Genotyping of marine viral haemorrhagic septicaemia virus isolated from the Flemish Cap by nucleotide sequence analysis and restriction fragment length polymorphism patterns

Abstract

A total of 14 viral haemorrhagic septicaemia virus (VHSV) isolates obtained from Greenland halibut Reinhardtius hippoglossoides caught at the Flemish Cap, a fishing ground in the North Atlantic Ocean near Newfoundland, were characterised using restriction fragment length polymorphism (RFLP) and nucleotide sequence analysis. RFLP analysis was performed on a 1259 bp fragment of the glycoprotein (G) gene, and a 305 nucleotide region within the nucleoprotein (N) gene was used for sequence analysis. Representative strains of the 4 established genotypes were employed for comparative purposes. Sequencing analysis indicated that the Flemish cap isolates grouped in Genotype 3, which also includes isolates from wild fish caught in the North Sea and coastal waters of the UK and Ireland, isolates derived from outbreaks of VHS in turbot farms in the British Isles, and an isolate from European eel Anguilla anguilla caught in northern France. Characterisation using RFLPs resulted in the development of a simple and reliable method of typing VHSV at the genotype level using a 2-step restriction analysis (2-SRA) assay.