNA/DNA binding activity</td><td align="left">N4141 – Q4253</td><td align="left">(VRLQ'AGNA)</td></tr><tr><td align="left">nsp10</td><td align="left">complex with nsp14: replication fidelity</td><td align="left">A4254 – Q4392</td><td align="left">(PMLQ'SADA)</td></tr><tr><td align="left">nsp11</td><td align="left">short peptide at the end of orf1a</td><td align="left">S4393 – V4405</td><td align="left">(end of orf1a)</td></tr><tr><td align="left">nsp12</td><td align="left">RNA-dependent RNA polymerase</td><td align="left">S4393 – Q5324</td><td align="left">(TVLQ'AVGA)</td></tr><tr><td align="left">nsp13</td><td align="left">helicase</td><td align="left">A5325 – Q5925</td><td align="left">(ATLQ'AENV)</td></tr><tr><td align="left">nsp14</td><td align="left">ExoN: 3′–5′ exonuclease</td><td align="left">A5926 – Q6452</td><td align="left">(TRLQ'SLEN)</td></tr><tr><td align="left">nsp15</td><td align="left">XendoU: poly(U)-specific endoribonuclease</td><td align="left">S6453 – Q6798</td><td align="left">(PKLQ'SSQA)</td></tr><tr><td align="left">nsp16</td><td align="left">2'-O-MT: 2'-O-ribose methyltransferase</td><td align="left">S6799 – N7096</td><td align="left">(end of orf1b)</td></tr></tbody></table></table-wrap><table-wrap id="T0003" orientation="portrait" position="float"><label>Table 3.</label><caption><title>Amino acid identity between the 2019 novel coronavirus and bat SARS-like coronavirus or human SARS-CoV.</title></caption><pmc-comment>OASIS TABLE HERE</pmc-comment><table frame="hsides" rules="groups"><colgroup><col width="1*"></col><col width="1*"></col><col width="1*"></col></colgroup><thead valign="bottom"><tr><th align="left">Amino acid identity (%)</th><th align="center">2019-nCoV</th><th align="center">2019-nCoV</th></tr><tr><th align="left"> </th><th align="center">vs. bat-SL-CoVZXC21</th><th align="center">vs. SARS-CoV</th></tr></thead><tbody><tr><td align="left">NSP1</td><td align="char" char=".">96</td><td align="char" char=".">84</td></tr><tr><td align="left">NSP2</td><td align="char" char=".">96</td><td align="char" char=".">68</td></tr><tr><td align="left">NSP3</td><td align="char" char=".">93</td><td align="char" char=".">76</td></tr><tr><td align="left">NSP4</td><td align="char" char=".">96</td><td align="char" char=".">80</td></tr><tr><td align="left">NSP5</td><td align="char" char=".">99</td><td align="char" char=".">96</td></tr><tr><td align="left">NSP6</td><td align="char" char=".">98</td><td align="char" char=".">88</td></tr><tr><td align="left">NSP7</td><td align="char" char=".">99</td><td align="char" char=".">99</td></tr><tr><td align="left">NSP8</td><td align="char" char=".">96</td><td align="char" char=".">97</td></tr><tr><td align="left">NSP9</td><td align="char" char=".">96</td><td align="char" char=".">97</td></tr><tr><td align="left">NSP10</td><td align="char" char=".">98</td><td align="char" char=".">97</td></tr><tr><td align="left">NSP11</td><td align="char" char=".">85</td><td align="char" char=".">85</td></tr><tr><td align="left">NSP12</td><td align="char" char=".">96</td><td align="char" char=".">96</td></tr><tr><td align="left">NSP13</td><td align="char" char=".">99</td><td align="char" char=".">100</td></tr><tr><td align="left">NSP14</td><td align="char" char=".">95</td><td align="char" char=".">95</td></tr><tr><td align="left">NSP15</td><td align="char" char=".">88</td><td align="char" char=".">89</td></tr><tr><td align="left">NSP16</td><td align="char" char=".">98</td><td align="char" char=".">93</td></tr><tr><td align="left">Spike</td><td align="char" char=".">80</td><td align="char" char=".">76</td></tr><tr><td align="left">Orf3a</td><td align="char" char=".">92</td><td align="char" char=".">72</td></tr><tr><td align="left">Orf3b</td><td align="char" char=".">32</td><td align="char" char=".">32</td></tr><tr><td align="left">Envelope</td><td align="char" char=".">100</td><td align="char" char=".">95</td></tr><tr><td align="left">Membrane</td><td align="char" char=".">99</td><td align="char" char=".">91</td></tr><tr><td align="left">Orf6</td><td align="char" char=".">94</td><td