Design of an epitope-based peptide vaccine against the SARS-CoV-2: a vaccine-informatics approach
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Abstract
The recurrent and recent global outbreak of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has turned into a global concern which has infected more than 42 million people all over the globe, and this number is increasing in hours. Unfortunately, no vaccine or specific treatment is available, which makes it more deadly. A vaccine-informatics 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 thymus cells (T-cells) and bone marrow or bursa-derived cells] in the surface glycoprotein (SG) of SARS-CoV-2 which is nontoxic and nonallergenic in nature, nonallergenic, highly antigenic and non-mutated in other SARS-CoV-2 virus strains. The population coverage analysis has found that cluster of differentiation 4 (CD4+) T-cell peptides showed higher cumulative population coverage over cluster of differentiation 8 (CD8+) peptides in the 16 different geographical regions of the world. We identified 12 peptides ((LTDEMIAQY, WTAGAAAYY, WMESEFRVY, IRASANLAA, FGAISSVLN, VKQLSSNFG, FAMQMAYRF, FGAGAALQI, YGFQPTNGVGYQ, LPDPSKPSKR, QTQTNSPRRARS and VITPGTNTSN) that are $80\hbox{--} 90\%$ identical with experimentally determined epitopes of SARS-CoV, and this will likely be beneficial for a quick progression of the vaccine design. Moreover, docking analysis suggested that the identified peptides are tightly bound in the groove of human leukocyte antigen molecules which can induce the T-cell response. Overall, this study allows us to determine potent peptide antigen targets in the SG on intuitive grounds, which opens up a new horizon in the coronavirus disease (COVID-19) research. However, this study needs experimental validation by in vitro and in vivo.
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SciScore for 10.1101/2020.05.03.074930: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Additionally, we check the sequence similarity of peptide sequences with other SG proteins of other SARS-CoV-19 isolates from different geographical regions using Clustal Omega tool[26] to analyze the variation in epitopes-sequences that can determine us whether the epitopes are conserved or have altered peptide ligands. 2. T-Cell Peptides Clustal Omegasuggested: (Clustal Omega, RRID:SCR_001591)Receptor grid was generated using Receptor grid generation in the Glide application by specifying the binding (active) site residues, which was identified by SiteMap tool[57]. SiteMapsuggested: …SciScore for 10.1101/2020.05.03.074930: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Additionally, we check the sequence similarity of peptide sequences with other SG proteins of other SARS-CoV-19 isolates from different geographical regions using Clustal Omega tool[26] to analyze the variation in epitopes-sequences that can determine us whether the epitopes are conserved or have altered peptide ligands. 2. T-Cell Peptides Clustal Omegasuggested: (Clustal Omega, RRID:SCR_001591)Receptor grid was generated using Receptor grid generation in the Glide application by specifying the binding (active) site residues, which was identified by SiteMap tool[57]. SiteMapsuggested: (Biositemaps, RRID:SCR_001976)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: Please consider improving the rainbow (“jet”) colormap(s) used on pages 21 and 22. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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