Antiviral efficacy versus host recovery: contrasting transcriptional footprints of four antivirals in human cytomegalovirus-infected brain organoids

Infection with human cytomegalovirus (HCMV) is common and usually asymptomatic in healthy individuals, but can cause severe neurological injury, particularly following congenital transmission. For symptomatic congenital infection, standard antiviral treatment is ganciclovir, with maribavir and letermovir as alternative direct-acting agents. However, their relative efficacy in clearing HCMV and restoring host transcription towards an uninfected state has not been directly assessed in a neural model. To address this, we infected human cerebral organoids with Merlin-strain HCMV and treated them for 14 days with aciclovir, ganciclovir, letermovir, or maribavir, comparing each with untreated infected organoids (NO). All four antivirals reduced HCMV RNA-seq reads relative to NO, but differed in both antiviral efficacy and their effects on host transcription. Combining new and existing data, we identified >2,500 differentially expressed host genes in infected versus uninfected organoids, with enrichment of neurodevelopmental and metabolic stress pathways. Relative to NO, antiviral treatment reduced viral load 3.3-fold with aciclovir, 20.1-fold with ganciclovir, 65.4-fold with letermovir, and 6.9-fold with maribavir. Aciclovir, ganciclovir, and maribavir produced few differentially expressed host genes relative to NO and no significant GO or KEGG enrichment. In contrast, letermovir altered 312 genes enriched for glycolysis and related metabolic processes. An mSigDB Hallmark pathway analysis showed minimal perturbation with aciclovir and letermovir, whereas ganciclovir and maribavir produced small but coordinated pathway-level shifts. This was partly in the same direction as control uninfected organoids but also with additional perturbations not seen in controls. These findings indicate that antiviral choice influences both HCMV clearance and the transcriptional state of infected neural tissue. The results support further evaluation of ganciclovir and letermovir in therapy of neural damage resulting from HCMV infection, particularly of the developing fetal brain.