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

Identifieur interne : 000C37 ( Pmc/Curation ); précédent : 000C36; suivant : 000C38

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

Auteurs : Jasper Fuk-Woo Chan [République populaire de Chine] ; Kin-Hang Kok [République populaire de Chine] ; Zheng Zhu [République populaire de Chine] ; Hin Chu [République populaire de Chine] ; Kelvin Kai-Wang To [République populaire de Chine] ; Shuofeng Yuan [République populaire de Chine] ; Kwok-Yung Yuen [République populaire de Chine]

Source :

RBID : PMC:7067204

Abstract

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.


Url:
DOI: 10.1080/22221751.2020.1719902
PubMed: 31987001
PubMed Central: 7067204

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PMC:7067204

Le document en format XML

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<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>
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<pmc article-type="research-article">
<pmc-dir>properties open_access</pmc-dir>
<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>
</pmc>
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