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One of the most valuable aquaculture fish in Europe is the rainbow trout,  Oncorhynchus mykiss , but the profitability of trout production is threatened by a highly lethal infectious disease, viral hemorrhagic septicemia (VHS), caused by the VHS virus (VHSV). For the past few decades, the subgenogroup  Ia  of VHSV has been the main cause of VHS outbreaks in European freshwater-farmed rainbow trout. Little is currently known, however, about the phylogenetic radiation of this  Ia  lineage into subordinate  Ia  clades and their subsequent geographical spread routes. We investigated this topic using the largest  Ia -isolate dataset ever compiled, comprising 651 complete  G  gene sequences: 209 GenBank  Ia  isolates and 442  Ia  isolates from this study. The sequences come from 11 European countries and cover the period 1971–2015. Based on this dataset, we documented the extensive spread of the  Ia  population and the strong mixing of  Ia  isolates, assumed to be the result of the Europe-wide trout trade. For example, the  Ia  lineage underwent a radiation into nine  Ia  clades, most of which are difficult to allocate to a specific geographic distribution. Furthermore, we found indications for two rapid, large-scale population growth events, and identified three polytomies among the  Ia  clades, both of which possibly indicate a rapid radiation. However, only about 4% of  Ia  haplotypes (out of 398) occur in more than one European country. This apparently conflicting finding regarding the Europe-wide spread and mixing of  Ia  isolates can be explained by the high mutation rate of VHSV. Accordingly, the mean period of occurrence of a single  Ia  haplotype was less than a full year, and we found a substitution rate of up to 7.813 × 10 −4  nucleotides per site per year. Finally, we documented significant differences between Germany and Denmark regarding their VHS epidemiology, apparently due to those countries’ individual handling of VHS.

Phylogeny of the Viral Hemorrhagic Septicemia Virus in European Aquaculture