Primary nasal viral infection rewires the tissue-scale memory response

The nasal mucosa is frequently the initial site of respiratory viral infection, replication, and transmission, but the cellular composition at homeostasis, during infection, and during a memory response are poorly understood. Here, we generated a single-cell RNA-sequencing (scRNA-seq) atlas of the murine nasal mucosa sampling three distinct regions before and during primary and secondary influenza A virus (IAV) infection. Primary infection was largely restricted to respiratory mucosa and induced stepwise changes in immune and epithelial cell type, subset, and state composition over time. Following viral clearance (14 dpi), rare, previously undescribed Krt13+ nasal immune-interacting floor epithelial (KNIIFE) cells expressing multiple genes with immune communication potential increased concurrently with tissue-resident memory T (TRM)-like cells and early IgG+/IgA+ plasmablasts. Proportionality analysis coupled with cell-cell communication inference, alongside validation by in situ microscopy, underscored the CXCL16–CXCR6 signaling axis between MDMs and effector CD8 T cells 8dpi and KNIIFE cells and TRM cells 14 dpi. Secondary influenza challenge with a homologous or heterologous strain administered 60 dpi induced an accelerated and coordinated myeloid and lymphoid response without epithelial proliferation, illustrating how tissue-scale memory to natural infection engages both myeloid and lymphoid cells to reduce epithelial regenerative burden. Raw and processed single-cell counts matrices can be accessed and downloaded from the Broad Institute Single-Cell Portal from studies SCP2216 and SCP 2221.