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Evolution and variation of 2019-novel coronavirus

View ORCID ProfileChenglong Xiong, Lufang Jiang, Yue Chen, Qingwu Jiang
doi: https://doi.org/10.1101/2020.01.30.926477
Chenglong Xiong
1Department of Public Health Microbiology, School of Public Health, Fudan University, Shanghai 200032, China
2School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai 200032, China
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  • ORCID record for Chenglong Xiong
Lufang Jiang
1Department of Public Health Microbiology, School of Public Health, Fudan University, Shanghai 200032, China
2School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai 200032, China
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Yue Chen
3School of Epidemiology and Public Health, Faculty of Medicine, University of Ottawa, Ottawa, Canada
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Qingwu Jiang
1Department of Public Health Microbiology, School of Public Health, Fudan University, Shanghai 200032, China
2School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai 200032, China
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  • For correspondence: jiangqw@fudan.edu.cn
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Abstract

Background The current outbreak caused by novel coronavirus (2019-nCoV) in China has become a worldwide concern. As of 28 January 2020, there were 4631 confirmed cases and 106 deaths, and 11 countries or regions were affected.

Methods We downloaded the genomes of 2019-nCoVs and similar isolates from the Global Initiative on Sharing Avian Influenza Database (GISAID and nucleotide database of the National Center for Biotechnology Information (NCBI). Lasergene 7.0 and MEGA 6.0 softwares were used to calculate genetic distances of the sequences, to construct phylogenetic trees, and to align amino acid sequences. Bayesian coalescent phylogenetic analysis, implemented in the BEAST software package, was used to calculate the molecular clock related characteristics such as the nucleotide substitution rate and the most recent common ancestor (tMRCA) of 2019-nCoVs.

Results An isolate numbered EPI_ISL_403928 showed different phylogenetic trees and genetic distances of the whole length genome, the coding sequences (CDS) of ployprotein (P), spike protein (S), and nucleoprotein (N) from other 2019-nCoVs. There are 22, 4, 2 variations in P, S, and N at the level of amino acid residues. The nucleotide substitution rates from high to low are 1·05 × 10−2 (nucleotide substitutions/site/year, with 95% HPD interval being 6.27 × 10−4 to 2.72 × 10−2) for N, 5.34 × 10−3 (5.10 × 10−4, 1.28 × 10−2) for S, 1.69 × 10−3 (3.94 × 10−4, 3.60 × 10−3) for P, 1.65 × 10−3 (4.47 × 10−4, 3.24 × 10−3) for the whole genome, respectively. At this nucleotide substitution rate, the most recent common ancestor (tMRCA) of 2019-nCoVs appeared about 0.253-0.594 year before the epidemic.

Conclusion Our analysis suggests that at least two different viral strains of 2019-nCoV are involved in this outbreak that might occur a few months earlier before it was officially reported.

  • List of abbreviations

    CoVs
    Coronaviruses
    2019-nCoV
    2019-novel coronavirus
    SARS-CoV
    severe acute respiratory syndrome coronavirus
    MERS-CoV
    Middle East respiratory syndrome coronavirus
    CDS
    coding sequence
    tMRCA
    the most recent common ancestor
    GISAID
    the Global Initiative on Sharing Avian Influenza Database
    ESSs
    Effective sample sizes
  • Copyright 
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    Posted January 30, 2020.
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    Evolution and variation of 2019-novel coronavirus
    Chenglong Xiong, Lufang Jiang, Yue Chen, Qingwu Jiang
    bioRxiv 2020.01.30.926477; doi: https://doi.org/10.1101/2020.01.30.926477
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    Evolution and variation of 2019-novel coronavirus
    Chenglong Xiong, Lufang Jiang, Yue Chen, Qingwu Jiang
    bioRxiv 2020.01.30.926477; doi: https://doi.org/10.1101/2020.01.30.926477

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