A large-scale single-cell transcriptomic atlas indicates the immune panorama of influenza A infection

Influenza A virus (IAV) infection has a wide clinical spectrum, from mild illness to life-threatening pneumonia, yet the underlying immune determinants of disease remain poorly defined. Here, we generated a large-scale single-cell transcriptomic atlas from peripheral blood, profiling more than 612,010 cells from 97 individuals, including healthy controls, and patients with mild, severe, or convalescent IAV infection. Our findings uncovered a core immune dichotomy that determines clinical severity: a protective, monocyte-centric antiviral state in mild disease versus a pathological, neutrophil- and myeloid-derived suppressor cell (MDSC)-driven hyperinflammatory state in severe infection. Severe disease was marked by a peripheral hyperinflammatory state, driven by specific monocyte and neutrophil subsets via the S100A8/9/12-TLR4/RAGE signaling axis, and was coupled with the expansion of granulocytic MDSCs that likely contribute to T cell paralysis. In contrast, mild disease was associated with a protective, monocyte-centric response characterized by robust antiviral interferon signaling and enhanced antigen presentation. This functional divergence extends to the adaptive immune system, where mild disease was associated with CD8⁺ T cells displaying a balance of high cytotoxicity and regulated exhaustion. In severe illness, however, T cells become profoundly dysfunctional, exhibiting signatures of metabolic stress and apoptosis alongside the emergence of pathogenic, pro-inflammatory regulatory T cells. Together, our atlas provides a high-resolution immunological blueprint of human IAV infection, delineates the cellular states and pathways that govern clinical trajectories and offers a critical resource for developing host-directed therapies.