Single cell sequencing analysis of respiratory syncytial virus–infected pediatric and adult human nose organoids reveals age differences, proliferative diversity and identifies novel cellular tropism

Respiratory syncytial virus (RSV) is a leading cause of infant death across the globe. Age is a significant factor that contributes to the severity of infection in young children. RSV primarily infects the ciliated cells of the airway epithelium, induces mucus hypersecretion, and impaired mucociliary clearance. Better understanding of RSV infection at the cellular level is needed for the development of effective therapeutic interventions. To investigate the age difference and comprehensively understand gene signatures associated with RSV infection, we performed single-cell transcriptomic analysis of adult and pediatric human nose organoids (HNOs) infected with RSV. Our analysis revealed a significant difference in transcriptomic signature associated with cellular differentiation and proliferative pathways between the adult and pediatric HNOs. Moreover, we found a distinct innate immune response to RSV infection, with pediatric HNO revealing a lower and dysregulated response. Through sub-clustering analysis of the ciliated cell population, we identified the primary ciliary cell as a novel and prominent susceptible ciliary cell type to RSV infection. Intriguingly and unexpectedly, we found that in the pediatric more than in the adult, HNO RSV infects other novel airway cells, including basal cells, and ionocytes/tuft cells, as demonstrated by increased RSV-gene counts and induction of interferon-related pathways. Together, our study provides the first HNO cell atlas dissecting the heterogeneity of RSV infection in airway epithelium between adult versus pediatric HNOs and identifies novel cell types that are susceptible to RSV infection, which altogether provides a key resource for research on RSV pathogenesis, therapeutics and vaccines.