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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 : 000191 ( Main/Exploration ); précédent : 000190; suivant : 000192

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

Descripteurs français

English descriptors

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


Affiliations:


Links toward previous steps (curation, corpus...)


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<term>Amino Acid Sequence</term>
<term>Betacoronavirus (genetics)</term>
<term>Betacoronavirus (isolation & purification)</term>
<term>China</term>
<term>Coronavirus Infections (virology)</term>
<term>Genome, Viral</term>
<term>Humans</term>
<term>Phylogeny</term>
<term>Pneumonia, Viral (virology)</term>
<term>Sequence Analysis, Protein</term>
<term>Travel</term>
<term>Viral Proteins (chemistry)</term>
<term>Viral Proteins (genetics)</term>
</keywords>
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<term>Analyse de séquence de protéine</term>
<term>Chine</term>
<term>Génome viral</term>
<term>Humains</term>
<term>Infections à coronavirus (virologie)</term>
<term>Phylogénie</term>
<term>Pneumopathie virale (virologie)</term>
<term>Protéines virales ()</term>
<term>Protéines virales (génétique)</term>
<term>Séquence d'acides aminés</term>
<term>Voyage</term>
</keywords>
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<term>Viral Proteins</term>
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<term>Viral Proteins</term>
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<term>China</term>
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<keywords scheme="MESH" qualifier="genetics" xml:lang="en">
<term>Betacoronavirus</term>
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<term>Protéines virales</term>
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<keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en">
<term>Betacoronavirus</term>
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<keywords scheme="MESH" qualifier="virologie" xml:lang="fr">
<term>Infections à coronavirus</term>
<term>Pneumopathie virale</term>
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<keywords scheme="MESH" qualifier="virology" xml:lang="en">
<term>Coronavirus Infections</term>
<term>Pneumonia, Viral</term>
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<keywords scheme="MESH" xml:lang="en">
<term>Amino Acid Sequence</term>
<term>Genome, Viral</term>
<term>Humans</term>
<term>Phylogeny</term>
<term>Sequence Analysis, Protein</term>
<term>Travel</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr">
<term>Analyse de séquence de protéine</term>
<term>Chine</term>
<term>Génome viral</term>
<term>Humains</term>
<term>Phylogénie</term>
<term>Protéines virales</term>
<term>Séquence d'acides aminés</term>
<term>Voyage</term>
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<keywords scheme="Wicri" type="geographic" xml:lang="fr">
<term>République populaire de Chine</term>
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<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>
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<name sortKey="Chu, Hin" sort="Chu, Hin" uniqKey="Chu H" first="Hin" last="Chu">Hin Chu</name>
<name sortKey="Kok, Kin Hang" sort="Kok, Kin Hang" uniqKey="Kok K" first="Kin-Hang" last="Kok">Kin-Hang Kok</name>
<name sortKey="Kok, Kin Hang" sort="Kok, Kin Hang" uniqKey="Kok K" first="Kin-Hang" last="Kok">Kin-Hang Kok</name>
<name sortKey="Kok, Kin Hang" sort="Kok, Kin Hang" uniqKey="Kok K" first="Kin-Hang" last="Kok">Kin-Hang Kok</name>
<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>
<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>
<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>
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<name sortKey="Yuan, Shuofeng" sort="Yuan, Shuofeng" uniqKey="Yuan S" first="Shuofeng" last="Yuan">Shuofeng Yuan</name>
<name sortKey="Yuan, Shuofeng" sort="Yuan, Shuofeng" uniqKey="Yuan S" first="Shuofeng" last="Yuan">Shuofeng Yuan</name>
<name sortKey="Yuan, Shuofeng" sort="Yuan, Shuofeng" uniqKey="Yuan S" first="Shuofeng" last="Yuan">Shuofeng Yuan</name>
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