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

Emerging Microbes & Infections
Jasper Fuk-Woo ChanKwok-Yung Yuen

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 evo...Continue Reading

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Citations

Feb 14, 2020·Journal of Medical Virology·Lei Zhang, Yunhui Liu
Feb 26, 2020·Journal of Medical Virology·Pengfei SunBo Pan
Mar 10, 2020·Emerging Microbes & Infections·Shan Lu
Mar 12, 2020·Emerging Infectious Diseases·Jennifer HarcourtNatalie J Thornburg
Mar 19, 2020·AJR. American Journal of Roentgenology·Dehan LiuChuansheng Zheng
Mar 21, 2020·Emerging Microbes & Infections·Michael J Loeffelholz, Yi-Wei Tang
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Mar 25, 2020·Emerging Microbes & Infections·Jianhui NieYouchun Wang
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Mar 3, 2020·Journal of Medical Virology·Hongzhou LuYi-Wei Tang
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Datasets Mentioned

BETA
AY278488
AY390556
AY391777
AY515512
MN975262
MG772934.1
MG772933.1
NC004718
KP886809
AY274119

Methods Mentioned

BETA
transfection

Software Mentioned

blast PREDiction ( PSIPRED )
CLUSTAL
MEGA X
BOXSHADE
RNAfold WebServer
Fold
TMHMM
PSI
blast PREDiction

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