Genomic classification of betanodavirus by molecular phylogenetic analysis of the coat protein gene.

Abstract

The classification of betanodavirus into four species was reviewed including newer and well-charac terised isolates. Six major clusters were identified, four of which were similar to the classic species. Two single iso late clusters were worth consideration as new species. Betanodaviruses are small (37 nm average) icosahedral viruses with two positive-stranded non-polyadenylated RNAs as its genome. RNA1 (3.1 kb) codes for the viral RNA-dependent RNA polymerase (protein A), while RNA2 (1.4 kb) codes for the coat protein [16]. A subge nomic RNA3 synthesized from RNA1 during early viral replication codes for protein B2 [17], which functions against the host RNA interference system [3, 8]. These viruses cause viral nervous necrosis (VNN) or viral encephalopathy and retinopathy (VER) in fin fishes. They were first identified as picorna-like virus particles [5] and later described as members of the family Nodaviridae [12]. Taxonomically, these viruses belong to the genus Betan odavirus of family Nodaviridae, with four species recog nised so far [16] based on similarities in the variable region of the viral coat protein (CP) gene (nt 604-1030) [14]. The currently recognized species are Redspotted grouper ner vous necrosis virus (RGNNV), Striped jack nervous necrosis virus (SJNNV), Tiger puffer nervous necrosis virus (TPNNV) and Barfin flounder nervous necrosis virus. (BFNNV), with SJNNV as the type species. The preferred temperature ranges of members of these species are 25-30 C, 20-25 C, 20 C and 15-20 C, respectively. Over 40 fish species have been reported to be suscep tible to betanodaviruses, and the number is steadily increasing [10, 13]. Since the first description 15 years ago, the taxonomy of betanodavirus has remained more or less the same irrespective of the huge number of virus isolates being reported from different geographical environments and from different fish hosts. Some modifications were proposed to the system [4, 11, 15, 19], but these have been largely restricted to the geographical area of the researcher. The study presented here is an attempt to analyze the global phylogenetic relationships among the viruses by comparing all isolates for which full-length coat protein (CP) gene ORF sequence information is available in the NCBI GenBank database. A short variable region in the CP gene is shown to be sufficient for determining the phylogenetics of these viruses [14], but the full-length CP gene ORF is used in this study to obtain more reliable results.