Predicting Epitope Candidates for SARS-CoV-2
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Abstract
Epitopes are short amino acid sequences that define the antigen signature to which an antibody binds. In light of the current pandemic, epitope analysis and prediction is paramount to improving serological testing and developing vaccines. In this paper, we leverage known epitope sequences from SARS-CoV, SARS-CoV-2 and other Coronaviridae and use those known epitopes to identify additional antigen regions in 62k SARS-CoV-2 genomes. Additionally, we present epitope distribution across SARS-CoV-2 genomes, locate the most commonly found epitopes, discuss where epitopes are located on proteins, and how epitopes can be grouped into classes. We also discuss the mutation density of different regions on proteins using a big data approach. We find that there are many conserved epitopes between SARS-CoV-2 and SARS-CoV, with more diverse sequences found in Nucleoprotein and Spike Glycoprotein.
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SciScore for 10.1101/2022.02.09.479786: (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 Default parameters were used to run BLASTN and an e-value threshold of 0.01 was chosen since that indicated statistically significant match44. BLASTNsuggested: (BLASTN, RRID:SCR_001598)To obtain position-based clustering of the epitopes, the following steps were carried out: 3.6 Identification of Epitopes on Protein: 3.6.1 Mutations in Proteins affecting Epitopes and Mutation Density: Certain epitopes were not found by MSA as exact subsequences on proteins. Proteinsuggested: NoneFirst, we compared the reference sequence from UniProt with the sequence of the protein structures deposited in … SciScore for 10.1101/2022.02.09.479786: (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 Default parameters were used to run BLASTN and an e-value threshold of 0.01 was chosen since that indicated statistically significant match44. BLASTNsuggested: (BLASTN, RRID:SCR_001598)To obtain position-based clustering of the epitopes, the following steps were carried out: 3.6 Identification of Epitopes on Protein: 3.6.1 Mutations in Proteins affecting Epitopes and Mutation Density: Certain epitopes were not found by MSA as exact subsequences on proteins. Proteinsuggested: NoneFirst, we compared the reference sequence from UniProt with the sequence of the protein structures deposited in the Protein Data Bank48, 49 and then we visualize the epitope positions in the 3D shape of the protein by selecting the protein deposited structure showing 100% identity with the consensus sequence. UniProtsuggested: (UniProtKB, RRID:SCR_004426)Thus, we generated four BLAST databases, one for each protein and cell type. BLASTsuggested: (BLASTX, RRID:SCR_001653)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: 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.
- No funding statement was detected.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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