Increased Potency and Breadth of SARS-CoV-2 Neutralizing Antibodies After a Third mRNA Vaccine Dose

  1. Frauke Muecksch
  2. Zijun Wang
  3. Alice Cho
  4. Christian Gaebler
  5. Tarek Ben Tanfous
  6. Justin DaSilva
  7. Eva Bednarski
  8. Victor Ramos
  9. Shuai Zong
  10. Brianna Johnson
  11. Raphael Raspe
  12. Dennis Schaefer-Babajew
  13. Irina Shimeliovich
  14. Mridushi Daga
  15. Kai-Hui Yao
  16. Fabian Schmidt
  17. Katrina G. Millard
  18. Martina Turroja
  19. Mila Jankovic
  20. Thiago Y. Oliveria
  21. Anna Gazumyan
  22. Marina Caskey
  23. Theodora Hatziioannou
  24. Paul D. Bieniasz
  25. Michel C. Nussenzweig

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Abstract

The omicron variant of SARS-CoV-2 infected very large numbers of SARS-CoV-2 vaccinated and convalescent individuals 1–3 . The penetrance of this variant in the antigen experienced human population can be explained in part by the relatively low levels of plasma neutralizing activity against Omicron in people who were infected or vaccinated with the original Wuhan-Hu-1 strain 4–7 . The 3 rd mRNA vaccine dose produces an initial increase in circulating anti-Omicron neutralizing antibodies, but titers remain 10-20-fold lower than against Wuhan-Hu-1 and are, in many cases, insufficient to prevent infection 7 . Despite the reduced protection from infection, individuals that received 3 doses of an mRNA vaccine were highly protected from the more serious consequences of infection 8 . Here we examine the memory B cell repertoire in a longitudinal cohort of individuals receiving 3 mRNA vaccine doses 9,10 . We find that the 3 rd dose is accompanied by an increase in, and evolution of, anti-receptor binding domain specific memory B cells. The increase is due to expansion of memory B cell clones that were present after the 2 nd vaccine dose as well as the emergence of new clones. The antibodies encoded by these cells showed significantly increased potency and breadth when compared to antibodies obtained after the 2 nd vaccine dose. Notably, the increase in potency was especially evident among newly developing clones of memory cells that differed from the persisting clones in targeting more conserved regions of the RBD. Overall, more than 50% of the analyzed neutralizing antibodies in the memory compartment obtained from individuals receiving a 3 rd mRNA vaccine dose neutralized Omicron. Thus, individuals receiving 3 doses of an mRNA vaccine encoding Wuhan-Hu-1, have a diverse memory B cell repertoire that can respond rapidly and produce antibodies capable of clearing even diversified variants such as Omicron. These data help explain why a 3 rd dose of an mRNA vaccine that was not specifically designed to protect against variants is effective against variant-induced serious disease.

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  1. ScreenIT

    SciScore for 10.1101/2022.02.14.480394: (What is this?)

