Molecular epidemiology and evolutionary dynamics of betanodavirus in southern Europe

Viral encephalopathy and retinopathy (VER) is one of the most devastating diseases for marine aquaculture, and similarly represents a threat to wild fish populations because of its high infectivity and broad host range. Betanodavirus, the causative agent of VER, is a small non-enveloped virus with a bipartite RNA genome comprising the RNA1 and RNA2 segments. We partially sequenced both RNA1 and RNA2 from 120 viral strains isolated from 2000 to 2009 in six different countries in Southern Europe. Phylogenetic analysis revealed the presence of the red-spotted grouper nervous necrosis virus (RGNNV) (n = 96) and striped jack nervous necrosis virus (SJNNV) (n = 1) genotypes in Southern Europe, with 23/120 samples classified as RGNNV/SJNNV reassortants. Viruses sampled from individual countries tended to cluster together suggesting a major geographic subdivision among betanodaviruses, although some phylogenetic evidence for viral gene flow was also obtained. Rates of nucleotide substitution were similar to those observed in a broad array of RNA viruses, and revealed a significantly higher evolutionary rate in the polymerase compared to the coat protein gene. This may reflect temperature adaptation of betanodaviruses, although a site-specific analysis of selection pressures identified relatively few selected sites in either gene. Overall, our analyses yielded novel data on the evolutionary dynamics and phylogeography of betanodaviruses and therein provides a more complete understanding of the distribution and evolution of different genotypes in Southern Europe.

► We sequenced genomes of 120 betanodaviruses isolated in 2000-2009 in Southern Europe. ► Phylogenetic analysis revealed the presence of the RGNNV and SJNNV genotypes. ► We identified RGNNV/SJNNV reassortant strains. ► The polymerase gene shows higher evolutionary rate compared to the coat protein gene. ► We observed a major geographic subdivision among betanodaviruses.