Integrated single-cell analysis unveils diverging immune features of COVID-19, influenza, and other community-acquired pneumonia

• Published in: eLife
• Main Authors: Alex R Schuurman, Tom DY Reijnders, Anno Saris, Ivan Ramirez Moral, Michiel Schinkel, Justin de Brabander, Christine van Linge, Louis Vermeulen, Brendon P Scicluna, W Joost Wiersinga, Felipe A Vieira Braga, Tom van der Poll
• Format: Article
• Language: English
• Published: eLife Sciences Publications Ltd 2021-08-01
• Subjects: PBMC; COVID-19; Pneumonia
• Online Access: https://elifesciences.org/articles/69661

The exact immunopathophysiology of community-acquired pneumonia (CAP) caused by SARS-CoV-2 (COVID-19) remains clouded by a general lack of relevant disease controls. The scarcity of single-cell investigations in the broader population of patients with CAP renders it difficult to distinguish immune features unique to COVID-19 from the common characteristics of a dysregulated host response to pneumonia. We performed integrated single-cell transcriptomic and proteomic analyses in peripheral blood mononuclear cells from a matched cohort of eight patients with COVID-19, eight patients with CAP caused by Influenza A or other pathogens, and four non-infectious control subjects. Using this balanced, multi-omics approach, we describe shared and diverging transcriptional and phenotypic patterns—including increased levels of type I interferon-stimulated natural killer cells in COVID-19, cytotoxic CD8 T EMRA cells in both COVID-19 and influenza, and distinctive monocyte compositions between all groups—and thereby expand our understanding of the peripheral immune response in different etiologies of pneumonia.