Molecular analysis of a public cross-neutralizing antibody response to SARS-CoV-2

  1. Meng Yuan
  2. Yiquan Wang
  3. Huibin Lv
  4. Timothy J.C. Tan
  5. Ian A. Wilson
  6. Nicholas C. Wu

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Abstract

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  1. Version published to 10.1016/j.celrep.2022.111650
  2. ScreenIT

    SciScore for 10.1101/2022.05.17.492220: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Dataset collection: The information on antibodies S24-223, P2B-1E4, 2-7, LY-CoV1404, XG005, XG031, and COV2-2268 were compiled in our previous study [12], whereas the information on XGv042, XGv264, XGv265, and XGv266 were compiled in CoV-AbDab [38].
    LY-CoV1404, XG005
    suggested: None
    Allele assignment of IGHV2-5/IGLV2-14-encoded RBD antibodies: For antibodies P2B-1E4, XG005, and XG031, the allele information was obtained from the original publications [14, 16].
    XG031
    suggested: None
    All “ambiguous” allele assignments in this study came from antibodies that do not have nucleotide sequence information available, namely XGv264, XGv265, and XGv266.
    XGv266
    suggested: None
    Software and Algorithms
    SentencesResources
    Somatic hypermutations were identified by IgBlast [25].
    IgBlast
    suggested: (IgBLAST, RRID:SCR_002873)
    Analysis of CDR H3 sequences: Sequence alignment was performed using MAFFT [40].
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    Sequence logos were generated by WebLogo [42].
    WebLogo
    suggested: (WEBLOGO, RRID:SCR_010236)

    Results from OddPub: Thank you for sharing your code.

    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.

    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 10.1101/2022.05.17.492220v1 on bioRxiv