Energetics based epitope screening in SARS CoV-2 (COVID 19) spike glycoprotein by Immuno-informatic analysis aiming to a suitable vaccine development

Amrita Banerjee; Dipannita Santra; Smarajit Maiti

As, we have analyzed the spike glycoprotein of COVID 19 which is an infectious particle, transmit from one infected individual to another, alleles of MHC class II were selected for viral epitope specificity analysis. Where HLA-DRB1*01:13 was observed to bind with 2B, 3B, 4B, 5B, 7B and 8B epitope sequences identified on the basis of IC50 value. Among them sequence IIAYTMSLGAENSVA (epitope 8B) was shown with lowest IC50 value of 7.11. On the other hand, HLA-DRB1*04:04 was found for both the sequence of TIMLCCMTSCCSCLK (epitope 5A) and SIIAYTMSLGAENSV (epitope 8A) on highest consensus percentile rank basis. Highest value of 9.5 was found for motif 5. Similarly HLA-DRB1*04:08 was observed for the sequences VRDPQTLEILDITPC (epitope 9A) with highest 9.50 and VSVITPGTNTSNQVA (epitope 10A) with 7.90 consensus percentile rank value. Individual MHC class II molecules were found for others ( Table 3 ). The threshold value of highest consensus percentile rank was selected as 10 for all. As a whole, highest Consensus percentile rank value of 10 was observed for sequence QQLIRAAEIRASANL (epitope 3A) and lowest IC50 value of 7.11 was observed for sequence IIAYTMSLGAENSVA (epitope 8B).