SARS-CoV-2 and other human coronaviruses: Mapping of protease recognition sites, antigenic variation of spike protein and their grouping through molecular phylogenetics

Infect Genet Evol. 2021 Apr:89:104729. doi: 10.1016/j.meegid.2021.104729. Epub 2021 Jan 23.

Abstract

In recent years, a total of seven human pathogenic coronaviruses (HCoVs) strains were identified, i.e., SARS-CoV, SARS-CoV-2, MERS-CoV, HCoV-OC43, HCoV-229E, HCoV-NL63, and HCoV-HKU1. Here, we performed an analysis of the protease recognition sites and antigenic variation of the S-protein of these HCoVs. We showed tissue-specific expression pattern, functions, and a number of recognition sites of proteases in S-proteins from seven strains of HCoVs. In the case of SARS-CoV-2, we found two new protease recognition sites, each of calpain-2, pepsin-A, and caspase-8, and one new protease recognition site each of caspase-6, caspase-3, and furin. Our antigenic mapping study of the S-protein of these HCoVs showed that the SARS-CoV-2 virus strain has the most potent antigenic epitopes (highest antigenicity score with maximum numbers of epitope regions). Additionally, the other six strains of HCoVs show common antigenic epitopes (both B-cell and T-cell), with low antigenicity scores compared to SARS-CoV-2. We suggest that the molecular evolution of structural proteins of human CoV can be classified, such as (i) HCoV-NL63 and HCoV-229E, (ii) SARS-CoV-2, and SARS-CoV and (iii) HCoV-OC43 and HCoV-HKU1. In conclusion, we can presume that our study might help to prepare the interventions for the possible HCoVs outbreaks in the future.

Keywords: Antigenic variation; Human coronavirus; Molecular phylogenetics; Protease recognition sites; S-protein.

MeSH terms

  • Antigenic Variation
  • Binding Sites
  • Coronavirus / classification
  • Coronavirus / immunology
  • Coronavirus / metabolism*
  • Epitopes, B-Lymphocyte / immunology
  • Epitopes, T-Lymphocyte / immunology
  • Humans
  • Peptide Hydrolases / metabolism*
  • Phylogeny*
  • SARS-CoV-2 / classification
  • SARS-CoV-2 / immunology
  • SARS-CoV-2 / metabolism*
  • Spike Glycoprotein, Coronavirus / metabolism*

Substances

  • Epitopes, B-Lymphocyte
  • Epitopes, T-Lymphocyte
  • Spike Glycoprotein, Coronavirus
  • Peptide Hydrolases