COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas

A dysfunctional immune response in coronavirus disease 2019 (COVID-19) patients is a recurrent theme impacting symptoms and mortality, yet a detailed understanding of pertinent immune cells is not complete. We applied single-cell RNA sequencing to 284 samples from 196 COVID-19 patients and controls and created a comprehensive immune landscape with 1.46 million cells. The large dataset enabled us to identify that different peripheral immune subtype changes are associated with distinct clinical features, including age, sex, severity, and disease stages of COVID-19. Severe acute respiratory syndrome coronavirus 2 (SARSCoV-2) RNA was found in diverse epithelial and immune cell types, accompanied by dramatic transcriptomic changes within virus-positive cells. Systemic upregulation of S100A8/A9, mainly by megakaryocytes and monocytes in the peripheral blood, may contribute to the cytokine storms frequently observed in severe patients. Our data provide a rich resource for understanding the pathogenesis of and developing effective therapeutic strategies for COVID-19.

Automated summary

The study revealed the presence of immune response dysfunction in COVID-19 patients, with different peripheral immune subtype changes associated with clinical features such as age, sex, severity, and disease stages. Additionally, dramatic transcriptomic changes were observed within virus-infected cells, and upregulation of S100A8/A9 in peripheral blood may contribute to the cytokine storms frequently observed in severe patients.