Symptomatic SARS-CoV-2 breakthrough infections broaden the repertoire of Spike-reactive CD4 T cells

SARS-CoV-2 breakthrough infections (BTI) are relatively common, but little is known in terms of differentiating responses associated with asymptomatic BTI (ABTI) versus symptomatic BTI (SBTI). Here, we investigated the impact of ABTI and SBTI on antibody and T cell responses towards Spike. SBTI donors had significantly higher plasma anti-Spike RBD IgG titers compared to both ABTI and SARS-CoV-2 vaccinated donors with no signs of previous infection (VAX) donors. While no impact of ABTI or SBTIs was found in the magnitude of Spike-specific CD4 and CD8 T cell responses, both ABTI and SBTI donors had significantly higher CD4 T cell responses towards non-Spike antigens. In-depth characterization of Spike-specific CD4 and CD8 T cells at scRNA/TCRseq level revealed that ABTI and SBTI induced different alterations of the CD4 compartment. These included a IFNGhigh skewed response among cytokine-producing cells, and a concurrent expansion of type II IFN-responsive TH17-like cells in SBTI. SBTI donors were further found to have an increased CD4 TCR repertoire diversity compared to VAX donors. ABTI-associated alterations of the Spike-specific compartment were intermediate between SBTI and VAX groups, likely reflecting lower antigen exposure and less inflammatory environment during ABTIs versus SBTIs. Overall design: Here, we used single-cell RNA sequencing (scRNAseq) and T cell receptor sequencing (scTCRseq) to characterize Spike (S)-specific T cell responses in VAX, ABTIs, and SBTIs, to define distinct immunological signatures related to T cell functionality and T cell subsets responding to antigen stimulation. We performed scRNAseq and scTCRseq on S-reactive CD4 T cells by sorting AIM+ (OX40+CD137+) cells following S megapool stimulation.