align="char" char=".">69</td></tr><tr><td align="left">Orf7a</td><td align="char" char=".">89</td><td align="char" char=".">85</td></tr><tr><td align="left">Orf7b</td><td align="char" char=".">93</td><td align="char" char=".">81</td></tr><tr><td align="left">Orf8/Orf8b</td><td align="char" char=".">94</td><td align="char" char=".">40</td></tr><tr><td align="left">Nucleoprotein</td><td align="char" char=".">94</td><td align="char" char=".">94</td></tr><tr><td align="left">Orf9b</td><td align="char" char=".">73</td><td align="char" char=".">73</td></tr></tbody></table></table-wrap></p><sec id="S003-S2001-S3001"><title>Spike</title><p>Spike glycoprotein comprised of S1 and S2 subunits. The S1 subunit contains a signal peptide, followed by an N-terminal domain (NTD) and receptor-binding domain (RBD), while the S2 subunit contains conserved fusion peptide (FP), heptad repeat (HR) 1 and 2, transmembrane domain (TM), and cytoplasmic domain (CP). We found that the S2 subunit of 2019-nCoV is highly conserved and shares 99% identity with those of the two bat SARS-like CoVs (SL-CoV ZXC21 and ZC45) and human SARS-CoV (<xref rid="F0002" ref-type="fig">Figure 2</xref>). Thus the broad spectrum antiviral peptides against S2 would be an important preventive and treatment modality for testing in animal models before clinical trials [<xref rid="CIT0018" ref-type="bibr">18</xref>]. Though the S1 subunit of 2019-nCoV shares around 70% identity to that of the two bat SARS-like CoVs and human SARS-CoV (<xref rid="F0003" ref-type="fig">Figure 3</xref>(A)), the core domain of RBD (excluding the external subdomain) are highly conserved (<xref rid="F0003" ref-type="fig">Figure 3</xref>(B)). Most of the amino acid differences of RBD are located in the external subdomain, which is responsible for the direct interaction with the host receptor. Further investigation of this soluble variable external subdomain region will reveal its receptor usage, interspecies transmission and pathogenesis. Unlike 2019-nCoV and human SARS-CoV, most known bat SARSr-CoVs have two stretches of deletions in the spike receptor binding domain (RBD) when compared with that of human SARS-CoV. But some Yunnan strains such as the WIV1 had no such deletions and can use human ACE2 as a cellular entry receptor. It is interesting to note that the two bat SARS-related coronavirus ZXC21 and ZC45, being closest to 2019-nCoV, can infect suckling rats and cause inflammation in the brain tissue, and pathological changes in lung & intestine. However, these two viruses could not be isolated in Vero E6 cells and were not investigated further. The two retained deletion sites in the Spike genes of ZXC21 and ZC45 may lessen their likelihood of jumping species barriers imposed by receptor specificity.
<fig id="F0002" orientation="portrait" position="float"><label>Figure 2.</label><caption><p>Comparison of protein sequences of Spike stalk S2 subunit. Multiple alignment of Spike S2 amino acid sequences of 2019-nCoV HKU-SZ-005b (accession number MN975262), bat SARS-like coronavirus isolates bat-SL-CoVZXC21 and bat-SL-CoVZXC45 (accession number MG772934.1 and MG772933.1, respectively) and human SARS coronavirus (accession number NC004718) was performed and displayed using CLUSTAL 2.1 and BOXSHADE 3.21 respectively. The black boxes represent the identity while the grey boxes represent the similarity of the four amino acid sequences.</p></caption><graphic xlink:href="TEMI_A_1719902_F0002_OB"></graphic></fig><fig-group id="F0003" orientation="portrait" position="float"><label>Figure 3.