Highlights d Low avidity and broad cross-reactivities of pre-existing SARS-CoV-2 memory T cells d Strong CCCoV-specific memory CD4 + T cell responses in all analyzed individuals d SARS-CoV-2-specific CD4 + T cells in COVID-19 patients lack cross-reactivity to CCCoVs d Low avidity and clonality of SARS-CoV-2-specific T cell responses in severe COVID-19

Coronavirus disease 2019 (COVID-19) displays high clinical variability but the parameters that determine disease severity are still unclear. Pre-existing T cell memory has been hypothesized as a protective mechanism but conclusive evidence is lacking. Here we demonstrate that all unexposed individuals harbor SARS-CoV-2-specific memory T cells with marginal cross-reactivity to common cold corona and other unrelated viruses. They display low functional avidity and broad protein target specificities and their frequencies correlate with the overall size of the CD4+ memory compartment reflecting the immunological age of an individual. COVID-19 patients have strongly increased SARS-CoV-2-specific inflammatory T cell responses that are correlated with severity. Strikingly however, patients with severe COVID-19 displayed lower TCR functional avidity and less clonal expansion. Our data suggest that a low avidity pre-existing T cell memory negatively impacts on the T cell response quality against neoantigens such as SARS-CoV-2, which may predispose to develop inappropriate immune reactions especially in the elderly. We propose the immunological age as an independent risk factor to develop severe COVID-19.

ObjectiveOne of the current hypotheses to explain the proinflammatory immune response in IBD is a dysregulated T cell reaction to yet unknown intestinal antigens. As such, it may be possible to identify disease-associated T cell clonotypes by analysing the peripheral and intestinal T-cell receptor (TCR) repertoire of patients with IBD and controls.DesignWe performed bulk TCR repertoire profiling of both the TCR alpha and beta chains using high-throughput sequencing in peripheral blood samples of a total of 244 patients with IBD and healthy controls as well as from matched blood and intestinal tissue of 59 patients with IBD and disease controls. We further characterised specific T cell clonotypes via single-cell RNAseq.ResultsWe identified a group of clonotypes, characterised by semi-invariant TCR alpha chains, to be significantly enriched in the blood of patients with Crohn’s disease (CD) and particularly expanded in the CD8+ T cell population. Single-cell RNAseq data showed an innate-like phenotype of these cells, with a comparable gene expression to unconventional T cells such as mucosal associated invariant T and natural killer T (NKT) cells, but with distinct TCRs.ConclusionsWe identified and characterised a subpopulation of unconventional Crohn-associated invariant T (CAIT) cells. Multiple evidence suggests these cells to be part of the NKT type II population. The potential implications of this population for CD or a subset thereof remain to be elucidated, and the immunophenotype and antigen reactivity of CAIT cells need further investigations in future studies.

The humoral immune response to severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) vaccination in patients with chronic inflammatory disease (CID) declines more rapidly with tumor necrosis factor‐α (TNF‐α) inhibition. Furthermore, the efficacy of current vaccines against Omicron variants of concern (VOC) including BA.2 is limited. Alterations within immune cell populations, changes in IgG affinity, and the ability to neutralize a pre‐VOC strain and the BA.2 virus were investigated in these at‐risk patients. Serum levels of anti‐SARS‐CoV‐2 IgG, IgG avidity, and neutralizing antibodies (NA) were determined in anti‐TNF‐α patients ( n = 10) and controls ( n = 24 healthy individuals; n = 12 patients under other disease‐modifying antirheumatic drugs, oDMARD) before and after the second and third vaccination by ELISA, immunoblot and live virus neutralization assay. SARS‐CoV‐2‐specific B‐ and T cell subsets were analysed by multicolor flow cytometry. Six months after the second vaccination, anti‐SARS‐CoV‐2 IgG levels, IgG avidity and anti‐pre‐VOC NA titres were significantly reduced in anti‐TNF‐α recipients compared to controls (healthy individuals: avidity: p ≤ 0.0001; NA: p = 0.0347; oDMARDs: avidity: p = 0.0012; NA: p = 0.0293). The number of plasma cells was increased in anti‐TNF‐α patients (Healthy individuals: p = 0.0344; oDMARDs: p = 0.0254), while the absolute number of SARS‐CoV‐2‐specific plasma cells 7 days after 2nd vaccination were comparable. Even after a third vaccination, these patients had lower anti‐BA.2 NA titres compared to both other groups. We show a reduced SARS‐CoV‐2 neutralizing capacity in patients under TNF‐α blockade. In this cohort, the plasma cell response appears to be less specific and shows stronger bystander activation. While these effects were observable after the first two vaccinations and with older VOC, the differences in responses to BA.2 were enhanced.

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