Analysis of Mutations in the Receptor Binding Domain of Spike Protein of SARS-COV 2 In Borno State, Nigeria and its Effect on Antigenic Properties

The high mutation rate and RNA nature of SARS-CoV-2 drive rapid evolution, emphasizing the pivotal role of inhibiting viral interaction with host cells for pharmaceutical intervention. The study was aimed to assess the influence of mutation on the receptor binding domain (RBD) of the Spike glycoprotein gene. A combination of experimental (wet lab) and computational (in silico) techniques was utilized. Ten (10) samples were analyzed by amplifying the receptor binding domain of the virus and sequenced using Sanger technique. Sequence alignment analysis was carried out using Clustal w, secondary structure predictions using Chou and Fasman tools, B-cell epitopes using the integrated BepiPred 2.0 prediction module and MHCI and MHCII epitopes using two servers, ProPredI and ProPred. Twenty mutations in the receptor binding domain of the samples were identified and the mutations exert varying degree of effects on the secondary structure of the protein. On the epitopes, 291 B cell epitopes and 307 MHC I, and 435 MHC II were identified. Among them, 79 MHC I and 20 MHC II are potential antigenic sites for multiple subunit vaccine production which were affected by various mutations. Differences were also observed in the number of strong and weak binders in MHCI and MHCII between the reference and the sequenced sample. While none of the mutations was among the prominent ones identified from other parts of the world, the result showed rapid mutation of the virus especially at the receptor binding domain which will be of significant effect. The results highlighted the impact of mutations on antigenic properties, providing valuable insights for future vaccine development strategies against SARS-CoV-2.