Aberrant host mRNA partitioning in Ebola virus condensates driven by RNA folding perpetuates species-dependent interferon response
RNA viruses form membraneless condensates in host cells to drive replication, but whether these compartments also regulate host RNAs remains unclear. Using MERFISH-based subcellular transcriptomics, we quantified cellular mRNA recruitment into Ebola virus condensates under basal and IFN-stimulated states. We find that in the basal state, cellular RNAs with minimally folded coding regions are selectively recruited. Under IFN-stimulation, however, interferon-stimulated genes (ISGs) with structured 3'UTRs concentrate in viral condensates. We find that both features, minimally folded coding regions and structured 3'UTRs, are conserved in the viral RNA genome, supporting viral genome retention in condensates. In parallel, for cellular mRNAs, we find that partitioning into condensates escapes decay, prolonging RNA-half-life, and amplifying rather than dampening ISG expression. Fruit bats, which do not experience severe disease for RNA viruses, instead have ISGs with reduced 3'UTR folding, and may evade condensate-sequestration, enabling balanced antiviral responses. This selective stabilization links condensate function to RNA regulation as a molecular determinant of viral and host co-evolution and disease pathogenesis.