Molecular epidemiology of Epizootic haematopoietic necrosis virus (EHNV)

Low genetic diversity of Epizootic haematopoietic necrosis virus (EHNV) was determined for the complete genome of 16 isolates spanning the natural range of hosts, geography and time since the first outbreaks of disease. Genomes ranged from 125,591–127,487 nucleotides with 97.47% pairwise identity and 106–109 genes. All isolates shared 101 core genes with 121 potential genes predicted within the pan-genome of this collection. There was high conservation within 90,181 nucleotides of the core genes with isolates separated by average genetic distance of 3.43 × 10−4 substitutions per site. Evolutionary analysis of the core genome strongly supported historical epidemiological evidence of iatrogenic spread of EHNV to naïve hosts and establishment of endemic status in discrete ecological niches. There was no evidence of structural genome reorganization, however, the complement of non-core genes and variation in repeat elements enabled fine scale molecular epidemiological investigation of this unpredictable pathogen of fish. •Accessible methodology enabled efficient determination of the complete genome for 16 isolates of EHNV.•EHNV isolates spanning 25 years, 2 host species and the known geographical distribution of the virus were >97.5% similar.•Genetic differentiation of EHNV was consistent with patterns of spread determined by traditional disease investigation.