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Evolutionary history, potential intermediate animal host, and cross-species analyses of SARS-CoV-2.
J Med Virol. 2020 06; 92(6):602-611.JM

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.

Authors+Show Affiliations

Hubei Engineering Research Center of Viral Vector, Wuhan University of Bioengineering, Wuhan, China.Immunology Innovation Team, School of Medicine, Ningbo University, Ningbo, China.Precision Cancer Center Airport Center, Tianjin Cancer Hospital Airport Hospital, Tianjin, China.Department of Microbiology, Weifang Center for Disease Control and Prevention, Weifang, China.Hubei Engineering Research Center of Viral Vector, Wuhan University of Bioengineering, Wuhan, China.HIV Databases, Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico.Department of Medicine, University of California San Diego, La Jolla, California.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

32104911

Citation

Li, Xingguang, et al. "Evolutionary History, Potential Intermediate Animal Host, and Cross-species Analyses of SARS-CoV-2." Journal of Medical Virology, vol. 92, no. 6, 2020, pp. 602-611.
Li X, Zai J, Zhao Q, et al. Evolutionary history, potential intermediate animal host, and cross-species analyses of SARS-CoV-2. J Med Virol. 2020;92(6):602-611.
Li, X., Zai, J., Zhao, Q., Nie, Q., Li, Y., Foley, B. T., & Chaillon, A. (2020). Evolutionary history, potential intermediate animal host, and cross-species analyses of SARS-CoV-2. Journal of Medical Virology, 92(6), 602-611. https://doi.org/10.1002/jmv.25731
Li X, et al. Evolutionary History, Potential Intermediate Animal Host, and Cross-species Analyses of SARS-CoV-2. J Med Virol. 2020;92(6):602-611. PubMed PMID: 32104911.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Evolutionary history, potential intermediate animal host, and cross-species analyses of SARS-CoV-2. AU - Li,Xingguang, AU - Zai,Junjie, AU - Zhao,Qiang, AU - Nie,Qing, AU - Li,Yi, AU - Foley,Brian T, AU - Chaillon,Antoine, Y1 - 2020/03/11/ PY - 2020/02/15/received PY - 2020/02/24/accepted PY - 2020/2/28/pubmed PY - 2020/7/1/medline PY - 2020/2/28/entrez KW - COVID-19 KW - SARS-CoV-2 KW - TMRCA KW - cross-species transmission KW - evolutionary rate KW - potential intermediate animal host SP - 602 EP - 611 JF - Journal of medical virology JO - J Med Virol VL - 92 IS - 6 N2 - 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. SN - 1096-9071 UR - https://www.unboundmedicine.com/medline/citation/32104911/Evolutionary_history_potential_intermediate_animal_host_and_cross_species_analyses_of_SARS_CoV_2_ L2 - https://doi.org/10.1002/jmv.25731 DB - PRIME DP - Unbound Medicine ER -