Identification of Epitope Against Omicron Variant of SARS-CoV-2: In Silico Vaccine Design Approach

Abstract

SARS-CoV-2, which causes COVID-19, resulted in a global pandemic, and there were millions of confirmed cases and deaths worldwide. The vaccines were developed and distributed to help control the spread of the virus. The numbers and information related to the COVID-19 pandemic have likely evolved. Therefore, rapid immunological epitope identification would be a useful screening technique for vaccine candidates. The aim of this study is to anticipate the protective epitopes for vaccine development using bioinformatics methods and resources The SARS-CoV-2 genome and protein sequences were retrieved. Furthermore, using the ABCpred server, sequential B-cell epitope analysis was carried out. The Ellipro algorithm was used to forecast discontinuous B-cell epitopes. Moreover, by utilising the NetCTL server, a sequential T-cell epitope analysis was carried out. Furthermore, the 3D structure of the peptide was created using the PEP-FOLD3 server, and the 3D structure of the HLA molecule was identified using the homology modelling tool. The molecular docking was performed by AutoDock Vina. There were 20 B-cell epitopes altogether, of which 11 are highly antigenic. After assessing the antigenicity and toxicity of each resultant epitope, it was determined that the epitope SVLYNLAPFFTFKCYG is highly antigenic. Then, out of the 6 T-cell epitopes we had found, "RSYSFRPTY" was chosen as the epitope most suited for further research. Consequently, 72.42% of the population is covered overall. The structure that was generated was refined and energyminimized. RSYSFRPTY's binding affinity to the groove of HLA-B*15:01 was determined by docking study to be -7.5 kcal/mol. PyMOL's visualisation of the docking result for predicting binding sites. The final B-cell and T-cell epitopes are “SVLYNLAPFFTFKCYG” and “RSYSFRPTY” in terms of antigenicity score and nonallergenic and nontoxic qualities. An in Silico study indicated that our hypothesised T cell epitope “RSYSFRPTY” had a greater affinity for binding with its receptor, which might elicit an immune response against the omicron variant.