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:

Li, Xiaojun  ^[1];

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Giorgi, Elena E. ^[2]; Marichannegowda, Manukumar Honnayakanahalli  ^[1];

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Foley, Brian ^[2]; Xiao, Chuan  ^[3];

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Kong, Xiang-Peng ^[4]; Chen, Yue ^[1]; Gnanakaran, S.  ^[2];

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Korber, Bette  ^[5];

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Gao, Feng  ^[6]

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+ Show Author Affiliations

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:

2020-05-29

Research Org.:

Los Alamos National Laboratory (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; eabb9153

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