Two doses of mRNA vaccine elicit cross-neutralizing memory B-cells against SARS-CoV-2 Omicron variant

  1. Ryutaro Kotaki
  2. Yu Adachi
  3. Saya Moriyama
  4. Taishi Onodera
  5. Shuetsu Fukushi
  6. Takaki Nagakura
  7. Keisuke Tonouchi
  8. Kazutaka Terahara
  9. Lin Sun
  10. Tomohiro Takano
  11. Ayae Nishiyama
  12. Masaharu Shinkai
  13. Kunihiro Oba
  14. Fukumi Nakamura-Uchiyama
  15. Hidefumi Shimizu
  16. Tadaki Suzuki
  17. Takayuki Matsumura
  18. Masanori Isogawa
  19. Yoshimasa Takahashi

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Abstract

SARS-CoV-2 Beta and Omicron variants have multiple mutations in the receptor-binding domain (RBD) allowing antibody evasion. Despite the resistance to circulating antibodies in those who received two doses of mRNA vaccine, the third dose prominently recalls cross-neutralizing antibodies with expanded breadth to these variants. Herein, we longitudinally profiled the cellular composition of persistent memory B-cell subsets and their antibody reactivity against these variants following the second vaccine dose. The vaccination elicited a memory B-cell subset with resting phenotype that dominated the other subsets at 4.9 months. Notably, most of the resting memory subset retained the ability to bind the Beta variant, and the memory-derived antibodies cross-neutralized the Beta and Omicron variants at frequencies of 59% and 29%, respectively. The preservation of cross-neutralizing antibody repertoires in the durable memory B-cell subset likely contributes to the prominent recall of cross-neutralizing antibodies following the third dose of the vaccine.

One Sentence Summary

Fully vaccinated individuals preserve cross-neutralizing memory B-cells against the SARS-CoV-2 Omicron variant.

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  1. ScreenIT

    SciScore for 10.1101/2021.12.24.474091: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: The present study was approved by the Institutional Review Board of the National Institute of Infectious
    Consent: All volunteers provided written informed consent prior to the enrollment.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Nucleocapsid antibody was analyzed by cobas e411 plus (Roche) with Elecsys Anti-SARS-CoV-2 (Roche), and <1 was evaluated as seronegative according to the manufacturer’s instructions.
    Anti-SARS-CoV-2
    suggested: None
    To obtain comparable titers of IgA to those of IgG, we normalized the IgA titers using a converting unit, which was calculated from the binding curves of CR3022 monoclonal antibodies prepared as human IgG1 and human IgA1 isotypes (20, 43).
    human IgA1
    suggested: None
    The cells were washed with the medium and stained with subsequent antibodies/reagents using the Brilliant Stain Buffer Plus (BD Biosciences) for 30 min at room temperature: FITC-conjugated anti-IgA (polyclonal rabbit F(ab’)2, Dako), BV421-conjugated anti-IgG (G18-145, BD Biosciences)
    anti-IgA
    suggested: None
    anti-IgG
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    The virus-plasma mixtures were placed on VeroE6/TMPRSS2 cells (JCRB1819) seeded in 96-well plates and cultured at 37 °C with 5% CO2 for 5 days.
    VeroE6/TMPRSS2
    suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)
    The plasmid vectors were transfected into 293T cells followed by infection with 0.5 MOI of G-complemented VSVΔG/Luc 24 h after the transfection (45), and then the uninfected viruses were washed out.
    293T
    suggested: None
    Recombinant DNA
    SentencesResources
    Briefly, the human codon-optimized DNA sequence encoding amino acids 331-529 of the SARS-CoV-2 spike (GenBank: MN994467) with an N-terminal signal peptide sequence (MIHSVFLLMFLLTPTESYVD) and C-terminal avi-tag and histidine-tag were cloned into the pCAGGS vector.
    pCAGGS
    suggested: RRID:Addgene_127347)
    To biotinylate RBD proteins, the RBD expression vectors were co-transfected into Expi293F cells together with the secreted BirA-Flag plasmid (Addgene) in the presence of 100 μM biotin.
    BirA-Flag
    suggested: RRID:Addgene_64395)
    Software and Algorithms
    SentencesResources
    Blood was collected in Vacutainer CPT tubes (BD Biosciences), followed by centrifugation at 1800 × g for 20 min.
    BD Biosciences
    suggested: (BD Biosciences, RRID:SCR_013311)
    Statistical analysis: The numerical data were statistically analyzed and visualized with GraphPad Prism 9 software (GraphPad)
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Flow cytometry data were analyzed using FlowJo software (BD Biosciences).
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)

    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:
    A primary limitation of our study is the lack of longitudinal analysis after the third dose of vaccines in our cohort. Therefore, we cannot determine the extents to which the numbers of cross-neutralizing Bmem subset correlate with the magnitudes of cross-neutralizing antibody responses following the third vaccine dose. Owing to the paucity of Bmem subsets, detailed phenotypic and transcriptomic characterization of the cross-neutralizing Bmem subset is hampered in this study. Finally, we focused on the neutralizing antibodies but non-neutralizing antibodies also confer the protection in vivo at least in animal models. The analysis on non-neutralizing and protective antibodies against the variants may generate the distinct outcome owing to the epitope difference.

    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.

  2. Version published to 10.1101/2021.12.24.474091v1 on bioRxiv