A Combination of Receptor-Binding Domain and N-Terminal Domain Neutralizing Antibodies Limits the Generation of SARS-CoV-2 Spike Neutralization-Escape Mutants

  1. Denise Haslwanter
  2. M. Eugenia Dieterle
  3. Anna Z. Wec
  4. Cecilia M. O’Brien
  5. Mrunal Sakharkar
  6. Catalina Florez
  7. Karen Tong
  8. C. Garrett Rappazzo
  9. Gorka Lasso
  10. Olivia Vergnolle
  11. Ariel S. Wirchnianski
  12. Robert H. Bortz
  13. Ethan Laudermilch
  14. J. Maximilian Fels
  15. Amanda Mengotto
  16. Ryan J. Malonis
  17. George I. Georgiev
  18. Jose A. Quiroz
  19. Daniel Wrapp
  20. Nianshuang Wang
  21. Kathryn E. Dye
  22. Jason Barnhill
  23. John M. Dye
  24. Jason S. McLellan
  25. Johanna P. Daily
  26. Jonathan R. Lai
  27. Andrew S. Herbert
  28. Laura M. Walker
  29. Kartik Chandran
  30. Rohit K. Jangra

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Abstract

The U.S. FDA has issued emergency use authorizations (EUAs) for multiple investigational monoclonal antibody (MAb) therapies for the treatment of mild to moderate COVID-19.

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  1. Version published to 10.1128/mbio.02473-21
  2. ScreenIT

    SciScore for 10.1101/2021.06.10.447999: (What is this?)

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

    Table 1: Rigor

    EthicsField Sample Permit: All the experiments described here with the authentic SARS-CoV-2 (Washington state isolate MT020880.1) were carried out in BSL-3 laboratories at USAMRIID, Frederick, MD as per Federal regulations under institutional biosafety committee-approved protocols.
    IACUC: Appropriate approvals from the Environmental Health and Safety Department and the Institutional Biosafety Committee at Albert Einstein College of Medicine were sought for using rVSV-SARS2 at biosafety level 2.
    IRB: The study protocol was approved by the Institutional Review Board (IRB) of the Albert Einstein College of Medicine (IRB number 2016-6137).
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Cells were immunostained with SARS-CoV-1 nucleocapsid protein-specific antibody (Sino Biologic; Cat# 40143-R001) and AlexaFluor 488 labeled secondary antibody.
    SARS-CoV-1 nucleocapsid protein-specific
    suggested: None
    In short, B-cells purified from donor PBMCs using the MACS Human B-Cells isolation kit (Miltenyi Biotec Miltenyi Biotec Cat# 130-091-151) were stained with a panel of antibodies: anti-human CD19 (PE-Cy7; Biolegend Cat# 302216), CD3 (PerCP-Cy5.5; Biolegend Cat# 30040), CD8 (PerCP-Cy5.5; Biolegend Cat# 344710), CD14 (PerCP-Cy5.5; Invitrogen Cat#
    anti-human CD19
    suggested: (BioLegend Cat# 302216, RRID:AB_314246)
    PE-Cy7
    suggested: None
    CD3
    suggested: (BioLegend Cat# 348805, RRID:AB_2889063)
    CD8
    suggested: (BioLegend Cat# 344710, RRID:AB_2044010)
    CD14
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Virus stocks were generated by growing the virus on Vero cells.
    Vero
    suggested: CLS Cat# 605372/p622_VERO, RRID:CVCL_0059)
    The inoculum was added to Vero-E6 cell monolayers in 96 well plates and incubated for 1 h at 37°C and 5% CO2.
    Vero-E6
    suggested: None
    Recombinant DNA
    SentencesResources
    A plaque-purified rVSV-SARS2 corresponding to the passage 9 (plaque #2 virus) described previously (31) was used for these studies.
    rVSV-SARS2
    suggested: None
    Software and Algorithms
    SentencesResources
    Viral infectivity was measured by automated enumeration of GFP-positive cells from captured images using a Cytation5 automated fluorescence microscope (BioTek) and analyzed using the Gen5 data analysis software (BioTek).
    Gen5
    suggested: (Gen5, RRID:SCR_017317)
    The half-maximal inhibitory concentration (IC50) of the mAbs or sera was calculated using a nonlinear regression analysis with GraphPad Prism software.
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Flow cytometry data was analyzed using FlowJo software.
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)

    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: Please consider improving the rainbow (“jet”) colormap(s) used on page 8. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

    Results from rtransparent:
    • No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
    • 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 10.1101/2021.06.10.447999v1 on bioRxiv