Aquabirnavirus Genome sequencing and assembly

The Infectious Pancreatic Necrosis Virus (IPNV) is a naked double stranded RNA virus with a bi-segmented genome within the family Birnaviridae, genus Aquabirnavirus. The small ORF of segment A encodes the VP5 protein, while the large ORF encodes the non-structural protease (VP4), the internal capsid component (VP3) and the major structural protein (VP2). The viral polymerase (VP1) is encoded by the genomic segment B. Basing on the phylogenetic analysis of the VP2 sequence, seven IPNV genogroups have been described so far (I-VII), corresponding to 10 different serotypes.IPNV was detected for the fist time in Italian trout farms in the late 70s and ultimately became endemic. To genetically characterize the viruses circulating in Italy and to understand their evolution, the VP1 and the VP2 complete sequences related to 75 IPNV strains isolated in the period 1978-2017 were analyzed. Data obtained showed that Italian IPNV were genetically poorly variable and clustered within genogroup 2 for VP1, and within genogroup V for VP2. The estimated evolutionary rates for the polymerase and the capsid protein genes were 2 × 10-4 sub/site/y and 1.92 × 10-4 sub/site/y, respectively. The mean dN/dS ratios estimated for both target sequences clearly indicated that IPNV was subjected to strong selective constraint. Interestingly, all the Italian strains showed a proline at position 217 (P217) and a threonine at position 221 (T221) which are associated with a low virulent phenotype.This paper represents the first extended study on the molecular characterization of IPNV in Italy, and provides new information on the evolutionary dynamics of this virus. Data gained will be of utmost importance to elucidate the mechanisms involved in the spread of IPNV in Italian trout farms and will provide useful information to understand the mechanisms at the base of Aquabirnaviruses evolution.