Array-based analysis of SARS-CoV-2, other coronaviruses, and influenza antibodies in convalescent COVID-19 patients

  1. Daniel J. Steiner
  2. John S. Cognetti
  3. Ethan P. Luta
  4. Alanna M. Klose
  5. Joseph Bucukovski
  6. Michael R. Bryan
  7. Jon J. Schmuke
  8. Phuong Nguyen-Contant
  9. Mark Y. Sangster
  10. David J. Topham
  11. Benjamin L. Miller

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Abstract

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  1. Version published to 10.1016/j.bios.2020.112643
  2. ScreenIT

    SciScore for 10.1101/2020.06.15.153064: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: Sera were drawn under a protocol approved by the University of Rochester Medical Center Institutional Review Board.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.
    Cell Line AuthenticationAuthentication: During development, several printing concentrations and/or solution pH values of each antigen were tested, along with sugar additives (glycerol, trehalose) in order to optimize spot uniformity and morphology as well as initial probe thickness.

    Table 2: Resources

    Antibodies
    SentencesResources
    Secondary antibodies were diluted to 1 μg/mL for both goat α-hIgG (Jackson Immunoresearch) and rabbit α-hIgM (Rockland, Inc.) in Adarza diluent.
    α-hIgG
    suggested: None
    α-hIgM
    suggested: None
    While anti-FITC spots were designed to serve as an intra-chip normalizer, these were not used as such due to the unexpected presence of anti-goat IgG antibodies in some single donor human serum samples.
    anti-FITC
    suggested: None
    anti-goat IgG
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    SARS-CoV2 nucleocapsid expressed in mammalian cells was obtained from RayBiotech, while HCoV-229E and HCoV-OC43 spike proteins (baculovirus-expressed) were obtained from Sino Biological.
    HCoV-229E
    suggested: None
    Software and Algorithms
    SentencesResources
    Aminereactive substrates for fabrication of AIR arrays were provided by Adarza BioSystems, Inc.
    Adarza BioSystems
    suggested: None
    The median intensity values were converted to median thickness values using a best-fit line to an experimentally derived reflectance model.14 Then, the median thickness values were further processed in Microsoft Excel as described below, and are referred to simply as “thickness” hereafter.
    Microsoft Excel
    suggested: (Microsoft Excel, RRID:SCR_016137)

    Results from OddPub: Thank you for sharing your data.

    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.

  3. Version published to 10.1101/2020.06.15.153064v1 on bioRxiv