Genetic diversity and epidemiology of infectious hematopoietic necrosis virus in Alaska

Forty-two infectious hematopoietic necrosis virus (IHNV) isolates from Alas ka were analyzed using the ribonuclease protection assay (RPA) and nucleoti de sequencing. RPA analyses, utilizing 4 probes, N5, N3 (N gene), GF (G gen e), and NV (NV gene), determined that the haplotypes of all 3 genes demonst rated a consistent spatial pattern. Virus isolates belonging to the most co mmon haplotype groups were distributed throughout Alaska, whereas isolates in small haplotype groups were obtained from only 1 site (hatchery, lake, e tc.). The temporal pattern of the GF haplotypes suggested a 'genetic acclim ation' of the G gene, possibly due to positive selection on the glycoprotei n. A pairwise comparison of the sequence data determined that the maximum n ucleotide diversity of the isolates was 2.75% (10 mismatches) for the NV ge ne, and 1.99% (6 mismatches) for a 301 base pair region of the G gene, indi cating that the genetic diversity of IHNV within Alaska is notably lower th an in the more southern portions of the IHNV North American range. Phylogen etic analysis of representative Alaskan sequences and sequences of 12 previ ously characterized IHNV strains from Washington. Oregon, Idaho, California (USA) and British Columbia (Canada) distinguished the isolates into cluste rs that correlated with geographic origin and indicated that the Alaskan an d British Columbia isolates may have a common viral ancestral lineage. Comp arisons of multiple isolates from the same site provided epidemiological in sights into viral transmission patterns and indicated that viral evolution, viral introduction, and genetic stasis were the mechanisms involved with I HN virus population dynamics in Alaska. The examples of genetic stasis and the overall low sequence heterogeneity of the Alaskan isolates suggested th at they are evolutionarily constrained. This study establishes a baseline o f genetic fingerprint patterns and sequence groups representing the genetic diversity of Alaskan IHNV isolates. This information could be used to dete rmine the source of an IHN outbreak and to facilitate decisions in fisherie s management of Alaskan salmonid stocks.