</label><caption><p>Comparison of protein sequences of A. Spike globular head S1, and B. S1 receptor-binding domain (RBD) subunit. Multiple alignment of Spike S1 amino acid sequences of 2019-nCoV HKU-SZ-005b (accession number MN975262), bat SARS-like coronavirus isolates bat-SL-CoVZXC21, bat-SL-CoVZXC45, bat-SL-CoV-YNLF_31C, bat-SL-CoV-YNLF_34C and bat SL-CoV HKU3-1 (accession number MG772934.1 and MG772933.1, KP886808, KP886809 and DQ022305, respectively), human SARS coronavirus GZ02 and Tor2 (accession number AY390556 and AY274119, respectively) and Paguma SARS-CoV (accession number AY515512) was performed and displayed using CLUSTAL 2.1 and BOXSHADE 3.21, respectively. The black background represents the identity while the grey background represents the similarity of the amino acid sequences. Orange box indicates the region of signal peptide, while green and blue boxes indicate the core domain and receptor binding domain respectively. Sequences of RBD, highlighted in (A) were used for comparison. External subdomain variable region of 2019-nCoV HKU-SZ-005b was predicted by comparison of amino acid similarity and published structural analysis [<xref rid="CIT0017" ref-type="bibr">17</xref>]. Purple box indicates the external subdomain region.</p></caption><fig id="F0003a" orientation="portrait" position="anchor"><graphic xlink:href="TEMI_A_1719902_F0003a_OC"></graphic></fig><fig id="F0003b" orientation="portrait" position="anchor"><graphic xlink:href="TEMI_A_1719902_F0003b_OC"></graphic></fig></fig-group></p></sec><sec id="S003-S2001-S3002"><title>Orf3b</title><p>A novel short putative protein with 4 helices and no homology to existing SARS-CoV or SARS-r-CoV protein was found within Orf3b (<xref rid="F0004" ref-type="fig">Figure 4</xref>). It is notable that SARS-CoV deletion mutants lacking orf3b replicate to levels similar to those of wild-type virus in several cell types [<xref rid="CIT0019" ref-type="bibr">19</xref>], suggesting that orf3b is dispensable for viral replication in vitro. But orf3b may have a role in viral pathogenicity as Vero E6 but not 293T cells transfected with a construct expressing Orf3b underwent necrosis as early as 6 h after transfection and underwent simultaneous necrosis and apoptosis at later time points [<xref rid="CIT0020" ref-type="bibr">20</xref>]. Orf3b was also shown to inhibit expression of IFN-β at synthesis and signalling [<xref rid="CIT0021" ref-type="bibr">21</xref>]. Subsequently, orf3b homologues identified from three bat SARS-related-CoV strains were C-terminally truncated and lacked the C-terminal nucleus localization signal of SARS-CoV [<xref rid="CIT0022" ref-type="bibr">22</xref>]. IFN antagonist activity analysis demonstrated that one SARS-related-CoV orf3b still possessed IFN antagonist and IRF3-modulating activities. These results indicated that different orf3b proteins display different IFN antagonist activities and this function is independent of the protein's nuclear localization, suggesting a potential link between bat SARS-related-CoV orf3b function and pathogenesis. The importance of this new protein in 2019-nCoV will require further validation and study.
<fig id="F0004" orientation="portrait" position="float"><label>Figure 4.</label><caption><p>Analysis of orf3b. A. Multiple alignment of orf3b protein sequence between 2019-nCoV (HKU-SZ-005b), SARS-CoV and SARS-related CoV. B. A novel putative short protein found in orf3b.</p></caption><graphic xlink:href="TEMI_A_1719902_F0004_OC"></graphic></fig></p></sec><sec id="S003-S2001-S3003"><title>Orf8</title><p>orf8 is an accessory protein found in the <italic>Betacoronavirus</italic> lineage B coronaviruses. Human SARS-CoVs isolated from early-phase patients, all civet SARS-CoVs, and other bat SARS-related CoVs contain full-length orf8 [<xref rid="CIT0023" ref-type="bibr">23</xref>]. However, a 29-nucleotide deletion, which causes the split of full length of orf8 into putative orf8a and orf8b, has been found in all SARS-CoV isolated from mid- and late- phase human patients [<xref rid="CIT0024" ref-type="bibr">24</xref>]. In addition, we have previously identified two bat SARS-related-CoV (Bat-CoV YNLF_31C and YNLF_34C) and proposed that the original SARS-CoV full-length orf8 is acquired from these two bat SARS-related-CoV [<xref rid="CIT0025" ref-type="bibr">25</xref>]. Since the SARS-CoV is the closest human pathogenic virus to the 2019-nCoV, we performed phylogenetic analysis and multiple alignments to investigate the orf8 amino acid sequences. The orf8 protein sequences used in the analysis derived from early phase SARS-CoV that includes full-length orf8 (human SARS-CoV GZ02), the mid- and