Homo sapiens Raw sequence reads. Homo sapiens

Mucosal antigen-specific T cells are pivotal for pathogen clearance and immune modulation in respiratory infections. Dysregulated T cell responses exacerbate COVID-19 severity, marked by cytokine storms and respiratory failure. Despite extensive description in peripheral blood, the characteristics of SARS-CoV-2-specific T cells in the lungs remain elusive. Here, we conducted integrated single-cell profiling of SARS-CoV-2-specific T cells in paired bronchoalveolar lavage fluid (BALF) and blood samples from 159 patients.