Evolution of infectious salmon anaemia virus (ISA virus)

Abstract

Infectious salmon anaemia virus, ISA virus (genus Isavirus, family Orthomyxoviridae), emerged in Norwegian salmon culture in the mid-80s. The genome consists of eight segments coding for at least 10 proteins. ISA viruses show many of similarities to influenza A viruses but differ in many important aspects such as the number of hosts, the host population structure and the route of transmission. The only known hosts and reservoirs for ISA viruses are salmonids found in countries surrounding the North Atlantic. In this study, four different segments of the genome of about 100 ISA viruses have been sequenced in an attempt to understand the evolution of ISA viruses and how these viruses are maintained in and transmitted between populations of farmed Atlantic salmon. The four gene segments code for the nucleoprotein (NP), the putative acid polymerase (PA), the fusion protein (F) and the haemagglutinin-esterase (HE). Analysis of these four genes showed that the substitution rates of the internal proteins (NP and PA) are lower than those of the two surface proteins (F and HE). All four segments are evolving at a lower rate than similar genes in influenza A viruses. The ISA virus populations consist of avirulent viruses and pathogenic strains with variable virulence in Atlantic salmon. Recombination resulting in inserts close to the proteolytic-cleavage site of the precursor F0 protein and deletions in the stalk region of the HE protein seem to be responsible for the transition from avirulent ISA viruses to pathogenic strains. It is also shown that reassortment is a frequent event among the dominating ISA viruses in farmed Atlantic salmon. The pattern that is obtained after phylogenetic analysis of the four gene segments from ISA viruses suggests that the variation is limited to a few distinct clades and that no major changes have occurred in the ISA virus population in Norway since the first viruses were isolated. Calculation of the time of most recent common ancestor (TMRCA) suggests that the Norwegian ISA viruses separated from the European subtype found in North America between 1932 and 1959. The TMRCA data also suggest that the ISA viruses in Chile were transmitted from Norway in the period from 1995 to 2007, depending on which of the four genes were used in the analysis.

Infectious salmon anaemia virus (ISAV) in Chilean Atlantic salmon (Salmo salar) aquaculture: emergence of low pathogenic ISAV-HPR0 and re-emergence of virulent ISAV-HPR∆: HPR3 and HPR14

“…There are no previous sequences for ISAV-HPR14 in Chile, but this virus was first detected in 2008 in XI Region [32]. The 2013 ISAV-HPR∆ viruses (ISAV-HPR3 and ISAV-HPR14) show very close similarity to the ISAV-HPR0_CGA/CH1390, CGA/CH1420, CGA/CH1656, and CGA/CH1673, (this study) and ISAV-HPR0_CH29/08 [21] (Figure 5, and Additional file 4: Figure S2). The relationship between ISAV-HPR0 and ISAV-HPR∆ has been previously described in Norway [18-21] and Faroe Islands [12], but this is the first report of ISA cases directly linked to the presence of ISAV-HPR0 that is enzootic in an area.…”

Whole-genome analysis of piscine reovirus (PRV) shows PRV represents a new genus in family Reoviridae and its genome segment S1 sequences group it into two separate sub-genotypes

“…In Chile, the presence of PRV in farmed Atlantic salmon reared in Chilean seawater was first detected in 2010 and published in a laboratory report in 2011 [26], which cited a high prevalence among the sites located in different areas of the Los Lagos region growing-up macro-zone. PRV could have been introduced to Chile through importation of Atlantic salmon eggs similarly to ISAV [37-39] albeit more recently than ISAV: most Atlantic salmon egg imports to Chile in 2008 were from Norway, and from 2009–2013 have been from Iceland [40]. In Chile, HSMI will be recommended to be included on the List 3 of high-risk diseases [25], thus ensuring active surveillance for it in Chilean aquaculture.…”

Microevolution of Renibacterium salmoninarum: evidence for intercontinental dissemination associated with fish movements

“…Eggs are typically produced in dedicated broodstock facilities before being moved to hatcheries for production of fry, which are then moved again to ongrowing sites (either seawater cages for Atlantic salmon, or larger tanks or raceways for rainbow trout). As with other intensive livestock production systems, frequent transport means that breaches in biosecurity can lead to the transmission of pathogens between premises (Plarre et al , 2012). Furthermore, evidence exists that other highly clonal bacterial diseases of salmonids have spread between continents in similar ways, likely via egg and live fish movements.…”