Molecular characterisation of infectious pancreatic necrosis viruses isolated from farmed fish in Finland

Abstract

Infectious pancreatic necrosis virus (IPNV) has been isolated annually since 1987 from salmonids without clinical signs at coastal fish farms in Finland. In the inland area, viral isolations were rare until 2012, when IPNV was detected at several freshwater fish farms. Between 2013 and 2015, the infection spread and IPNV was continuously isolated from several farms, both inland and on the coast. The aim of this study was to genetically characterise the IPNV isolates collected from Finnish coastal and inland fish farms over the last 15 years, and to detect genetic changes that may have occurred in the virus populations during the study period. The partial VP2 gene sequence from 88 isolates was analysed. In addition, a complete genomic coding sequence was obtained from 11 isolates. Based on the genetic analyses, Finnish IPNV isolates belong to three genogroups: 2, 5 and 6. The genetic properties of the isolates appear to vary between inland farms producing juveniles and food fish farms in the coastal region: the inland farms harboured genogroup 2 isolates, whereas at coastal farms, all three genogroups were detected. Little genetic variation was observed within the Finnish genogroup 2 and 5 isolates, whereas among the genogroup 6 isolates, two subgroups were detected. All isolates studied demonstrated amino acid patterns in the viral VP2 gene previously associated with avirulence. However, increased mortality was detected at some of the farms, indicating that more research is needed to clarify the relationship between the pathogenicity and genetic properties of IPNV isolates from different genogroups.

The Infectious Pancreatic Necrosis Virus (IPNV) and its Virulence Determinants: What is Known and What Should be Known

“…On the other hand, stress is an important parameter influencing the disease, and in the farming system it depends on the physicochemical conditions of the water, inappropriate nutrition, manipulation of the fish, and the density of the fish population in the facility. To this regard, the excessive density of cultured fish, a very important and often ignored parameter, has a double effect on the artificial environment in farms: on the one hand, it provokes stress in the fish, which is known to affect host defenses and has been reported to trigger outbreaks in asymptomatic carriers [78,79]; on the other hand, high fish densities favor virus transmission and virus evolution to high virulent types [80]. Therefore, it is clear that fish density represents a very important parameter in fish mortalities by IPNV.…”

“…The capacity of the host to defend against virus invasion and proliferation, its immune response-described in Section 3.3-depends, to a large extent, on its physiological state, and stress has a great influence on it and hence on the reduction of the effectivity of the defense barriers and on the development of the disease [78,79,81]. Another approach to understand the variable susceptibility of fish is more related to genetics, since it has been demonstrated that different lines of the same species, with the same age, and under the same conditions, can respond differently to infection of the same viral strain.…”

“…Although for some authors VP5 activity does not depend on its size, and even though apoptosis is not dependent of that protein [54,57,108], others defended the anti-apoptotic activity of the protein [52] and stated that a deletion in the 15 kDa normal VP5 protein might affect its activity and, therefore, viruses expressing a truncated 12 kDa VP5 should be more benign. To this regard, Davies et al [99] noted that all the Australian strains from healthy fish that they sequenced had a deletion at the N-terminal; however, other authors found that differences in VP5 size in field isolates were not related to the level of disease [79,109]. In IBDV, a clear association between the size of the protein and the virulence of the strain has been demonstrated in field isolates [61]; thus, the very virulent IBDV strains exhibit a large ORF and the low virulent ones have shorter forms.…”

Wild fish are negligible transmitters of viral haemorrhagic septicaemia virus (VHSV) genotype Id in the VHS restriction zone in Finland

“…Additionally, a sprivivirus was isolated from all fish species in this infection trial (Table 2). Spriviviruses grow in the same cell cultures as those used for VHSV isolation and were confirmed by sequencing (Holopainen et al 2017).…”

“…The probe was 5'-end labelled with FAM and 3'-end labelled with TAMRA (Table 3). We used a threshold cycle (C t ) cut-off value of 36 as estimated in our earlier study (Vennerström et al 2017).…”