Design of an Epitope-Based Peptide Vaccine against the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2): A Vaccine-informatics Approach

Abstract

The recurrent and recent global outbreak of SARS-COV-2 has turned into a global concern which has infected more than one million people all over the globe, and this number is increasing in hours. Unfortunate no vaccine or specific treatment is available, which make it more deadly.An immunoinformatics approach has shown significant breakthrough in peptide-based epitope mapping and opens the new horizon in vaccine development. In this study, we have identified a total of 15 antigenic peptides (including T and B Cells) in the surface glycoprotein of SARS-CoV-2 which found to be 100% conserved with other SARS coronaviruses. Furthermore, the population coverage analysis has found that CD4 + T-cell peptides showed higher cumulative population coverage over to CD8 + peptides in the 16 different geographical regions in the world. Notably, only 09 out of 15 peptides (LTDEMIAQY, IRASANLAA, FGAISSVLN, VKQLSSNFG, FAMQMAYRF, FGAGAALQ, VITPGTNTS, WTAGAAAYY and QTQTNSPRRARS) that have 8 0 % െ 9 0 % identity with experimentally identified epitopes of different organisms including SARS-CoV and this will likely be beneficial for a quick progression of the vaccine design. Moreover, docking analysis suggested that these peptides are tightly bound in the groove of HLA molecules which can induce the T-cell response. Overall this study allows us to determine potent peptide antigen targets in surface glycoprotein on intuitive grounds which open up a new horizon in COVID-19 research. However, this study needs experimental validation by in vitro and in vivo. low affinity)(16). We chose those peptides (epitopes) only which have binding affinity 4 0 0 ݊ ݉ for the further analysis. Next, we check the probability of selected peptides for naturally processed and tied with MHC molecule by using MHC-NP tool(20).

Identification of immunodominant linear epitopes from SARS-CoV-2 patient plasma

“…Other antibodies with neutralizing activities have been discovered through different methodologies [20][21][22][23][24][25]. The rapid propagation of SARS-CoV-2 stimulated several studies predicting the antigenic parts of the viral proteins in silico [26][27][28][29][30][31][32], and analyzing SARS-CoV-1 epitopes that were conserved in this new coronavirus [33][34][35][36]. More recently, the first reports of experimental epitope mapping of the SARS-CoV-2 were deposited on repositories [37][38][39][40][41][42].…”

Computationally Optimized SARS-CoV-2 MHC Class I and II Vaccine Formulations Predicted to Target Human Haplotype Distributions

“…We used EvalVax to evaluate peptide vaccines and megapools proposed by other publications ( Lee and Koohy, 2020 ; Fast et al., 2020 ; Poran et al., 2020 ; Bhattacharya et al., 2020 ; Baruah and Bose, 2020 ; Abdelmageed et al., 2020 ; Ahmed et al., 2020 ; Srivastava et al., 2020 ; Herst et al., 2020 ; Vashi et al., 2020 ; Akhand et al., 2020 ; Mitra et al., 2020 ; Khan et al., 2020 ; Banerjee et al., 2020 ; Ramaiah and Arumugaswami, 2020 ; Gupta et al., 2020 ; Saha and Prasad, 2020 ; Tahir ul Qamar et al, 2020 ; Singh et al., 2020 ; Yarmarkovich et al., 2020 ; Grifoni et al., 2020a ; Nerli and Sgourakis, 2020 ; Yazdani et al., 2020 ; Ismail et al., 2020 ) on metrics including EvalVax-Unlinked and EvalVax-Robust population coverage at different per-individual number of peptide-HLA hits thresholds, expected per-individual number of peptide-HLA hits in White, Black, and Asian populations, percentage of peptides that are predicted to be glycosylated, peptides observed to mutate with a probability greater than 0.001, or peptides that sit on known cleavage sites. We define “normalized coverage” as the mean expected per-individual number of peptide-HLA hits for a vaccine divided by the number of peptides in the vaccine.…”

Computationally validated SARS-CoV-2 CTL and HTL Multi-Patch vaccines, designed by reverse epitomics approach, show potential to cover large ethnically distributed human population worldwide

“…On the other hand, the multi-epitope vaccine involves fusion of multiple epitopes identified from the proteome of the SARS-CoV-2 by short peptide linkers. Several subunit and multi-epitope-based vaccine designs have been published claiming potential to activate CD4 and CD8 T-cell immune response driving long-term robust adaptive immunity in the vast majority of the population (Abdelmageed et al, 2020 ; Ahmed et al, 2020 ; Akhand et al, 2020 ; An et al, 2000 ; Banerjee et al, 2020 ; Baruah & Bose, 2020 ; Bhattacharya et al, 2020 ; Fast & Chen, 2020 ; Gragert et al, 2013 ; Gupta et al, 2020 ; Herst et al, 2020 ; Ismail et al, 2020 ; Khan et al, 2020 ; Lee & Koohy, 2020 ; Liu et al, 2020 ; Lu et al, 2014 ; Mitra et al, 2020 ; Nerli & Sgourakis, 2020 ; Poran et al, 2020 ; Ramaiah & Arumugaswami, 2020 ; Saha & Prasad, 2020 ; Sheikhshahrokh et al, 2020 ; Singh et al, 2020 ; Srivastava et al, 2020a ; 2020b ; Ul Qamar et al, 2020 ; Vashi et al, 2020 ; Yarmarkovich, Farrel et al, 2020; Yazdani et al, 2020 ). Numerous highly antigenic regions have also been reported from SARS-CoV-2 proteins, which have been recognized with a large population coverage by favorable binding with large number of HLA allele distributed among different ethnic human population across the world (Grifoni et al, 2020b ; Yarmarkovich, Warrington, et al, 2020 ).…”