Genetic and Structural Analysis of SARS-CoV-2 Spike Protein for Universal Epitope Selection
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Abstract
Evaluation of immunogenic epitopes for universal vaccine development in the face of ongoing SARS-CoV-2 evolution remains a challenge. Herein, we investigate the genetic and structural conservation of an immunogenically relevant epitope (C662–C671) of spike (S) protein across SARS-CoV-2 variants to determine its potential utility as a broad-spectrum vaccine candidate against coronavirus diseases. Comparative sequence analysis, structural assessment, and molecular dynamics simulations of C662–C671 epitope were performed. Mathematical tools were employed to determine its mutational cost. We found that the amino acid sequence of C662–C671 epitope is entirely conserved across the observed major variants of SARS-CoV-2 in addition to SARS-CoV. Its conformation and accessibility are predicted to be conserved, even in the highly mutated Omicron variant. Costly mutational rate in the context of energy expenditure in genome replication and translation can explain this strict conservation. These observations may herald an approach to developing vaccine candidates for universal protection against emergent variants of coronavirus.
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SciScore for 10.1101/2021.08.30.458222: (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 For Alpha, Beta, Gamma, and Delta VOCs, the associated mutations were introduced by using Modeller 10.1.36 All-atom explicit-solvent simulations were performed by using GROMACS 2020.3.37,38 Each system was solvated by using TIP3P water molecules,39 with a 10-Å buffer between the protein and the edge of the box. Modellersuggested: (MODELLER, RRID:SCR_008395)GROMACSsuggested: (GROMACS, RRID:SCR_014565)All analyses were performed in MATLAB R2018a. MATLABsuggested: (MATLAB, RRID:SCR_001622)Results from OddPub: Thank you for sharing your data.
Results from LimitationRecognizer: An explicit …SciScore for 10.1101/2021.08.30.458222: (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 For Alpha, Beta, Gamma, and Delta VOCs, the associated mutations were introduced by using Modeller 10.1.36 All-atom explicit-solvent simulations were performed by using GROMACS 2020.3.37,38 Each system was solvated by using TIP3P water molecules,39 with a 10-Å buffer between the protein and the edge of the box. Modellersuggested: (MODELLER, RRID:SCR_008395)GROMACSsuggested: (GROMACS, RRID:SCR_014565)All analyses were performed in MATLAB R2018a. MATLABsuggested: (MATLAB, RRID:SCR_001622)Results from OddPub: Thank you for sharing your data.
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: We did not find any issues relating to colormaps.
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.
Results from scite Reference Check: We found no unreliable references.
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