Imbalance of Regulatory and Cytotoxic SARS-CoV-2-Reactive CD4⁺ T Cells in COVID-19

The contribution of CD4⁺ T cells to protective or pathogenic immune responses to SARS-CoV-2 infection remains unknown. Here, we present single-cell transcriptomic analysis of >100,000 viral antigen-reactive CD4⁺ T cells from 40 COVID-19 patients. In hospitalized patients compared to non-hospitalized patients, we found increased proportions of cytotoxic follicular helper cells and cytotoxic T helper (T_H) cells (CD4-CTLs) responding to SARS-CoV-2 and reduced proportion of SARS-CoV-2-reactive regulatory T cells (T_REG). Importantly, in hospitalized COVID-19 patients, a strong cytotoxic T_FH response was observed early in the illness, which correlated negatively with antibody levels to SARS-CoV-2 spike protein. Polyfunctional T_H1 and T_H17 cell subsets were underrepresented in the repertoire of SARS-CoV-2-reactive CD4⁺ T cells compared to influenza-reactive CD4⁺ T cells. Together, our analyses provide insights into the gene expression patterns of SARS-CoV-2-reactive CD4⁺ T cells in distinct disease severities.