High-Resolution Linear Epitope Mapping of the Receptor Binding Domain of SARS-CoV-2 Spike Protein in COVID-19 mRNA Vaccine Recipients

  1. Yuko Nitahara
  2. Yu Nakagama
  3. Natsuko Kaku
  4. Katherine Candray
  5. Yu Michimuko
  6. Evariste Tshibangu-Kabamba
  7. Akira Kaneko
  8. Hiromasa Yamamoto
  9. Yasumitsu Mizobata
  10. Hiroshi Kakeya
  11. Mayo Yasugi
  12. Yasutoshi Kido

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Abstract

Establishing vaccine-based population immunity has been the key factor in attaining herd protection. Thanks to expedited worldwide research efforts, the potency of mRNA vaccines against the coronavirus disease 2019 (COVID-19) is now incontestable.

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  1. Version published to 10.1128/spectrum.00965-21
  2. Version published to 10.1101/2021.07.03.21259953v2 on medRxiv
  3. ScreenIT

    SciScore for 10.1101/2021.07.03.21259953: (What is this?)

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

    Table 1: Rigor

    EthicsConsent: All subjects provided written consent before participating in this study.
    IRB: This study was approved by the institutional review board of Osaka City University (#2020-003) and the Graduate School of Life and Environmental sciences and the Graduate School of Sciences, Osaka Prefecture University.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Antibodies targeting the viral nucleocapsid protein (Anti-N IgG) was also performed on vaccine recipients to screen unrecognized exposure to SARS-CoV-2 prior to the vaccination (Abbot SARS-CoV-2 IgG assay, USA) (23)
    Anti-N IgG
    suggested: None
    After fixation (4% paraformaldehyde, 15 minutes), cells were permeabilized (0.1% TritonX100, 15 minutes) and incubated with rabbit anti-spike monoclonal antibodies (Sino biological, China) (1:1000, 1 hour at 37°C).
    anti-spike monoclonal antibodies ( Sino biological , China )
    suggested: None
    Synthesized arrays were probed with sera at a 1:400 dilution followed by incubation with horseradish peroxidase conjugated goat anti-human IgA +IgG +IgM polyclonal antibody at a 1:30,000 dilution.
    anti-human IgA +IgG
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    The monolayer of VeroE6 cells (National Institutes of Biomedical Innovation, Health and Nutrition, Japan) were then absorbed with the mixtures at 37°C.
    VeroE6
    suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)
    Software and Algorithms
    SentencesResources
    Half-maximal neutralization titers (NT50) of the neutralization assay were calculated using GraphPad Prism 9.1.0.221 and Microsoft Excel for Microsoft 365 MSO (16.0.14026.20202).
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Microsoft Excel
    suggested: (Microsoft Excel, RRID:SCR_016137)
    The images to depict the recognized epitopes are shown using The PyMOL Molecular Graphics System, Version 1.2r3pre, Schrödinger, LLC.
    PyMOL
    suggested: (PyMOL, RRID:SCR_000305)

    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:
    Limitations: There are several limitations in our study. The severity of the COVID-19 patients evaluated in this study was high (seven out of ten were critical) with comorbidities, whereas the vaccine recipients were relatively healthy without major comorbidities. The age was distributed in both groups. This analysis was focused exclusively on the linear epitope profile targeting RBD. Experimental observations on compositional epitopes nor epitopes outside the RBD region was not made in this study. Nonetheless, our results reporting the mRNA vaccine’s broader RBD epitope variety are in concordance with preceding reports. This result was consistent with the recently reported immune profile of Moderna vaccines (37).

    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.

  4. Version published to 10.1101/2021.07.03.21259953v1 on medRxiv