Spatially Resolved Microglial State Transitions Govern Strain-Specific Zika Neuropathogenesis

Neurotropic viral infections produce strain-dependent neurological outcomes, yet how viral strain differences reorganize the brain microenvironment to shape disease severity remains poorly understood. Using high-resolution spatial transcriptomics integrated with paired single-cell RNA-seq and infection-aware cell-type annotation, we constructed a spatiotemporal atlas of Zika virus (ZIKV) infection in the mouse brain, comparing African and Asian strains at 4 and 6 days post-infection. ZIKV spreads preferentially through pericallosal white-matter pathways, and microglia mount spatially compartmentalized state transitions whose effects extend to uninfected bystander cells, establishing infection as a tissue-level immune process. We identify disease-associated microglia (DAM) as the cellular state that mediates viral containment: DAM accumulate where viral burden stabilizes, and their density inversely correlates with infection within local microenvironments. This containment depends on ApoE-Trem2-Tyrobp signaling from infected cells, which sustains DAM differentiation through Bcl3, Nfkb2, and Klf12-driven repression of inflammatory programs. In African strain infection, coordinated downregulation of ApoE ligands and the Trem2 receptor locks microglia into an Irf1-driven inflammatory state and produces spatially structured loss of oligodendrocytes, astrocytes, and neurons in dorsal cortical and callosal-adjacent regions, with concurrent suppression of myelination, axon guidance, and GABAergic transmission programs. Together, our work links viral strain identity to spatially restricted microglial state transitions and the regional fate of neural circuits, providing mechanistic insight into how neurotropic viruses drive neurological disease.