Ostreid Herpesvirus OsHV-1 remains one of the most significant issues facing Pacific oyster aquaculture, and continues to cause disease in oyster growing regions worldwide. Our understanding of how the virus interacts with oysters has developed, but the exact locations and routes of infection remain cryptic. Here we performed an immersion challenge between Pacific oysters and OsHV-1 µVar and assessed the whole-animal response over a 72-hour infection cycle with a bespoke single nuclei RNA-seq analysis. New methods of nuclei isolation were optimised before cells were processed with Parse Biosciences Evercode and sequenced by Illumina. Across eight samples, we generated 2.2 billion reads in 22,000 nuclei. Results allow us to characterise gene expression in a range of cells from different tissues, including muscle, haemocyte, mantle, hepatopancreas, adductor muscle, digestive epithelia and gill (Figure 1). We were in addition able to characterise viral transcripts and host responses in cells undergoing infection. Results demonstrate that infection at all stages is highly specific to one cell type and that the response previously observed in whole tissue bulk RNA-seq is likely driven by gene expression changes in one cell type. Within this presentation we will describe some of the challenges associated with performing single nuclei RNA-seq in animals for which there is limited genome annotation and some of the methods that can be used to overcome these.