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Biological databases contain a wealth of valuable information that can contribute to the enrichment of virtually any area. However, the exponential growth of information together with its dissemination through virtual networks has become a double-edged sword, promoting synonymy that leads to confusion and chaos. Organization of data is a big effort that must be accompanied by clarity, both in the deposited data and in the publications arising from them. In this report, an effort is made to organize the information related to infectious salmon anemia virus and its classification based on the variability of genomic segment 6.

Infectious salmon anaemia virus, ISA virus (genus Isavirus, family Orthomyxoviridae), emerged in Norwegian salmon culture in the mid-80s. The genome consists of eight segments coding for at least 10 proteins. ISA viruses show many of similarities to influenza A viruses but differ in many important aspects such as the number of hosts, the host population structure and the route of transmission. The only known hosts and reservoirs for ISA viruses are salmonids found in countries surrounding the North Atlantic. In this study, four different segments of the genome of about 100 ISA viruses have been sequenced in an attempt to understand the evolution of ISA viruses and how these viruses are maintained in and transmitted between populations of farmed Atlantic salmon. The four gene segments code for the nucleoprotein (NP), the putative acid polymerase (PA), the fusion protein (F) and the haemagglutinin-esterase (HE). Analysis of these four genes showed that the substitution rates of the internal proteins (NP and PA) are lower than those of the two surface proteins (F and HE). All four segments are evolving at a lower rate than similar genes in influenza A viruses. The ISA virus populations consist of avirulent viruses and pathogenic strains with variable virulence in Atlantic salmon. Recombination resulting in inserts close to the proteolytic-cleavage site of the precursor F0 protein and deletions in the stalk region of the HE protein seem to be responsible for the transition from avirulent ISA viruses to pathogenic strains. It is also shown that reassortment is a frequent event among the dominating ISA viruses in farmed Atlantic salmon. The pattern that is obtained after phylogenetic analysis of the four gene segments from ISA viruses suggests that the variation is limited to a few distinct clades and that no major changes have occurred in the ISA virus population in Norway since the first viruses were isolated. Calculation of the time of most recent common ancestor (TMRCA) suggests that the Norwegian ISA viruses separated from the European subtype found in North America between 1932 and 1959. The TMRCA data also suggest that the ISA viruses in Chile were transmitted from Norway in the period from 1995 to 2007, depending on which of the four genes were used in the analysis.

Infectious salmon anaemia virus (ISAV), genus Isavirus (family Orthomyxoviridae), is present in all large salmon (Salmo salar)-producing countries around the North Atlantic. The target species for this virus are members of the genus Salmo, but the virus may also replicate in other salmonids introduced to the North Atlantic (Oncorhychus spp.). Existing ISA virus isolates can be divided into two major genotypes, a North American (NA) and a European (EU) genotype, based on phylogenetic analysis of the genome. The EU genotype can be subdivided into several highly supported clades based on analysis of segments 5 (fusion protein gene) and 6 (hemagglutinin-esterase gene). In 1999 an ISA virus belonging to the NA genotype was isolated from Coho salmon in Chile, and in 2007 the first outbreaks of ISA in farmed Atlantic salmon was observed. Several salmon farms in Chile were affected by the disease in 2007, and even more farms in 2008. In this study, ISA virus has been isolated from salmon in a marine farm suffering an outbreak of the disease in 2008 and from smolts with no signs of ISA in a fresh water lake. Sequencing of the partial genome of these ISA viruses, followed by phylogenetic analysis including genome sequences from members of the NA and EU genotypes, showed that the Chilean ISA virus belongs to the EU genotype. The Chilean ISA virus groups in a clade with exclusively Norwegian ISA viruses, where one of these isolates was obtained from a Norwegian brood stock population. All salmonid species in the southern hemisphere have been introduced from Europe and North America. The absence of natural hosts for ISA viruses in Chile excludes the possibility of natural reservoirs in this country, and the close relationship between contemporary ISA virus strains from farmed Atlantic salmon in Chile and Norway suggest a recent transmission from Norway to Chile. Norway export large amounts of Atlantic salmon embryos every year to Chile; hence, the best explanation for the Norwegian ISA virus in Chile is transmission via these embryos, i.e. vertical or transgenerational transmission. This supports other studies showing that the ISA virus can be transmitted vertically.

In the present study, 24 smolt production sites were screened for the presence of infectious salmon anaemia virus (ISAV) with the help of a specific real-time RT PCR assay, and 22 of these sites had smolts that were positive. If these smolt production sites are representative for the prevalence of ISAV in Norwegian smolts, then most marine production sites must be considered to be positive for ISAV. In addition, 92 European ISAV isolates have been genotyped based on the hemagglutinin-esterase gene (HE), and their distribution pattern was analysed. This pattern has been coupled to information about the origin of smolt, eggs, and broodfish in those cases where it has been possible to obtain such information, and with information about ISAV in neighbouring farms. The pattern suggests that an important transmission route for the ISAV could be that the salmon farming industry in Norway is circulating some of the isolates in the production cycle, i.e. some sort of vertical or transgenerational transmission may occur. It has also been shown that avirluent ISAV isolates are fairly common in Norwegian farmed salmon. Based on this, it is hypothesized that the change from avirulent to virulent ISAV isolates is a stochastic event that is dependent on the replication frequency of the virus and the time available for changes in a highly polymorphic region (HPR) of the HE gene to occur. This, and the possibility that only avirluent ISAV isolates are vertically transmitted, may explain why ISA most often occurs at marine sites and why no more than about 15 farms get ISA every year in Norway.