OmniVira

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

Xiaojun Li1 Elena E Giorgi2 Manukumar Honnayakanahalli Marichannegowda1 Brian Foley2 Chuan Xiao3 Xiang-Peng Kong4 Yue Chen1 S Gnanakaran2 Bette Korber2,5 Feng Gao6,7
Affiliations 7 institutions
  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. New Mexico Consortium, Los Alamos, NM 87545, USA.
  6. Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA. [email protected].
  7. National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China.
PMID32937441 DOI10.1126/sciadv.abb9153 Year2020 Journal Science advances Sci Adv Languageeng Statusepublish

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.

Supporting text Virus Host Location
Recombination, Genetic 59 Amino Acid Sequence 128 Angiotensin-Converting Enzyme 2 177 Animals 1948 Betacoronavirus 78 Binding Sites 89 Chiroptera 371 Coronavirus Infections 171 COVID-19 425 Evolution, Molecular 176 Genome, Viral 317 Humans 1440 Pandemics 108 Peptidyl-Dipeptidase A 57 Phylogeny 805 Pneumonia, Viral 42 Protein Structure, Tertiary 29 SARS-CoV-2 453 Sequence Alignment 51 ACE2 protein, human 87

Evidence records

1 total
Genomic Evolution
1 records · 1 evidence types
Evidence type Phylogenetic Evolution
1 records
OVE4142 Phylogenetic Evolution
Key finding

Comparative phylogenetic analysis revealed similar purifying selection among bat, pangolin, and human coronaviruses, supporting a shared evolutionary mechanism underlying coronavirus emergence.

Virus
Coronaviridae
Host
bats Chiroptera Natural host pangolins Manidae Natural host human Homo sapiens Natural host
Location
Not specified
Supporting text

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.

Genes or proteins
spike | receptor binding motif (RBM) | other genes
Analysis methods
phylogenetic analysis | comparative genomic analysis | selection pressure analysis