late-phase SARS-CoV that includes the split orf8b (human SARS-CoV Tor2), civet SARS-CoV (paguma SARS-CoV), two bat SARS-related-CoV containing full-length orf8 (bat-CoV YNLF_31C and YNLF_34C), 2019-nCoV, the other two closest bat SARS-related-CoV to 2019-nCoV SL-CoV ZXC21 and ZC45), and bat SARS-related-CoV HKU3-1 (<xref rid="F0005" ref-type="fig">Figure 5</xref>(A)). As expected, orf8 derived from 2019-nCoV belongs to the group that includes the closest genome sequences of bat SARS-related-CoV ZXC21 and ZC45. Interestingly, the new 2019-nCoV orf8 is distant from the conserved orf8 or orf8b derived from human SARS-CoV or its related viruses derived from civet (paguma SARS-CoV) and bat (bat-CoV YNLF_31C and YNLF_34C). This new orf8 of 2019-nCoV does not contain known functional domain or motif. An aggregation motif VLVVL (amino acid 75–79) has been found in SARS-CoV orf8b (<xref rid="F0005" ref-type="fig">Figure 5</xref>(B)) which was shown to trigger intracellular stress pathways and activates NLRP3 inflammasomes [<xref rid="CIT0026" ref-type="bibr">26</xref>], but this is absent in this novel orf8 of 2019-nCoV. Based on a secondary structure prediction, this novel orf8 has a high possibility to form a protein with an alpha-helix, following with a beta-sheet(s) containing six strands (<xref rid="F0005" ref-type="fig">Figure 5</xref>(C)).
<fig id="F0005" orientation="portrait" position="float"><label>Figure 5.</label><caption><p>Analysis of orf8 to show novel putative protein. (A) Phylogenetic analysis of orf8 amino acid sequences of 2019-nCoV HKU-SZ-005b (accession number MN975262), bat SARS-like coronavirus isolates bat-SL-CoVZXC21 and bat-SL-CoVZXC45 (accession number MG772934.1 and MG772933.1, respectively) and human SARS coronavirus (accession number AY274119) was performed using the neighbour-joining method with bootstrap 1000. The evolutionary distances were calculated using the JTT matrix-based method. (B) Multiple alignment was performed and displayed using CLUSTAL 2.1 and BOXSHADE 3.21, respectively. The black background represents the identity while the grey background represents the similarity of the amino acid sequences. (C) Structural analysis of Orf8 was performed using PSI-blast-based secondary structure PREDiction (PSIPRED). Predicted helix structure (h) and strand (s) were boxed with red and yellow respectively.</p></caption><graphic xlink:href="TEMI_A_1719902_F0005_OC"></graphic></fig></p></sec><sec id="S003-S2001-S3004"><title>Phylogenetic relationship among 2019-nCoV and other βCoVs</title><p>The genome of 2019-nCoV has overall 89% nucleotide identity with bat SARS-related-CoV SL-CoVZXC21 (MG772934.1), and 82% with human SARS-CoV BJ01 2003 (AY278488) and human SARS-CoV Tor2 (AY274119). The phylogenetic trees constructed using the amino acid sequences of orf1a/b and the 4 structural genes (S, E, M, and N) were shown (<xref rid="F0006" ref-type="fig">Figure 6</xref>(A–E)). For all these 5 genes, the 2019-nCoV was clustered with lineage B βCoVs. It was most closely related to the bat SARS-related CoVs ZXC21 and ZC45 found in Chinese horseshoe bats (<italic>Rhinolopus sinicus</italic>) collected from Zhoushan city, Zhejiang province, China between 2015 and 2017. Thus this novel coronavirus should belong to the genus <italic>Betacoronavirus</italic>, subgenus <italic>Sabecovirus</italic> (previously lineage 2b of Group 2 coronavirus). SARS-related coronaviruses have been found continuously especially in horseshoe bat species in the last 13 years. Between 2003 and 2018, 339 complete SARS-related coronavirus genomes have been sequenced, including 274 human SARS-CoV, 18 civet SARS coronavirus, and 47 bat SARS-related coronaviruses mainly from <italic>Rhinolophus</italic> bat species. Together, they formed a distinct subclade among other lineage B βCoVs. These results suggested that the 2019-nCoV might have also originated from bats. But we cannot ascertain whether another intermediate or amplification animal host infected by 2019-nCoV could be found in the epidemiological market, just as in the case of Paguma civets for SARS-CoV.
