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Emergence of SARS-CoV-2 through Recombination and Strong Purifying Selection

View ORCID ProfileXiaojun Li, Elena E. Giorgi, Manukumar Honnayakanahalli Marichann, Brian Foley, Chuan Xiao, Xiang-Peng Kong, Yue Chen, Bette Korber, Feng Gao
doi: https://doi.org/10.1101/2020.03.20.000885
Xiaojun Li
1Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
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Elena E. Giorgi
2Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
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Manukumar Honnayakanahalli Marichann
1Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
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Brian Foley
2Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
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Chuan Xiao
3Department of Chemistry and Biochemistry, The University of Texas at El Paso, El Paso, TX 79968, USA
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Xiang-Peng Kong
4Department of Biochemistry and Molecular Pharmacology, Grossman School of Medicine, New York University, New York, NY 10016
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Yue Chen
1Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
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Bette Korber
2Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
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Feng Gao
1Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
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  • For correspondence: fgao@duke.edu
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Abstract

COVID-19 has become a global pandemic caused by a novel coronavirus SARS-CoV-2. Understanding the origins of SARS-CoV-2 is critical for deterring future zoonosis and for drug discovery and vaccine development. We show evidence of strong purifying selection around the receptor binding motif (RBM) in the spike gene and in other genes among bat, pangolin and human coronaviruses, indicating similar strong evolutionary constraints in different host species. We also demonstrate that SARS-CoV-2’s entire RBM was introduced through recombination with coronaviruses from pangolins, possibly a critical step in the evolution of SARS-CoV-2’s ability to infect humans. Similar purifying selection in different host species and frequent recombination among coronaviruses suggest a common evolutionary mechanism that could lead to new emerging human coronaviruses.

One Sentence Summary Extensive Recombination and Strong Purifying Selection among coronaviruses from different hosts facilitate the emergence of SARS-CoV-2

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Posted March 24, 2020.
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Emergence of SARS-CoV-2 through Recombination and Strong Purifying Selection
Xiaojun Li, Elena E. Giorgi, Manukumar Honnayakanahalli Marichann, Brian Foley, Chuan Xiao, Xiang-Peng Kong, Yue Chen, Bette Korber, Feng Gao
bioRxiv 2020.03.20.000885; doi: https://doi.org/10.1101/2020.03.20.000885
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Emergence of SARS-CoV-2 through Recombination and Strong Purifying Selection
Xiaojun Li, Elena E. Giorgi, Manukumar Honnayakanahalli Marichann, Brian Foley, Chuan Xiao, Xiang-Peng Kong, Yue Chen, Bette Korber, Feng Gao
bioRxiv 2020.03.20.000885; doi: https://doi.org/10.1101/2020.03.20.000885

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