Piscine orthoreovirus
Piscine orthoreovirus (PRV) is a species in the genus "Orthoreovirus" that infects fish exclusively, PRV was first discovered in 2010 in farmed Atlantic salmon exhibiting Heart and Skeletal Muscle Inflammation (HSMI) and has been found present at higher concentration in fish with various diseases. These diseases include HSMI, jaundice syndrome, proliferative darkening syndrome and erythrocytic body inclusion syndrome. PRV is thought to mainly affect aquacultured and maricultured fish stocks, and recent research has been focused around the susceptibility of wild stock. However, whether PRV is virulent with respect to HSMI remains a topic of debate. PRV has been  in the public eye mostly due to a potential linkage to farmed Atlantic Salmon exhibiting HSMI. Public concern has been raised regarding the possibility of open ocean-net farms transmitting PRV to wild salmon populations and being a factor in declining populations. PRV has not been confirmed to be pathogenic in wild salmon stocks. Classification. Phylogenetic analysis of each segment of the PRV genome initially placed PRV in the "Reoviridae" family, subfamily "Spinareovirinae", based on sequence and structural similarity to known reoviruses. Upon discovery, phylogenetic sequence analysis indicated PRV was equally related to viruses in the genera "Orthoreovirus" and "Aquareovirus . As a result, it was suggested that PRV evolved separately from a common ancestor related to both Orthoreovirus" and "Aquareovirus" in the subfamily "Spinareovirinae". Currently, PRV is officially classified as an Orthoreovirus. Placement into the genus "Orthoreovirus" has been argued for the following reasons: Opposing arguments to placement in "Orthoreovirus", Genome and structure. Genome. "Piscine orthoreovirus" has a segmented dsRNA genome made up of 10 individual linear segments, cumulatively measuring around 23,600bp. It has a GC content of 47%. Each segment has conserved terminal sequences. The 3' end sequence (UCAUC-3') is the same as "Orthoreovirus" and "Aquareovirus". The 5' end  sequence (5'-GAUAAA/U) is unique to PRV. These segments are referred to as L1-3 (Long), M1-3(Medium) and S1-4 (Short) based on length and comparison with homologous segments in "Orthoreovirus" and "Aquareovirus". L1 is the longest at 3916bp and S4 the shortest at 1040bp. Eleven proteins are confirmed to be encoded. S1 exhibits bicistronicity with 2 overlapping open reading frames, while the remaining proteins are either confirmed as monocistronic or have been thought to be bicistronic with no further evidence. The proteins that each segment encodes for are as follows, using a standardized naming system across reovirus genera : Subdivisions. Piscine orthoreovirus has been grouped into multiple different genotypes based on sequence diversity. Although multiple ways of subdividing PRV have been proposed, the system most often used in the literature subdivides PRV into Genotypes I and II, which are further divided into Ia and Ib, and IIa and IIb, respectively. These divisions and subdivisions are based on sequence diversity within segment S1. Genotype I (PRV-1). Ia. This sub genotype of PRV is found primarily in farmed Atlantic salmon in Norway, Chile and Canada. It has been associated with populations exhibiting HSMI. It has been found in farmed Chinook salmon  in Canada exhibiting Jaundice syndrome, as well as farmed Rainbow trout and Coho showing HSMI like symptoms in Chile and Canada. Ib. This sub genotype of PRV is found primarily in farmed Atlantic and Coho salmon in Norway and Chile, additionally being found in farmed Rainbow trout in Chile. It has been present in many salmon with HSMI. It has also been found in Coho populations exhibiting Jaundice syndrome. Genotype II. Genotype II was first discovered when comparing the S1 sequences among farmed Atlantic salmon in Chile, and further reiterated with both M2 and whole genome analysis. Despite being within  one genotype, the sub genotypes IIa and IIb exhibit much higher inter-sequence diversity than do Ia and Ib. IIa (PRV-3). PRV-3 has been associated with pathological heart lesions in rainbow trout. It has also been found in farmed Coho Salmon, Brown trout, and Rainbow trout exhibiting HSMI across Northern Europe and Chile. It has also been found in wild brown trout with proliferative darkening syndrome in Central Europe. Comparison with PRV-2 shows an 80.1% and 90.5% similarity for nucleotides and amino acids, respectively. Comparison with PRV-1 showed a 72.9% similarity in nucleotide sequence and 80.0% amino acid sequence similarity . IIb (PRV-2). PVR-2 has only been found in farmed Coho salmon in Japan exhibiting Erythrocytic Inclusion Body Syndrome (EIBS). Only one genome of PRV-2 has been sequenced thus far, which has reduced confidence in phylogenetic placements. Comparison with PRV-1 showed a 73.4% and 80.3% similarity in nucleotide sequence and amino acid sequence, respectively. Structure. As a member of genus "Orthoreovirus", the virion form of PRV is a non-enveloped icosahedral capsid with two layers, the outer and core. The diameter of the total virion encompassing the outer layer is approximately 70 nm, with the inner core layer measuring around 39  nm in diameter. The inner layer consists of the shell protein, λ3, as well as the inner clamp protein σ2, which is thought to play a role in the structural stabilization of the icosahedron. The outer layer is thought to play a stabilizing role for the inner capsid and is made up of μ1(Outer