Persistence of T Cell and Antibody Responses to SARS-CoV-2 Up to 9 Months after Symptom Onset

  1. Jaclyn C Law
  2. Melanie Girard
  3. Gary Y C Chao
  4. Lesley A Ward
  5. Baweleta Isho
  6. Bhavisha Rathod
  7. Karen Colwill
  8. Zhijie Li
  9. James M Rini
  10. Feng Yun Yue
  11. Samira Mubareka
  12. Allison J McGeer
  13. Mario A Ostrowski
  14. Jennifer L Gommerman
  15. Anne-Claude Gingras
  16. Tania H Watts

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Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induces T cell, B cell, and Ab responses that are detected for several months in recovered individuals. Whether this response resembles a typical respiratory viral infection is a matter of debate. In this study, we followed T cell and Ab responses in 24 mainly nonhospitalized human subjects who had recovered from PCR-confirmed SARS-CoV-2 infection at two time points (median of 45 and 145 d after symptom onset). Ab responses were detected in 95% of subjects, with a strong correlation between plasma and salivary anti-spike (anti-S) and anti—receptor binding domain IgG, as well as a correlation between circulating T follicular helper cells and the SARS-CoV-2–specific IgG response. T cell responses to SARS-CoV-2 peptides were determined using intracellular cytokine staining, activation markers, proliferation, and cytokine secretion. All study subjects had a T cell response to at least one SARS-CoV-2 Ag based on at least one T cell assay. CD4+ responses were largely of the Th1 phenotype, but with a lower ratio of IFN-γ– to IL-2–producing cells and a lower frequency of CD8+:CD4+ T cells than in influenza A virus (IAV)-specific memory responses within the same subjects. Analysis of secreted molecules also revealed a lower ratio of IFN-γ to IL-2 and an altered cytotoxic profile for SARS-CoV-2 S- and nucleocapsid-specific responses compared with IAV-specific responses. These data suggest that the memory T cell phenotype after a single infection with SARS-CoV-2 persists over time, with an altered cytokine and cytotoxicity profile compared with long-term memory to whole IAV within the same subjects.

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  1. Version published to 10.4049/jimmunol.2100727
  2. ScreenIT

    SciScore for 10.1101/2021.06.08.21258518: (What is this?)

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

    Table 1: Rigor

    EthicsConsent: Human subjects and sample preparation: Individuals who had recovered from COVID-19 as confirmed by positive nasopharyngeal COVID-19 PCR upon presentation, were recruited to RISC-CoV through participating hospitals in the Toronto Invasive Bacterial Diseases Network, with informed consent, to donate blood and saliva, as approved by the University of Toronto Research Ethics Board (REB protocol number 00027673 to THW).
    IRB: Human subjects and sample preparation: Individuals who had recovered from COVID-19 as confirmed by positive nasopharyngeal COVID-19 PCR upon presentation, were recruited to RISC-CoV through participating hospitals in the Toronto Invasive Bacterial Diseases Network, with informed consent, to donate blood and saliva, as approved by the University of Toronto Research Ethics Board (REB protocol number 00027673 to THW).
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    ELISA assays for detecting antibodies in plasma: An automated chemiluminescent ELISA assay was used to analyze the levels of IgG, IgA and IgM antibodies to the spike trimer, its RBD, and the nucleocapsid, essentially as in (12)with the following modifications.
    IgM
    suggested: None
    To define the cutoff for positive antibody calls for each antigen for IgG, 3 standard deviations from the mean of the log negative control distribution from 20 different runs collected over 4 months was used as a cut-off to define positivity in each individual assay.
    antigen for IgG
    suggested: (RIKEN Institute for Developmental Biology Cat# MS8407-3, RRID:AB_2783560)
    Enzyme-linked immunosorbent assays to detect Spike and RBD-specific IgG and IgA antibodies in saliva were completed as described in reference (12).
    RBD-specific IgG
    suggested: None
    IgA
    suggested: None
    Software and Algorithms
    SentencesResources
    Cells were first stained with anti-human CCR7 [clone G043H7 (BioLegend, San Diego, CA)] at 37°C for 10 min, followed by staining with Fixable Viability Dye eFluor™ 506 (eBiosciences, Thermofisher, Mississauga, Ontario) to discern viable cells, anti-human CD3 [clone UCHT1 (BioLegend)], CXCR5 [clone J252D4 (
    BioLegend)]
    suggested: None
    Samples were washed twice, then resuspended in FACS buffer and acquired on the BD LSRFortessa X-20 flow cytometer using FACSDiva software.
    FACSDiva
    suggested: (BD FACSDiva Software, RRID:SCR_001456)
    Data and Statistical analysis: Flow cytometry data were analyzed using FlowJo v10.7.1 (BD Biosciences)
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)
    Statistical analyses were performed using GraphPad Prism v9.1.1. “Δ” in figure labels represents values for which background signal has been subtracted.
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    These data were visualized using the Seaborn data visualization library for Python (https://joss.theoj.org/papers/10.21105/joss.03021).
    Python
    suggested: (IPython, RRID:SCR_001658)

    Results from OddPub: Thank you for sharing your data.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    A caveat to these estimates is that the T cell frequencies based on ICC were low, potentially rendering them less quantitative. Nonetheless, our results are quite similar to those of Dan et al. (34), who reported a half-life of 6 months for CD8+ T cell responses and 3 months for CD4+ T cell responses, by analyzing paired samples based on activation markers. SARS-CoV-2 specific proliferative responses of CD4+ T cells were more stable between time point one and two than the proliferative responses of CD8+ T cells, perhaps reflecting the higher proportion of Tcm in the CD4+ population and a higher proportion of Temra in the CD8+ T cell populations. Bilich, et al. reported stable CD8+ T cell responses and increasing CD4+ T cell responses over 2 time points (median 40 and 159 days) based on ICC or ELIspot assays, in a cohort of SARS-CoV-2 convalescent subjects, most with mild disease (36). However, the study of Bilich et al. (36) was focused on a series of defined epitopes, whereas the study of Dan et al. (34) and the present study used overlapping peptide pools covering the full Ag sequences. Thus, although the overall T cell response to SARS-CoV-2 declines over time, it is possible that subsets of epitope-specific T cells form longer lived subsets, which displace other T cells over time. The responses to IAV in our study were about 2-3 times more stable than the response to SARS-CoV-2 within the same subjects. As boosting is known to increase the duration of T cell immunity (53)...

    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.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

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  3. Version published to 10.1101/2021.06.08.21258518v1 on medRxiv