The plasmablast response to SARS-CoV-2 mRNA vaccination is dominated by non-neutralizing antibodies and targets both the NTD and the RBD

  1. Fatima Amanat
  2. Mahima Thapa
  3. Tinting Lei
  4. Shaza M. Sayed Ahmed
  5. Daniel C. Adelsberg
  6. Juan Manuel Carreno
  7. Shirin Strohmeier
  8. Aaron J. Schmitz
  9. Sarah Zafar
  10. Julian Q Zhou
  11. Willemijn Rijnink
  12. Hala Alshammary
  13. Nicholas Borcherding
  14. Ana Gonzalez Reiche
  15. Komal Srivastava
  16. Emilia Mia Sordillo
  17. Harm van Bakel
  18. The Personalized Virology Initiative
  19. Jackson S. Turner
  20. Goran Bajic
  21. Viviana Simon
  22. Ali H. Ellebedy
  23. Florian Krammer

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Abstract

In this study we profiled vaccine-induced polyclonal antibodies as well as plasmablast derived mAbs from individuals who received SARS-CoV-2 spike mRNA vaccine. Polyclonal antibody responses in vaccinees were robust and comparable to or exceeded those seen after natural infection. However, the ratio of binding to neutralizing antibodies after vaccination was greater than that after natural infection and, at the monoclonal level, we found that the majority of vaccine-induced antibodies did not have neutralizing activity. We also found a co-dominance of mAbs targeting the NTD and RBD of SARS-CoV-2 spike and an original antigenic-sin like backboost to seasonal human coronaviruses OC43 and HKU1. Neutralizing activity of NTD mAbs but not RBD mAbs against a clinical viral isolate carrying E484K as well as extensive changes in the NTD was abolished, suggesting that a proportion of vaccine induced RBD binding antibodies may provide substantial protection against viral variants carrying single E484K RBD mutations.

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  1. Version published to 10.1101/2021.03.07.21253098v2 on medRxiv
  2. ScreenIT

    SciScore for 10.1101/2021.03.07.21253098: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: Human subjects and specimen collection: The study protocols for the collection of clinical specimens from individuals with and without SARS-CoV-2 infection by the Personalized Virology Initiative were reviewed and approved by the Mount Sinai Hospital Institutional Review Board (IRB-16-16772; IRB-16-00791; IRB-20-03374).
    Consent: All participants provided written informed consent prior to collection of specimen and clinical information.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    For mouse samples, anti-mouse IgG conjugated to HRP was used at the same dilution (Rockland antibodies and assays; catalog #610-4302).
    anti-mouse IgG
    suggested: (Rockland Cat# 610-4302, RRID:AB_219682)
    Specifically, a mouse anti-histidine antibody (Takara; catalog #631212) was used as a positive control to detect proteins with a hexa-histidine tag.
    anti-histidine
    suggested: None
    After 24 hours, cells were permeabilized and stained using an anti-nucleoprotein antibody 1C7 as discussed in detail earlier (Amanat et al., 2020b; Sun et al., 2020).
    anti-nucleoprotein
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Viruses and cells: Vero.E6 cells (ATCC #CRL-1586) cells were maintained in culture using Dulbecco’s Modified Eagles Medium (DMEM, Gibco) which was supplemented with 10% fetal bovine serum (FBS, Corning) and antibiotics solution containing 10,000 units/mL of penicillin and 10,000 µg/mL of streptomycin (Pen Strep, Gibco)(10).
    Vero.E6
    suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)
    Software and Algorithms
    SentencesResources
    ELISA: Ninety-six well plates (Immulon 4 HBX; Thermo Scientific) were coated overnight at 4°C with recombinant proteins at a concentration of 2 ug/ml in PBS (Gibco; Life Technologies) and 50 uls/well.
    Gibco
    suggested: None
    All data was analyzed in Graphpad Prism 7.
    Graphpad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Serial dilutions of serum samples were made in 1X minimal essential medium (MEM; Life Technologies) starting at a dilution of 1:20.
    MEM
    suggested: (E-mem, RRID:SCR_016081)
    For mutation analysis, heavy chains of mAbs and single-cell BCRs first underwent V(D)J gene annotation using IgBLAST (v1.14.0) (Ye et al., 2013) with human reference (release 201931-4) from the international ImMunoGeneTics information system (IMGT) (Giudicelli et al., 2005) and then parsing using Change-O (v0.4.6)
    IgBLAST
    suggested: (IgBLAST, RRID:SCR_002873)
    Structure visualization: Structural figures were modeled and rendered in Pymol (The PyMOL Molecular Graphics System, Version 2.4 Schrödinger, LLC).
    PyMOL
    suggested: (PyMOL, RRID:SCR_000305)

    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: We detected the following sentences addressing limitations in the study:
    In one vaccinee not a single RBD binding mAbs was isolated with the caveats that the overall number of mAbs derived from that individual were low and their polyclonal serum antibody responses included RBD recognition. These data suggest that the NTD, which also harbors neutralizing epitopes, is - at least - as important as the RBD and warrants as much attention. In fact, five out of seven neutralizing antibodies isolated in this study bound to the NTD and only two targeted the RBD. Thus, a re-evaluation of the B cell responses to natural SARS-CoV-2 infection with unbiased approaches is needed to understand if the co-dominance of NTD and RBD is vaccine specific or also seen upon natural infection. Further characterization of the mAbs obtained in this study showed a complete loss of neutralization against an authentic, replication-competent variant virus that harbored extensive changes in the NTD. These observations may explain why a reduction in neutralization against the viral variant of concern B.1.17 is seen in some studies despite the fact the N501Y substitution in the RBD of this variant does not significantly impact binding and neutralizing activity (Emary et al., 2021). We also assessed the impact of different RBD mutations on affinity towards human ACE2. Interestingly, N501Y increased the affinity by five-fold. This increase in receptor binding affinity may contribute to the higher infectivity of B.1.1.7, which carries this mutation in its RBD. In contrast, introductio...

    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 10.1101/2021.03.07.21253098v1 on medRxiv