Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient

  1. Daming Zhou
  2. Helen M. E. Duyvesteyn
  3. Cheng-Pin Chen
  4. Chung-Guei Huang
  5. Ting-Hua Chen
  6. Shin-Ru Shih
  7. Yi-Chun Lin
  8. Chien-Yu Cheng
  9. Shu-Hsing Cheng
  10. Yhu-Chering Huang
  11. Tzou-Yien Lin
  12. Che Ma
  13. Jiandong Huo
  14. Loic Carrique
  15. Tomas Malinauskas
  16. Reinis R. Ruza
  17. Pranav N. M. Shah
  18. Tiong Kit Tan
  19. Pramila Rijal
  20. Robert F. Donat
  21. Kerry Godwin
  22. Karen R. Buttigieg
  23. Julia A. Tree
  24. Julika Radecke
  25. Neil G. Paterson
  26. Piyada Supasa
  27. Juthathip Mongkolsapaya
  28. Gavin R. Screaton
  29. Miles W. Carroll
  30. Javier Gilbert-Jaramillo
  31. Michael L. Knight
  32. William James
  33. Raymond J. Owens
  34. James H. Naismith
  35. Alain R. Townsend
  36. Elizabeth E. Fry
  37. Yuguang Zhao
  38. Jingshan Ren
  39. David I. Stuart
  40. Kuan-Ying A. Huang

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Abstract

No abstract available

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  1. Version published to 10.1038/s41594-020-0480-y
  2. ScreenIT

    SciScore for 10.1101/2020.06.12.148387: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementConsent: The study protocol and informed consent were approved by the ethics committee at the Chang Gung Medical Foundation and the Taoyuan General Hospital, Ministry of Health and Welfare, Taiwan.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    PBMCs were stained with a mix of fluorescent-labelled antibodies to cellular surface markers, including anti-CD3 (BD Biosciences,
    anti-CD3
    suggested: None
    Sorted single cells were used to produce human IgG monoclonal antibodies as previously described26.
    human IgG
    suggested: None
    The anti-influenza human monoclonal antibody BS 1A (in house), anti-SARS Spike monoclonal antibody CR3022 and convalescent serum were used as controls.
    anti-influenza
    suggested: None
    anti-SARS
    suggested: None
    ACE2 expressing cells were then FACS sorted post staining with RBD-6H followed by a secondary anti-His AlexaFluor 647 labelled antibody.
    anti-His
    suggested: None
    30 μL of biotinylated RBD (using EZ-link Sulfo-NHS-Biotin (A39256; Life Technologies)) at 25 nM was added to the titrated antibodies.
    Sulfo-NHS-Biotin
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Expression vectors that carry variable domains of heavy and light chains were transfected into the 293T cell line for expression of recombinant full-length human IgG monoclonal antibodies in serum-free transfection medium.
    293T
    suggested: NCBI_Iran Cat# C498, RRID:CVCL_0063)
    Immunofluorescence assay: SARS-CoV-2 (strain CDC-4) infected Vero E6 cells were prepared and fixed with acetone in the biosafety level 3 (BSL-3) laboratory following biosafety rules and guidelines27.
    Vero E6
    suggested: None
    Cell-based ACE2 blocking assays: MDCK-SIAT1 cells were stably transfected with human ACE2 cDNA using a second-generation lentiviral vector.
    MDCK-SIAT1
    suggested: ECACC Cat# 05071502, RRID:CVCL_Z936)
    Software and Algorithms
    SentencesResources
    Inhibitory concentration at 50 % (IC50) of the antibodies against RBD was determined using non-linear regression [inhibitor] versus normalised response curve fit using GraphPad Prism 8.
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Structural comparisons used SHP39, residues forming the RBD/Fab interface were identified with PISA40, figures were prepared with PyMOL (The PyMOL Molecular Graphics System, Version 1.2r3pre, Schrodinger, LLC).
    PyMOL
    suggested: (PyMOL, RRID:SCR_000305)
    Contrast-transfer-function (CTF) of full-dose and non-weighted micrographs was estimated within a CryoSPARC wrapper for Gctf-v1.0642.
    CryoSPARC
    suggested: (cryoSPARC, RRID:SCR_016501)

    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.

  3. Version published to 10.1101/2020.06.12.148387v1 on bioRxiv