Humoral immune responses against seasonal coronaviruses predict efficiency of SARS-CoV-2 spike targeting, FcγR activation, and corresponding COVID-19 disease severity

  1. Jose L. Garrido
  2. Matias Medina
  3. Felipe Bravo
  4. Sarah McGee
  5. Francisco Fuentes
  6. Mario Calvo
  7. James W. Bowman
  8. Christopher D. Bahl
  9. Maria Inés Barría
  10. Rebecca A. Brachman
  11. Raymond A. Alvarez

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Abstract

Despite SARS-CoV-2 being a “novel” coronavirus, several studies suggest that detection of anti-spike IgG early in infection may be attributable to the amplification of humoral memory responses against seasonal hCoVs in severe COVID-19 patients. In this study, we examined this concept by characterizing anti-spike IgG from a cohort of non-hospitalized convalescent individuals with a spectrum of COVID-19 severity. We observed that anti-spike IgG levels positively correlated with disease severity, higher IgG cross-reactivity against betacoronaviruses (SARS-CoV-1 and OC43), and higher levels of proinflammatory Fc gamma receptor 2a and 3a (FcγR2a & FcγR3a) activation. In examining the levels of IgG targeting betacoronavirus conserved and immunodominant epitopes versus disease severity, we observed a positive correlation with the levels of IgG targeting the conserved S2’FP region, and an inverse correlation with two conserved epitopes around the heptad repeat (HR) 2 region. In comparing the levels of IgG targeting non-conserved epitopes, we observed that only one of three non-conserved immunodominant epitopes correlated with disease severity. Notably, the levels of IgG targeting the receptor binding domain (RBD) were inversely correlated with severity. Importantly, targeting of the RBD and HR2 regions have both been shown to mediate SARS-CoV-2 neutralization. These findings show that, aside from antibody (Ab) targeting of the RBD region, humoral memory responses against seasonal betacoronaviruses are potentially an important factor in dictating COVID-19 severity, with anti-HR2-dominant Ab profiles representing protective memory responses, while an anti-S2’FP dominant Ab profiles indicate deleterious recall responses. Though these profiles are masked in whole antigen profiling, these analyses suggest that distinct Ab memory responses are detectable with epitope targeting analysis. These findings have important implications for predicting severity of SARS-CoV-2 infections (primary and reinfections), and may predict vaccine efficacy in subpopulations with different dominant antibody epitope profiles.

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  1. ScreenIT

    SciScore for 10.1101/2021.09.14.460338: (What is this?)

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

    Table 1: Rigor

    EthicsConsent: Blood samples were collected after obtaining signed informed consent in accordance with institutionally approved IRB protocols.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    After incubation, plates were washed three times and incubated for 30 minutes at room temperature with cross-absorbed goat anti-human IgG-horseradish peroxidase (HRP)-conjugated secondary antibody (ThermoFisher Scientific; A18811) diluted to a 1:2500 dilution in ELISA wash buffer.
    anti-human IgG-horseradish
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    For this assay, 293T cells are transfected with SARS-CoV-2 spike expression vector and co-cultured with either a FcγR2a, or FcγR3a, CD4+ Jurkat reporter cell line, which expresses firefly luciferase upon FcγR activation.
    Jurkat
    suggested: TKG Cat# TKG 0209, RRID:CVCL_0065)
    To quantify background (i.e., IgG activation-independent) luciferase production, reporter cells were co-cultured with the spike-expressing 293T cells in the absence of any IgG.
    293T
    suggested: CCLV Cat# CCLV-RIE 1018, RRID:CVCL_0063)
    Software and Algorithms
    SentencesResources
    Lithium heparin-coated tubes were used for blood collection and plasma was isolated using Ficoll-Hypaque (GE Healthcare; 17-1440-03) in accordance with manufacturer’s instructions.
    GE Healthcare
    suggested: (GE Healthcare, RRID:SCR_000004)
    Polyclonal IgG was isolated from 200μl of donor plasma using a protein A/G spin column kit, followed by desalting using Zeba spin columns according to manufacturer’s instructions (ThermoFisher Scientific; 89892)
    ThermoFisher Scientific
    suggested: None
    The optical density at 450 nm (OD450) was measured using a BioTek Powerwave HT plate reader using Gen5 software.
    Gen5
    suggested: (Gen5, RRID:SCR_017317)
    The data were quantified using Flow Jo software (Tree Star, Inc).
    Flow Jo
    suggested: (FlowJo, RRID:SCR_008520)
    Statistical analysis: Statistical and data analyses were performed using GraphPad Prism 8.4.3, R 4.0.4, and R Studio 1.4.1103.
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Graphs were generated in Prism and R Studio and statistical differences between two groups were calculated by Mann-Whitney U-test.
    Prism
    suggested: (PRISM, RRID:SCR_005375)
    Scatter plots, bar graphs, heatmaps, and polar plots were visualized with ggplot2 (v3.3.3 R Studio).
    ggplot2
    suggested: (ggplot2, RRID:SCR_014601)
    The completed data were scaled to unit variance using FactoMineR (v2.4 R studio).
    FactoMineR
    suggested: (FactoMineR, RRID:SCR_014602)

    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:
    One caveat to the previous studies that found FcγR activity to be critical for effective humoral immunity is that all of those studies were conducted with neutralizing IgG. Therefore, we cannot rule out that FcγR activation in the absence of a neutralizing response does not contribute to severe COVID-19 pathogenesis, as may be the case with individuals with anti-S2’FP dominant IgG profiles. Therefore, it will be important to dissect how IgG-targeting of neutralizing and non-neutralizing epitopes influences the relationship between FcγR activation and disease outcomes. Additionally, it will be important to examine the contribution of FcγR activation to systemic inflammation and control of virus replication in animal models that faithfully mimic human FcγR-signaling effects. In conclusion, the data presented here demonstrate that immunological history—particularly antibody repertoire from seasonal betacoronaviruses—predicts and potentially determines COVID-19 disease severity. Specifically, an anti-HR2-dominant Ab profile represents an efficient protective recall response, an anti-S2’FP dominant Ab profile suggests a deleterious inefficient recall response, and a predominantly anti-RBD profile likely reflects a protective de novo response. These data become particularly important in assessing epitope-targeting early in disease, which could allow earlier interventions with treatments like monoclonal Ab therapies, preventing progression to ARDS. Additionally, assessing the humora...

    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.

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  2. Version published to 10.1101/2021.09.14.460338v1 on bioRxiv