Fig. 2: At the time of intubation, the alveolar space in patients with severe SARS-CoV-2 pneumonia is enriched for T cells and monocytes and contains alveolar macrophages containing SARS-CoV-2 RNA and expressing interferon-response genes.

a, Hierarchical clustering of flow cytometry data from BAL samples collected within 48 h of intubation. Column headers are colour-coded by the diagnosis and presence or absence of co-infection (infection status). Samples were clustered by Euclidean distance using Ward’s method. AM, alveolar macrophages. b, Proportions of cells detected within 48 h of intubation (q < 0.05, pairwise Wilcoxon rank-sum tests with FDR correction). Comparisons are not significant unless otherwise noted. c, k-means clustering of the 1,194 significantly variable genes (q < 0.05, likelihood-ratio test) across diagnoses. Columns represent each individual sample and are clustered using Ward’s method. Column headers are colour-coded by the diagnosis and presence or absence of a co-infecting pathogen (infection status). Representative genes and GO biological processes are shown for each cluster. In b, c, infection status refers only to the COVID-19 and ‘other viral pneumonia’ groups; blanks in these groups refer to samples for which microbiology data were incomplete and infectious status could not be determined; ‘viral infection only’ refers to viral pathogens as the only detected pathogen in a sample and ‘viral infection with bacterial or fungal co-infection’ refers to detection of a viral pathogen with one or more bacterial or fungal co-pathogens.