Transcriptome analysis of HSV-1 infected dorsal root ganglia and large intestinal musculara

Following genital HSV-1 infection in mice, virus spreads to and infects the sensory neurons of the dorsal root ganglia (DRG) and the enteric neurons situated within the large intestinal musculara (LIM). We used RNA sequencing to simultaneously study the host and viral transcriptomes at these two distinct sites of infection. We find that transcription across the HSV-1 genome is weak and incomplete in sensory neurons whereas all known HSV-1 coding genes are robustly expressed in the enteric neurons. Furthermore, a T cell activation signature dominated the immune response to HSV-1 infection in the DRG. In contrast, an innate inflammatory signature was observed in the LIM. Duplicate samples of DRG and LIM from mock or HSV-1 infected mice were collected six days post infection. mRNA transcriptome profiles were generated by deep sequencing using the Illumina 2500 HiSeq platform.