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.

COVID-19, an emerging coronavirus infection: advances and prospects in designing and developing vaccines, immunotherapeutics, and therapeutics

“…The interactions between these epitopes and their corresponding MHC class I molecules were studied further by using molecular dynamics simulations and found that the CTL epitopes bind with MHC class I peptide-binding grooves via multiple contacts, thus indicating their potential for generating immune responses. 30 Such epitopes may possess the ideal characteristics to become part of COVID-19 vaccine candidates. The nucleocapsid (N) protein as well as the potential B cell epitopes of the E protein of MERS-CoV has been suggested as probable immunoprotective targets that induce both T-cell and neutralizing antibody responses.…”

Immune-epidemiological parameters of the novel coronavirus – a perspective

“…As the analysis of protein sequences has shown, eight HLA-DR epitopes that are located in the Spike, Envelope, and Membrane of the 2019-nCoV play an essential part in the obstruction of the immune surveillance [29]. Also, there are B-cell and cytotoxic T lymphocyte epitopes that are uniquely present on the surface glycoprotein of 2019-nCoV [36]. These epitopes are likely a vaccine target for the 2019-nCoV.…”

SARS-CoV-2 proteome microarray for mapping COVID-19 antibody interactions at amino acid resolution

“…The identification of B-cell and T-cell epitopes for SARS-COV-2 proteins is critical for the development of effective diagnostic tests and vaccine, especially for structural N and S proteins, which had been predicted by bioinformatics 19,20 . For example, there are several RT-PCR tests for detecting COVID-19 that target the S or N protein genome 21 .…”