Phylogeny of betanodaviruses and molecular evolution of their RNA polymerase and coat proteins

The betanodaviruses are the causative agent of the disease viral nervous necrosis in fishes. Betanodavirus genome consists of two single-stranded positive-sense RNA molecules (RNA1 and RNA2). RNA1 gene encodes the RNA polymerase, named also protein A, while RNA2 encodes the coat protein precursor, the CPp protein. We investigated the evolutionary relationships among betanodaviruses working on partial sequences of both RNA1 and RNA2. Phylogenetic analyses were performed by applying a maximum likelihood approach. The phylogenetic relationships among the major betanodavirus clades SJNNV-IV, TPNNV-III, BFNNV-II and RGNNV-I were resolved differently in the trees obtained, respectively, from RNA1 and RNA2 multiple alignments. The alternative topologies were corroborated by strong bootstrap values. The molecular evolution of proteins A and CPp was also investigated. Protein A appeared to have evolved under strong purifying selection while the CPp protein was subject to both purifying and neutral selection in different amino acid residues. Intragenic recombination in RNA1 and RNA2 genes was investigated by applying several methods and was not detected. Conversely reassortment of RNA1 and RNA2 genes was demonstrated in some isolates. Finally RNA1 and RNA2 genes substitution rates do not follow a clock-like behavior thus impeding estimation of a possible origin time for Betanodavirus genus.