Immunoinformatics mapping of potential epitopes in SARS-CoV-2 structural proteins

PLoS One. 2021 Nov 15;16(11):e0258645. doi: 10.1371/journal.pone.0258645. eCollection 2021.


All approved coronavirus disease 2019 (COVID-19) vaccines in current use are safe, effective, and reduce the risk of severe illness. Although data on the immunological presentation of patients with COVID-19 is limited, increasing experimental evidence supports the significant contribution of B and T cells towards the resolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Despite the availability of several COVID-19 vaccines with high efficacy, more effective vaccines are still needed to protect against the new variants of SARS-CoV-2. Employing a comprehensive immunoinformatic prediction algorithm and leveraging the genetic closeness with SARS-CoV, we have predicted potential immune epitopes in the structural proteins of SARS-CoV-2. The S and N proteins of SARS-CoV-2 and SARS-CoVs are main targets of antibody detection and have motivated us to design four multi-epitope vaccines which were based on our predicted B- and T-cell epitopes of SARS-CoV-2 structural proteins. The cardinal epitopes selected for the vaccine constructs are predicted to possess antigenic, non-allergenic, and cytokine-inducing properties. Additionally, some of the predicted epitopes have been experimentally validated in published papers. Furthermore, we used the C-ImmSim server to predict effective immune responses induced by the epitope-based vaccines. Taken together, the immune epitopes predicted in this study provide a platform for future experimental validations which may facilitate the development of effective vaccine candidates and epitope-based serological diagnostic assays.

MeSH terms

  • Amino Acid Sequence
  • COVID-19 Vaccines / chemistry
  • COVID-19 Vaccines / immunology
  • Computational Biology*
  • Databases as Topic
  • Epitope Mapping*
  • Epitopes, B-Lymphocyte / chemistry
  • Epitopes, B-Lymphocyte / immunology
  • Epitopes, T-Lymphocyte / chemistry
  • Epitopes, T-Lymphocyte / immunology
  • Histocompatibility Antigens Class I / metabolism
  • Humans
  • Models, Molecular
  • Protein Conformation
  • Reproducibility of Results
  • SARS-CoV-2 / immunology*
  • Viral Structural Proteins / chemistry
  • Viral Structural Proteins / immunology*


  • COVID-19 Vaccines
  • Epitopes, B-Lymphocyte
  • Epitopes, T-Lymphocyte
  • Histocompatibility Antigens Class I
  • Viral Structural Proteins

Grants and funding

The author(s) received no specific funding for this work.