Integrated multi-trophic aquaculture (IMTA) is an alternative approach to mono-culture aquaculture that reduces environmental impacts of commercial aquaculture systems by combining the cultivation of fed species with extractive species. Shellfish play a critical role in IMTA systems by filter-feeding particulate-bound organic nutrients. They may also increase or decrease disease risk on farms by serving as reservoirs or barriers for important finfish pathogens such as infectious salmon anaemia virus (ISAV). This study aimed to optimize culture and molecular assays in shellfish tissues and to determine the fate of ISAV in mussels, Mytilus edulis. To determine detection limits, qRT-PCR and culture assays in both CHSE- and ASK cells were optimized in ISAV-inoculated mussel tissue homogenates. Both qRT-PCR and culture assays performed in ASK cells had comparable detection limits of 102.8 TCID50 mL−1. The ISAV RNA genome was consistently detected in digestive gland tissue of ISAV-exposed mussels. Viable ISAV was not detected in mussel tissues by culture analysis in CHSE- and ASK cells. The fact that qRT-PCR analysis resulted in positive cycle threshold (CT) values that corresponded to the detectable range of ISAV in ASK culture assays suggests that little to no viable ISAV particles are present in the mussel tissues.