Evolutionary history, potential intermediate animal host, and cross-species analyses of SARS-CoV-2
Corresponding Author
Xingguang Li
Hubei Engineering Research Center of Viral Vector, Wuhan University of Bioengineering, Wuhan, China
Correspondence Dr Xingguang Li and Prof Yi Li, Hubei Engineering Research Center of Viral Vector, Wuhan University of Bioengineering, Wuhan, 430415, China.
Email: [email protected] (X. L.) and [email protected] (Y. L.) Prof Brian T. Foley, HIV Databases, Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87544.
Email: [email protected] Dr Antoine Chaillon, Department of Medicine, University of California San Diego, La Jolla, CA 92093-0679.
Email: [email protected]
Search for more papers by this authorJunjie Zai
Immunology Innovation Team, School of Medicine, Ningbo University, Ningbo, China
Search for more papers by this authorQiang Zhao
Precision Cancer Center Airport Center, Tianjin Cancer Hospital Airport Hospital, Tianjin, China
Search for more papers by this authorQing Nie
Department of Microbiology, Weifang Center for Disease Control and Prevention, Weifang, China
Search for more papers by this authorCorresponding Author
Yi Li
Hubei Engineering Research Center of Viral Vector, Wuhan University of Bioengineering, Wuhan, China
Correspondence Dr Xingguang Li and Prof Yi Li, Hubei Engineering Research Center of Viral Vector, Wuhan University of Bioengineering, Wuhan, 430415, China.
Email: [email protected] (X. L.) and [email protected] (Y. L.) Prof Brian T. Foley, HIV Databases, Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87544.
Email: [email protected] Dr Antoine Chaillon, Department of Medicine, University of California San Diego, La Jolla, CA 92093-0679.
Email: [email protected]
Search for more papers by this authorCorresponding Author
Brian T. Foley
HIV Databases, Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
Correspondence Dr Xingguang Li and Prof Yi Li, Hubei Engineering Research Center of Viral Vector, Wuhan University of Bioengineering, Wuhan, 430415, China.
Email: [email protected] (X. L.) and [email protected] (Y. L.) Prof Brian T. Foley, HIV Databases, Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87544.
Email: [email protected] Dr Antoine Chaillon, Department of Medicine, University of California San Diego, La Jolla, CA 92093-0679.
Email: [email protected]
Search for more papers by this authorCorresponding Author
Antoine Chaillon
Department of Medicine, University of California San Diego, La Jolla, California
Correspondence Dr Xingguang Li and Prof Yi Li, Hubei Engineering Research Center of Viral Vector, Wuhan University of Bioengineering, Wuhan, 430415, China.
Email: [email protected] (X. L.) and [email protected] (Y. L.) Prof Brian T. Foley, HIV Databases, Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87544.
Email: [email protected] Dr Antoine Chaillon, Department of Medicine, University of California San Diego, La Jolla, CA 92093-0679.
Email: [email protected]
Search for more papers by this authorCorresponding Author
Xingguang Li
Hubei Engineering Research Center of Viral Vector, Wuhan University of Bioengineering, Wuhan, China
Correspondence Dr Xingguang Li and Prof Yi Li, Hubei Engineering Research Center of Viral Vector, Wuhan University of Bioengineering, Wuhan, 430415, China.
Email: [email protected] (X. L.) and [email protected] (Y. L.) Prof Brian T. Foley, HIV Databases, Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87544.
Email: [email protected] Dr Antoine Chaillon, Department of Medicine, University of California San Diego, La Jolla, CA 92093-0679.
Email: [email protected]
Search for more papers by this authorJunjie Zai
Immunology Innovation Team, School of Medicine, Ningbo University, Ningbo, China
Search for more papers by this authorQiang Zhao
Precision Cancer Center Airport Center, Tianjin Cancer Hospital Airport Hospital, Tianjin, China
Search for more papers by this authorQing Nie
Department of Microbiology, Weifang Center for Disease Control and Prevention, Weifang, China
Search for more papers by this authorCorresponding Author
Yi Li
Hubei Engineering Research Center of Viral Vector, Wuhan University of Bioengineering, Wuhan, China
Correspondence Dr Xingguang Li and Prof Yi Li, Hubei Engineering Research Center of Viral Vector, Wuhan University of Bioengineering, Wuhan, 430415, China.
Email: [email protected] (X. L.) and [email protected] (Y. L.) Prof Brian T. Foley, HIV Databases, Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87544.
Email: [email protected] Dr Antoine Chaillon, Department of Medicine, University of California San Diego, La Jolla, CA 92093-0679.
Email: [email protected]
Search for more papers by this authorCorresponding Author
Brian T. Foley
HIV Databases, Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
Correspondence Dr Xingguang Li and Prof Yi Li, Hubei Engineering Research Center of Viral Vector, Wuhan University of Bioengineering, Wuhan, 430415, China.
Email: [email protected] (X. L.) and [email protected] (Y. L.) Prof Brian T. Foley, HIV Databases, Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87544.
Email: [email protected] Dr Antoine Chaillon, Department of Medicine, University of California San Diego, La Jolla, CA 92093-0679.
Email: [email protected]
Search for more papers by this authorCorresponding Author
Antoine Chaillon
Department of Medicine, University of California San Diego, La Jolla, California
Correspondence Dr Xingguang Li and Prof Yi Li, Hubei Engineering Research Center of Viral Vector, Wuhan University of Bioengineering, Wuhan, 430415, China.
Email: [email protected] (X. L.) and [email protected] (Y. L.) Prof Brian T. Foley, HIV Databases, Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87544.
Email: [email protected] Dr Antoine Chaillon, Department of Medicine, University of California San Diego, La Jolla, CA 92093-0679.
Email: [email protected]
Search for more papers by this authorXingguang Li, Junjie Zai, and Qiang Zhao contributed equally to this study.
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.
Highlights
We 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.
CONFLICT OF INTERESTS
The authors declare that there are no conflict of interests.
Supporting Information
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| jmv25731-sup-0001-Figure_S1.tif2.9 MB | Supporting information |
| jmv25731-sup-0002-Figure_S2.tif1.1 MB | Supporting information |
| jmv25731-sup-0003-Figure_S3.tif3.5 MB | Supporting information |
| jmv25731-sup-0004-Figure_S4.tif1.2 MB | Supporting information |
| jmv25731-sup-0005-Figure_S5.tif1 MB | Supporting information |
| jmv25731-sup-0006-Figure_S6.png20 KB | Supporting information |
| jmv25731-sup-0007-TableS1.xlsx23.1 KB | Supporting information |
| jmv25731-sup-0008-supmat.docx12.6 KB | Supporting information |
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