Identification of cytotoxic t-cell and b-cell epitopes in the nucleocapsid phosphoprotein of sars-cov-2 using immunoinformatics

Abstract

Last December, a novel coronavirus emerged in Wuhan city, China. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes a high intense acute respiratory syndrome with elevation mortality. Nucleocapsid phosphoprotein (NP) is one of the most structural proteins of the virus. NP possesses active immunogenicity for T-cell response. Because NP considered as a potential vaccine target, our study goal was to identify the cytotoxic T-cell (CTL) and B-cell epitopes inside NP peptides. Methods. We used a series of popular immunoinformatics and algorithm tools such as FASTA-NCBI, CLUSTAL-OMGA, T-COFFEE, SWISS-MODEL, CTLPred and its branches. Results. Homology modeling and alignment of SARS-CoV-2 NP showed high conserved residues compared with related sequences. Different types of the major histocompatibility complex (MHC) alleles were identified, specifically human leukocyte antigens (HLA-A) affinity for NP. We also demonstrate six B-cell epitopes with a high score above the threshold. Conclusions. We recorded high binder HLA-A*02:01 alleles matched between the novel coronavirus SARS-CoV-2 NP and the Bat coronavirus SARS-Bat-CoV NP. Identification of CTL response and B-cell predictions will be helpful in reverse immunogenetic approaches, hence in the strategy process of the plausible design of the vaccine.