Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan.
Identifieur interne : 000724 ( Main/Exploration ); précédent : 000723; suivant : 000725Genomic 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 :
- Emerging microbes & infections [ 2222-1751 ] ; 2020.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Protéines virales.
- virologie : Infections à coronavirus, Pneumopathie virale.
- Analyse de séquence de protéine, Chine, Génome viral, Humains, Phylogénie, Protéines virales, Séquence d'acides aminés, Voyage.
- Wicri :
- geographic : République populaire de Chine.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Viral Proteins.
- chemical , genetics : Viral Proteins.
- geographic : China.
- genetics : Betacoronavirus.
- isolation & purification : Betacoronavirus.
- virology : Coronavirus Infections, Pneumonia, Viral.
- Amino Acid Sequence, Genome, Viral, Humans, Phylogeny, Sequence Analysis, Protein, Travel.
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.
DOI: 10.1080/22221751.2020.1719902
PubMed: 31987001
Affiliations:
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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 wicri:level="1"><nlm:affiliation>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region</wicri:regionArea><wicri:noRegion>Hong Kong Special Administrative Region</wicri:noRegion></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 wicri:level="1"><nlm:affiliation>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong 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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></keywords><keywords scheme="Wicri" type="geographic" xml:lang="fr"><term>République populaire de Chine</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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 <i>betacoronavirus</i>. 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.</div></front></TEI><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><country name="République populaire de Chine"><noRegion><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></noRegion><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="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="Yuan, Shuofeng" sort="Yuan, Shuofeng" uniqKey="Yuan S" first="Shuofeng" last="Yuan">Shuofeng Yuan</name><name sortKey="Yuen, Kwok Yung" sort="Yuen, Kwok Yung" uniqKey="Yuen K" first="Kwok-Yung" last="Yuen">Kwok-Yung Yuen</name><name sortKey="Zhu, Zheng" sort="Zhu, Zheng" uniqKey="Zhu Z" first="Zheng" last="Zhu">Zheng Zhu</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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