SARS-CoV-2 Epitopes Are Recognized by a Public and Diverse Repertoire of Human T Cell Receptors

  1. Alina S. Shomuradova
  2. Murad S. Vagida
  3. Savely A. Sheetikov
  4. Ksenia V. Zornikova
  5. Dmitry Kiryukhin
  6. Aleksei Titov
  7. Iuliia O. Peshkova
  8. Alexandra Khmelevskaya
  9. Dmitry V. Dianov
  10. Maria Malasheva
  11. Anton Shmelev
  12. Yana Serdyuk
  13. Dmitry V. Bagaev
  14. Anastasia Pivnyuk
  15. Dmitrii S. Shcherbinin
  16. Alexandra V. Maleeva
  17. Naina T. Shakirova
  18. Artem Pilunov
  19. Dmitry B. Malko
  20. Ekaterina G. Khamaganova
  21. Bella Biderman
  22. Alexander Ivanov
  23. Mikhail Shugay
  24. Grigory A. Efimov

Reviewed by

Read the full article See related articles

Discuss this preprint

Start a discussion What are Sciety discussions?

Listed in

Log in to save this article

Abstract

No abstract available

Article activity feed

  1. ScreenIT

    SciScore for 10.1101/2020.05.20.20107813: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementConsent: All donors signed the informed consent approved by the National Research Center for Hematology ethical committee before the enrollment.
    IACUC: Additionally, 10 healthy hematopoietic stem cell donor samples and 10 healthy donor serum samples were obtained from the blood bank with the approval of the local ethical committee.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    COVID-19 was confirmed either by positive SARS-CoV-2 RT-PCR test or retrospectively by the detection of anti-RBD antibodies.
    anti-RBD
    suggested: None
    After, plates were washed two times with PBS and then two times with PBS, containing 0.05% Tween-20, followed by incubation with biotinylated anti-human IFN-γ Detection antibody for 2h at room temperature (RT).
    anti-human IFN-γ
    suggested: None
    Next, the wells were washed 3 times and were incubated for one more hour with 100 μL of anti-human IgG monoclonal HRP-conjugated antibodies (supplied with RBD ELISA Kit).
    anti-human IgG
    suggested: None
    Software and Algorithms
    SentencesResources
    Predicted proteasomal cleavage score of the C-terminal amino acid was estimated using NetChop 3.1 (Nielsen, Lundegaard et al. 2005).
    NetChop
    suggested: None
    Data were analyzed using FlowJo Software.
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)

    Results from OddPub: Thank you for sharing your code and data.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    Our findings are in line with that with acaveat that we observed the significant increase of SARS-CoV-2 S-protein reactive T-cells in healthy donors sampled during the COVID-19 pandemic (Figure 2c and 2d). Combined with the complete lack of SARS-CoV-2 specific antibodies in that group this suggests that some of the donors may have had contact with SARS-CoV-2 before blood sampling. Due to cross-reactivity induced by other coronaviruses their T cells might have protected them from developing the full scale infection. This is illustrated by the case of p1477 who is known to cohabited with COVID-19 patient but was negative in multiple PCR tests, did not have any COVID-19 typical or flu-like symptoms and had no detectable antibodies to any of the SARS-CoV-2 antigens. This hypothesis, although, needs to be validated on a larger cohort of donors. As others have shown before, we observed that significantly more CD4+ cells in convalescent donors express HLA-DR and CD38 (Braun, Loyal et al. 2020, Thevarajan, Nguyen et al. 2020). We have also shown the same tendency for CD8+ T cells, though the difference was not significant (Figure 2g). As was shown before (Weiskopf, Schmitz et al. 2020) the majority of SARS-CoV-2 specific CD4+ belonged to the TCM subpopulation while CD8+ were predominantly of TTE and TEM phenotype. In this work we used the IFNγ-secretion upon antigen stimulation as a criterion of antigen-specific cells. This approach might potentially miss some relevant T cells as the...

    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: Please consider improving the rainbow (“jet”) colormap(s) used on page 6. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

    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.

    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 10.1016/j.immuni.2020.11.004
  3. Version published to 10.1101/2020.05.20.20107813 on medRxiv