Piscine orthoreovirus sequences in escaped farmed Atlantic salmon in Washington and British Columbia

Abstract

Background Piscine orthoreovirus (PRV) is an emergent virus in salmon aquaculture belonging to the family Reoviridae . PRV is associated with a growing list of pathological conditions including heart and skeletal inflammation (HSMI) of farmed Atlantic salmon. Despite widespread PRV infection in commercially farmed Atlantic salmon, information on PRV prevalence and on the genetic sequence variation of PRV in Atlantic salmon on the north Pacific Coast is limited. Methods Feral Atlantic salmon caught in Washington State and British Columbia following a large containment failure at a farm in northern Puget Sound were sampled. Fish tissues were tested for PRV by RT-qPCR assay for segment L1 and conventional RT-PCR for PRV segment S1. The PCR products were sequenced and their relationship to PRV strains in GenBank was determined using phylogenetic analysis and nucleotide and amino acid homology comparisons. Results Following the escape of 253,000 Atlantic salmon from a salmon farm in Washington State, USA, 72/73 tissue samples from 27 Atlantic salmon captured shortly after the escape tested PRV-positive. We estimate PRV-prevalence in the source farm population at 95% or greater. The PRV found in the fish was identified as PRV sub-genotype Ia and very similar to PRV from farmed Atlantic salmon in Iceland. This correlates with the source of the fish in the farm. Eggs of infected fish were positive for PRV indicating the possibility of vertical transfer and spread with fish egg transports. Conclusions PRV prevalence was close to 100% in farmed Atlantic salmon that were caught in Washington State and British Columbia following a large containment failure at a farm in northern Puget Sound. The PRV strains present in the escaped Atlantic salmon were very similar to the PRV strain reported in farmed Atlantic salmon from the source hatchery in Iceland that was used to stock commercial aquaculture sites in Washington State. This study emphasizes the need to screen Atlantic salmon broodstock for PRV, particularly where used to supply eggs to the global Atlantic salmon farming industry thereby improving our understanding of PRV epidemiology. Electronic supplementary material The online version of this article (10.1186/s12985-019-1148-2) contains supplementary material, which is available to authorized users.

Genomes reveal genetic diversity of Piscine orthoreovirus in farmed and free-ranging salmonids from Canada and USA

“…These authors suggested that the grouping of PRV-1 into sub-genogroups 1a and 1 b did not adequately describe the genetic patterns in their larger dataset. Kibenge et al. (2019) reported separation of sequences into the two genogroups 1a and 1 b, with sequences from the northeast Pacific grouping with sequences from Iceland, Norway, and Chile within 1a.…”

A molecular assessment of infectious agents carried by Atlantic salmon at sea and in three eastern Canadian rivers, including aquaculture escapees and North American and European origin wild stocks

“…PRV-1 S1 sequences from both aquaculture escapees differed from those isolated from wild fish at sea (Greenland-collected), and PRV-1 was not detected in either wild river-sampled population in this study. It is worth noting that the PRV-1 variants observed both in Greenland and in eastern Canada all clustered with the Norwegian "wild-type" variant, classified in some studies as PRV-1a (Kibenge et al 2019) that, based on the S1 segment, is divergent from PRV-1b, has been proposed to be of higher virulence (Dhamotharan et al 2019) and has been shown to be the causative agent of heart and skeletal muscle inflammation (HSMI) (Wessel et al 2017). However, HSMI has been diagnosed in farmed Atlantic salmon in western Canada in association with PRV-1a (Di Cicco et al 2017).…”

Piscine orthoreovirus: Biology and distribution in farmed and wild fish

“…The initial genome naming and annotation of PRV proposed that L1, L2, L3, M1, M2, M3, S1, S2, S3 and S4 segments code for the λ1, λ2, λ3, μ2, μ1, μNS, σ3/p13, σ2, σNS and σ1 proteins, respectively (Palacios et al., 2010). This scheme was followed by Kibenge et al (2013) when establishing the first PRV genome in GenBank (GCA_002829625.1) and has been followed by a number of subsequent researchers (Di Cicco et al., 2017; Kibenge et al., 2019; Polinski, Marty, Snyman, & Garver, 2019; Takano et al., 2016). However, one early study reversed the naming of L1 and L3 so that the term L1 would be used to identify the segment that codes λ3, similar to the terminology applied to an analog, mammalian orthoreovirus (MRV) (Markussen et al., 2013).…”

“…Current data suggest that this was a result of a single introduction prior to 1987 (Siah et al, in press ). A second introduction of PRV‐1a via importation of Atlantic Salmon into Washington state from Iceland appears to have occurred within the last decade (Kibenge et al., 2019; Siah et al, in press ); however, it is as yet unclear if this introduction will result in regional establishment of this second PRV‐1a variant in the North Pacific. PRV‐1 is also hypothesized to have been introduced to Chile from both North Pacific and North Atlantic sources, possibly in multiple introduction events (Siah et al, in press ).…”

“…In the Pacific region, PRV‐1 has been detected along the west coast of the United States and Canada as well as in Chile (Godoy et al., 2016; Marty et al., 2015; Purcell et al., 2018). Both PRV‐1a and ‐1b subgroups are present in Norway, Chile and Denmark (Dhamotharan et al., 2019; Siah et al, in press ), whereas in all other regions, including all North Atlantic countries apart from Norway, the PRV‐1a genogroup has (as yet) been the only subgroup identified (Dhamotharan et al., 2019; Kibenge et al., 2013, 2019; Siah et al, in press ; Siah et al., 2015).…”