Abstract
The aquatic virus, infectious pancreatic necrosis virus (IPNV), is known to infect various farmed fish, in particular salmonids, and is responsible for large economic losses in the aquaculture industry. Common practices to detect the virus include qPCR tests based on specific primers and serum neutralization tests for virus serotyping. Following the potential presence of IPNV viruses in a fish farm in Scotland containing vaccinated and IPNV-resistant fish, the common serotyping of the IPNV isolates was not made possible. This led us to determine the complete genome of the new IPNV isolates in order to investigate the cause of the serotyping discrepancy. Next-generation sequencing using the Illumina technology along with the sequence-independent single primer amplification (SISPA) approach was conducted to fully characterize the new Scottish isolates. With this approach, the full genome of two isolates, V1810–4 and V1810–6, was determined and analyzed. The potential origin of the virus isolates was investigated by phylogenetic analyses along with tridimensional and secondary protein structure analyses. These revealed the emergence of a new variant from one of the main virus serotypes, probably caused by the presence of selective pressure exerted by the vaccinated IPNV-resistant farmed fish.
Highlights
Infectious pancreatic necrosis virus (IPNV) is an economically relevant pathogen of farmed Atlantic salmon (Salmo salar Linnaeus 1758) and rainbow trout (Oncorhynchus mykissWalbaum 1792)
Amino acid residues at position 217 and 221 have been shown to be linked to virulence types (virulent (T217, A221), persistent (P217, T221), avirulent (T217, T221) and low virulent (P217, A221)) and infectious pancreatic necrosis virus (IPNV) is classified into seven genogroups (I-VII) according to 10 known serotypes [6,7,8,9,10,11,12,13]
Tissue samples were inoculated on CHSE-214 cells, and culture was performed at 22 ◦ C, 4% CO2 in Eagle’s minimum essential medium (EMEM) with 10% fetal bovine serum (FBS) 1× non-essential amino acids and 2 μM L-glutamine
Summary
Infectious pancreatic necrosis virus (IPNV) is an economically relevant pathogen of farmed Atlantic salmon (Salmo salar Linnaeus 1758) and rainbow trout (Oncorhynchus mykissWalbaum 1792). Segment B encodes the RNA-dependent RNA polymerase (RdRp/VP1) [1,2,3,4,5]. The VP2 protein contains a variable domain in the central region between the amino acid residues 183–335, which is an important antigenic site with two hypervariable regions at residues 239–257 and 271–284 [6]. It should be noted that discrepancies among studies regarding the virulence profile of VP2 have been highlighted in a recent review from Dopazo [14]. It suggests that genetic factors from the host and environmental factors linked to the geographic location could contribute to different degrees of VP2 virulence connected to different different amino acid patterns
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