User:Babbo99/Piscine Orthoreovirus

My Sandbox for the Piscine reovirus project

Genomics
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.

Orthoreoviruses are made up of 10-12 segments typically, and are dsRNA icosahedral non enveloped.

This new species had segments L1-3, M1-3, S1-4 (10 total) S1 and S4 are polycistronic.

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).

There is equal separation between aquareoviridae and orthoreoviridae, suggesting that they are somewhere in between.

'''-For each segment, there is an identical and conserved 3' end sequence (UCAUC-3') to Orthoreoviridae and Aquareoviridae. The 5' end sequence (5'-GAUAAA/U) shows complete uniqueness within PRV.'''

Really good in-depth analysis of the PRV genome

Two-layered capsid.

Receptor-mediated endocytosis.

Lipid layer penetration by (UNKNOWN???)

Lambda-1 protein acts as a helicase/triphosphatase, lambda 2 as a guanylyltransferase and lambda 3 as RdRP

(-) Sense, so transcripts are both replicated & translated

Discovered p13, suggested that S2 and L2 may be bicistronic

S4 was determined to encode the PRV cell attachment protein sigma1

Argued that since syncytia aren't common in viral cells, likely no fusogenic protein exists.

PRV has 47% GC content in its genome which falls directly into the range of 44-48%, while aquareoviruses fall in the range of 52-60%.

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)

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

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 I a, while coho grouped in 1a or 1b

-Farmed Coho additionally grouped into subgenotype II.

-h

Suggested that PRV is more similar to orthoreoviridae on the basis of having 10 segments instead of 11 segments.

S1 is bicistronic, and has 2 overlapping ORF's

ORF1 has no homology to any of the ortho/aquareoviridae known.

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

The S4 region was not homologous to any other reoviridae.

Thought to have lacked an outer fiber protein characteristic in most orthoreoviridae before this paper.

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.

Predicted that the S4 segment encodes certain signature motifs that indicate it encodes for a fiber protein, the first for orthoreoviridae not to be in a polycistronic segment.

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.

Interesting article tracing the lineage between Orthoreoviridae and Aquareoviridae. May be good for sequence-specific information/protein differences.

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 subgenotypes Ia/Ib, and IIa and IIb, respectively   . These groupings are based on sequence diversity within segment S1.

Genotype I (PRV-1)

Ia-

Ib

Genotype 2

Genotype 2 was first discovered when comparing the S1 sequences among farmed Atlantic salmon in Chile

IIa (PRV-3)

Also known as PRV-3, this sub-genotype

IIb (PRV-2)

Also known as PRV-2, this sub-genotype