OmniVira

SARS-CoV-2 spillover transmission due to recombination event.

Nariman Shahhosseini1 Gary Wong1,2 Gary P Kobinger1,3,4,5 Sadegh Chinikar6,7
Affiliations 7 institutions
  1. Département de Microbiologie-Infectiologie et d'Immunologie, Université Laval, Québec City, Québec, Canada.
  2. Pasteur Institute of Shanghai, China.
  3. Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada.
  4. Department of Immunology, University of Manitoba, Winnipeg, Manitoba, Canada.
  5. Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA.
  6. Institute of Virology, University of Veterinary Medicine, Vienna, Austria.
  7. Pasteur Institute of Tehran, Iran.
PMID33615041 DOI10.1016/j.genrep.2021.101045 Year2021 Journal Gene reports Gene Rep Languageeng Statusppublish

Abstract

In late 2019, a novel Coronavirus emerged in China. Perceiving the modulating factors of cross-species virus transmission is critical to elucidate the nature of virus emergence. Using bioinformatics tools, we analyzed the mapping of the SARS-CoV-2 genome, modeling of protein structure, and analyze the evolutionary origin of SARS-CoV-2, as well as potential recombination events. Phylogenetic tree analysis shows that SARS-CoV-2 has the closest evolutionary relationship with Bat-SL-CoV-2 (RaTG13) at the scale of the complete virus genome, and less similarity to Pangolin-CoV. However, the Receptor Binding Domain (RBD) of SARS-CoV-2 is almost identical to Pangolin-CoV at the aa level, suggesting that spillover transmission probably occurred directly from pangolins, but not bats. Further recombination analysis revealed the pathway for spillover transmission from Bat-SL-CoV-2 and Pangolin-CoV. Here, we provide evidence for recombination event between Bat-SL-CoV-2 and Pangolin-CoV that resulted in the emergence of SARS-CoV-2. Nevertheless, the role of mutations should be noted as another influencing factor in the continuing evolution and resurgence of novel SARS-CoV-2 variants.

Supporting text Virus Host Location
Bat-SL-CoV-2, Bat SARS like Coronavirus 2 1 CoV, coronavirus 2 COVID-19, coronavirus disease 2019 1 hACE2, human angiotensin-converting enzyme 2 1 MERS, Middle East Respiratory Syndrome 2 Mutation 222 Pandemic 15 Phylogenetics 29 RBD, receptor binding domain 1 Recombination 40 SARS, severe acute respiratory syndrome 2 SARS-CoV-2 550 Virulence 116

Evidence records

3 total
Genomic Evolution
3 records · 2 evidence types
Evidence type Recombination or Reassortment
2 records
OVE4553 Recombination or Reassortment
Key finding

SARS-CoV-2 emerged through a recombination event between Bat-SL-CoV-2 and Pangolin-CoV.

Virus
SARS-related coronavirus Severe acute respiratory syndrome coronavirus 2
Host
Not specified
Location
Not specified
Supporting text

Here, we provide evidence for recombination event between Bat-SL-CoV-2 and Pangolin-CoV that resulted in the emergence of SARS-CoV-2.

Event type
recombination
OVE4552 Recombination or Reassortment
Key finding

SARS-CoV-2 spillover transmission probably occurred directly from pangolins to humans, but not from bats.

Virus
Severe acute respiratory syndrome coronavirus 2
Host
pangolins Manidae Natural host human Homo sapiens Natural host
Location
China
Supporting text

In late 2019, a novel Coronavirus emerged in China. The Receptor Binding Domain (RBD) of SARS-CoV-2 is almost identical to Pangolin-CoV at the aa level, suggesting that spillover transmission probably occurred directly from pangolins, but not bats.

Event type
recombination
Evidence type Phylogenetic Evolution
1 records
OVE4550 Phylogenetic Evolution
Key finding

Complete genome phylogenetic analysis shows that SARS-CoV-2 clusters most closely with Bat-SL-CoV-2 (RaTG13) and is more distantly related to Pangolin-CoV, indicating an evolutionary relationship among these coronaviruses.

Virus
Severe acute respiratory syndrome coronavirus 2 Coronaviridae SARS-related coronavirus
Host
bats Chiroptera Natural host pangolins Manidae Natural host
Location
Not specified
Supporting text

Phylogenetic tree analysis shows that SARS-CoV-2 has the closest evolutionary relationship with Bat-SL-CoV-2 (RaTG13) at the scale of the complete virus genome, and less similarity to Pangolin-CoV.

Genes or proteins
complete genome
Analysis methods
phylogenetic tree analysis