Extrafollicular B cell responses correlate with neutralizing antibodies and morbidity in COVID-19

  1. Matthew C. Woodruff
  2. Richard P. Ramonell
  3. Doan C. Nguyen
  4. Kevin S. Cashman
  5. Ankur Singh Saini
  6. Natalie S. Haddad
  7. Ariel M. Ley
  8. Shuya Kyu
  9. J. Christina Howell
  10. Tugba Ozturk
  11. Saeyun Lee
  12. Naveenchandra Suryadevara
  13. James Brett Case
  14. Regina Bugrovsky
  15. Weirong Chen
  16. Jacob Estrada
  17. Andrea Morrison-Porter
  18. Andrew Derrico
  19. Fabliha A. Anam
  20. Monika Sharma
  21. Henry M. Wu
  22. Sang N. Le
  23. Scott A. Jenks
  24. Christopher M. Tipton
  25. Bashar Staitieh
  26. John L. Daiss
  27. Eliver Ghosn
  28. Michael S. Diamond
  29. Robert H. Carnahan
  30. James E. Crowe
  31. William T. Hu
  32. F. Eun-Hyung Lee
  33. Ignacio Sanz

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Abstract

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  1. Version published to 10.1038/s41590-020-00814-z
  2. Version published to 10.1101/2020.04.29.20083717v2 on medRxiv
  3. ScreenIT

    SciScore for 10.1101/2020.04.29.20083717: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: Human Subjects: All research was approved by the Emory University Institutional Review Board (Emory IRB numbers IRB00058507, IRB00057983, and IRB00058271) and was performed in accordance with all relevant guidelines and regulations.
    Consent: Written informed consent was obtained from all participants or, if they were unable to provide informed consent, obtained from designated healthcare surrogates.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Median Fluorescent Intensity (MFI) using combined or individual detection antibodies (anti-IgA/anti-IgG/anti-IgM) was measured using the Luminex xPONENT software.
    anti-IgA/anti-IgG/anti-IgM
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Nucleocapsid (N) protein expressed from E. coli (N-terminal His6) was obtained from Raybiotech (230-01104-100) and the Receptor Binding Domain (RBD) of Spike protein expressed from HEK293 was obtained from the laboratory of Dr. Jens Wrammert37.
    HEK293
    suggested: None
    Software and Algorithms
    SentencesResources
    Peripheral blood was collected in either heparin sodium tubes (PBMCs) (BD Diagnostic Systems) or serum tubes (serum) (BD Diagnostic Systems).
    BD Diagnostic Systems
    suggested: None
    Study data were collected and managed using REDCap electronic data capture tools hosted at Emory University35 Peripheral Blood Mononuclear Cell Isolation and Plasma Collection: Peripheral blood samples were collected in heparin sodium tubes and processed within 6 hours of collection.
    REDCap
    suggested: (REDCap, RRID:SCR_003445)
    All samples were concatenated to create a single composite, and a UMAP algorithm for dimensionality reduction was applied using the UMAP plugin (V3.1) available on the FlowJo Exchange.
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)
    Custom plotting such as Ag-specific response curves was performed using the ggplot2 library for base analysis, and then post-processed in Adobe Illustrator.
    ggplot2
    suggested: (ggplot2, RRID:SCR_014601)
    Adobe Illustrator
    suggested: (Adobe Illustrator, RRID:SCR_010279)
    Circos plotting was carried out using Circos software, version 0.69-9.
    Circos
    suggested: (Circos, RRID:SCR_011798)
    Lineage trees were claculated using GLaMST (Grow Lineages along Minimum Spanning Tree) software36, run on matlab, and then visualized in R using the iGraph package, version 1.2.4.2.
    matlab
    suggested: (MATLAB, RRID:SCR_001622)
    iGraph
    suggested: (igraph, RRID:SCR_019225)
    Statistical analyses were performed directly in R, or in Graphpad Prism, version 8.2.1.
    Graphpad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Statistical Analysis: Statistical analysis was carried out using Prism statistical analysis software.
    Prism
    suggested: (PRISM, RRID:SCR_005375)

    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 10.1101/2020.04.29.20083717v1 on medRxiv