Capsid protein) as well as σ3 (Outer Clamp Protein). Additionally, the outer layer has fiber proteins (σ1) that mediate viral attachment and entry into the host. PRV is a turreted reovirus, exhibiting a turret protein (λ2) on the five-fold axes of its inner capsid icosahedron . The homologous proteins for L2 in MRV and ARV have both guanyltransferase and methyltransferase activity. Although not entirely conserved, the active regions of (λ2) exhibit fidelity to MRV and ARV sequences, suggesting λ2 is the turret protein and that it plays a similar role in the 5' capping of transcribed viral mRNA. Discovery. PRV was first identified in 2010 via high throughput DNA sequencing and bioinformatics approaches which determined the virus was present in maricultured Atlantic salmon affected by Heart and Skeletal Muscle Inflammation (HSMI), and while control of the spread of PRV was advised, a causal relationship between PRV  and HSMI was not demonstrated at that time. In 2012, several wild fish species off the coast of Norway tested positive for PRV indicating that PRV is present in wild populations, however the majority of sample tests yielded negative results indicating low prevalence of PRV off the Norwegian coast. There has been speculation that PRV 1a was introduced to the West Coast of North America from a North Atlantic source. PRV 1a was introduced to Chile from North Pacific and North Atlantic sources. Distribution. PRV has been found to have a nearly worldwide distribution with various studies detecting the presence  of PRV in fisheries in the Atlantic off the coast of the UK, Ireland, and Norway, as well as in both the Atlantic and Pacific Coasts off of North and South America. PRV has been detected in pacific farmed and wild fish species as far north as Alaska, and as far south as Chile. PRV-1 is less common in wild salmon than it is in farmed salmon, and while wild Sea Trout tend to exhibit PRV-3 infection, the same can not be said for wild Atlantic Salmon populations. Interaction with host. Infection dynamics. The kinetics of PRV infection have been  identified into three distinct phases: There are complications in determining the possible outcomes of PRV infection. Each genotype has been shown to lead to circulatory disease; however, high-load PRV infections have also occurred in non-diseased salmon and trout. Disease. PRV and HSMI. While Norwegian strains of PRV have led to HSMI outbreaks, it's uncertain if HSMI develops as a result of infection with North American strains of PRV as various salmon and trout have been found to have detectable PRV infections despite an apparent absence of HSMI. Research in Norway has indicated that injecting tissue from fish  exhibiting HSMI into healthy fish leads to HSMI, but this causal relationship seems to be more difficult to demonstrate with PRV variants found off the west coast of Canada. So far, only Atlantic Salmon in Norway have had causation proven, while correlation with disease has been found in other cases, but causation has yet to be proven. Wild salmon from British Columbia, such as Coho, Chinook and Sockeye are susceptible to infection by PRV, and exhibit similar viral loads to farmed Atlantic salmon, but have not been reported to exhibit symptoms of HSMI. Disease prevention. HSMI is one of the  most significant diseases in Atlantic salmon aquaculture in Norway. In efforts to mitigate this disease, attempts have been made to develop vaccines which target PRV-1 using deactivated viral particles, and DNA which codes for proteins with sequences derived from PRV; neither treatment prevented infection with PRV, but the effects of HSMI were lessened with both treatments. Various dietary formulations have been tried in attempts to lower the severity of HSMI, and some efforts have been made to select for fish with genetic variants which confer resistance. One method of disease prevention may be to disinfect the surface of fish eggs  prior to introduction to the farm, as removing PRV from a confined system after the fact requires rigorous disinfection, letting the system rest free of hosts, and thorough regular testing. Prevalence in aquaculture. PRV has been found to be most prevalent in Europe, and the Americas with relatively few reports in Asia. The prevalence of PRV varies greatly depending on the region and host species. PRV surveillance occurs most significantly in North America and Norway Europe: PRV-1 has been present in Norwegian farmed Atlantic Salmon since roughly 1988; within the rest of Europe, PRV is suspected to be common, but  reports in some countries remain limited. Iceland has reported finding high PRV-1 prevalence in its Atlantic salmon. In 2018, PRV-3 was reported at Brown Trout and Rainbow trout farms in Denmark and Germany. North America: PRV seems to exhibit high infectivity in North America, with a single infected fish often resulting in infection of a farms entire fish stock. PRV-1 tends to be initially detected following the return of farmed salmon from seawater. It’s likely that PRV-1 has been present in North America for decades, or possibly longer. South America: In Chile, farmed Atlantic salmon show high rates of  PRV-1 infection, while wild fish populations show low rates of infection. Rainbow trout show high rates of infection with PRV-1. Asia: Within Asia, PRV-2 has only been found in Japan and it has been linked to Erythrocytic Inclusion Body Syndrome (EIBS) in farmed Coho Salmon. Host range. PRV has been found in a range of aquacultured/wild host species such as: