Sampling SARS-CoV-2 Proteomes for Predicted CD8 T-Cell Epitopes as a Tool for Understanding Immunogenic Breadth and Rational Vaccine Design
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Abstract
Predictive models for vaccine design have become a powerful and necessary resource for the expeditiousness design of vaccines to combat the ongoing SARS-CoV-2 global pandemic. Here we use the power of these predicted models to assess the sequence diversity of circulating SARS-CoV-2 proteomes in the context of an individual’s CD8 T-cell immune repertoire to identify potential. defined regions of immunogenicity. Using this approach of expedited and rational CD8 T-cell vaccine design, it may be possible to develop a therapeutic vaccine candidate with the potential for both global and local coverage.
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SciScore for 10.1101/2020.08.15.250647: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization For comparison, set-building was performed a second time using randomly selected proteomes instead of choosing the proteome that resulted in the greatest increase of peptide coverage. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
No key resources detected.
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: We detected the following sentences addressing limitations in the study:However, limitations in both these studies including that …
SciScore for 10.1101/2020.08.15.250647: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization For comparison, set-building was performed a second time using randomly selected proteomes instead of choosing the proteome that resulted in the greatest increase of peptide coverage. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
No key resources detected.
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: We detected the following sentences addressing limitations in the study:However, limitations in both these studies including that ORF1ab peptides were not examined in one study, the sample size in both was small, peptides were generated from the reference strain and the HLA Class 1 distribution was limited, may mean that potential regions of interest have been overlooked. We identified 409 predicted CD8 peptides that have 100% conservation within our sample set with >90% of the predicted epitopes contained within either the ORF1ab polypeptide or spike glycoprotein. Furthermore, the predicted epitopes appear to cluster within a ∼550 a.a region of the spike glycoprotein (amino acid 319-865) and within 2 regions of the ORF1ab polypeptide (amino acid positions 2750-3250 and 4500-5500). Future experimental testing of these epitopes would confirm whether natural infection induces CD8 T-cell responses targeting these regions, but from an in silico perspective they offer a potential target for developing a therapeutic T-cell vaccine that warrants further investigation.
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.
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