Two distinct phylogenetic clades of infectious hematopoietic necrosis virus overlap within the Columbia River basin

Abstract

Infectious hematopoietic necrosis virus (IHNV), an aquatic rhabdovirus, causes a highly lethal disease of salmonid fish in North America. To evaluate the genetic diversity of IHNV from throughout the Columbia River basin, excluding the Hagerman Valley, Idaho, the sequences of a 303 nt region of the glycoprotein gene (mid-G) of 120 virus isolates were determined. Sequence comparisons revealed 30 different sequence types, with a maximum nucleotide diversity of 7.3% (22 mismatches) and an intrapopulational nucleotide diversity of 0.018. This indicates that the genetic diversity of IHNV within the Columbia River basin is 3-fold higher than in Alaska, but 2-fold lower than in the Hagerman Valley, Idaho. Phylogenetic analyses separated the Columbia River basin IHNV isolates into 2 major clades, designated U and M. The 2 clades geographically overlapped within the lower Columbia River basin and in the lower Snake River and tributaries, while the upper Columbia River basin had only U clade and the upper Snake River basin had only M clade virus types. These results suggest that there are co-circulating lineages of IHNV present within specific areas of the Columbia River basin. The epidemiological significance of these findings provided insight into viral traffic patterns exhibited by IHNV in the Columbia River basin, with specific relevance to how the Columbia River basin IHNV types were related to those in the Hagerman Valley. These analyses indicate that there have likely been 2 historical events in which Hagerman Valley IHNV types were introduced and became established in the lower Columbia River basin. However, the data also clearly indicates that the Hagerman Valley is not a continuous source of waterborne virus infecting salmonid stocks downstream. KEY WORDS: Columbia River basin · IHNV · Rhabdovirus · Epidemiology · Salmonids Resale or republication not permitted without written consent of the publisherDis Aquat Org 55: [187][188][189][190][191][192][193][194][195][196][197][198][199][200][201][202][203] 2003 ture with chinook salmon and steelhead culture, the occurrence of IHNV in the Columbia River basin became much less apparent. Prior to the late-1970s, IHNV was isolated only sporadically within the Columbia River basin. A survey conducted in 1970 by Amend and Wood for IHNV in Washington salmon indicated that IHNV was not present in stocks of chinook O. tshawytscha or coho O. kisutch, and only a portion of the sockeye salmon were found to be infected (Amend & Wood 1972). In Oregon, during the 1970s, IHN disease was observed in stocks of rainbow trout, steelhead trout, chinook salmon and kokanee salmon, but the virus was endemic to only 2 facilities (Mulcahy et al. 1980, Groberg & Fryer 1983, Groberg et al. 1983. In 1977, an area of the Columbia River basin located in Hagerman Valley, Idaho, began to experience high mortalities at rainbow trout aquaculture facilities (Busch 1983). The virus spread over the next 3 years to become endemic to the Hagerman Valley. During the subsequent years of 1980 ...

Genotyping of Korean isolates of infectious hematopoietic necrosis virus (IHNV) based on the glycoprotein gene

“…Subsequently, Garver et al [3] and Kurath et al [7] revealed three major genogroups, denoted upper (U), middle (M) and lower (L), correlating with the geographic areas in the Pacific Northwest of North America. The genogroup U includes isolates from Alaska, British Columbia, Washington coastal watersheds and the Columbia River basin; the genogroup M includes isolates from the Columbia River basin and Idaho; and the genogroup L includes isolates from California and the southern Oregon coast.…”

“…The IHNV genome is a non-segmented and single-stranded negative-sense RNA with approximately 11,000 nucleotides containing six genes in the order 3'-N-P-M-G-NV-L-5' encoding the nucleocapsid protein (N), phosphoprotein (P), matrix protein (M), glycoprotein (G), non-virion protein (NV) and polymerase (L) genes, respectively [6,9]. The G, N and NV genes have been used for analyses of IHNV evolution, diversity and phylogenetic relationship among the worldwide isolates [1,3,7,10,11,16,17].…”

Genotipificacion y relacion hospedador especifica del virus de la necrosis pancreatica infecciosa en Chile

“…graphpad.com/quickcalcs/contingency1/), resultando la relación en ambos casos como altamente significativa entre las variables (P < 0,001). Este tipo de relación hospedador-específica también ha sido reportada para otros virus de salmónidos, como el virus de la Necrosis Hematopoyética Infecciosa (IHNV) en Norteamérica, donde la mayoría de los aislados de los genogrupos denominados U y M, provienen predo-minantemente de salmón rojo (Oncorhynchus nerka) y trucha arcoíris, respectivamente (Garver et al, 2003). Estudios basados en desafíos experimentales con ambas especies y genogrupos han mostrado que esta relación está asociada a una virulencia específica para cada hospedador (i.e., mortalidad causada por la infección), la cual depende principalmente de la capacidad del virus de entrar en el pez hospedador y de replicarse rá- Tapia et al (2015).…”

First Record of Infectious Haematopoietic Necrosis Virus in Rainbow Trout Fry in Croatia

“…RT-PCR was done using single step RT-PCR system (Access, Promega) and nested PCR with HotStartTaq polymerase (Qiagen). Primers and reaction conditions were described previously Garver et al 2003). Nested PCR products were purified by a QIAquick gel extraction kit (Qiagen) and sequenced by an "ABI PRISM ® 3100-Avant Genetic Analyzer" DNA sequencer (Applied Biosystems).…”

“…Reverse transcriptase-polymerase chain reaction (RT-PCR), which detects specific parts of the IHNV genome, has been described (W inton and Einer-Jensen 2002) and approved by OIE as a valuable confirmation method for the IHNV diagnosis (OIE 2003). Further molecular characterisation, based on the sequence comparison of the glycoprotein (G) and non-virion (NV) genes from the different IHNV isolates proved to be useful in understanding and explanation of IHNV spreading, evolution and origin (Troyer et al 2000;Kurath et al 2003;Troyer and Kurath 2003;Garver et al 2003). Phylogenetic analysis of partial G gene sequences (Mid-G, 303 nucleotide region coding antigenic determinants) from the North American IHNV isolates revealed 3 major virus genogroups.…”