Mikrobiol. Z. 2021; 83(1):78-86.
doi: https://doi.org/10.15407/microbiolj83.01.078

Identification of Cytotoxic T-Cell and B-Cell Epitopes in the Nucleocapsid Phosphoprotein
of SARS-COV-2 Using Immunoinformatics

A.A. Dawood

University of Mosul
Almajmuaa Str., Mosul, 41002, Nineveh, Iraq

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.

Keywords: Nucleocapsid phosphoprotein, SARS-CoV, Immunoinformatics, MHC epitope, Cytotoxic T-cells, Affinity.

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