Limited nasal interferon production contributes to delayed respiratory virus clearance and suboptimal vaccine responses

Acute lower respiratory infections are the primary cause of global mortality in post-neonatal children. Most respiratory viruses primarily involve upper airway infection and inflammation, yet nasal responses are poorly characterized. Using a mouse model of human metapneumovirus (HMPV), we found viral burden was higher in nasal airways and exhibited delayed clearance. Despite high burden, there was low nasal expression of type I and III interferon (IFN). Single-cell RNA-sequencing (scRNA-seq) from HMPV-infected mice showed lower nasal interferon-stimulated gene (ISG) expression and nasal enrichment of genes negatively regulating IFN. scRNA-seq of COVID-19 patients confirmed lower ISG expression in upper airways. HMPV infection downregulated nasal expression of interferon regulatory factor-3, suggesting a mechanism for limited response. To rescue the quiescent environment, we administered type I or III IFN to upper airways early post-infection, leading to lower nasal HMPV titer and virus-specific CD8+ T-cell upregulation. Intranasal immunization adjuvanted with type I or III IFN improved immune response, reduced clinical disease, and enhanced viral clearance in HMPV and influenza infection. IFN adjuvant increased recruitment of dendritic cells, resident-memory T-cells, and neutralizing antibodies. These findings reveal locally suppressed IFN production contributes to a quiescent nasal immune landscape that delays viral clearance and impairs mucosal vaccine responses.