A recurring YYDRxG pattern in broadly neutralizing antibodies to a conserved site on SARS-CoV-2, variants of concern, and related viruses

  1. Hejun Liu
  2. Chengzi I. Kaku
  3. Ge Song
  4. Meng Yuan
  5. Raiees Andrabi
  6. Dennis R. Burton
  7. Laura M. Walker
  8. Ian A. Wilson

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Abstract

Studying the antibody response to SARS-CoV-2 informs on how the human immune system can respond to antigenic variants as well as other SARS-related viruses. Here, we structurally and functionally characterized a potent human antibody ADI-62113 that also neutralizes SARS-CoV- 2 variants of concern and cross-reacts with many other sarbecoviruses. A YYDRxG motif encoded by IGHD3-22 in CDR H3 facilitates targeting to a highly conserved epitope on the SARS-CoV-2 receptor binding domain. A computational search for a YYDRxG pattern in publicly available sequences identified many antibodies with broad neutralization activity against SARS-CoV-2 variants and SARS-CoV. Thus, the YYDRxG motif represents a common convergent solution for the human humoral immune system to counteract sarbecoviruses. These findings also suggest an epitope targeting strategy to identify potent and broadly neutralizing antibodies that can aid in the design of pan-sarbecovirus vaccines and antibody therapeutics.

Short Summary

Decryption of a recurrent sequence feature in anti-SARS-CoV-2 antibodies identifies how potent pan-sarbecovirus antibodies target a conserved epitope on the receptor binding domain.

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  1. ScreenIT

    SciScore for 10.1101/2021.12.15.472864: (What is this?)

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

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    The IgG antibodies and Fabs were purified with a CaptureSelect™ CH1-XL Matrix column (Thermo Fisher Scientific) for affinity purification and a HiLoad Superdex 200 pg column (Cytiva) for size exclusion chromatography.
    IgG
    suggested: None
    Sequences of the antibodies against SARS-CoV-2 were included in further analysis.
    SARS-CoV-2
    suggested: None
    11 antibody (BioLegend, 901524), PE-conjugated goat anti-human IgG polyclonal antibodies (Southern Biotech, 2040-09), and propidium iodide (Invitrogen, P1304MP) for 20 minutes on ice.
    anti-human IgG
    suggested: (SouthernBiotech Cat# 2040-09, RRID:AB_2795648)
    2040-09
    suggested: (SouthernBiotech Cat# 2040-09, RRID:AB_2795648)
    Experimental Models: Cell Lines
    SentencesResources
    Pseudovirus production and neutralization assays: Plasmids encoding SARS-CoV, SARS-CoV-2, or other variants of the spike protein, with the ER retrieval signal removed were co-transfected with MLV-gag/pol and MLV-CMV-Luciferase plasmids into HEK293T cells to generate pseudoviruses.
    HEK293T
    suggested: KCB Cat# KCB 200744YJ, RRID:CVCL_0063)
    Right before the end of the incubation, HeLa-hACE2 cells were suspended with culture medium at a concentration of 2 x 105/ml.
    HeLa-hACE2
    suggested: None
    Recombinant DNA
    SentencesResources
    Expression and purification of SARS-CoV-2 RBD: The receptor-binding domain (RBD) (residues 333-529) of the SARS-CoV-2 spike (S) protein (GenBank: QHD43416.1), was cloned into a customized pFastBac vector (Ekiert et al., 2011), and fused with an N-terminal gp67 signal peptide and C-terminal His6 tag (Yuan et al., 2020).
    pFastBac
    suggested: RRID:Addgene_1925)
    Software and Algorithms
    SentencesResources
    YYDRxG pattern search: Over 205,000 antibody sequences including heavy and light chains were retrieved from GenBank using Biopython program (Cock et al., 2009), supplemented with sequences reported in previous publications (Cho et al., 2021; Gaebler et al., 2021; Robbiani et al., 2020; Z. Wang, J. C. C. Lorenzi, et al., 2021; Z. Wang, F. Muecksch, et al., 2021; Z. Wang, F. Schmidt, et al., 2021), and then subjected to repertoire analysis using PyIR program (Soto et al., 2020) implemented with IgBLAST (Ye et al., 2013).
    Biopython
    suggested: (Biopython, RRID:SCR_007173)
    PyIR
    suggested: None
    IgBLAST
    suggested: (IgBLAST, RRID:SCR_002873)
    Sequence analysis and surface conservation: Sequences of sarbecoviruses were retrieved from GenBank using Biopython program, aligned using MUSCLE program (Edgar, 2004) built in European Bioinformatics Institute (EBI) web services (Madeira et al., 2019) and scored for surface conservation in ConSurf server (Ashkenazy et al., 2016; Landau et al., 2005).
    MUSCLE
    suggested: (MUSCLE, RRID:SCR_011812)
    The conserved surface of SARS-CoV-2 RBD was visualized using the PyMOL program (Schrödinger, LLC).
    PyMOL
    suggested: (PyMOL, RRID:SCR_000305)
    Iterative model building and refinement were carried out in COOT (Emsley & Cowtan, 2004) and PHENIX (Acta Crystallographica Section D: Biological CrystallographyAdams et al., 2010), respectively.
    COOT
    suggested: (Coot, RRID:SCR_014222)
    Epitope and paratope residues, as well as their interactions, were identified with the PISA program (Krissinel & Henrick, 2007) using calculated buried surface area (BSA >0 Å2) as the criterion.
    PISA
    suggested: (PISA, RRID:SCR_015749)
    Binding curves were fitted with four-parameter non-linear regression analysis to calculate the apparent equilibrium binding constant (KDApp) in GraphPad Prism 9.
    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.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

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  2. Version published to 10.1101/2021.12.15.472864v1 on bioRxiv