Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding

Citation

Material Information

Title:
Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding
Series Title:
The Lancet
Creator:
Lu, Roujian
Zhao, Xiang
Li, Juan
Niu, Pehua
Yang, Bo
Wu, Honglong
Wang, Wenling
Song, Hao
Huang, Baoying
Zhu, Na
Bi, Yuhai
Ma, Xuejun
Zhan, Faxian
Wang, Liang
Hu, Tao
Zhou, Hong
Hu, Zhenhong
Zhou, Weimin
Zhao, Li
Chen, Jing
Meng, Yao
Wang, Ji
Lin, Yang
Yuan, Jianyeng
Xie, Zhihao
Ma, Jinmin
Liu, William J.
Wang, Dayan
Xu, Wenbo
Holmes, Edward C.
Gao, George F.
Wu, Guizhen
Chen, Weijun
Shi, Weifeng
Tan, Wenjie
Publisher:
The Lancet
Publication Date:
Language:
English

Subjects

Subjects / Keywords:
Genomic Characterization ( local )
Epidemiology ( local )
2019 Novel Coronavirus ( local )
Virus ( local )
Coronavirus ( local )
Genre:
serial ( sobekcm )

Notes

Abstract:
Background In late December, 2019, patients presenting with viral pneumonia due to an unidentified microbial agent were reported in Wuhan, China. A novel coronavirus was subsequently identified as the causative pathogen, provisionally named 2019 novel coronavirus (2019-nCoV). As of Jan 26, 2020, more than 2000 cases of 2019-nCoV infection have been confirmed, most of which involved people living in or visiting Wuhan, and human-to-human transmission has been confirmed. Methods We did next-generation sequencing of samples from bronchoalveolar lavage fluid and cultured isolates from nine inpatients, eight of whom had visited the Huanan seafood market in Wuhan. Complete and partial 2019-nCoV genome sequences were obtained from these individuals. Viral contigs were connected using Sanger sequencing to obtain the full-length genomes, with the terminal regions determined by rapid amplification of cDNA ends. Phylogenetic analysis of these 2019-nCoV genomes and those of other coronaviruses was used to determine the evolutionary history of the virus and help infer its likely origin. Homology modelling was done to explore the likely receptor-binding properties of the virus. Findings The ten genome sequences of 2019-nCoV obtained from the nine patients were extremely similar, exhibiting more than 99·98% sequence identity. Notably, 2019-nCoV was closely related (with 88% identity) to two bat-derived severe acute respiratory syndrome (SARS)-like coronaviruses, bat-SL-CoVZC45 and bat-SL-CoVZXC21, collected in 2018 in Zhoushan, eastern China, but were more distant from SARS-CoV (about 79%) and MERS-CoV (about 50%). Phylogenetic analysis revealed that 2019-nCoV fell within the subgenus Sarbecovirus of the genus Betacoronavirus, with a relatively long branch length to its closest relatives bat-SL-CoVZC45 and bat-SL-CoVZXC21, and was genetically distinct from SARS-CoV. Notably, homology modelling revealed that 2019-nCoV had a similar receptor-binding domain structure to that of SARS-CoV, despite amino acid variation at some key res
Original Version:
The Lancet, Vol. 395, no. 10224 (2020-01-29).

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University of South Florida Library
Holding Location:
University of South Florida
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