A third vaccination with a single T cell epitope protects against SARS-CoV-2 infection in the absence of neutralizing antibodies

  1. Iris N. Pardieck
  2. Esmé T.I. van der Gracht
  3. Dominique M.B. Veerkamp
  4. Felix M. Behr
  5. Suzanne van Duikeren
  6. Guillaume Beyrend
  7. Jasper Rip
  8. Reza Nadafi
  9. Tetje C. van der Sluis
  10. Elham Beyranvand Nejad
  11. Nils Mülling
  12. Dena J. Brasem
  13. Marcel G.M. Camps
  14. Sebenzile K. Myeni
  15. Peter J. Bredenbeek
  16. Marjolein Kikkert
  17. Yeonsu Kim
  18. Luka Cicin-Sain
  19. Tamim Abdelaal
  20. Klaas P.J.M. van Gisbergen
  21. Kees L.M.C. Franken
  22. Jan Wouter Drijfhout
  23. Cornelius J.M. Melief
  24. Gerben C.M. Zondag
  25. Ferry Ossendorp
  26. Ramon Arens

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Abstract

Understanding the mechanisms and impact of booster vaccinations can facilitate decisions on vaccination programmes. This study shows that three doses of the same synthetic peptide vaccine eliciting an exclusive CD8 + T cell response against one SARS-CoV-2 Spike epitope protected all mice against lethal SARS-CoV-2 infection in the K18-hACE2 transgenic mouse model in the absence of neutralizing antibodies, while only a second vaccination with this T cell vaccine was insufficient to provide protection. The third vaccine dose of the single T cell epitope peptide resulted in superior generation of effector-memory T cells in the circulation and tissue-resident memory T (T RM ) cells, and these tertiary vaccine-specific CD8 + T cells were characterized by enhanced polyfunctional cytokine production. Moreover, fate mapping showed that a substantial fraction of the tertiary effector-memory CD8 + T cells developed from remigrated T RM cells. Thus, repeated booster vaccinations quantitatively and qualitatively improve the CD8 + T cell response leading to protection against otherwise lethal SARS-CoV-2 infection.

Summary

A third dose with a single T cell epitope-vaccine promotes a strong increase in tissue-resident memory CD8 + T cells and fully protects against SARS-CoV-2 infection, while single B cell epitope-eliciting vaccines are unable to provide protection.

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    SciScore for 10.1101/2021.12.15.472838: (What is this?)

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

    Table 1: Rigor

    EthicsIACUC: All animal experiments were approved by the Animal Experiments Committee of LUMC and performed according to the recommendations and guidelines set by LUMC and by the Dutch Experiments on Animals Act.
    Euthanasia Agents: K18-hACE2 transgenic mice were anaesthetized with isoflurane gas and intranasally infected with 5 × 103 plaque forming units (PFU) of SARS-CoV-2 in a total volume of 50 μl DMEM.
    Sex as a biological variableAt the start of the experiments, male and female mice were 6-8 weeks old.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Antigen-binding ELISA: ELISAs were performed to determine antibody titers in sera.
    Antigen-binding ELISA
    suggested: (Ling-Chu Hung / Animal Health Research Institute, Council of Agriculture, Executive Yuan, Taiwan Cat# 12-Hung-03 m& 20 ORF3 7D3, RRID:AB_2827541)
    Plates were again washed and then incubated with 1:4000 dilution of horse radish peroxidase (HRP) conjugated antimouse IgG secondary antibody (SouthernBiotech, cat. 1030-05) and incubated for 1h at RT.
    antimouse IgG
    suggested: (Roche Cat# 760-500, RRID:AB_2753116)
    Flow cytometry: Fluorescently labelled antibodies against the following mouse antigens were used: CD3 (clone 145-2C11, BD Biosciences),
    CD3
    suggested: None
    Mass cytometry and analysis: Metal-conjugated antibodies were either purchased from Fluidigm or were generated by conjugation of lanthanide metal isotopes to anti-mouse antibodies using the Maxpar X8 Polymer method according to the manufacturer’s protocol (Fluidigm).
    anti-mouse
    suggested: None
    Anti-PE and anti-APC were added and incubated for 45 minutes.
    Anti-PE
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Thereupon, 2 × 104 Vero-E6 (ATCC CRL-1586) cells that were seeded in 96-well plates were inoculated with serum and virus.
    Vero-E6
    suggested: None
    Experimental Models: Organisms/Strains
    SentencesResources
    Mice: Wild-type C57BL/6 mice were obtained from Charles River Laboratories, Jackson Laboratory or Janvier Labs.
    C57BL/6
    suggested: None
    The K18-hACE2 transgenic mice, expressing the human ACE2 receptor (hACE2) under control of the cytokeratin 18 (K18) promoter (41), were obtained from the Jackson Laboratory (B6.Cg-Tg(K18-ACE2)2Prlmn/J), and bred in-house.
    B6.Cg-Tg(K18-ACE2)2Prlmn/J)
    suggested: RRID:IMSR_JAX:034860)
    K18-hACE2 transgenic mice were anaesthetized with isoflurane gas and intranasally infected with 5 × 103 plaque forming units (PFU) of SARS-CoV-2 in a total volume of 50 μl DMEM.
    K18-hACE2
    suggested: RRID:IMSR_GPT:T037657)
    Adoptive T cell transfers: Spleens of OT-I Hobit reporter × ROSA26-eYFP LT mice were isolated and subsequently CD8+ T cells were isolated by negative selection using MicroBeads (130-104-075, Miltenyi Biotec) according to the manufacturer’s protocol.
    ROSA26-eYFP LT
    suggested: None
    Software and Algorithms
    SentencesResources
    Subsequently, MHC class I tetramer-specific CD8+ T cells were selected in FlowJo for subsequent analysis.
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)
    Using FlowSOM, 14 clusters were identified per analysis.
    FlowSOM
    suggested: (FlowSOM, RRID:SCR_016899)
    Statistical analysis: Statistical analyses were performed using Cytofast or GraphPad Prism (La Jolla, CA, Unites States).
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)

    Results from OddPub: Thank you for sharing your 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 10.1101/2021.12.15.472838v1 on bioRxiv