Viruses that infect fungi have a ubiquitous distribution and play an important role in structuring fungal communities. Most of these viruses have an unusual life history in that they are propagated exclusively via asexual reproduction or fission of fungal cells. This asexual mode of transmission intimately ties viral reproductive success to that of its fungal host, and should select for viruses that have minimal deleterious impact on the fitness of their hosts. Accordingly, viral infections of fungi frequently do not measurably impact fungal growth, and in some instances increase the fitness of the fungal host. Here we determine the impact of the loss of co-infection by LA virus and the virus-like particle M1 upon global gene expression of the fungal host Saccharomyces cerevisiae, and provide evidence supporting the idea that coevolution has selected for viral infection minimally impacting host gene expression.