Figure 2.

Severe outcomes are associated with transitions between neutrophil states

(A) Heatmap of marker genes for all patients grouped by subtype using NMF clustering (STAR Methods).

(B) UMAPs of scRNA data from Bonn Cohort 2.⁹

(C) Network diagram displaying relationships between NMF subtype marker genes and published neutrophil signature genes.

(D) Volcano plot of genes DE between COVID-19⁺ severe and non-severe patients. Colored points indicate log₂(FC) > 0.5 and p < 10⁻⁴.

(E) Bar plots of proportions of COVID-19⁺ samples in each NMF cluster. Bar heights indicate percentages of COVID-19⁺ samples for each time point separately. ∗q < 0.05, ∗∗q < 0.01 by Fisher’s exact test for each time point separately, with false discovery rate (FDR) correction across all days.

(F and G) GSEA for genes DE between COVID-19⁺ severe and non-severe patients.

See also Figures S2 and S3 and Table S2.