Multi-omic analysis identifies mitochondrial dysfunction as a conserved driver of acute severity and long-term complications in RSV infection
Respiratory syncytial virus (RSV) is a leading cause of lower respiratory tract infection in infants, older adults, and immunocompromised individuals. The molecular mechanisms linking acute RSV infection to disease severity and long-term complications remain incompletely understood. Herein, we conducted a comprehensive multi-omic analysis of 12 independent datasets encompassing epigenomics, transcriptomics, proteomics, and metabolomics across diverse systems, including in vitro infection models, clinical cohorts, longitudinal pediatric studies, vaccination models, and multiple viral strains. Across these experimental platforms and omic analysis, RSV consistently triggered suppression of oxidative phosphorylation (OXPHOS), alongside HIF-1-driven glycolytic metabolism and mitochondrial stress response. This coordinated reprogramming was consistent across transcriptomic, proteomic, and chromatin datasets. In adult challenge studies, symptomatic individuals exhibited prolonged OXPHOS suppression and greater activation of HIF-1 immune signaling than asymptomatic individuals. Similarly, pediatric intensive care cohorts showed comparable signatures associated with severe disease. Vaccinated mice showed attenuation of infection-induced metabolic disruption, further supporting a link between mitochondrial dysfunction and disease severity. Longitudinal analyses in pediatric samples revealed that these metabolic alterations persist for up to 1-year post-infection, with sustained metabolic dysfunction, persistent epigenetic remodeling, and single-cell evidence of epithelial remodeling, including depletion of multiciliated cells, expansion of secretory populations, and prolonged OXPHOS suppression, in children who developed wheezing. Comparative analysis across RSV strains revealed variable OXPHOS suppression and variable HIF-1 activation, indicating strain-specific differences in metabolic reprogramming. Together, these findings establish mitochondrial dysfunction as a central and conserved feature of RSV pathogenesis, encompassing acute severity, viral strain variation, and long-term complications, and highlight mitochondrial pathways as promising therapeutic targets to mitigate both acute disease severity and post-viral sequelae. Ultimately, demonstrating that distinct viral lineages drive unique bioenergetic phenotypes establishes a foundation for predictive molecular epidemiology and gaining insight into host-pathogen dynamics in response to novel interventions. HighlightsO_LIMulti-omic integration of 13 independent RSV datasets reveals mitochondrial dysfunction as a conserved hallmark of infection. C_LIO_LIRSV consistently suppresses oxidative phosphorylation (OXPHOS) while activating HIF-1 signaling, glycolysis, mitochondrial stress responses, and immune pathways. C_LIO_LIGreater mitochondrial dysfunction correlates with increased disease severity, persists in children who develop wheezing, and is partially ameliorated by vaccination. C_LIO_LIDistinct RSV strains display variable patterns of metabolic reprogramming, linking viral genetic diversity to differential host mitochondrial responses. C_LI