Extended Data Fig. 4: The BAL fluid from patients with SARS-CoV-2 pneumonia is persistently enriched for T cells irrespective of superinfection status.
From: Circuits between infected macrophages and T cells in SARS-CoV-2 pneumonia
a, Heat map of flow cytometry data demonstrating composition of BAL samples from all time points, grouped by diagnosis and ordered by the duration of mechanical ventilation. Column headers are colour-coded by the diagnosis, duration of mechanical ventilation (white indicates chronically ventilated patients), and presence or absence of superinfection (infection status). ‘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/fungal superinfection’ refers to detection of a viral pathogen with one or more bacterial or fungal co-pathogens. b, Comparison of percentage of CD206lo and CD206hi alveolar macrophages between early (<48 h after intubation) and late (>48 h of mechanical ventilation) samples (q < 0.05, pairwise Wilcoxon rank-sum tests with FDR correction). c, Comparison of CD4+ and CD8+ T cell and neutrophil abundance in the COVID-19 group, with and without superinfection in early and late sampling. Superinfection is represented by lighter bars. Differences between groups are not significant after FDR correction.
