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Title: Emergence of SARS-CoV-2 through recombination and strong purifying selection

Abstract

COVID-19 has become a global pandemic caused by the novel coronavirus SARS-CoV-2. Understanding the origins of SARS-CoV-2 is critical for deterring future zoonosis, discovering new drugs, and developing a vaccine. We show evidence of strong purifying selection around the receptor binding motif (RBM) in the spike and other genes among bat, pangolin, and human coronaviruses, suggesting similar 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, together with frequent recombination among coronaviruses, suggests a common evolutionary mechanism that could lead to new emerging human coronaviruses.

Authors:
ORCiD logo [1];  [2]; ORCiD logo [1];  [2]; ORCiD logo [3];  [4];  [1]; ORCiD logo [2]; ORCiD logo [5]; ORCiD logo [6]
  1. Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA.
  2. Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87544, USA.
  3. Department of Chemistry and Biochemistry, The University of Texas at El Paso, El Paso, TX 79968, USA.
  4. Department of Biochemistry and Molecular Pharmacology, Grossman School of Medicine, New York University, New York, NY 10016, USA.
  5. Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87544, USA., New Mexico Consortium, Los Alamos, NM 87545, USA.
  6. Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA., National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China.
Publication Date:
Research Org.:
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE Laboratory Directed Research and Development (LDRD) Program; USDOE National Nuclear Security Administration (NNSA)
OSTI Identifier:
1635592
Alternate Identifier(s):
OSTI ID: 1726193
Report Number(s):
LA-UR-20-22544
Journal ID: ISSN 2375-2548; /advances/6/27/eabb9153.atom
Grant/Contract Number:  
89233218CNA000001; 20200554ECR
Resource Type:
Published Article
Journal Name:
Science Advances
Additional Journal Information:
Journal Name: Science Advances Journal Volume: 6 Journal Issue: 27; Journal ID: ISSN 2375-2548
Publisher:
AAAS
Country of Publication:
United States
Language:
English
Subject:
60 APPLIED LIFE SCIENCES

Citation Formats

Li, Xiaojun, Giorgi, Elena E., Marichannegowda, Manukumar Honnayakanahalli, Foley, Brian, Xiao, Chuan, Kong, Xiang-Peng, Chen, Yue, Gnanakaran, S., Korber, Bette, and Gao, Feng. Emergence of SARS-CoV-2 through recombination and strong purifying selection. United States: N. p., 2020. Web. https://doi.org/10.1126/sciadv.abb9153.
Li, Xiaojun, Giorgi, Elena E., Marichannegowda, Manukumar Honnayakanahalli, Foley, Brian, Xiao, Chuan, Kong, Xiang-Peng, Chen, Yue, Gnanakaran, S., Korber, Bette, & Gao, Feng. Emergence of SARS-CoV-2 through recombination and strong purifying selection. United States. https://doi.org/10.1126/sciadv.abb9153
Li, Xiaojun, Giorgi, Elena E., Marichannegowda, Manukumar Honnayakanahalli, Foley, Brian, Xiao, Chuan, Kong, Xiang-Peng, Chen, Yue, Gnanakaran, S., Korber, Bette, and Gao, Feng. Fri . "Emergence of SARS-CoV-2 through recombination and strong purifying selection". United States. https://doi.org/10.1126/sciadv.abb9153.
@article{osti_1635592,
title = {Emergence of SARS-CoV-2 through recombination and strong purifying selection},
author = {Li, Xiaojun and Giorgi, Elena E. and Marichannegowda, Manukumar Honnayakanahalli and Foley, Brian and Xiao, Chuan and Kong, Xiang-Peng and Chen, Yue and Gnanakaran, S. and Korber, Bette and Gao, Feng},
abstractNote = {COVID-19 has become a global pandemic caused by the novel coronavirus SARS-CoV-2. Understanding the origins of SARS-CoV-2 is critical for deterring future zoonosis, discovering new drugs, and developing a vaccine. We show evidence of strong purifying selection around the receptor binding motif (RBM) in the spike and other genes among bat, pangolin, and human coronaviruses, suggesting similar 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, together with frequent recombination among coronaviruses, suggests a common evolutionary mechanism that could lead to new emerging human coronaviruses.},
doi = {10.1126/sciadv.abb9153},
journal = {Science Advances},
number = 27,
volume = 6,
place = {United States},
year = {2020},
month = {5}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1126/sciadv.abb9153

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Cited by: 10 works
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