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Viral, bacterial, and parasitic diseases are among the primary causes of mortality and economic loss for the bivalve farming sector.

Among the countries analyzed by the project, in France and Ireland, the oyster sector has suffered major problems due to the oyster virus (OsHV-1 µVar), which causes mortality rates of up to 80-100% in juvenile Crassostrea gigas during the summer months, when water temperatures exceed 16°C. More recently, adult oysters have been affected by Vibrio aestuarianus, a Gram-negative bacterium responsible for high mortality in Pacific oysters and often associated with summer mortality events. Regarding the flat oyster (Ostrea edulis), the parasites Bonamia ostreae and Marteilia refringens have almost eliminated historical Irish production.

Health challenges are also crucial in the project's other partner countries, varying according to the main farmed species. In Spain, Bonamia and Marteilia infections have severely limited the historic flat oyster production in Galicia. The common mussel (Mytilus galloprovincialis), although considered a more hardy and resistant species, is often attacked by parasites such as the copepod Mytilicola intestinalis and must contend with bacterial outbreaks of the Vibrio genus, which can cause high mortality in the larval stage or in weakened specimens.

In Italy, the health alert directly affects not only mussels (prone to Marteilia and opportunistic bacteria), but above all clam farming, particularly the European clam Ruditapes philippinarum, a national excellence. Clams are threatened by pathogens such as the protozoan Perkinsus olseni, responsible for perkinsosis, which causes severe tissue inflammation, and the bacterium Vibrio tapetis, responsible for Brown Ring Disease, which attacks the shell and stunts its growth.

In Greece, where bivalve molluscs farming focuses almost exclusively on mussels, health issues have become inseparable from climate concerns. Increasingly prolonged and frequent summer heatwaves cause severe physiological and thermal stress in mollusks; this condition, in addition to causing the byssus to break and the mussels to fall to the bottom, causes immunosuppression and paves the way for deadly systemic infections by opportunistic pathogenic bacteria (especially Vibrio spp.), triggering devastating mass mortality events for local producers.

Pathogen detection methods rely primarily on molecular biology techniques (real-time PCR) and histological tests conducted by national reference laboratories. Current solutions do not provide cures (impossible in the open sea) but focus on mitigation: genetic selection of resistant strains in hatchery, modifications to husbandry practices (lowering baskets deep enough to avoid temperature fluctuations), and rigorous biosecurity measures to prevent the movement of infected animals.