Opposing cell-type preferences for binding and replication shape influenza A virus infection in human airways

Influenza A viruses (IAVs) pose a threat to human health. Although receptor specificity, polymerase adaptation, and airway tropism have been studied extensively, it remains unresolved how they combine to shape tropism in airway epithelia. Here, we show that avian IAVs infect ciliated and secretory cells but preferentially bind to ciliated cells because of higher apical α2,3-linked sialic acid levels. As replication levels are comparable between cell types, this translates into overall preference for ciliated cells. Human IAVs also preferentially bind to ciliated cells despite comparable α2,6-linked sialic acid abundance. Instead, they show higher viral RNA and protein levels in secretory cells, linked to their compatibility with human ANP32 proteins and modestly higher ANP32A/B expression in this cell type, resulting in equal infection levels across cell types. Our findings redefine IAV tropism in the human airway as a stage-resolved process shaped by the interplay between apical glycans, viral binding, polymerase cofactor compatibility, and cell-type-specific replication capacity, moving beyond receptor-centric models.