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

Lancet
Roujian LuWenjie Tan

Abstract

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. 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. The ten genome sequences of 2019-nCoV obtained from the nine patients were extremely...Continue Reading

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Datasets Mentioned

BETA
MG772933.1
MG772934
AY390556
GU190215

Methods Mentioned

BETA
bronchoalveolar lavage
PCR
light microscopy

Software Mentioned

Geneious
CLCBio
RAxML
Primer
Swiss
RapSearch
Mafft
Blast
SimPlot
OLIGO Primer Analysis

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