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Evolutionary history, potential intermediate animal host, and cross-species analyses of SARS-CoV-2.
Li, Xingguang; Zai, Junjie; Zhao, Qiang; Nie, Qing; Li, Yi; Foley, Brian T; Chaillon, Antoine.
  • Li X; Hubei Engineering Research Center of Viral Vector, Wuhan University of Bioengineering, Wuhan, China.
  • Zai J; Immunology Innovation Team, School of Medicine, Ningbo University, Ningbo, China.
  • Zhao Q; Precision Cancer Center Airport Center, Tianjin Cancer Hospital Airport Hospital, Tianjin, China.
  • Nie Q; Department of Microbiology, Weifang Center for Disease Control and Prevention, Weifang, China.
  • Li Y; Hubei Engineering Research Center of Viral Vector, Wuhan University of Bioengineering, Wuhan, China.
  • Foley BT; HIV Databases, Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico.
  • Chaillon A; Department of Medicine, University of California San Diego, La Jolla, California.
J Med Virol ; 92(6): 602-611, 2020 06.
Article in English | MEDLINE | ID: covidwho-153847
ABSTRACT
To investigate the evolutionary history of the recent outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China, a total of 70 genomes of virus strains from China and elsewhere with sampling dates between 24 December 2019 and 3 February 2020 were analyzed. To explore the potential intermediate animal host of the SARS-CoV-2 virus, we reanalyzed virome data sets from pangolins and representative SARS-related coronaviruses isolates from bats, with particular attention paid to the spike glycoprotein gene. We performed phylogenetic, split network, transmission network, likelihood-mapping, and comparative analyses of the genomes. Based on Bayesian time-scaled phylogenetic analysis using the tip-dating method, we estimated the time to the most recent common ancestor and evolutionary rate of SARS-CoV-2, which ranged from 22 to 24 November 2019 and 1.19 to 1.31 × 10-3 substitutions per site per year, respectively. Our results also revealed that the BetaCoV/bat/Yunnan/RaTG13/2013 virus was more similar to the SARS-CoV-2 virus than the coronavirus obtained from the two pangolin samples (SRR10168377 and SRR10168378). We also identified a unique peptide (PRRA) insertion in the human SARS-CoV-2 virus, which may be involved in the proteolytic cleavage of the spike protein by cellular proteases, and thus could impact host range and transmissibility. Interestingly, the coronavirus carried by pangolins did not have the RRAR motif. Therefore, we concluded that the human SARS-CoV-2 virus, which is responsible for the recent outbreak of COVID-19, did not come directly from pangolins.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Pneumonia, Viral / Genome, Viral / Coronavirus Infections / Pandemics / Spike Glycoprotein, Coronavirus / Betacoronavirus Type of study: Observational study / Prognostic study / Randomized controlled trials Limits: Animals / Humans Language: English Journal: J Med Virol Year: 2020 Document Type: Article Affiliation country: Jmv.25731

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Pneumonia, Viral / Genome, Viral / Coronavirus Infections / Pandemics / Spike Glycoprotein, Coronavirus / Betacoronavirus Type of study: Observational study / Prognostic study / Randomized controlled trials Limits: Animals / Humans Language: English Journal: J Med Virol Year: 2020 Document Type: Article Affiliation country: Jmv.25731