Daily Viral Kinetics and Innate and Adaptive Immune Response Assessment in COVID-19: a Case Series

  1. Pauline Vetter
  2. Christiane S. Eberhardt
  3. Benjamin Meyer
  4. Paola Andrea Martinez Murillo
  5. Giulia Torriani
  6. Fiona Pigny
  7. Sylvain Lemeille
  8. Samuel Cordey
  9. Florian Laubscher
  10. Diem-Lan Vu
  11. Adrien Calame
  12. Manuel Schibler
  13. Frederique Jacquerioz
  14. Géraldine Blanchard-Rohner
  15. Claire-Anne Siegrist
  16. Laurent Kaiser
  17. Arnaud M. Didierlaurent
  18. Isabella Eckerle

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Abstract

This work is particularly important because it simultaneously assessed the virology, immunology, and clinical presentation of the same subjects, whereas other studies assess these separately. We describe the detailed viral and immune profiles of the first five patients infected by SARS-CoV-2 and quarantined in Geneva, Switzerland. Viral loads peaked at the very beginning of the disease, and infectious virus was shed only during the early acute phase of disease. No infectious virus could be isolated by culture 7 days after onset of symptoms, while viral RNA was still detectable for a prolonged period. Importantly, we saw that all patients, even those with mild symptoms, mount an innate response sufficient for viral control (characterized by early activated cytokines and monocyte responses) and develop specific immunity as well as cellular and humoral SARS-CoV-2-specific adaptive responses, which already begin to decline a few months after the resolution of symptoms.

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  1. Version published to 10.1128/msphere.00827-20
  2. ScreenIT

    SciScore for 10.1101/2020.07.02.20143271: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: Ethical approval was waived by the local ethics committee (BASEC Req-2020-00143); written informed consent for sample collection and coded data gathering was obtained from each patient.
    Consent: Ethical approval was waived by the local ethics committee (BASEC Req-2020-00143); written informed consent for sample collection and coded data gathering was obtained from each patient.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    T cells were stained in PBS with LIVE/DEAD™ Stain Kit to exclude dead cells, anti-CD3, -CD4, -CD8, -CD38 and anti-HLA-DR antibodies and were then fixed and permeabilized.
    anti-CD3
    suggested: (BD Biosciences Cat# 341004, RRID:AB_400448)
    -CD4
    suggested: None
    -CD8
    suggested: None
    -CD38
    suggested: None
    anti-HLA-DR
    suggested: None
    Anti-Granzyme B and anti-Ki67 antibodies were used for intracellular staining.
    Anti-Granzyme B
    suggested: None
    anti-Ki67
    suggested: None
    For phenotyping of monocytes, cells were stained with FcR binding inhibitor, anti-CD3, -HLA-DR, -CD40, -CD123, -CD169, -CD20, -CCR2, -CD14, -CD16, -CD86, -CD163 and anti-CCR7 antibodies.
    anti-CD3 , -HLA-DR , -CD40 , -CD123 , -CD169 , -CD20 , -CCR2 , -CD14 , -CD16
    suggested: None
    -CD86
    suggested: None
    -CD163
    suggested: None
    anti-CCR7
    suggested: None
    Antibody assays: S1 domain-specific IgG and IgA antibody response was measured using a commercially available kit (Euroimmun AG, Lübeck, Germany, #EI 2606-9601 G and EI 2606-9601 A) according to the manufacturer’s instructions.
    IgA
    suggested: None
    IgG, IgA and IgM antibody titers were determined using a SARS-CoV-2 complete spike (S) protein-based rIFA [21, 22]
    IgM
    suggested: None
    Neutralizing antibodies were quantified on VeroE6 cells infected with a VSV-based SARS-CoV-2 pseudotype expressing a 19-amino-acid, C-terminal truncated spike protein [23-25] (NCBI Reference sequence: NC_045512.2) with serially diluted sera.
    C-terminal truncated spike protein
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Viral culture was performed on VeroE6 cells as previously described [19].
    VeroE6
    suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)
    Software and Algorithms
    SentencesResources
    All data were acquired the same day on a Fortessa II cytometer (BD Biosciences) and analyzed using FlowJo software (V10, Tree Star)
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)

    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:
    Our study has limitations. Although we were able to perform a comprehensive analysis of the immune response and viral shedding, the description is limited to five patients (with early time points missing for P5, and later time points missing for P2) and our interpretation of the association between viral load, innate and adaptive responses in patients with mild COVID-19 requires confirmation with a larger sample size. Finally, we were unable to follow all patients for late time points and cannot reach a conclusion about the durability of SARS-CoV-2 specific immunity according to disease pattern.

    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.
    • Thank you for including a protocol registration statement.

    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 10.1101/2020.07.02.20143271v1 on medRxiv