Immunoglobulin G1 Fc glycosylation as an early hallmark of severe COVID-19

  1. Tamas Pongracz
  2. Jan Nouta
  3. Wenjun Wang
  4. Krista E. van Meijgaarden
  5. Federica Linty
  6. Gestur Vidarsson
  7. Simone A. Joosten
  8. Tom H.M. Ottenhoff
  9. Cornelis H. Hokke
  10. Jutte J.C. de Vries
  11. Sesmu M. Arbous
  12. Anna H.E. Roukens
  13. Manfred Wuhrer

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Abstract

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  1. Version published to 10.1016/j.ebiom.2022.103957
  2. ScreenIT

    SciScore for 10.1101/2021.11.18.21266442: (What is this?)

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

    Table 1: Rigor

    EthicsConsent: After informed consent was obtained from the patient or his/her relatives, longitudinal sampling was performed for the duration of the hospital admission, and one convalescent sample was obtained at the outpatient follow-up appointment, which was scheduled six weeks after hospital discharge.
    IRB: The Medical Ethics Committee Leiden-Den Haag-Delft (NL73740.058.20) approved the study.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power AnalysisStatistical sample size calculation was not performed, the sample size was determined based on availability.

    Table 2: Resources

    Antibodies
    SentencesResources
    2.7 Antibody titer measurement: Semi-quantitative detection of SARS-CoV-2 anti-nucleocapsid (N) protein IgG was performed on the Abbott Architect platform.21-23 In this antibody chemiluminescent microparticle immunoassay (CMIA) test, the SARS-CoV-2 antigen coated paramagnetic microparticles bind to the IgG antibodies that attach to the viral nucleocapsid protein in human serum samples.
    anti-nucleocapsid ( N ) protein IgG
    suggested: None
    IgG
    suggested: None
    Quantitative detection of SARS-CoV-2 anti-S1/S2 IgG antibodies was performed using the DiaSorin LIAISON platform.
    anti-S1/S2 IgG
    suggested: None
    Semi-quantitative detection of SARS-CoV-2 anti-RBD IgM antibodies was performed using the Wantai IgM-ELISA (CE-IVD) kit (Sanbio).24 Briefly, the IgM u-chain capture method was used to detect IgM antibodies using a double-antigen sandwich immunoassay using mammalian cell-expressed recombinant antigens containing the RBD of the spike protein of SARS-CoV-2 and the immobilized and horseradish peroxidase-conjugated antigen.
    anti-RBD IgM
    suggested: None
    horseradish peroxidase-conjugated antigen .
    suggested: None
    Semi-quantitative detection of SARS-CoV-2 anti-S1 IgA antibodies was performed using the Euroimmun IgA 2-step ELISA.
    anti-S1 IgA
    suggested: None
    Software and Algorithms
    SentencesResources
    2.6 Cytokine measurements by cytometric bead array: Circulating cytokine and chemokine levels were determined in serum using commercially available bead based multiplex assays using the BioPLex 100 system for acquisition as previously described.
    BioPLex
    suggested: (BioPlex, RRID:SCR_016144)
    2.7 Antibody titer measurement: Semi-quantitative detection of SARS-CoV-2 anti-nucleocapsid (N) protein IgG was performed on the Abbott Architect platform.21-23 In this antibody chemiluminescent microparticle immunoassay (CMIA) test, the SARS-CoV-2 antigen coated paramagnetic microparticles bind to the IgG antibodies that attach to the viral nucleocapsid protein in human serum samples.
    Abbott Architect
    suggested: (Abbott ARCHITECT i1000sr System, RRID:SCR_019328)
    All statistical analyses and visualizations were performed in R, version 4.1.0 (R Foundation for Statistical Computing, Vienna, Austria) and RStudio, version 1.4.1717 (RStudio, Boston, MA). 2.10 Role of funding source: The funders had no role in study design, data collection, data analysis, data interpretation, or writing of the report.
    RStudio
    suggested: (RStudio, RRID:SCR_000432)

    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.

    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 10.1101/2021.11.18.21266442v1 on medRxiv