Comparisons among the complete genomes of four betanodavirus genotypes

Abstract

Betanodaviruses, the causative agents of viral nervous necrosis in marine fish, have bipartite positive-sense RNA genomes and have been classified (based on analysis of RNA2 sequences) into 4 genotypes: tiger puffer nervous necrosis virus (TPNNV), barfin flounder nervous necrosis virus (BFNNV), striped jack nervous necrosis virus (SJNNV), and redspotted grouper nervous necrosis virus (RGNNV). Full-length genomes of TPNNV and BFNNV were sequenced for the first time in this study. Their sequence data and those of SJNNV and RGNNV retrieved from GenBank were compared in order to investigate the relationships among the 4 genotypes. Between TPNNV and BFNNV, sequence identities were relatively high in RNA1 and encoded Protein A, but were not significantly high in RNA2 or the coat protein (CP). Similarly, between BFNNV and RGNNV, the amino acid sequences of CP were highly similar, but identities of RNA1, RNA2, and Protein A sequences were not especially high. Furthermore, multiple alignment data of the 4 genotypes of RNA2 sequences revealed that the TPNNV and SJNNV sequences have the same sizes of gaps and extra sequences at the same positions. Collectively, these apparent contradictions in sequence identity suggest that betanodavirus genomes have been constructed via complex evolutionary processes. KEY WORDS: Betanodavirus · Complete genomic sequence · RNA1 · RNA2 · Tiger puffer nervous necrosis virus · Barfin flounder nervous necrosis virus Resale or republication not permitted without written consent of the publisherDis Aquat Org 80: [113][114][115][116][117][118][119][120][121] 2008 betanodavirus isolates from France, Spain, Tunisia, and Tahiti were classified as RGNNV, and were further divided into 2 distinct subtypes (Thiéry et al. 2004). Phylogenetic analysis of betanodaviruses has been commonly performed using the T4 sequences. However, in some studies, the T2 region (Nishizawa et al. 1994), which covers a larger RNA2 sequence than T4, is also utilized for phylogenetic analysis (e.g. Grotmol et al. 2000, Chi et al. 2003, Johansen et al. 2004. Clinical disease caused by SJNNV and TPNNV has only been reported in striped jack Pseudocaranx dentex and tiger puffer Takifugu rubripes, respectively. However, recently, SJNNV was found in European sea bass Dicentrarchus labrax, sea bream Sparus aurata and Senegalese sole Solea senegalensis farmed in the Iberian Peninsula -though the samples used were from subclinically infected fish (Thiéry et al. 2004, Cutrín et al. 2007). BFNNV has been isolated from some coldwater species, such as barfin flounder Verasper moseri, Pacific cod Gadus macrocephalus, and Atlantic halibut Hippoglossus hippoglossus. RGNNV has a broad host range and causes disease among a variety of warm-water fish species, particularly groupers and sea bass (Munday et al. 2002).As mentioned earlier, betanodavirus isolates have been characterized based on similarities in the partial RNA2 sequences. Thus, not much is known about the RNA1 sequences and the remaining RNA2 region. So far, complete nuc...

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

“…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].…”

Viral encephalopathy and retinopathy in aquaculture: a review

“…Among the different species of betanodaviruses, amino acid sequences of RdRp protein and capsid protein share 87–99% and 77–100% of identity, respectively [82–98% for the complete RNA1 nucleic sequence and 76–99% for the RNA2 segment (Okinaka & Nakai )]. The topology of phylogenetic trees based on RNA1 and RNA2 distinguishes several clades, suggesting a high diversity despite relatively strong purifying selection on most codons (Panzarin et al .…”

Complete genome sequence and pathogenic analysis of a new betanodavirus isolated from shellfish

“…Additionally, KSNNV‐KOR1 appears to be an ancient member of the Betanodavirus , as it forms a group in a primitive branch extending distantly from all the other previously reported betanodaviruses in both phylogenetic trees for RNA1 and RNA2 (Figure c,d). In the same point of view, KSNNV may have evolved via reshuffling events between RNA1 and RNA2 of different genotypes based on the cross‐similarity of segments including BFNNV‐SJNNV in RNA1, and RGNNV‐BFNNV and SJNNV‐TPNNV in RNA2 (Dalla Valle et al, ; Okinaka & Nakai, ). In addition, both the gap regions of 2 aa in ORF and 21 nt in 3′‐UTR in RNA2 (aa236–aa237 of ORF and nt1122–nt1142 of 3′‐UTR in KSNNV‐KOR1 RNA2) were used to determine the RGNNV‐BFNNV and SJNNV‐TPNNV sister relationship (Okinaka & Nakai, ; Figures and ).…”

“…In the same point of view, KSNNV may have evolved via reshuffling events between RNA1 and RNA2 of different genotypes based on the cross‐similarity of segments including BFNNV‐SJNNV in RNA1, and RGNNV‐BFNNV and SJNNV‐TPNNV in RNA2 (Dalla Valle et al, ; Okinaka & Nakai, ). In addition, both the gap regions of 2 aa in ORF and 21 nt in 3′‐UTR in RNA2 (aa236–aa237 of ORF and nt1122–nt1142 of 3′‐UTR in KSNNV‐KOR1 RNA2) were used to determine the RGNNV‐BFNNV and SJNNV‐TPNNV sister relationship (Okinaka & Nakai, ; Figures and ). Interestingly, KSNNV‐KOR1 contained extra sequences at the two gap regions in RNA2 (aa236–aa237 of ORF and nt1122–nt1142 of 3′‐UTR in KSNNV‐KOR1 RNA2).…”