Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan
pmid: 31987001
pmc: PMC7067204
Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan
(Uploaded by Plazi for the Bat Literature Project) 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.
- University of Hong Kong - Shenzhen Hospital China (People's Republic of)
- University of Hong Kong China (People's Republic of)
- Li Ka Shing Faculty of Medicine, University of Hong Kong Hong Kong
Wuhan, China, Epidemiology, Pneumonia, Viral, Immunology, bats, bat, Infectious and parasitic diseases, RC109-216, Genome, Viral, Microbiology, Betacoronavirus, Viral Proteins, Sequence Analysis, Protein, Chiroptera, Virology, Drug Discovery, Humans, Animalia, Amino Acid Sequence, Chordata, genome, Phylogeny, SARS, Travel, genome ; COVID-19 ; respiratory ; SARS-CoV ; SARS ; Wuhan ; emerging ; virus ; bioinformatics ; Coronavirus, SARS-CoV-2, emerging, COVID-19, Articles, Biodiversity, General Medicine, respiratory, QR1-502, Coronavirus, Infectious Diseases, Mammalia, Parasitology, Coronavirus Infections
Wuhan, China, Epidemiology, Pneumonia, Viral, Immunology, bats, bat, Infectious and parasitic diseases, RC109-216, Genome, Viral, Microbiology, Betacoronavirus, Viral Proteins, Sequence Analysis, Protein, Chiroptera, Virology, Drug Discovery, Humans, Animalia, Amino Acid Sequence, Chordata, genome, Phylogeny, SARS, Travel, genome ; COVID-19 ; respiratory ; SARS-CoV ; SARS ; Wuhan ; emerging ; virus ; bioinformatics ; Coronavirus, SARS-CoV-2, emerging, COVID-19, Articles, Biodiversity, General Medicine, respiratory, QR1-502, Coronavirus, Infectious Diseases, Mammalia, Parasitology, Coronavirus Infections
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