Potential CD8+ T Cell Cross-Reactivity Against SARS-CoV-2 Conferred by Other Coronavirus Strains

  1. Chloe H. Lee
  2. Mariana Pereira Pinho
  3. Paul R. Buckley
  4. Isaac B. Woodhouse
  5. Graham Ogg
  6. Alison Simmons
  7. Giorgio Napolitani
  8. Hashem Koohy

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Abstract

No abstract available

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  1. Version published to 10.3389/fimmu.2020.579480
  2. ScreenIT

    SciScore for 10.1101/2020.05.20.107292: (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
    SentencesResources
    The Repitope package was retrieved from GitHub repository (https://github.com/masato-ogishi/Repitope.git).
    Repitope
    suggested: None
    Visualization of private and public peptides: The conservation of peptides across coronavirus strains before and after MHC binding and immunogenicity prediction were visualized by ‘venn’ function from R venn v1.9 package and upset function from R UpSetR v1.4.0 package.
    R UpSetR
    suggested: None
    To identify shared peptides with up to two amino acid tolerance, the best matching peptides were identified by ‘pairwiseAlignment’ from Biostrings v2.40.2 package using BLOSUM62 matrix, gapOpening of 100 and gapExtension of 100, followed by hamming distance to filter only peptide pairs with less than or equal to two amino acid difference.
    Biostrings
    suggested: (Biostrings, RRID:SCR_016949)

    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.
    • 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.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  3. Version published to 10.1101/2020.05.20.107292v1 on bioRxiv