T and B cell Epitope analysis of SARS-CoV-2 S protein based on immunoinformatics and experimental research

J Cell Mol Med. 2021 Jan;25(2):1274-1289. doi: 10.1111/jcmm.16200. Epub 2020 Dec 15.


COVID-19 caused by SARS-CoV-2 is pandemic with a severe morbidity and mortality rate across the world. Despite the race for effective vaccine and drug against further expansion and fatality rate of this novel coronavirus, there is still lack of effective antiviral therapy. To this effect, we deemed it necessary to identify potential B and T cell epitopes from the envelope S protein. This can be used as potential targets to develop anti-SARS-CoV-2 vaccine preparations. In this study, we used immunoinformatics to identify conservative B and T cell epitopes for S proteins of SARS-CoV-2, which might play roles in the initiation of SARS-CoV-2 infection. We identified the B cell and T cell peptide epitopes of S protein and their antigenicity, as well as the interaction between the peptide epitopes and human leucocyte antigen (HLA). Among the B cell epitopes, 'EILDITPCSFGGVS' has the highest score of antigenicity and great immunogenicity. In T cell epitopes, MHC-I peptide 'KIADYNYKL' and MHC-II peptide 'LEILDITPC' were identified as high antigens. Besides, docking analysis showed that the predicted peptide 'KIADYNYKL' was closely bound to the HLA-A*0201. The results of molecular dynamics simulation through GROMACS software showed that 'HLA-A*0201~peptide' complex was very stable. And the peptide we selected could induce the T cell response similar to that of SARS-CoV-2 infection. Moreover, the predicted peptides were highly conserved in different isolates from different countries. The antigenic epitopes presumed in this study were effective new vaccine targets to prevent SARS-CoV-2 infection.

Keywords: SARS-CoV-2; T and B cell epitopes; T cell immune response; immunoinformatics; molecular dynamics simulation; vaccine design.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • COVID-19 / immunology*
  • COVID-19 Vaccines / immunology
  • Epitopes, B-Lymphocyte / immunology*
  • Epitopes, T-Lymphocyte / immunology*
  • HLA-A Antigens / immunology
  • Histocompatibility Antigens Class II / immunology
  • Humans
  • Molecular Dynamics Simulation
  • Pandemics / prevention & control
  • SARS-CoV-2 / immunology*
  • Spike Glycoprotein, Coronavirus / immunology*
  • Viral Vaccines / immunology


  • COVID-19 Vaccines
  • Epitopes, B-Lymphocyte
  • Epitopes, T-Lymphocyte
  • HLA-A Antigens
  • Histocompatibility Antigens Class II
  • Spike Glycoprotein, Coronavirus
  • Viral Vaccines
  • spike protein, SARS-CoV-2