Viruses of phytoplankton alter their host metabolism and physiology. This viral reprogramming of algal cells modulates oceanic biogeochemistry. OtV-5 is a Nucleocytoplasmic large DNA virus infecting the smallest free-living eukaryote, the green pico-alga Ostreococcus tauri. In eukaryotes, there is a link between their genomic 3D organisation and gene expression. NCLDVs hijack their host's cellular machinery and alter their gene expression, resulting in the repression or activation of host genes. However, it is unclear how NCLDVs manipulate the host's chromatin, as there is a link between gene expression and chromatin conformation. Here, we used a combination of RNA-seq and Hi-C (high-throughput chromatin conformation capture) to determine how OtV-5 alters the genomic structure and gene expression of O. tauri during infection. In addition to anticipated transcriptomic changes within the host, we found that the virus has different states due to the kinetic classes of its genes. Hi-C data showed differences in chromatin conformation between non-infected and infected algal cells, with the virus preferentially contacting certain regions of the host genome. These findings demonstrate how a large DNA virus degrades the chromatin structure of its algal host to modulate its gene expression during infection and how multi-omics studies may provide a better understanding of host-virus interactions.