Temporally resolved single-cell RNA sequencing reveals protective and pathological responses during herpes simplex virus 1 CNS infection

We profile the transcriptomic changes in the infected brain stem at the single-cell level with temporal resolution, supported by GeoMx spatial transcriptomic data. Microglia proportions increased during infection, while blood-brain barrier cells declined. Transcriptional analysis revealed strong antiviral and inflammatory responses, and impairment of physiological brain activities. This study highlights the complex immune response in virus-infected brains, balancing infection elimination with immunopathology. Overall design: We allowed the infection of HSV-1 to progress for days 4, 6, and 8. Brainstem of HSV1 infected mice and control mice were collected for scRNA sequencing