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

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ABSTRACT SARS-CoV-2 breakthrough infections (BTIs) 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 toward 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 toward 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 an IFNG high -skewed response among cytokine-producing cells and a concurrent expansion of type II IFN-responsive T H 17-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. IMPORTANCE SARS-CoV-2 mRNA vaccines have been shown to induce robust T-cell responses, crucial for long-term protection against severe SARS-CoV-2 infection. Hybrid immunity, created by a combination of vaccination and infection, has been associated with improved protection against severe SARS-CoV-2 infection. Here, we have investigated the impact of asymptomatic and symptomatic breakthrough infections (BTIs) on T-cell responses toward Spike, compared to donors that have only received mRNA SARS-CoV-2 vaccines. Symptomatic, and to a lesser extent asymptomatic, BTIs broadened the repertoire of Spike-reactive CD4 T cells and induced a more pro-inflammatory Spike-reactive T-cell response capable of enhancing activation of TH17-like cells. These findings represent the first characterization of T-cell responses in ABTI in comparison to SBTI, and in comparison to vaccinated individuals (VAX) who did not experience BTIs.

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