In our study we observed increased abundance of microglia in the brain stem following HSV-1 infection, and also that microglia are a prime source of transcripts for Ifnb1 and Tnfa, and to a lesser extent also Il1b and Il6. Interestingly, we observed that microglia undergo a profound and diverse change in subpopulation composition upon infection, with none of the subpopulations being present in the uninfected brain stem areas sequenced being detectable on day 6 post infection. Here, IL6 is linked to infection.