Deciphering the quality of SARS‐CoV‐2 specific T‐cell response associated with disease severity, immune memory and heterologous response

  1. Alberto Pérez‐Gómez
  2. Carmen Gasca‐Capote
  3. Joana Vitallé
  4. Francisco J. Ostos
  5. Ana Serna‐Gallego
  6. María Trujillo‐Rodríguez
  7. Esperanza Muñoz‐Muela
  8. Teresa Giráldez‐Pérez
  9. Julia Praena‐Segovia
  10. María D. Navarro‐Amuedo
  11. María Paniagua‐García
  12. Manuel García‐Gutiérrez
  13. Manuela Aguilar‐Guisado
  14. Inmaculada Rivas‐Jeremías
  15. María Reyes Jiménez‐León
  16. Sara Bachiller
  17. Alberto Fernández‐Villar
  18. Alexandre Pérez‐González
  19. Alicia Gutiérrez‐Valencia
  20. Mohammed Rafii‐El‐Idrissi Benhnia
  21. Daniela Weiskopf
  22. Alessandro Sette
  23. Luis F. López‐Cortés
  24. Eva Poveda
  25. Ezequiel Ruiz‐Mateos
  26. Virgen del Rocío Hospital COVID‐19 and COHVID‐GS Working Teams

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Abstract

SARS‐CoV‐2 specific T‐cell response has been associated with disease severity, immune memory and heterologous response to endemic coronaviruses. However, an integrative approach combining a comprehensive analysis of the quality of SARS‐CoV‐2 specific T‐cell response with antibody levels in these three scenarios is needed. In the present study, we found that, in acute infection, while mild disease was associated with high T‐cell polyfunctionality biased to IL‐2 production and inversely correlated with anti‐S IgG levels, combinations only including IFN‐γ with the absence of perforin production predominated in severe disease. Seven months after infection, both non‐hospitalised and previously hospitalised patients presented robust anti‐S IgG levels and SARS‐CoV‐2 specific T‐cell response. In addition, only previously hospitalised patients showed a T‐cell exhaustion profile. Finally, combinations including IL‐2 in response to S protein of endemic coronaviruses were the ones associated with SARS‐CoV‐2 S‐specific T‐cell response in pre‐COVID‐19 healthy donors’ samples. These results could have implications for protective immunity against SARS‐CoV‐2 and recurrent COVID‐19 and may help for the design of new prototypes and boosting vaccine strategies.

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  1. Version published to 10.1002/ctm2.802
  2. ScreenIT

    SciScore for 10.1101/2021.12.28.474325: (What is this?)

