Distinct antibody repertoires against endemic human coronaviruses in children and adults

  1. Taushif Khan
  2. Mahbuba Rahman
  3. Fatima Al Ali
  4. Susie S.Y. Huang
  5. Manar Ata
  6. Qian Zhang
  7. Paul Bastard
  8. Zhiyong Liu
  9. Emmanuelle Jouanguy
  10. Vivien Beziat
  11. Aurélie Cobat
  12. Gheyath K. Nasrallah
  13. Hadi M. Yassine
  14. Maria K. Smatti
  15. Amira Saeed
  16. Isabelle Vandernoot
  17. Jean-Christophe Goffard
  18. Guillaume Smits
  19. Isabelle Migeotte
  20. Filomeen Haerynck
  21. Isabelle Meyts
  22. Laurent Abel
  23. Jean-Laurent Casanova
  24. Mohammad R. Hasan
  25. Nico Marr

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Abstract

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  1. Version published to 10.1172/jci.insight.144499
  2. Version published to 10.1101/2020.06.21.163394v2 on bioRxiv
  3. ScreenIT

    SciScore for 10.1101/2020.06.21.163394: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: The human subject research described here had been approved by the institutional research ethics boards of Sidra Medicine, Qatar Biobank, INSERM, and Erasme Hospital.
    RandomizationFor the purpose of this study, specimen from male Qatari nationals 19 to 66 years of age (Supplementary Table S1) were selected from a larger blood donor cohort including 5983 individuals, and then age-matched male donors with other nationalities were randomly selected (Supplementary Figure S1).
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variableStudy design and samples: We performed a retrospective analysis of deidentified or coded plasma and serum samples collected from three different human cohorts, namely: i) 400 healthy male adult blood donors (ABD) of a blood bank in Qatar with diverse ethnic background and nationality (Supplementary Figure S1A); ii) 800 adult male and female Qatari nationals and long-term residents of Qatar who are participating in a national cohort study— the Qatar Biobank (QBB)—and who represent the general local population in the State of Qatar [32]; and iii) 231 pediatric subjects with Qatari nationality who were admitted to, or visited outpatient clinics of, Sidra Medicine.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Software: Open source Python modules with in-house scripts were used to test for associations (statsmodel v0.11), to filter differentially enrichment peptides and to perform different statistical tests (sklearn v0.23, scipy v1.14.1).
    Python
    suggested: (IPython, RRID:SCR_001658)
    scipy
    suggested: (SciPy, RRID:SCR_008058)
    Multiple sequence alignments were done using the MAFFT [73, 74] via EMBL-EBI’s web services and Java Alignment Viewer (Jalview) for visualization [75].
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    Jalview
    suggested: (Jalview, RRID:SCR_006459)
    Protein structures graphics were generated using PyMOL (Schrödinger).
    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: 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.

  4. Version published to 10.1101/2020.06.21.163394v1 on bioRxiv