Single-cell landscape of bronchoalveolar immune cells in COVID-19 patients

Immune characteristics associated with Coronavirus Disease-2019 (COVID-19) severity are currently unclear. We characterized bronchoalveolar lavage fluid (BALF) immune cells from patients with varying severity of COVID-19 disease and from healthy subjects using single-cell RNA-sequencing. Proinflammatory monocyte-derived macrophages were abundant in the BALF from severe COVID-9 patients. Moderate cases were characterized by the presence of highly clonally expanded tissue-resident CD8+ T cells. This atlas of the bronchoalveolar immune-microenvironment suggests potential mechanisms underlying pathogenesis and recovery in COVID-19. Overall design: Using 10x genomics to measure single-cell RNA sequence (scRNA-seq)/TCR-seq to comprehensively characterize the lung immune microenvironment in the bronchoalveolar lavage fluid (BALF) from 6 severe and 3 moderate COVID-19 patients and 3 healthy control.