Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan.
Identifieur interne : 000273 ( PubMed/Curation ); précédent : 000272; suivant : 000274Genomic 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
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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><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">31987001</PMID><DateCompleted><Year>2020</Year><Month>03</Month><Day>16</Day></DateCompleted><DateRevised><Year>2020</Year><Month>03</Month><Day>25</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">2222-1751</ISSN><JournalIssue CitedMedium="Internet"><Volume>9</Volume><Issue>1</Issue><PubDate><Year>2020</Year></PubDate></JournalIssue><Title>Emerging microbes & infections</Title><ISOAbbreviation>Emerg Microbes Infect</ISOAbbreviation></Journal><ArticleTitle>Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan.</ArticleTitle><Pagination><MedlinePgn>221-236</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1080/22221751.2020.1719902</ELocationID><Abstract><AbstractText>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.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Chan</LastName><ForeName>Jasper Fuk-Woo</ForeName><Initials>JF</Initials><Identifier Source="ORCID">0000-0001-6336-6657</Identifier><AffiliationInfo><Affiliation>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, People's Republic of China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kok</LastName><ForeName>Kin-Hang</ForeName><Initials>KH</Initials><Identifier Source="ORCID">0000-0003-3426-332X</Identifier><AffiliationInfo><Affiliation>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhu</LastName><ForeName>Zheng</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chu</LastName><ForeName>Hin</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>To</LastName><ForeName>Kelvin Kai-Wang</ForeName><Initials>KK</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, People's Republic of China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yuan</LastName><ForeName>Shuofeng</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yuen</LastName><ForeName>Kwok-Yung</ForeName><Initials>KY</Initials><AffiliationInfo><Affiliation>Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, People's Republic of China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>01</Month><Day>28</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Emerg Microbes 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