A draft genome combined with transcriptomics reveals unique aspects of Phocine herpesvirus-1 infections in the brains of harbor seals

Phocine herpesvirus (PhHV-1) is a viral pathogen belonging to the genus Varicellovirus. Its high prevalence, morbidity, and mortality in harbor seals makes PhHV-1 an important virus for pinniped conservation. The genome of PhHV-1 has yet to be sequenced and the infection dynamics of this virus in brain tissues has yet to be examined. Thus, we used California harbor seal brain tissue samples for deep sequencing to characterize both the genome and transcriptome of PhHV-1. In this study, we identified that PhHV-1 contains 75 genes. In the transcriptome analysis, we identified four different gene expression profiles that may represent different stages of viral infection in the brain. Transcriptional activity was also detected within tandem repeats that may be important for reactivation, infection, or latency in neuronal tissue. In addition, we confirmed previous research studies that closest known relative to PhHV-1 is the canine herpesvirus-1 (CHV-1). In all, we provide here omic data to illuminate the phylogenetic relationships, infection pathways, and genomic structure of PhHV-1 infecting the brains of pinnipeds.