A conserved immune trajectory of recovery in hospitalized COVID-19 patients

  1. Cassandra E. Burnett
  2. Trine Line Hauge Okholm
  3. Iliana Tenvooren
  4. Diana M. Marquez
  5. Stanley Tamaki
  6. Priscila Munoz Sandoval
  7. The UCSF COMET Consortium
  8. Carolyn S. Calfee
  9. Carolyn M. Hendrickson
  10. Kirsten N. Kangelaris
  11. Charles R. Langelier
  12. Matthew F. Krummel
  13. Prescott G. Woodruff
  14. David J. Erle
  15. K. Mark Ansel
  16. Matthew H. Spitzer

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Abstract

Many studies have provided insights into the immune response to COVID-19; however, little is known about the immunological changes and immune signaling occurring during COVID-19 resolution. Individual heterogeneity and variable disease resolution timelines obscure unifying immune characteristics. Here, we collected and profiled >200 longitudinal peripheral blood samples from patients hospitalized with COVID-19, with other respiratory infections, and healthy individuals, using mass cytometry to measure immune cells and signaling states at single cell resolution. COVID-19 patients showed a unique immune composition and an early, coordinated and elevated immune cell signaling profile, which correlated with early hospital discharge. Intra-patient time course analysis tied to clinically relevant events of recovery revealed a conserved set of immunological processes that accompany, and are unique to, disease resolution and discharge. This immunological process, together with additional changes in CD4 regulatory T cells and basophils, accompanies recovery from respiratory failure and is associated with better clinical outcomes at the time of admission. Our work elucidates the biological timeline of immune recovery from COVID-19 and provides insights into the fundamental processes of COVID-19 resolution in hospitalized patients.

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  1. ScreenIT

    SciScore for 10.1101/2022.03.15.484467: (What is this?)

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

    Table 1: Rigor

    EthicsConsent: Human subjects: Patients, or a designated surrogate, provided informed consent to participate in the study.
    IRB: The study is approved by the UCSF Institutional Review Board: IRB 20-30497.
    Field Sample Permit: Peripheral blood sample collection and processing: Blood samples were collected in one EDTA tube and processed within 6 hours of collection.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    No key resources detected.

    Results from OddPub: Thank you for sharing your code and 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 10.1101/2022.03.15.484467v1 on bioRxiv