CD8+ T-Cell Responses in COVID-19 Convalescent Individuals Target Conserved Epitopes From Multiple Prominent SARS-CoV-2 Circulating Variants

  1. Andrew D Redd
  2. Alessandra Nardin
  3. Hassen Kared
  4. Evan M Bloch
  5. Andrew Pekosz
  6. Oliver Laeyendecker
  7. Brian Abel
  8. Michael Fehlings
  9. Thomas C Quinn
  10. Aaron A R Tobian

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Abstract

This study examined whether CD8+ T-cell responses from coronavirus disease 2019 convalescent individuals (n = 30) potentially maintain recognition of the major severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants (alpha, beta, gamma; n = 45 mutations assessed). Only 1 mutation found in Beta variant-spike overlapped with a previously identified epitope (1/52), suggesting that virtually all anti-SARS-CoV-2 CD8+ T-cell responses should recognize these newly described variants.

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  1. Version published to 10.1093/ofid/ofab143
  2. ScreenIT

    SciScore for 10.1101/2021.02.11.21251585: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: This study was approved by the Johns Hopkins Institutional Review Board, and all participants provided informed consent.
    Consent: This study was approved by the Johns Hopkins Institutional Review Board, and all participants provided informed consent.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    No key resources detected.

    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:
    It should be noted that this study had several limitations including the relatively small size of the population examined. In addition, the participants in the study were all from North America and were selected in part on the presence of one or more of the target HLA types examined (73% coverage of the continental US population). It will be important to examine for T cell escape in more diverse HLA types moving forward. These data highlight the potential significant role of a multi-epitope T cell response in limiting viral escape, and partly mediate protection from disease caused by the SARS-CoV-2 variants. It is important that vaccines used for widespread campaigns generate strong multivalent T-cell responses in addition to NAb and other humoral responses in order to optimize efficacy against the current SARS-CoV-2 and emerging strains. It will also be important to continue to monitor the breadth, magnitude, and durability of the anti-SARS-CoV-2 T cell responses in recovered and vaccinated individuals as part of any assessment to determine if booster vaccinations are needed.

    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.
    • No funding statement was detected.
    • 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.

  3. Version published to 10.1101/2021.02.11.21251585v1 on medRxiv