General information about infection tracing and phylogenetic analyses
Sequencing specific parts of the virus’s or bacterium’s genome is used for infection tracing. The sequences are then compared to previously identified sequences, and through phylogenetic analysis, one can determine the relationship between the different variants. This can also provide insights into where the infection may have been introduced.
Blue Analytics has its own equipment for sequencing and performs phylogenetic (relationship-based) analyses summarized in a report.
We offer specific analyses for the viruses mentioned below. Feel free to contact us if you would like to have other agents mapped.
ILAV
Virulence testing and relationship analysis for infection tracing
Infectious salmon anemia virus (ISAV) can lead to the disease infectious salmon anemia (ISA). During ISA outbreaks, a control area is typically established by the Norwegian Food Safety Authority to combat the disease and prevent further spread.
ILAS is a single-stranded RNA virus in the Orthomyxoviridae family. ISAV consists of 8 RNA segments and exists in a non-virulent form (HPR0) and a virulent form (HPRΔ). HPR stands for Highly Polymorphic Region.
Mutations in segment 5 (fusion protein) and segment 6 (hemagglutinin esterase) are associated with changes in virulence, and there are indications that when changes (deletions) in a specific part of segment 6 (HPR region) coincide with a mutation in segment 5 (fusion protein), clinical disease can occur in infected fish.
There are also intermediate phases where the virus is mutated in segment 6 (HPRΔ) but not virulent since there is no change in segment 5.
Blue Analytics can sequence ISAV-HPR and the fusion protein, even at low virus levels. Our analyses can be used for virulence verification and contact tracing.
IPNV
Relationship analysis for contact tracing
Infectious pancreatic necrosis virus (IPNV) can lead to the disease infectious pancreatic necrosis (IPN).
IPNV is a double-stranded RNA virus in the Birnaviridae family, where the genome consists of two segments (segment A and segment B). Segment A distinguishes the different IPNV variants from each other and codes for the outer and inner capsid proteins of the virus particle. Additionally, segment A codes for a protease and immunosuppressive proteins that help the virus infect the host.
For infection tracing, we offer sequencing of segment A from positive IPNV samples.
SAV
Differentiation between different virus variants
Salmonid alphavirus (SAV) causes the disease pancreas disease (PD).
SAV is a single-stranded RNA virus in the Togaviridae family. In Norway, it is the virus variants SAV2 and SAV3 that cause disease in salmon and trout.
Blue Analytics can offer sequencing to differentiate between the different SAV variants.