Cross-Neutralization of a SARS-CoV-2 Antibody to a Functionally Conserved Site Is Mediated by Avidity

  1. Hejun Liu
  2. Nicholas C. Wu
  3. Meng Yuan
  4. Sandhya Bangaru
  5. Jonathan L. Torres
  6. Tom G. Caniels
  7. Jelle van Schooten
  8. Xueyong Zhu
  9. Chang-Chun D. Lee
  10. Philip J.M. Brouwer
  11. Marit J. van Gils
  12. Rogier W. Sanders
  13. Andrew B. Ward
  14. Ian A. Wilson

Reviewed by

Read the full article See related articles

Listed in

Log in to save this article

Abstract

No abstract available

Article activity feed

  1. ScreenIT

    SciScore for 10.1101/2020.08.02.233536: (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

    Antibodies
    SentencesResources
    For the COVA1-16 IgG 1 antibody, suspension HEK293F cells (Invitrogen, cat no. R79007) were cultured in FreeStyle medium (Gibco) and co-transfected with the two IgG plasmids expressing the corresponding HC and LC in a 1:1 ratio at a density of 0.8-1.2 million cells/mL in a 1:3 ratio with 1 mg/L PEImax (Polysciences).
    COVA1-16 IgG 1
    suggested: None
    Competition studies of antibodies with ACE-2 receptor: For competition assays, COVA1-16 IgG, CR3022 IgG, and human ACE2-Fc were all diluted to 250 nM.
    COVA1-16 IgG, CR3022 IgG
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Pseudovirus neutralization assay: Neutralization assays were performed using SARS-CoV and SARS-CoV-2 S-pseudotyped HIV-1 virus and HEK-293T/ACE2 cells as described previously [59].
    HEK-293T/ACE2
    suggested: None
    In brief, pseudotyped virus was produced by co-transfecting expression plasmids of SARS-CoV S and SARS-COV-2Δ19 S proteins (GenBank; AAP33697.1 and MT449663.1, respectively) with an HIV backbone expressing NanoLuc luciferase (pHIV-1NL4-3 ΔEnv-NanoLuc) in HEK293T cells (ATCC, CRL-11268).
    HEK293T
    suggested: ATCC Cat# CRL-11268, RRID:CVCL_1926)
    Software and Algorithms
    SentencesResources
    Iterative model building and refinement were carried out in COOT [52] and PHENIX [53], respectively.
    COOT
    suggested: (Coot, RRID:SCR_014222)
    PHENIX
    suggested: (Phenix, RRID:SCR_014224)
    Micrographs were collected using Leginon [55] and the images were transferred to Appion for processing.
    Leginon
    suggested: (Leginon, RRID:SCR_016731)
    Selected 3D classes were auto-refined on Relion and used to make figures with UCSF Chimera.
    Relion
    suggested: (RELION, RRID:SCR_016274)
    Protein concentrations were determined by Nanodrop using the proteins peptidic molecular weight and extinction coefficient as determined by the online ExPASy software (ProtParam).
    ExPASy
    suggested: None
    The inhibitory concentration (IC50) was determined as the concentration of IgG or Fab that neutralized 50% of the pseudotyped virus using GraphPad Prism software (version 8.3.0).
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Sequence conservation analysis: RBD protein sequences from SARS-CoV and SARS-related coronavirus (SARSr-CoV) strains were retrieved from the following accession codes: Multiple sequence alignment of the RBD sequences was performed by MUSCLE version 3.8.31 [60].
    MUSCLE
    suggested: (MUSCLE, RRID:SCR_011812)
    Sequence logos were generated by WebLogo [61].
    WebLogo
    suggested: (WEBLOGO, RRID:SCR_010236)

    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.

  2. Version published to 10.1016/j.immuni.2020.10.023
  3. Version published to 10.1101/2020.08.02.233536v1 on bioRxiv