In silico mutagenesis of human ACE2 with S protein and translational efficiency explain SARS-CoV-2 infectivity in different species

PLoS Comput Biol. 2020 Dec 7;16(12):e1008450. doi: 10.1371/journal.pcbi.1008450. eCollection 2020 Dec.


The coronavirus disease COVID-19 constitutes the most severe pandemic of the last decades having caused more than 1 million deaths worldwide. The SARS-CoV-2 virus recognizes the angiotensin converting enzyme 2 (ACE2) on the surface of human cells through its spike protein. It has been reported that the coronavirus can mildly infect cats, and ferrets, and perhaps dogs while not pigs, mice, chicken and ducks. Differences in viral infectivity among different species or individuals could be due to amino acid differences at key positions of the host proteins that interact with the virus, the immune response, expression levels of host proteins and translation efficiency of the viral proteins among other factors. Here, first we have addressed the importance that sequence variants of different animal species, human individuals and virus isolates have on the interaction between the RBD domain of the SARS-CoV-2 spike S protein and human angiotensin converting enzyme 2 (ACE2). Second, we have looked at viral translation efficiency by using the tRNA adaptation index. We find that integration of both interaction energy with ACE2 and translational efficiency explains animal infectivity. Humans are the top species in which SARS-CoV-2 is both efficiently translated as well as optimally interacting with ACE2. We have found some viral mutations that increase affinity for hACE and some hACE2 variants affecting ACE2 stability and virus binding. These variants suggest that different sensitivities to coronavirus infection in humans could arise in some cases from allelic variability affecting ACE2 stability and virus binding.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Angiotensin-Converting Enzyme 2 / genetics*
  • Animals
  • COVID-19 / genetics*
  • COVID-19 / virology*
  • Computer Simulation
  • Crystallography, X-Ray
  • Humans
  • Immune System
  • Mutagenesis*
  • Protein Binding
  • Protein Biosynthesis*
  • Protein Domains
  • Protein Folding
  • Protein Interaction Mapping
  • Protein Structure, Secondary
  • Proteome
  • SARS-CoV-2
  • Species Specificity
  • Spike Glycoprotein, Coronavirus / genetics*


  • Proteome
  • Spike Glycoprotein, Coronavirus
  • spike protein, SARS-CoV-2
  • ACE2 protein, human
  • Angiotensin-Converting Enzyme 2

Grants and funding

We acknowledge the support of the Centre for Genomic Regulation (CRG) Technology & Business Development Office (TBDO) for support with licensing information, the CRG Tecnologías de Información y Comunicación (TIC) for assistance with web hosting, and the Scientific Information Technologies (SIT) for distributed computing, the Spanish Ministry of Science and Innovation (MICINN), ‘Centro de Excelencia Severo Ochoa’, the CERCA Programme/Generalitat de Catalunya, the Spanish Ministry of Science and Innovation (MICINN) to the EMBL partnership. The project that gave rise to these results was supported by a fellowship from “la Caixa” Foundation (ID 100010434; fellowship code LCF/BQ/DI19/11730061). The work of X.H. has been supported by a PhD fellowship from the Fundación Ramón Areces.