Extended Data Fig. 7: Viral load–based stratification of host response in DENV2-infected cells.

a. Ridge plot showing the distribution of viral RNA levels across transcriptional clusters. Cells are grouped into two major infection states—quiescent infection (blue) and active infection (red)—based on host transcriptomic profiles. Although overall viral load can be similar between states, active cells display a robust host response, while quiescent cells remain largely unresponsive. b. Viral load across infection groups, colored by cell cycle phase (G1, S, G2/M). c. UMAP embeddings of infected cells colored by cell cycle phase (top) and infection group (bottom): quiescent_lowVL, quiescent_highVL, active_lowVL, active_highVL. d. Gene expression across four states. Cells were stratified into quiescent/active × low/high viral load groups. Dot plot shows expression patterns of differentially expressed genes. e. GO enrichment analysis for genes differentially expressed between high and low viral load cells within each infection state. Top: In quiescent response, high-load cells are enriched for chromatin remodeling, RNA splicing, and nucleosome-related processes. Bottom: In active response, high-load cells show enrichment for unfolded protein response (UPR), ER stress, and protein targeting to membranes. f. Violin plots showing module scores for key biological processes across the four infection groups. Enrichment significance was assessed using a one-sided over-representation test (hypergeometric test), with P values adjusted for multiple comparisons using the Benjamini–Hochberg FDR. Significance is indicated as ***FDR < 0.001, **FDR < 0.01, and *FDR < 0.05.