Molecular epidemiology of betanodaviruses isolated from sea bass and sea bream cultured along the Tunisian coasts

Abstract

Viral nervous necrosis (VNN) is a serious viral disease affecting farmed sea bass (Dicentrarchus labrax). Only scarce molecular data are available on the disease-causing betanodavirus populations in Tunisia. Therefore, we carried out the first molecular survey of betanodaviruses in farmed sea bass and sea bream (Sparus aurata) along the Tunisian coasts. Among 81 samples from five farms, 20 tested positive with RT-PCR, not only in clinical cases but also in asymptomatic fish before and during outbreaks. Positive fish were found in all farms, except in one farm investigated in the south of Tunisia. Sequencing the fragments of both genomic components (RNA1 and RNA2) in 16 isolates revealed that the Tunisian viruses were related to the red-spotted grouper nervous necrosis virus (RGNNV) genotype. Furthermore, the newly sequenced isolates were generally highly related to one another suggesting a recent common ancestor. They also showed high identities with other isolates obtained from wild fishes in the Mediterranean, but were slightly more divergent from strains recently obtained from farmed fishes in the Mediterranean. The poor genetic diversity of the viral population along the Tunisian coasts is striking. One hypothesis is that it is the result of the maintenance of a homogenous genetic pool among infected wild fish, groupers for instance and subsequent dissemination to farmed fish over the seasons.

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

“…Comparison of a partial sequence from the coat protein gene of the wild isolates showed a similarity ranging from 94% to 97% to the Tunisian nodaviruses retrieved from farmed sea bass and sea bream [4,24]. In addition, the similarity with the rest of the genotypes was ranging from 88% to 97% (data not shown).…”

“…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].…”

First generic one step real-time Taqman RT-PCR targeting the RNA1 of betanodaviruses

“…When used in conventional PCR, the oPVP154-155 primer set proved to be useful alone to detect RGNNV isolates during an epidemiological study in sea bass and sea bream in Tunisian farms (Haddad-Boubaker et al, 2013). A Taqman probe was therefore added to the method to increase specificity in an attempt to extend the method to the widest possible panel of hosts.…”

“…It is rapid, sensitive, specific and has a potential for being used routinely in different geographic regions and host species with a very high chance of detecting any isolate. An additional advantage of the targeted region is its potential, after sequencing, for providing a rough genotyping in order to identify the viral species (Haddad-Boubaker et al, 2013). In addition, the region targeted by the Taqman probe is subjected to rare variations.…”

Viral nervous necrosis in gilthead sea bream (Sparus aurata) caused by reassortant betanodavirus RGNNV/SJNNV: an emerging threat for Mediterranean aquaculture

“…Indeed, this species has often been reared in close vicinity to sea bass in areas where VNN is endemic. Interestingly, most of the VNN outbreaks in seabass were associated to the RGNNV species202122, which suggested that maybe sea bream was not susceptible to this specific virus species. This finding was supported also under experimental conditions.…”