Integrated single-cell analysis reveals interferon-driven immune signatures in a DENV1 human infection model.

Abstract

Dengue virus infection triggers complex innate and adaptive immune responses, yet the molecular mechanisms that shape early antiviral immunity remain incompletely defined. We performed longitudinal single-cell multi-omics profiling of peripheral blood mononuclear cells from four flavivirus-naive adults experimentally infected with DENV-1, integrating 5' scRNA-seq with paired surface proteomics. Across 95,841 high-quality cells collected at baseline and on days 8 and 10 post-infection, we observed a strong interferon-driven transcriptional response accompanied by marked immune-cell redistribution, including expansion of monocytes and transient reductions in dendritic cells and double-negative T cells. Cytotoxic and helper lymphocyte populations, particularly naive, central memory, and effector memory CD8 T cells, showed extensive crosstalk with monocytes and NK cells, reflecting coordinated cytokine production and cytotoxic activation. Early B cell activation was evident through increased immunoglobulin gene expression. Innate sensing pathways, including RIG-I and Toll-like signaling, were activated across NK, T, and B cell subsets, while also demonstrating enrichment of antigen processing and apoptosis programs. Pro-inflammatory and cytotoxic signatures peaked at day 8, supported by broad upregulation of interferon-stimulated, pro-apoptotic, and regulatory genes. Together, these findings define a robust IFN-driven antiviral state and coordinated activation of immune cell subsets, providing new insights into the immune dynamics of primary dengue infection. ImportanceDengue virus infects millions of people each year, but the early immune events that shape disease outcomes are still unclear. Most studies measure average responses across all blood cells, which hides how individual cell types react. By tracking thousands of single immune cells from volunteers infected with dengue virus under controlled conditions, we show how the immune system rapidly reorganizes during the first days of infection. Many cell types activate antiviral programs, communicate with one another, and shift their behavior in a coordinated way, driven by strong interferon activity. These results provide a clearer view of how early immune responses unfold in humans and identify cellular processes that may influence who develops more severe illness.