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

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...

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Published in	Emerging microbes & infections Vol. 9; no. 1; pp. 221 - 236
Main Authors	Chan, Jasper Fuk-Woo, Kok, Kin-Hang, Zhu, Zheng, Chu, Hin, To, Kelvin Kai-Wang, Yuan, Shuofeng, Yuen, Kwok-Yung
Format	Journal Article
Language	English
Published	United States Taylor & Francis 01.01.2020 Taylor & Francis Ltd Taylor & Francis Group
Subjects	Amino Acid Sequence Antiviral drugs Betacoronavirus - genetics Betacoronavirus - isolation & purification bioinformatics China Coronavirus Coronavirus Infections - virology Coronaviruses COVID-19 emerging genome Genome, Viral Genomes Humans Original Phylogeny Pneumonia Pneumonia, Viral - virology respiratory SARS SARS-CoV-2 Sequence Analysis, Protein Travel Viral Proteins - chemistry Viral Proteins - genetics virus Wuhan China genome Coronavirus Wuhan bioinformatics SARS respiratory virus emerging
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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.
AbstractList	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. 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. 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.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. 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 . 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.
Author	Chu, Hin To, Kelvin Kai-Wang Chan, Jasper Fuk-Woo Yuen, Kwok-Yung Kok, Kin-Hang Zhu, Zheng Yuan, Shuofeng
Author_xml	– sequence: 1 givenname: Jasper Fuk-Woo orcidid: 0000-0001-6336-6657 surname: Chan fullname: Chan, Jasper Fuk-Woo organization: Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong – sequence: 2 givenname: Kin-Hang orcidid: 0000-0003-3426-332X surname: Kok fullname: Kok, Kin-Hang email: khkok@hku.hk organization: Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong – sequence: 3 givenname: Zheng surname: Zhu fullname: Zhu, Zheng organization: Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong – sequence: 4 givenname: Hin surname: Chu fullname: Chu, Hin organization: Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong – sequence: 5 givenname: Kelvin Kai-Wang orcidid: 0000-0002-1921-5824 surname: To fullname: To, Kelvin Kai-Wang organization: Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong – sequence: 6 givenname: Shuofeng surname: Yuan fullname: Yuan, Shuofeng organization: Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong – sequence: 7 givenname: Kwok-Yung surname: Yuen fullname: Yuen, Kwok-Yung email: kyyuen@hku.hk organization: Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/31987001$$D View this record in MEDLINE/PubMed
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References	e_1_3_4_4_1 e_1_3_4_3_1 e_1_3_4_2_1 e_1_3_4_9_1 e_1_3_4_8_1 e_1_3_4_7_1 e_1_3_4_20_1 e_1_3_4_6_1 e_1_3_4_5_1 e_1_3_4_23_1 e_1_3_4_24_1 e_1_3_4_21_1 Saitou N (e_1_3_4_13_1) 1987; 4 e_1_3_4_22_1 e_1_3_4_27_1 e_1_3_4_28_1 e_1_3_4_25_1 e_1_3_4_26_1 e_1_3_4_12_1 e_1_3_4_10_1 e_1_3_4_11_1 e_1_3_4_16_1 e_1_3_4_17_1 e_1_3_4_14_1 e_1_3_4_15_1 e_1_3_4_18_1 e_1_3_4_19_1 32133926 - Emerg Microbes Infect. 2020 Dec;9(1):540
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Snippet	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...
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SubjectTerms	Amino Acid Sequence Antiviral drugs Betacoronavirus - genetics Betacoronavirus - isolation & purification bioinformatics China Coronavirus Coronavirus Infections - virology Coronaviruses COVID-19 emerging genome Genome, Viral Genomes Humans Original Phylogeny Pneumonia Pneumonia, Viral - virology respiratory SARS SARS-CoV-2 Sequence Analysis, Protein Travel Viral Proteins - chemistry Viral Proteins - genetics virus Wuhan
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Title	Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan
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