User:Babbo99/Piscine Orthoreovirusedits

Piscine orthoreovirus (PRV) is an Orthoreovirus genus which infects a variety of fish species, and has been found present at higher concentration in fish with various diseases. These diseases include heart and skeletal muscle inflammation (HSMI), jaundice syndrome, proliferative darkening syndrome, 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 pathogenic, specifically with respect to HSMI, has not been unanimously agreed upon. PRV has been in the public eye mostly due to high presence in farmed Atlantic Salmon exhibiting HSMI. Public concern has been raised about the possibility of PRV in open ocean farms transmitting to wild populations, being a factor in the decline of wild salmon in areas such as the Pacific Northwest.

Article about the decline of salmon in british columbia

This article classified PRV, and then did the original histopathology studies on HSMI salmon. It found viral levels much higher in salmon exhibiting HSMI, suggesting a correlation.

Sigma one & sigma 3 sequences were completely distinct to orthoreoviridae/ aquareoviridae in this study, which led to the phylogenetic tree branching off of the last common ancestor of these two (a separate family).

Really good in-depth analysis of the PRV genome

• The homologous proteins for L2 in MRV and ARV are guanyltransferases and methyltransferases. Although not entirely conserved, the active regions of L2 are mostly conserved, suggesting this is the turret protein, and plays a similar role in the 5' capping of transcribed viral mRNA.

This article characterized the genome of PRV in Canadian and Chilean salmon phylogenetically.

• They characterized the reading frames, and then proceeded to classify the PRV in Norway, Canada and Chile as genotype 1, and strain 1a or 1b (Based on their S1 sequences)

• Because PRV has 10 segments and not 11, it is more similar to orthoreoviridae and not aquareoviridae.
  
• Genomic analysis also suggested that the virus originated in Norway, and has evolved into subgenotypes 1a and 1b, based on the nucleotide sequences produced by their S1 segments. The Canadian and Chilean strains matched to 1a and 1b respectively, which they suggested meant an origin in Norway and introduction to Canada and Chile in recent years.
• S1 is bicistronic, but S4 is not.

• Salmon in Canada and Norway were divergent in S1/S4

Overview of PRV genotypes and sub genotype phylogeny, and what type of fish have been found in each.

Studied genomes in Northwest Pacific and Northwest Atlantic. Showed that PRV in Pacific originated in the Atlantic. In terms of whether or not PRV was evolving differently between farmed Atlantic and wild pacific, they found no evidence.

Great overview of current distribution/genomic data in the introduction.

Discovery of a new subtype in Japan, in Coho salmon (Subgenotypes as well)

• Analyzed S1 and λ3 to determine that a new type of PRV was present in salmon.

Discovery of other subtypes

• -Found a new subtype in brown trout frequenting river systems in Central Europe. This subtype was detected in salmon exhibiting proliferative darkening syndrome (PDS)

Proposed standardized naming system for reoviridae proteins

Article for the function of mu-NS

Article that categorized the genotypes of PRV into 4 different types

Article that differentiated subgenotype 2

• Chilean Atlantic Salmon grouped as Ia, while coho grouped in 1a or 1b

• Farmed Coho additionally grouped into subgenotype II.

Proof that piscine reovirus is non-fusogenic, also good for the function of specific segments.

• No homologues were identified for the clamp proteins found in both aquareoviridae and orthoreoviridae originally.

• This study argued that because they found what appeared to be a fiber protein encoded in PRV, it was more closely related to orthoreoviridae,

• This study also found that the sequences of the 9 homologous protein regions aligned closer to orthoreoviridae than aquareoviridae.
• S1 ORF1 is a clamp protein sequence and S1 ORF2 is p13. What is p13?
• What is the overall structure of the virus genome?
• Piscine reovirus has a segmented dsRNA genome made up of 10 individual linear segments, cumulatively measuring around 23,600bp.
• These segments are referred to as Long L1-3, Medium M 1-3 and Short S1-4 in order of decreasing length, with L1 being 4000bp and S4 being 1000bp.

Article on each subgenotype found to date.

M2 segment diversity comparison revealed even more robust divergence between I and II

80.1% sequence similarity observed with PRV-1

Article against PRV causing disease in BC salmon

What does each segment do?

The 10 segments encode 11 proteins in total. S1 exhibits bicistronicity with 2 overlapping open reading frames. The proteins that each segment encodes for are as follows, using a standardized naming system across reovirus genera

• L1-λ3 - Shell Protein
• L2-λ2 -Turret Protein
• L3-λ1 -RdRP
• M1-μ2 -NTPase
• M2-μ1 - Outer Capsid Protein
• M3-μNS, unknown function.
• S1-σ3, Outer clamp protein
• p13, Cytotoxic nonstructural protein.
• S2-σ2 Core Clamp Protein
• S3-σNS, unknown function.
• S4-σ1 Viral attachment Protein

How has it varied?

Piscine reovirus 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 it into 2 genotypes, I and II, which further divide sub genotypes Ia/Ib, and IIa and IIb, respectively. These groupings are based on sequence diversity within segment S1.

Genotype I (PRV-1)

Ia- This subgenotype 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 showing HSMI like symptoms in Chile and Canada.

Ib- This subgenotype of PRV is found primarily in farmed Atlantic salmon in Norway and Chile, additonally being found in farmed Rainbow trout in Chile.

Genotype 2

Genotype 2 was first discovered when comparing the S1 sequences among farmed Atlantic salmon in Chile, and further reiterated with both M2 and whole genome analysis

IIa (PRV-3)

Also known as PRV-3, this sub-genotype has been found in farmed Coho Salmon, Brown trout and Rainbow trout exhibiting HSMI-like symptoms across Northern Europe and Chile. It has also been found in wild Brown trout with proliferative darkening syndrome in northern Europe.

IIb (PRV-2)

Also known as PRV-2, this sub-genotype has only been found in farmed Coho salmon in Japan exhibiting Erythrocytic Inclusion Body Syndrome (EIBS).

It has been found that PRV 1 has been around for decades and because of that, it has the most diverse phylogenetic landscape of PRV in North America. Within the subtypes, PRV 1a and 1b, there seems to be distinct variation between the S1 and M2 segments. It has been speculated that there have been specific alterations between the S1 and M2 segments of PRV 1b. Both have been found to cause HSMI in Atlantic Salmon and a HSMI-like disease in Rainbow trout and Coho salmon. In Canada, PRV-1a has been found to cause Jaundice disease in Chinook salmon.