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

    Table 1: Rigor

    EthicsConsent: All participants provided written informed consent before participation in the study and the study was conducted in accordance with Good Clinical Practice.
    IRB: The study was performed in compliance with all relevant ethical regulations and the protocol (DRO-1006) for studies with human participants was approved by the Institutional Review Board of the Rockefeller University.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Plates were washed 6 times with washing buffer and then incubated with anti-human IgG, IgM or IgA secondary antibody conjugated to horseradish peroxidase (HRP) (Jackson Immuno Research
    anti-human IgG
    suggested: None
    IgA
    suggested: None
    The half-maximal neutralization titers for plasma (NT50) or half-maximal and 90% inhibitory concentrations for monoclonal antibodies (IC50 and IC90) were determined using four-parameter nonlinear regression (least squares regression method without weighting; constraints: top=1, bottom=0) (GraphPad Prism).
    IC90
    suggested: None
    The enriched B cells were incubated in Flourescence-Activated Cell-sorting (FACS) buffer (1× PBS, 2% FCS, 1 mM ethylenediaminetetraacetic acid (EDTA)) with the following anti-human antibodies (all at 1:200 dilution): anti-CD20-PECy7 (BD Biosciences, 335793), anti-CD3-APC-eFluro 780 (Invitrogen, 47-0037-41)
    anti-CD20-PECy7
    suggested: None
    anti-CD3-APC-eFluro 780
    suggested: None
    For B cell phenotype analysis, in addition to above antibodies, B cells were also stained with following anti-human antibodies (all at 1:200 dilution): anti-IgD-BV650 (BD, 740594), anti-CD27-BV786 (BD biosciences, 563327), anti-CD19-BV605 (Biolegend, 302244), anti-CD71-PerCP-Cy5.5 (Biolegend, 334114), anti-IgG-PECF594 (BD, 562538), anti-IgM-AF700 (Biolegend, 314538), anti-IgA-Viogreen (Miltenyi Biotec, 130-113-481)
    anti-human
    suggested: (Abnova Cat# H00007360-A01, RRID:AB_563327)
    anti-IgD-BV650
    suggested: None
    anti-CD27-BV786
    suggested: None
    anti-CD19-BV605
    suggested: None
    anti-CD71-PerCP-Cy5.5
    suggested: None
    anti-IgM-AF700 ( Biolegend , 314538) , anti-IgA-Viogreen ( Miltenyi Biotec , 130-113-481)
    suggested: None
    The frequency distributions of human V genes in anti-SARS-CoV-2 antibodies from this study was compared to 131,284,220 IgH and IgL sequences generated by41 and downloaded from cAb-Rep42, a database of human shared BCR clonotypes available at https://cab-rep.c2b2.columbia.edu/.
    anti-SARS-CoV-2
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Briefly, 293T (CRL-11268) cells were obtained from ATCC, and the cells were transfected with pNL4-3ΔEnv-nanoluc and pSARS-CoV-2-SΔ19, particles were harvested 48 hours post-transfection, filtered and stored at −80°C.
    293T
    suggested: ATCC Cat# CRL-11268, RRID:CVCL_1926)
    Recombinant DNA
    SentencesResources
    Briefly, 293T (CRL-11268) cells were obtained from ATCC, and the cells were transfected with pNL4-3ΔEnv-nanoluc and pSARS-CoV-2-SΔ19, particles were harvested 48 hours post-transfection, filtered and stored at −80°C.
    pNL4-3ΔEnv-nanoluc
    suggested: None
    pSARS-CoV-2-SΔ19
    suggested: None
    Software and Algorithms
    SentencesResources
    The average of its signal was used for normalization of all the other values on the same plate with Excel software before calculating the area under the curve using Prism V9.1(GraphPad).
    Excel
    suggested: None
    Prism
    suggested: (PRISM, RRID:SCR_005375)
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)
    For monoclonal antibodies, the ELISA half-maximal concentration (EC50) was determined using four-parameter nonlinear regression (GraphPad Prism V9.1).
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    3,000 units/ml RNasin Ribonuclease Inhibitors (Promega, N2615) per well using a FACS Aria III and FACSDiva software (Becton Dickinson) for acquisition and FlowJo for analysis.
    FACSDiva
    suggested: (BD FACSDiva Software, RRID:SCR_001456)
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)
    For B cell phenotype analysis, in addition to above antibodies, B cells were also stained with following anti-human antibodies (all at 1:200 dilution): anti-IgD-BV650 (BD, 740594), anti-CD27-BV786 (BD biosciences, 563327), anti-CD19-BV605 (Biolegend, 302244), anti-CD71-PerCP-Cy5.5 (Biolegend, 334114), anti-IgG-PECF594 (BD, 562538), anti-IgM-AF700 (Biolegend, 314538), anti-IgA-Viogreen (Miltenyi Biotec, 130-113-481)
    Biolegend , 314538) , anti-IgA-Viogreen ( Miltenyi Biotec
    suggested: None
    Miltenyi
    suggested: (Miltenyi Biotec, RRID:SCR_008984)
    Sequence analysis was performed using MacVector.
    MacVector
    suggested: (MacVector, RRID:SCR_015700)

    Results from OddPub: Thank you for sharing your code and 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 10.1101/2022.02.14.480394v1 on bioRxiv