Respiratory syncytial virus load-dependent ciliated cell dedifferentiation and downregulation of immune response genes

Abstract

Respiratory syncytial virus (RSV) can cause severe lower respiratory tract infections in infants, older adults, and individuals with chronic or immunocompromising conditions. To understand how RSV affects airway cells, we infected primary human airway epithelial cultures with RSV and analyzed infected and bystander cells using time-resolved single-cell RNA sequencing and imaging. RSV mainly infected ciliated cells, triggering a virus load-dependent shutdown of genes involved in ciliogenesis, antigen presentation, and innate sensing, including key interferon (IFN) and pattern recognition pathways. Only a subset of infected cells produced type I and III IFNs, while bystander cells exhibited strong IFN-stimulated gene (ISG) signatures. Neither IFN treatment nor ISG induction eliminated infection, but IRF1, an antiviral transcription factor not suppressed by RSV, remained robustly expressed. Ectopic IRF1 expression in vitro reduced viral replication. These findings reveal how RSV evades antiviral defenses and highlight IRF1 as a potential target for therapeutic intervention.