Low evolutionary rate of infectious pancreatic necrosis virus (IPNV) in Italy is associated with reduced virulence in trout

Infectious pancreatic necrosis virus (IPNV) is a naked double-stranded RNA virus with a bi-segmented genome that is classified within the family Birnaviridae, genus Aquabirnavirus. IPNV was first detected in Italian trout farms in the late 1970s and ultimately became endemic. To characterize the evolution of IPNV circulating in Italy, particularly whether there is a link between evolutionary rate and virulence, we obtained and analyzed the VP1 (polymerase) and the pVP2 (major capsid protein precursor) sequences from 75 IPNV strains sampled between 1978 and 2017. These data revealed that the Italian IPNV exhibit relatively little genetic variation over the sampling period, falling into four genetic clusters within a single genogroup (group 2 for VP1 and genogroup V for pVP2) and contained one example of inter-segment reassortment. The mean evolutionary rates for VP1 and pVP2 were estimated to be 1.70 and 1.45 × 10(−4) nucleotide substitutions per site, per year, respectively, and hence significantly lower than those seen in other Birnaviruses. Similarly, the relatively low ratios of non-synonymous (d(N)) to synonymous (d(S)) nucleotide substitutions per site in both genes indicated that IPNV was subject to strong selective constraints, again in contrast to other RNA viruses infecting salmonids that co-circulate in the same area during the same time period. Notably, all the Italian IPNV harbored a proline at position 217 (P(217)) and a threonine at position 221 (T(221)) in pVP2, both of which are associated with a low virulence phenotype. We therefore suggest the lower virulence of IPNV may have resulted in reduced rates of virus replication and hence lower rates of evolutionary change. The data generated here will be of importance in understanding the factors that shape the evolution of Aquabirnaviruses in nature.