Fig. 2: Single-cell transcriptomics revealed murine astrovirus preferentially infects actively secreting goblet cells.

a Aggregated data of all duodenal epithelial cells (n = 2973 individual cells) from both infected and uninfected (n = 4 mice/group) as represented by t-SNE clustering and colored according to unique cell cluster based on transcriptional profiling. b Overlapping epithelial cell clusters from infected animals (dark blue) and uninfected animals (light blue) indicated that infection does not drive massive changes in epithelial cell populations. c Infected cells with detectable murine astrovirus are highlighted within the black box that includes all goblet cells. Subset analysis on goblet cells alone showed overlapping clusters of cells from infected (dark blue) and uninfected (light blue) animals. t-SNE clustering indicated four subpopulations of goblet cells as indicated by shape of each dot. d Cell clusters susceptible to infection are noted by overlay of murine astrovirus expression in grayscale. Murine astrovirus-susceptible cell clusters overlap with cells expressing high levels of mucus-related genes (Muc2, Fcgbp, Clca1, Zg16) as noted by darker colors. e Violin plots of mucus-related gene expression compared across infected (dark blue) and uninfected animals (light blue). f Gene set enrichment analysis indicating secretion pathways were significantly enriched in infected cells compared with uninfected cells using a weighted Kolmogorov–Smirnov-like statistic. Significance was estimated using an empirical phenotype-based permutation test and adjusted for multiple comparisons by first normalizing the gene set enrichment scores and calculating the false discovery rate (FDR) for each. Darker colors denote higher normalized enrichment scores (NES) for each gene set on the y-axis and an FDR q value < 0.2 is noted with a dotted line on the x-axis.