DEVELOPMENT AND APPLICATION OF A FAST AND SENSITIVE AMPLICON-BASED METHOD FOR WHOLE GENOME
The virulent Infectious Salmon Anaemia Virus (ISAV-HPRΔ) is an Orthomyxovirus that causes Infectious Salmon Anaemia (ISA) , an important disease of farmed Atlantic salmon (Salmon salar ). It caused a major epidemic in the Faroe Islands in the early 2000. The non virulent ISAV-HPR0 variant causes a transient epithelial infection localised to the gills and skin and has been identified as the progenitor of all virulent ISAV-HPRΔ variants. ISAV-HPR0 has been shown to circulate in freshwater RAS smolt farms and marine farms and is potentially introduced from the environment, thus highlighting the paramount importance of biosecurity in smolt farms. A previous study based on the partial sequencing of ISAV-HPR0 segment 6 has suggested that ISAV-HPR0, once introduced, can persist over time in the smolt farms. Mounting evidence also suggests t hat ISAV-HPR0 mutation in these farms can cause disease outbreaks when introduced in marine sites. To date, there has no t been a successful cultivation of ISAV-HPR0. Our study utilises an in-house developed, fast, and efficient ISAV whole genome sequencing method to understand the transmission and evolutionary dynamics of ISAV-HPR0 between land-based smolt farms and marine sites in the Faroe Islands.
Approximately 100 HPR0 positive samples collected over time (2007 to 2024) and space (8 smolt and 23 marine farms) were subjected to whole genome sequencing. Twenty-five samples were sequenced on MiSeq, and all other samples will be sequenced on the Nanopore GridION. In addition, HPR0-positive aerosol samples collected from certain smolt stations close to the sea will be included.
The Illumina MiSeq sequencing yielded high- quality complete genome sequences from all the field samples. Preliminary phylogenetic analysis of the complete genomes shows that identical ISAV-HPR0 variants persist in the smolt farms as " house strain" over several years. We also show the recurrence of an old HPR0 variant in a smolt farm after total disinfection. Preliminary analysis also suggests the introduction of ISAV-HRP0 into the smolt farms from the external environment. The comprehensive whole genome data is expected to provide insights into the transmission dynamics and genetic variability of ISAV-HPR0, including how naïve RAS smolt farms, which are Closed Containment Systems (CCS) without prior detection, are increasingly testing positive.
This study was funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 956481.