Anti-SARS-CoV-2 receptor-binding domain antibody evolution after mRNA vaccination

  1. Alice Cho
  2. Frauke Muecksch
  3. Dennis Schaefer-Babajew
  4. Zijun Wang
  5. Shlomo Finkin
  6. Christian Gaebler
  7. Victor Ramos
  8. Melissa Cipolla
  9. Pilar Mendoza
  10. Marianna Agudelo
  11. Eva Bednarski
  12. Justin DaSilva
  13. Irina Shimeliovich
  14. Juan Dizon
  15. Mridushi Daga
  16. Katrina G. Millard
  17. Martina Turroja
  18. Fabian Schmidt
  19. Fengwen Zhang
  20. Tarek Ben Tanfous
  21. Mila Jankovic
  22. Thiago Y. Oliveria
  23. Anna Gazumyan
  24. Marina Caskey
  25. Paul D. Bieniasz
  26. Theodora Hatziioannou
  27. Michel C. Nussenzweig

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Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection produces B cell responses that continue to evolve for at least a year. During that time, memory B cells express increasingly broad and potent antibodies that are resistant to mutations found in variants of concern 1 . As a result, vaccination of coronavirus disease 2019 (COVID-19) convalescent individuals with currently available mRNA vaccines produces high levels of plasma neutralizing activity against all variants tested 1,2 . Here we examine memory B cell evolution five months after vaccination with either Moderna (mRNA-1273) or Pfizer-BioNTech (BNT162b2) mRNA vaccine in a cohort of SARS-CoV-2-naive individuals. Between prime and boost, memory B cells produce antibodies that evolve increased neutralizing activity, but there is no further increase in potency or breadth thereafter. Instead, memory B cells that emerge five months after vaccination of naive individuals express antibodies that are similar to those that dominate the initial response. While individual memory antibodies selected over time by natural infection have greater potency and breadth than antibodies elicited by vaccination, the overall neutralizing potency of plasma is greater following vaccination. These results suggest that boosting vaccinated individuals with currently available mRNA vaccines will increase plasma neutralizing activity but may not produce antibodies with equivalent breadth to those obtained by vaccinating convalescent individuals.

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  1. Version published to 10.1038/s41586-021-04060-7
  2. Version published to 10.1101/2021.07.29.454333v2 on bioRxiv
  3. ScreenIT

    SciScore for 10.1101/2021.07.29.454333: (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 FACS buffer (1× PBS, 2% FCS, 1 mM 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-human
    suggested: (GenWay Biotech Inc. Cat# 18-202-335793-0.1 mg, RRID:AB_1981874)
    anti-CD20-PECy7
    suggested: None
    anti-CD3-APC-eFluro 780
    suggested: None
    For plasmablast single-cell sorting, in addition to above antibodies, B cells were also stained with anti-CD19-BV605 (Biolegend, 302244), and single CD3-CD8-CD14-CD16-CD19+CD20-Ova-RBD-PE+RBD-AF647+ plasmablasts were sorted as described above.
    anti-CD19-BV605
    suggested: None
    For B cell phenotype analysis, in addition to above antibodies, B cells were also stained with following anti-human antibodies: anti-IgD-BV421 (Biolegend, 348226), anti-CD27-FITC (BD biosciences, 555440), anti-CD19-BV605 (Biolegend, 302244), anti-CD71-PerCP-Cy5.5 (Biolegend, 334114), anti-IgG-PECF594 (BD biosciences, 562538), anti-IgM-AF700 (Biolegend, 314538), anti-IgA-Viogreen (Miltenyi Biotec, 130-113-481)
    anti-human antibodies: anti-IgD-BV421 ( Biolegend , 348226
    suggested: None
    anti-CD27-FITC
    suggested: (Millipore Cat# FCMAB191F, RRID:AB_10807274)
    anti-CD71-PerCP-Cy5.5
    suggested: None
    anti-IgG-PECF594
    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 by54 and downloaded from cAb-Rep55, 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 cells were transfected with pNL4-3ΔEnv-nanoluc and pSARS-CoV-2-SΔ19, particles were harvested 48 hpt, filtered and stored at −80°C.
    293T
    suggested: None
    Recombinant DNA
    SentencesResources
    Briefly, 293T cells were transfected with pNL4-3ΔEnv-nanoluc and pSARS-CoV-2-SΔ19, particles were harvested 48 hpt, 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)
    For monoclonal antibodies, the EC50 was determined using four-parameter nonlinear regression (GraphPad Prism V9.1).
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Proteins: Mammalian expression vector encoding the RBD of SARS-CoV-2 (GenBank MN985325.1; S protein residues 319-539) was previously described50.
    Proteins
    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).
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Single CD3-CD8-CD14-CD16−CD20+Ova−RBD-PE+RBD-AF647+ B cells were sorted into individual wells of 96-well plates containing 4 μl of lysis buffer (0.5× PBS, 10 mM DTT, 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: anti-IgD-BV421 (Biolegend, 348226), anti-CD27-FITC (BD biosciences, 555440), anti-CD19-BV605 (Biolegend, 302244), anti-CD71-PerCP-Cy5.5 (Biolegend, 334114), anti-IgG-PECF594 (BD biosciences, 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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  4. Version published to 10.1101/2021.07.29.454333v1 on bioRxiv