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

    Table 1: Rigor

    EthicsConsent: Written or oral informed consent was obtained from all participants.
    IRB: The study was approved by the Ethics Committee of the Virgen Macarena and Virgen del Rocio University Hospital (protocol code “pDCOVID”; internal code 0896-N-20).
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    The stimulation was performed in the presence of 10 µg/mL of brefeldin A (Sigma Chemical Co, St. Louis, MO) and 0.7 µg/mL of monensin (BD Biosciences) protein transport inhibitors, anti-CD107a-BV650 (clone H4A3; BD Biosciences, USA) monoclonal antibody and purified CD28 and CD49d as previously described (22).
    anti-CD107a-BV650
    suggested: None
    Quantification of anti-S SARS-CoV-2 and endemic coronaviruses IgG antibodies: Anti-S IgG SARS-CoV-2 and endemic coronaviruses (NL63, OC43, 229E and HKU1) levels were measured by ELISA as previously described (4,16,23,24).
    endemic coronaviruses IgG antibodies: Anti-S IgG SARS-CoV-2 and endemic coronaviruses (NL63, OC43, 229E and HKU1) levels
    suggested: None
    Anti-S IgG SARS-CoV-2
    suggested: None
    NL63
    suggested: (Virostat Cat# 3879, RRID:AB_2889994)
    HKU1
    suggested: None
    Secondary antibodies, streptavidin-horseradish peroxidase-conjugated mouse anti-human IgG (Hybridoma Reagent Laboratory, Baltimore, MD, #HP6043-HRP) was used at a 1: 2,000 dilutions in 1% milk containing 0.05% Tween-20 in PBS.
    anti-human IgG
    suggested: (LSBio (LifeSpan Cat# LS-C6452-25, RRID:AB_834632)
    Software and Algorithms
    SentencesResources
    Immunophenotyping and intracellular cytokine staining: Both cultured PBMCs and cells for phenotypical analysis were washed (1800 rpm, 5 min, room temperature) with Phosphate-buffered saline (PBS) and incubated 35 min at room temperature (RT) with LIVE/DEAD Fixable Aqua Dead Cell Stain (Life Technologies), anti-CD14-BV510 (clone MφP9), anti-CD19-BV510 (clone SJ25C1), anti-CD56-BV510 (clone NMCAM16.2), anti-CD3-BV711 (clone SP34-2), anti-CD45RA-FITC (clone L48), anti-CD8-APC (clone SK-1), anti-CD27-APCH7 (clone M-T271), anti-PD-1-BV786 (CD279, clone EH12-1), anti-CD38 (clone HIT2), anti-CD28 (clone CD28.2) (all of them from BD Bioscience); anti-TIGIT-PerCPCy5.5 (clone A15153G) and anti-HLA-DR (clone L243) (from BioLegend).
    BD Bioscience)
    suggested: None
    PBMCs were washed with PBS and fixed and permeabilized with BD Cytofix/CytoPerm following manufacturer’s protocol (Cat. No. 554714, BD Bioscience), and intracellularly stained at 4°C for 30 min with anti-IL-2-BV421 (clone MQ1-17H12), anti-IFN-γ-PE-Cy7 (clone B27) (BD Bioscience), anti-TNF-α-AF700 (clone Mab11) (BD Pharmingen), anti-Perforin-PE (clone B-D48) (BioLegend).
    BD Cytofix/CytoPerm
    suggested: None
    BD Bioscience
    suggested: (BD Biosciences, RRID:SCR_013311)
    Data were analyzed using the FlowJo 10.7.1 software (Treestar, Ashland, OR).
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)
    Statistical Analysis: Non-parametric statistical analyses were performed using Statistical Package for the Social Sciences software (SPSS 25.0; SPSS, Inc., Chicago, IL), RStudio Version 1.3.959 and GraphPad Prism version 8.0 (GraphPad Software, Inc.).
    Statistical Package for the Social Sciences
    suggested: (SPSS, RRID:SCR_002865)
    SPSS
    suggested: (SPSS, RRID:SCR_002865)
    RStudio
    suggested: (RStudio, RRID:SCR_000432)
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)

    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:
    One limitation of this study is that all patients included were recruited in the first wave of COVID-19 in Spain, in those dates, experimental therapies with very limited but transitory immunosuppressive effects were administered what may have affected the levels of immune parameters in acute infection. However, in those patients who were treated with IFN-β and corticosteroids, samples were collected time enough after these therapies to reverse the potential effects (24 days [7 – 28] and 9 days [1 – 21], respectively) what may have not affected the results presented herein. Seven months post-infection, one potential bias may come from the group of hospitalized subjects that were composed by patients with previous mild (42%) or severe (58%) disease, however, as no differences were found in any parameter associated to T-cell response (data not shown) between this two subgroups, they formed part of the same group of previously hospitalized and were compared with non-hospitalized patients. ICS needs a notable amount of cells to be assayed, this avoid us to perform endemic virus-specific T-cell response in COVID-19 samples; however, it has allowed us to obtain comprehensive data about the quality of SARS-CoV-2 specific T-cell response. Finally, anti-S IgG levels were assayed against the whole S protein and not for RBD, cross-reactive reaction cannot be excluded and results have to be interpreted taking this into account. In the same way, further research is needed to confirm and c...

    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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  3. Version published to 10.1101/2021.12.28.474325v1 on bioRxiv