Molecular detection and characterization of nodavirus in several marine fish species from the northeastern Atlantic

Abstract

Nodaviruses (NNV) are responsible for causing disease outbreaks mainly in hatcheryreared larvae and juveniles of a wide variety of fishes throughout the world. This disease has seriously limited the culture of marine fishes over the last decade. In the Atlantic provinces of Canada, disease caused by a nodavirus was first reported in juvenile Atlantic cod being reared in Nova Scotia, in 1999. More recently, disease outbreaks caused by nodavirus have been identified in hatcheryreared Atlantic cod and haddock in Newfoundland and New Brunswick, respectively, and along the east coast of the USA. The presence of NNV in wild Atlantic cod adults and wild winter flounder has also been reported. Nodaviruses were isolated from cultured Atlantic cod and haddock, as well as from wild winter flounder from a variety of geographical localities, and their virus coat (capsid) protein genes were partially sequenced. An analysis of the data indicates that all of the nodaviruses isolated from eastern North America were closely related to one another, but that they were distinct from the European isolates already sequenced. Regardless of host species, isolates from close geographical localities were more similar than those from distant geographical areas. At the protein level, differences in coat protein sequences were seen only for strains isolated from Atlantic cod originating from Newfoundland. Our results suggest that NNV may have been present in the Atlantic off Canada and on the east coast of the USA for some time, and has evolved to form a monophyletic group, distinct from other isolates found in cold-water species. Non-lethal methods for detection of NNV are necessary to develop management strategies for this disease, and would be an asset to diagnosticians and producers. Based on the results of this study, new primers were designed and developed for an improved RT-PCR assay able to detect North Atlantic nodaviruses in ovarian fluids, eggs and other tissues. The application of this test to field samples is discussed. KEY WORDS: Nodaviruses · RT-PCR · Phylogenetic analysis · Atlantic cod · Haddock Resale or republication not permitted without written consent of the publisherDis Aquat Org 62: [181][182][183][184][185][186][187][188][189] 2004 der (Pleuronectes americanus) has been reported from Atlantic Canada (Barker et al. 2002, Cusack 2002. Nodavirus infection has been reported in cultured juveniles of Atlantic cod from the UK, with low mortality rates (approximately 2%) observed over a 3-mo period (Starkey et al. 2001).Nodaviruses are small non-enveloped viruses, and their genome consists of 2 sense RNA strands. RNA1 (3.1 kb) of striped jack NNV encodes a putative RNAdependent RNA polymerase (RdRp) and RNA2 (1.4 kb) encodes the capsid protein precursor (Mori et al. 1992). To date, comparisons between the nucleotide sequences of a variable region of the capsid protein referred to as T4 (Nishizawa et al. 1994) have led to the division of the genus Betanodavirus into 7 type species: barfin flounder nervous necros...

Nodaviruses in Wild Fish Population Collected Around Aquaculture Cage Sites from Coastal Areas of Tunisia

“…The evolutionary history was inferred using the UPGMA method [25].The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) is shown next to the branches [23]. The evolutionary distances were computed using the Kimura 2-parameter method [26] and are in the units of the number of base substitutions per site [27][28][29][30]. GenBank accession numbers and references for nucleotide sequences are as follow: EU826138.1 [31], EF617326 [32], NC_013461 [33], KF386164 [34], KY354698.1 [35], GU826692.1 [36], HE796793.1 [37], KY354694.1 [35], HE796789.1 [37], HE796797.1 [37], HE796788.1 [37], HE796791.1 [37], HE796790.1 [37], HE796785.1 [37], HE796798.1 [37], HE796799.1 [37], HE796794.1 [37], HE796786.1 [37], AJ698093.1 [38], AF318942.1 [39], AF499774.1 [40], HE796795.1 [37], HE796796.1 [37], HE796787.1 [37], HE796784 [37], KM588181.1 [41], KP455642.1 [42], AY284968.1 [43], HE796792.1 [37], JN190021.1 [44].…”

Betanodavirus of Marine and Freshwater Fish: Distribution, Genomic Organization, Diagnosis and Control Measures

“…Till date, PCR is the main diagnostic test that is being used by most of laboratories. The sensitivity of this test depends on the strain of betanodavirus which is being targeted; hence specific primers are continuing to be developed [40]. Nested RT-PCR has been found to be 10-100 times more sensitive than the previously reported RT-PCR methods [29,117].…”

“…It has been observed that betanodavirus strains tend to be geographically related rather than to the fish species from which it has been isolated [40]. To ensure that the fish are as healthy as possible, a useful and practical approach would be vaccination of fish and boosting their immune system.…”

Viruses of Freshwater Finfish in the Asian–Pacific Region

“…The RNA1 encodes for non-structural RNA-dependent RNA polymerase and RNA2 encodes the coat protein. At least five genotypes based on coat protein have been described from different geographical locations [21]. The typical histological picture of vacuolating necrosis of neural cells of the brain, retina and spinal cord aids in diagnosis of this disease.…”