Vaccination Reduces Shedding of Salmonid Alphavirus Subtype 3, but Bacterial Co‐Infection Influences the Effect

ABSTRACT Waterborne horizontal transmission of viral diseases in fish relies on the release of infectious virus particles (termed shedding) into the aquatic environment. Both the rate and duration of shedding are critical for efficient viral spread, making interventions that reduce shedding valuable for disease control. While vaccines primarily aim to protect individuals from infection and severe disease, they should ideally also limit pathogen transmission by reducing shedding. In this study, we evaluated the capacity of two commercial vaccines—Clynav (DNA vaccine) and AlphaJect Micro 1‐PD (inactivated whole‐virus vaccine) to reduce Salmonid alphavirus subtype 3 (SAV3) shedding following experimental infection of Atlantic salmon post‐smolts. In individually housed fish, AlphaJect Micro 1‐PD significantly reduced the proportion of SAV3‐shedding fish, duration of shedding, and cumulative shedding, while Clynav significantly reduced shedding duration and the proportion of shedding fish. In cohort tanks (each containing 60 fish), all of which had concurrent inadvertent Tenacibaculum dicentrarchi co‐infection, AlphaJect Micro 1‐PD significantly reduced the cumulative shedding but increased the duration of shedding. In comparison, Clynav vaccination reduced both cumulative shedding and shedding duration, though not significantly. These results demonstrate the potential of vaccines to limit SAV3 transmission, while also highlighting how co‐infections likely influence vaccine efficacy.