Immunoinformatics-aided identification of T cell and B cell epitopes in the surface glycoprotein of 2019-nCoV

J Med Virol. 2020 May;92(5):495-500. doi: 10.1002/jmv.25698. Epub 2020 Mar 3.


The 2019 novel coronavirus (2019-nCoV) outbreak has caused a large number of deaths with thousands of confirmed cases worldwide, especially in East Asia. This study took an immunoinformatics approach to identify significant cytotoxic T lymphocyte (CTL) and B cell epitopes in the 2019-nCoV surface glycoprotein. Also, interactions between identified CTL epitopes and their corresponding major histocompatibility complex (MHC) class I supertype representatives prevalent in China were studied by molecular dynamics simulations. We identified five CTL epitopes, three sequential B cell epitopes and five discontinuous B cell epitopes in the viral surface glycoprotein. Also, during simulations, the CTL epitopes were observed to be binding MHC class I peptide-binding grooves via multiple contacts, with continuous hydrogen bonds and salt bridge anchors, indicating their potential in generating immune responses. Some of these identified epitopes can be potential candidates for the development of 2019-nCoV vaccines.

Keywords: 2019-nCoV; COVID-19; SARS-CoV-2; coronavirus; epitope prediction; immunoinformatics.

MeSH terms

  • Betacoronavirus / immunology*
  • COVID-19
  • China
  • Computational Biology*
  • Coronavirus Infections
  • Epitopes, B-Lymphocyte / immunology*
  • Epitopes, T-Lymphocyte / immunology*
  • Histocompatibility Antigens Class I / immunology*
  • Humans
  • Molecular Dynamics Simulation
  • Pneumonia, Viral
  • Protein Structure, Tertiary
  • SARS-CoV-2
  • Viral Envelope Proteins / immunology*


  • Epitopes, B-Lymphocyte
  • Epitopes, T-Lymphocyte
  • Histocompatibility Antigens Class I
  • Viral Envelope Proteins