Rapid Amplicon Sequencing of Salmon Gill Poxvirus Genomes

Atlantic salmon farming is an increasingly important global source of food and one of the most important industries in the Faroe Islands. Atlantic salmon farming has been associated with epidemics of infectious diseases that threaten not only local production, but also wild fish populations, because large-scale intensive marine farming facilitates selective conditions for pathogen evolution and transmission. To sustain the growth potential in Faroese aquaculture disease control is fundamental. Salmon gill pox virus (SGPV) regularly causes severe disease and high mortalities at Faroese salmon smolt farms. As only one full length SGPV genome has been published, we lack in-depth knowledge about the genetic characteristics of SGPV which is crucial to answer some fundamental epidemiological question such as: is SGPV circulating as house strains in the smolt farms or are new strains introduced on a regular basis from the environment? Is the varying severity of SGPV outbreaks caused by evolution of virulence or merely a result of interaction between the host genetics and/or environmental stressors? Has SGPV the potential to transmit vertically from parent to their offspring?
To answer these questions, we here aim to set up a rapid and cost-effective amplicon-based whole-genome sequencing method for SGPV (RASPOX) which can be used for real-time tracing of infection in the three production stages of Atlantic salmon and thus, provide the aquaculture industry with a tool for fast evidence-based decision making in mitigation of SGPV emergence and spread in smolt farms.