<fig-group id="F0006" orientation="portrait" position="float"><label>Figure 6.</label><caption><p>Phylogenetic tree construction by the neighbour joining method was performed using MEGA X software, with bootstrap values being calculated from 1000 trees using amino acid sequences of (A) orf1ab polypeptide; (B) Spike glycoprotein; (C) Envelope protein; (D) Membrane protein; (E) Nucleoprotein.</p></caption><fig id="F0006a" orientation="portrait" position="anchor"><graphic xlink:href="TEMI_A_1719902_F0006a_OC"></graphic></fig><fig id="F0006b" orientation="portrait" position="anchor"><graphic xlink:href="TEMI_A_1719902_F0006b_OC"></graphic></fig><fig id="F0006c" orientation="portrait" position="anchor"><graphic xlink:href="TEMI_A_1719902_F0006c_OC"></graphic></fig><fig id="F0006d" orientation="portrait" position="anchor"><graphic xlink:href="TEMI_A_1719902_F0006d_OC"></graphic></fig><fig id="F0006e" orientation="portrait" position="anchor"><graphic xlink:href="TEMI_A_1719902_F0006e_OC"></graphic></fig></fig-group></p></sec><sec id="S003-S2001-S3005"><title>RNA secondary structures</title><p>As shown in <xref rid="F0007" ref-type="fig">Figure 7</xref>(A–C), the SARS-CoV 5′-UTR contains SL1, SL2, SL3, SL4, S5, SL5A, SL5B, SL5C, SL6, SL7, and SL8. The SL3 contains trans–cis motif [<xref rid="CIT0027" ref-type="bibr">27</xref>]. The SL1, SL2, SL3, SL4, S5, SL5A, SL5B, and SL5C structures were similar among the 2019-nCoV, human SARS-CoV and the bat SARS-related ZC45. In the 2019-nCoV, part of the S5 found was inside the orf1a/b (marked in red), which was similar to SARS-CoV. In bat SARS-related CoV ZC45, the S5 was not found inside orf1a/b. The 2019-nCoV had the same SL6, SL7, and SL8 as SARS-CoV, and an additional stem loop. Bat SARS-related CoV ZC45 did not have the SARS-COV SL6-like stem loop. Instead, it possessed two other stem loops in this region. All three strains had similar SL7 and SL8. The bat SARS-like CoV ZC45 also had an additional stem loop between SL7 and SL8. Overall, the 5′-UTR of 2019-nCoV was more similar to that of SARS-CoV than the bat SARS-related CoV ZC 45. The biological relevance and effects of virulence of the 5′-UTR structures should be investigated further. The 2019-nCoV had various 3′-UTR structures, including BSL, S1, S2, S3, S4, L1, L2, L3, and HVR (<xref rid="F0007" ref-type="fig">Figure 7</xref>(D–F)). The 3′-UTR was conserved among 2019-nCoV, human SARS-CoV and SARS-related CoVs [<xref rid="CIT0027" ref-type="bibr">27</xref>].
<fig-group id="F0007" orientation="portrait" position="float"><label>Figure 7.</label><caption><p>Secondary structure prediction and comparison in the 5′-untranslated region (UTR) and 3′-UTR using the RNAfold WebServer (with minimum free energy and partition function in Fold algorithms and basic options. The SARS 5′- and 3′- UTR was used as a reference to adjust the prediction results.(A) SARS-CoV 5'-UTR; (B) 2019-nCoV (HKU-SZ-005b) 5'-UTR; (C) ZC45 5'-UTR; (D) SARS-CoV 3'-UTR; (E) 2019-nCoV (HKU-SZ-005b) 3'-UTR; (F) ZC45 3'-UTR.</p></caption><fig id="F0007a" orientation="portrait" position="anchor"><graphic xlink:href="TEMI_A_1719902_F0007a_OC"></graphic></fig><fig id="F0007b" orientation="portrait" position="anchor"><graphic xlink:href="TEMI_A_1719902_F0007b_OC"></graphic></fig></fig-group></p><p>In summary, 2019-nCoV is a novel lineage B <italic>Betacoronavirus</italic> closely related to bat SARS-related coronaviruses. It also has unique genomic features which deserves further investigation to ascertain their roles in viral replication cycle and pathogenesis. More animal sampling to determine its natural animal reservoir and intermediate animal host in the market is important. 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