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

• 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
• ISSN: 2222-1751; 2222-1751
• DOI: 10.1080/22221751.2020.1719902

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.