OmniVira

SARS-CoV-2 spike protein predicted to form complexes with host receptor protein orthologues from a broad range of mammals.

S D Lam1,2 N Bordin2 V P Waman2 H M Scholes2 P Ashford2 N Sen2,3 L van Dorp4 C Rauer2 N L Dawson2 C S M Pang2 M Abbasian2 I Sillitoe2 S J L Edwards5 F Fraternali6 J G Lees7 J M Santini2 C A Orengo8
Affiliations 8 institutions
  1. Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
  2. Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK.
  3. Indian Institute of Science Education and Research, Pune, 411008, India.
  4. UCL Genetics Institute, University College London, London, WC1E 6BT, UK.
  5. Department of Science and Technology Studies, University College London, London, WC1E 6BT, UK.
  6. Randall Division of Cell and Molecular Biophysics, Guy's Campus, New Hunt's House, King's College London, London, SE1 1UL, UK.
  7. Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, OX3 OBP, UK.
  8. Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK. [email protected].
PMID33020502 DOI10.1038/s41598-020-71936-5 Year2020 Journal Scientific reports Sci Rep Languageeng Statusepublish

Abstract

SARS-CoV-2 has a zoonotic origin and was transmitted to humans via an undetermined intermediate host, leading to infections in humans and other mammals. To enter host cells, the viral spike protein (S-protein) binds to its receptor, ACE2, and is then processed by TMPRSS2. Whilst receptor binding contributes to the viral host range, S-protein:ACE2 complexes from other animals have not been investigated widely. To predict infection risks, we modelled S-protein:ACE2 complexes from 215 vertebrate species, calculated changes in the energy of the complex caused by mutations in each species, relative to human ACE2, and correlated these changes with COVID-19 infection data. We also analysed structural interactions to better understand the key residues contributing to affinity. We predict that mutations are more detrimental in ACE2 than TMPRSS2. Finally, we demonstrate phylogenetically that human SARS-CoV-2 strains have been isolated in animals. Our results suggest that SARS-CoV-2 can infect a broad range of mammals, but few fish, birds or reptiles. Susceptible animals could serve as reservoirs of the virus, necessitating careful ongoing animal management and surveillance.

Supporting text Virus Host Location
Phylogeny 805 Angiotensin-Converting Enzyme 2 177 Animals 1948 Betacoronavirus 78 Humans 1440 Mammals 92 Molecular Docking Simulation 5 Mutation 209 Peptidyl-Dipeptidase A 57 Protein Binding 193 SARS-CoV-2 453 Spike Glycoprotein, Coronavirus 274 ACE2 protein, human 87 spike glycoprotein, SARS-CoV 16

Evidence records

1 total
Genomic Evolution
1 records · 1 evidence types
Evidence type Phylogenetic Evolution
1 records
OVE4188 Phylogenetic Evolution
Key finding

Phylogenetic analysis confirmed that human SARS-CoV-2 strains isolated from animals cluster within human lineages, indicating evolutionary relatedness across hosts.

Virus
Severe acute respiratory syndrome coronavirus 2
Host
animals Metazoa Context pending
Location
Not specified
Supporting text

Finally, we demonstrate phylogenetically that human SARS-CoV-2 strains have been isolated in animals.

Analysis methods
phylogenetic analysis