Spatial epitranscriptomic profiling of Zika virus-infected human brain organoids

This dataset includes spatially-resolved full-length transcriptome and A-to-I RNA editome profiles of Zika virus (ZIKV)-infected human brain organoids derived from induced pluripotent stem cells (iPSCs). To investigate virus-host interactions and the spatial dynamics of viral infection, brain organoids were infected with ZIKV and subjected to immunohistochemistry to define regions of interest (ROIs) by cell type (SOX2+ neural progenitor cells vs TUJ1+ neurons) and infection status. Specific ROIs were microdissected using Spatially-resolved Laser Activated Cell Sorting (SLACS).Both host and viral transcriptomes were reconstructed, enabling simultaneous analysis of gene expression, viral gene abundance, mutational landscape of viral genomes, and adenosine-to-inosine (A-to-I) RNA editing in each spatially-defined ROI. ZIKV-infected NPCs showed stronger metabolic and transcriptomic perturbations than neurons. Moreover, RNA editing profiles showed altered A-to-I editing patterns, particularly in mitochondrial and immune-related genes, suggesting post-transcriptional remodeling by viral infection.Viral genomes were assembled and mutation rates were assessed in each region, highlighting spatial heterogeneity in ZIKV evolution across organoid zones. Viral evolution trajectories were inferred from sequence divergence, indicating intra-organoid adaptation from NPCs to neurons.This dataset provides a valuable spatial-epitranscriptomic resource to dissect host-pathogen interactions at single-base and regional resolution in a physiologically relevant model of ZIKV neuroinfection.