Potential T-cell and B-cell Epitopes of 2019-nCoV

Abstract

As of Feb 16th 2020, 2019-nCoV has infected more than 51,857 people across 26 countries and claimed 1666 lives. 2019-nCoV is a novel form of coronavirus that causes COVID-19 and has high similarity with SARS-CoV. No approved vaccine yet exists for 2019-nCoV or any form of coronavirus. Here we use computational tools from structural biology and machine learning to identify 2019-nCoV T-cell and B-cell epitopes based on viral protein antigen presentation and antibody binding properties. These epitopes can be used to develop more effective vaccines and identify neutralizing antibodies. We identified 405 viral peptides with good antigen presentation scores for both human MHC-I and MHC-II alleles, and two potential neutralizing B-cell epitopes near the 2019-nCoV spike protein receptor binding domain (440-460 and 494-506). Analyzing mutation profiles of 68 viral genomes from four continents, we identified 96 coding-change mutations. These mutations are more likely to occur in regions with good MHC-I presentation scores (p=0.02). No mutations are present near the spike protein receptor binding domain. We validated our computational pipeline with SARS-CoV experimental data.Both humoral immunity provided by B-cell antibodies and cellular immunity provided by T-cells are essential for effective vaccines [10,11]. Though humans can usually mount an antibody response . CC-BY-NC 4.0

A Multi-Epitope Vaccine Against Sars-Cov-2 Directed Towards the Latin American Population: An Immunoinformatics Approach

“…In HLA-I molecules, we found a greater number of predicted agglutinations associated with the C locus, with a median of 82 agglutinations. In the complete dataset, B*27:05 (n = 8) was the least frequent allele, whereas C*08:01 (n = 98) was the most frequent; this has been reported in other populations 56 . Thus, the C locus should be a focus of future research on increased recognition of SARS-CoV-2 and could be used in future rational vaccine formulations.…”

“…The adjuvant Pan DR T helper epitope (PADRE) was also attached to the construct; it is relevant in multi-epitope constructs given its ability to potently stimulate the innate and humoral immune systems through generation of high and speci c IgG titers. It can also overcome barriers, indicated by the high diversity among HLA molecules; hence, it reaches a larger population and is safe 56,57 . Towards the C terminal, a peptide domain capable of interacting with M cells and mediating up to an 8-fold increase in intestinal absorption was added 58 .…”

Analysis of the full genome sequences of SARS-CoV-2 isolates to determine antigenic proteins and epitopes to be used for the development of a vaccine or a diagnostic approach for COVID-19

“…These findings indicate that the abovementioned epitopes may have promising neutralizing effect against SARS-CoV-2. In a previous in silico study, five different epitopes (SYGFQPTNGVGYQPY; SQSIIAYTMSLGAEN; IPTNFTISVTTEILP; AAAYYVGYLQPRTFL; APHGVVFLHVTYVPA) related to both MHC-I and II were predicted in S protein 51 and only one of them overlapped with a highly antigenic epitope (PTNFTISVTTEILPV) predicted in our study. In another in silico study, 14 epitopes were predicted in S protein for T cells 52 and six of them were detected to overlap with epitopes predicted in our study.…”

Shared Antigen-specific CD8+ T cell Responses Against the SARS-COV-2 Spike Protein in HLA A*02:01 COVID-19 Participants

“…These matched reasonably well with published lists of putative antigens. [10][11][12] We then utilized standard plasmid cloning techniques, followed by mammalian cell transfection and expression, to build a library of soluble, secreted peptide-major histocompatibility complexes (pMHCs), in which each library element is a single chain trimer (SCT) that contains the peptide antigen covalently linked to the β-2 microglobulin subunit linked to the HLA subunit ( Fig. 1A).…”