Abstract

Influenza A viruses of divergent pathogenicity elicit distinct host immune responses, yet the underlying cellular and spatial dynamics remain poorly defined. Here, we integrate single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics to systematically compare the immune landscapes in murine lungs following infection with seasonal H1N1 or a highly pathogenic avian influenza H5N1 virus belonging to clade 2.3.2.1. Analysis of 84,162 immune cells identifies 12 distinct cell types, suggesting that H1N1 infection is associated with robust interferon and inflammatory responses, characterized by alveolar macrophage depletion and extensive infiltration of monocytes and neutrophils. In contrast, H5N1 clade 2.3.2.1 infection is characterized by attenuated interferon signaling, delayed monocyte activation, dysregulated neutrophil maturation, and impaired intercellular communication—features that may be distinct from previously characterized H5N1 strains. Spatial mapping indicates distinct distribution and interaction patterns of immune cells between the two infections. Functional validation through myeloid cell depletion supports the critical role of the monocyte-macrophage axis in disease progression. These findings provide a high-resolution atlas of pulmonary immune responses to influenza viruses of differing pathogenicity and highlight cell-type-specific mechanisms of immune modulation.