UMAP clustering and differential abundance analysis of BAL immune cells. (A) UMAP visualization of all quality-controlled cells from pig BAL scRNA-seq analysis, colored by cell type and annotated with cluster numbers. Top: DPI 1 dataset; bottom: DPI 20 dataset. (B) Proportions of Tregs (cluster 4b) at 20 DPI by scRNA-seq in CD4 T cells (top) and over the time course by flow cytometry (bottom). (C) Proportions of further cell clusters with significant differences between 135-infected and ISU-1-infected pigs within the CD4 T-cell population at 20 DPI. Nonconventional T cells (NCT), macrophages (M), mitotic CD8 T cells (mCD8 T Cells).