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

Abstract

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.

Figure 1

Interactions between cytotoxic T lymphocyte binding epitopes and human leukocyte antigen (HLA) chains of corresponding major histocompatibility complex class I supertype representative during molecular dynamics simulations. A, Residue‐residue contacts (X: epitope, Y: HLA) were mapped in contact map matrices. B, Salt bridge‐forming residues were detected in three complexes. C, Continuous hydrogen bonds were observed between all epitopes and corresponding HLA chains throughout the simulations

Figure 2

Discontinuous B cell epitopes in 2019‐nCoV surface glycoprotein and structure validation by Ramachandran plot. Left—five discontinuous B cell epitopes identified in the modeled structure, detailed in Table 3. Right—ramachandran plot indicated a high proportion of residues to be located within the favored and allowed regions. 2019‐nCoV, 2019 novel coronavirus

Figure 3

Visualization of frequency‐based differences in residues of sequential CTL and B cell epitopes across bat coronavirus, MERS‐coronavirus and SARS‐coronavirus. CTL, cytotoxic T lymphocyte; MERS, Middle East respiratory syndrome; SARS, severe acute respiratory syndrome