Discriminating cross-reactivity in polyclonal IgG1 responses against SARS-CoV-2 variants of concern

  1. Danique M. H. van Rijswijck
  2. Albert Bondt
  3. Max Hoek
  4. Karlijn van der Straten
  5. Tom G. Caniels
  6. Meliawati Poniman
  7. Dirk Eggink
  8. Chantal Reusken
  9. Godelieve J. de Bree
  10. Rogier W. Sanders
  11. Marit J. van Gils
  12. Albert J. R. Heck

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Abstract

Existing assays to measure antibody cross-reactivity against different SARS-CoV-2 spike (S) protein variants lack the discriminatory power to provide insights at the level of individual clones. Using a mass spectrometry-based approach we are able to monitor individual donors’ IgG1 clonal responses following a SARS-CoV-2 infection. We monitor the plasma clonal IgG1 profiles of 8 donors who had experienced an infection by either the wild type Wuhan Hu-1 virus or one of 3 VOCs (Alpha, Beta and Gamma). In these donors we chart the full plasma IgG1 repertoires as well as the IgG1 repertoires targeting the SARS-CoV-2 spike protein trimer VOC antigens. The plasma of each donor contains numerous anti-spike IgG1 antibodies, accounting for <0.1% up to almost 10% of all IgG1s. Some of these antibodies are VOC-specific whereas others do recognize multiple or even all VOCs. We show that in these polyclonal responses, each clone exhibits a distinct cross-reactivity and also distinct virus neutralization capacity. These observations support the need for a more personalized look at the antibody clonal responses to infectious diseases.

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  1. Version published to 10.1038/s41467-022-33899-1
  2. Version published to 10.1101/2022.02.24.481778v2 on bioRxiv
  3. ScreenIT

    SciScore for 10.1101/2022.02.24.481778: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: , location AMC, in the Netherlands and approved by the local ethical committee of the AMC (NL 73281.018.20).
    Consent: All individuals included in this study gave written informed consent before participating.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    All S constructs were verified by Sanger sequencing and the protein was subsequently produced in human embryonic kidney (HEK) 293F cells (Thermo Fisher Scientific) and purified as previously described (4, 8).
    HEK
    suggested: RRID:CVCL_6642)
    293F
    suggested: RRID:CVCL_D615)
    Pseudo-viruses were produced by co-transfecting the SARS-CoV-2-S expression plasmid with the pHIV-1NL43 ΔEnv-NanoLuc reporter virus plasmid in HEK293T cells (ATCC, CRL-11268), as previously described (13).
    HEK293T
    suggested: ATCC Cat# CRL-11268, RRID:CVCL_1926)
    Shortly, HEK293T/ACE2 cells, kindly provided by Dr. Paul Bieniasz (13), were seeded at a density of 20,000 cells/well in a 96-well plate coated with 50 μg/mL poly-L-lysine one day prior to the start of the neutralization assay.
    HEK293T/ACE2
    suggested: None
    Recombinant DNA
    SentencesResources
    The genes were ordered as gBlock gene fragments (Integrated DNA Technologies) and cloned Pst I/Not I in a pPPI4 expression vector containing a hexahistidine (his) tag with Gibson Assembly (Thermo Fisher Scientific).
    pPPI4
    suggested: None
    Pseudo-virus construction: The WT, Alpha, Beta and Gamma pseudovirus S constructs were ordered as gBlock gene fragments (Integrated DNA Technologies) and cloned using SacI and Apal in the pCR3 SARS-CoV-2-SΔ19 expression plasmid (13) using Gibson Assembly (ThermoFisher).
    pCR3 SARS-CoV-2-SΔ19
    suggested: None
    Pseudo-viruses were produced by co-transfecting the SARS-CoV-2-S expression plasmid with the pHIV-1NL43 ΔEnv-NanoLuc reporter virus plasmid in HEK293T cells (ATCC, CRL-11268), as previously described (13).
    pHIV-1NL43 ΔEnv-NanoLuc
    suggested: None
    Software and Algorithms
    SentencesResources
    The LC was directly coupled to an Orbitrap Exploris 480 mass spectrometer with BioPharma option (Thermo Fisher Scientific, Bremen, Germany).
    BioPharma
    suggested: (TransCelerate BioPharma, RRID:SCR_003728)
    Data analysis: The retention times and masses of each of the Fab molecules were retrieved from the generated RAW files using BioPharmaFinder 3.2 (Thermo Scientific).
    BioPharmaFinder
    suggested: None
    Further data analysis was performed using in-house scripts using Python 3.8.3 (with libraries: Pandas 1.0.5, Numpy 1.18.5, Scipy 1.5.0, matplotlib 3.2.2 and seaborn 0.11.0).
    Python
    suggested: (IPython, RRID:SCR_001658)
    Numpy
    suggested: (NumPy, RRID:SCR_008633)
    Scipy
    suggested: (SciPy, RRID:SCR_008058)
    matplotlib
    suggested: (MatPlotLib, RRID:SCR_008624)
    The inhibitory concentration (IC50) and neutralization titers (ID50) were determined as the NAb concentration and plasmadilution at which infectivity was inhibited by 50%, respectively, using a non-linear regression curve fit (GraphPad Prism software version 8.3).
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)

    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.

    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.

  4. Version published to 10.1101/2022.02.24.481778v1 on bioRxiv