Structural basis for potent neutralization of SARS-CoV-2 and role of antibody affinity maturation

  1. Nicholas K. Hurlburt
  2. Emilie Seydoux
  3. Yu-Hsin Wan
  4. Venkata Viswanadh Edara
  5. Andrew B. Stuart
  6. Junli Feng
  7. Mehul S. Suthar
  8. Andrew T. McGuire
  9. Leonidas Stamatatos
  10. Marie Pancera

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Abstract

SARS-CoV-2 is a betacoronavirus virus responsible for the COVID-19 pandemic. Here, we determine the X-ray crystal structure of a potent neutralizing monoclonal antibody, CV30, isolated from a patient infected with SARS-CoV-2, in complex with the receptor binding domain. The structure reveals that CV30 binds to an epitope that overlaps with the human ACE2 receptor binding motif providing a structural basis for its neutralization. CV30 also induces shedding of the S1 subunit, indicating an additional mechanism of neutralization. A germline reversion of CV30 results in a substantial reduction in both binding affinity and neutralization potential indicating the minimal somatic mutation is needed for potently neutralizing antibodies against SARS-CoV-2.

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  1. Version published to 10.1038/s41467-020-19231-9
  2. ScreenIT

    SciScore for 10.1101/2020.06.12.148692: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    Briefly, plasmids expressing the HIV-1 Gag and pol (pHDM540 Hgpm2), HIV-1Rev (pRC-CMV-rev1b), HIV-1 Tat (pHDM-tat1b), the SARS-CoV-2 spike (pHDM-SARS-CoV-2 Spike) and a luciferase/GFP reporter (pHAGE-CMV-Luc2-IRES542 ZsGreen-W) were co-transfected into 293T cells at a 1:1:1:1.6:4.6 ratio using 293 Free transfection reagent according to the manufacturer’s instructions.
    293T
    suggested: None
    72 hours later the culture supernatant was harvested, clarified by centrifugation and frozen at -80°C. 293 cells stably expressing ACE2 (HEK-293T-hACE2) were seeded at a density of 4×103 cells/well in a 100 µL volume in 96 well flat bottom tissue culture plates.
    293
    suggested: NIH-ARP Cat# 103-306, RRID:CVCL_0045)
    The media was aspirated from 293T-ACE2 cells and 100 µL of the virus-antibody mixture was added.
    293T-ACE2
    suggested: RRID:CVCL_YZ65)
    Software and Algorithms
    SentencesResources
    Structural figures were made in Pymol.
    Pymol
    suggested: (PyMOL, RRID:SCR_000305)
    The antibody concentration that neutralized 50% of infectivity (IC50) was interpolated from the neutralization curves determined using the log(inhibitor) vs. response -- Variable slope (four parameters) fit using automatic outlier detection in Graphpad Prism Software.
    Graphpad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)

    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

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  3. Version published to 10.1101/2020.06.12.148692v1 on bioRxiv