Human brain cell types shape host-rabies virus transcriptional interactions revealing a preexisting pro-viral astrocyte subpopulation

How virus-host cell interactions and innate immune antagonism shape neurotropic infection dynamics across diverse brain cell types are largely unknown. To “unmask” and study how innate immune inhibition affects cell type-specific transcriptional regulation of the human and viral genome, we performed single-cell RNA sequencing of human brain cell co-cultures, comparing an isolate of rabies virus (RABV) to its mutant incapable of antagonizing interferon- and NF-κB-dependent responses. RABV gene expression was shaped by host cell type. RABV induced small-scale, cell-type conserved transcriptional programs that likely support infection by 1) hijacking negative transcriptional feedback of pro-viral factors while 2) reducing anti-viral RNAs. Unexpectedly, disinhibited innate immune signaling increased RABV transcription, most strikingly in an infection-independent “pro-viral” astrocyte subpopulation. Further analysis suggested that “pro-viral”-like astrocytes are a rare subtype in the human brain and are primed to protect the brain during viral infection in concert with interferon-sensitive microglia recalcitrant to infection.