Extensive Phylogenetic Analysis of Piscine Orthoreovirus Genomic Sequences Shows the Robustness of Subgenotype Classification

Abstract

Piscine orthoreovirus (PRV) belongs to the family Reoviridae and has been described mainly in association with salmonid infections. The genome of PRV consists of about 23,600 bp, with 10 segments of double-stranded RNA, classified as small (S1 to S4), medium (M1, M2 and M3) and large (L1, L2 and L3); these range approximately from 1000 bp (segment S4) to 4000 bp (segment L1). How the genetic variation among PRV strains affects the virulence for salmonids is still poorly understood. The aim of this study was to describe the molecular phylogeny of PRV based on an extensive sequence analysis of the S1 and M2 segments of PRV available in the GenBank database to date (May 2020). The analysis was extended to include new PRV sequences for S1 and M2 segments. In addition, subgenotype classifications were assigned to previously published unclassified sequences. It was concluded that the phylogenetic trees are consistent with the original classification using the PRV genomic segment S1, which differentiates PRV into two major genotypes, I and II, and each of these into two subgenotypes, designated as Ia and Ib, and IIa and IIb, respectively. Moreover, some clusters of country- and host-specific PRV subgenotypes were observed in the subset of sequences used. This work strengthens the subgenotype classification of PRV based on the S1 segment and can be used to enhance research on the virulence of PRV.

Genetic grouping and geographic distribution of Piscine orthoreovirus-1 (PRV-1) in farmed Atlantic salmon in Norway

“…Two groups were defined as high-virulent and two as low-virulent, whereas the remaining four groups were of unknown virulence. Previous phylogenetic studies have focused on nucleotide sequences, especially segment S1 [ 14 , 16 – 18 ], but also partly on whole genome analysis [ 19 , 28 ]. This has aided in description of the evolutionary relationships and geographical distribution of PRV-1.…”

“…Previous phylogenetic analyses of segment S1 cluster PRV-1 into two main monophyletic groups, which has been referred to as Ia and Ib [ 16 , 17 ]. However, the established classification of PRV-1 into Ia and Ib has important limitations with respect to virulence.…”

“…Thereafter, the virus isolates were grouped into genogroups (High, Low, Unknown) based on the combinations of the five segments compared to those of the reference isolates. The grouping on segment S1 in the present study into S1 (σ3) Group A or B correspond to Ia and Ib of the established classification system [ 16 , 17 ]. However, the classification of the present study takes into account the combination of all five segments linked to virulence which is the basis for the genogroups (High, Low, Unknown).…”

“…The genome segments sort into three groups: small (S1–S4), medium (M1–M3) and large (L1–L3) which encodes for at least 11 proteins; 8 structural, and 3 non-structural [ 7 ]. Segment S1 has been extensively used for phylogenetic analysis of PRV-1 [ 14 , 16 – 18 ]. Analysis of segment S1 groups PRV-1 into two main monophyletic clades, which has been referred to as sub-genotype Ia and Ib [ 16 , 17 ].…”

“…Segment S1 has been extensively used for phylogenetic analysis of PRV-1 [ 14 , 16 – 18 ]. Analysis of segment S1 groups PRV-1 into two main monophyletic clades, which has been referred to as sub-genotype Ia and Ib [ 16 , 17 ]. Other studies have reported four S1 groups (I–IV), where group I is consistent with Ib and group II, II and IV are comprised within Ia [ 14 , 18 ].…”