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Evolutionary history, potential intermediate animal host, and cross-species analyses of SARS-CoV-2

Journal Article · · Journal of Medical Virology
DOI:https://doi.org/10.1002/jmv.25731· OSTI ID:1774437
 [1];  [2];  [3];  [4];  [1];  [5];  [6]
  1. Wuhan Univ. of Bioengineering (China)
  2. Ningbo Univ. (China)
  3. Tianjin Cancer Hospital Airport Hospital, Tianjin (China). Precision Cancer Center Airport Center
  4. Weifang Center for Disease Control and Prevention (China)
  5. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  6. Univ. of California San Diego, La Jolla, CA (United States)
+ Show Author Affiliations

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. Additionally, 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.

Research Organization:
Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
Sponsoring Organization:
USDOE; National Natural Science Foundation of China (NNSFC); National Institutes of Health (NIH)
Grant/Contract Number:
89233218CNA000001
OSTI ID:
1774437
Report Number(s):
LA-UR--20-22399
Journal Information:
Journal of Medical Virology, Journal Name: Journal of Medical Virology Journal Issue: 6 Vol. 92; ISSN 0146-6615
Publisher:
WileyCopyright Statement
Country of Publication:
United States
Language:
English

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Selectomic and Evolvability Analyses of the Highly Pathogenic Betacoronaviruses SARS-CoV-2, SARS-CoV, and MERS-CoV dataset January 2020

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
COVID-19
SARS-CoV-2
TMRCA
cross-species transmission
epidemiology
evolution
evolutionary rate
potential intermediate animal host
virology