Abstract
<title>Abstract</title> <p>Respiratory syncytial virus (RSV) causes substantial pediatric lower respiratory tract disease, but the host programs that separate directly infected airway cells from exposed bystander cells are still not fully resolved. We reanalyzed public single-cell RNA sequencing data from RSV-infected human induced pluripotent stem cell-derived respiratory organoids and used viral transcript capture to distinguish mock cells, RSV RNA-negative bystander cells and RSV RNA-positive cells. RSV-positive cells made up 12.61% of the atlas and showed viral-load-linked stress, epithelial injury-repair, paracrine remodeling, CD73/adenosine and metabolic programs, not merely stronger interferon responses. Bystander cells, by contrast, were enriched for interferon-stimulated and antiviral sensing states. Curated ligand-receptor analysis, exploratory virtual perturbation, multi-layer host-target ranking and drug-signature reversal highlighted IL11, PSAT1, GREM1, PTGS2, SERPINE1, NT5E/CD73 and TNFRSF12A/Fn14 as candidate host nodes. External organoid bulk RNA-seq (GSE263272), antibody-treated organoid scRNA-seq used as a treatment-endpoint reference (GSE263271), primary airway epithelial data (GSE32139) and an in-house RSV time-course qPCR screen supported the injury-remodeling model, while showing that individual candidates vary by context. In silico perturbation placed NT5E/CD73 among network-relevant secondary-tier nodes and ranked the SYK inhibitor Fostamatinib/R406 highly in drug-signature reversal. These findings set priorities for experimental follow-up but do not establish functional rescue or therapeutic efficacy. Together, the study defines a focused set of RSV organoid host-response candidates for functional screening.</p>