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

Overview

Journal Pathogens

Date 2021 Jan 12

PMID 33430212

Citations 5

Authors

Marcos Godoy

Daniel A Medina

Rudy Suarez

Sandro Valenzuela

Jaime Romero

Molly Kibenge

Yingwei Wang

Frederick Kibenge

Affiliations

Soon will be listed here.

Abstract

(PRV) belongs to the family 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.

Citing Articles

PRV-1 Virulence in Atlantic Salmon Is Affected by Host Genotype.

Polinski M, Gross L, Groman D, Alarcon M, Braceland M, Booman M Viruses. 2025; 17(2).

PMID: 40007040 PMC: 11860446. DOI: 10.3390/v17020285.

PRV-1b and PRV-3a infection is associated with the same clinical disease in coho salmon (Oncorhynchus kisutch) farmed in Chile: unraveling the pathogenesis of the orthoreoviral cardiomyopathy and hemolytic jaundice (OCHJ).

Rozas-Serri M, Ildefonso R, Pena A, Jaramillo V, Correa R, Barrientos S Vet Res. 2025; 56(1):17.

PMID: 39833914 PMC: 11748349. DOI: 10.1186/s13567-024-01435-2.

Detection, sequencing, and tissue distribution of piscine orthoreovirus 2-like virus in diseased coho salmon in Alaska.

Eckstrand C, Torrevillas B, Wolking R, Bradway D, Reno J, McMenamin-Snekvik K J Vet Diagn Invest. 2024; 36(3):338-345.

PMID: 38693675 PMC: 11110780. DOI: 10.1177/10406387241250119.

Analyses and Insights into Genetic Reassortment and Natural Selection as Key Drivers of Evolution.

Solarte-Murillo L, Reyes H, Ojeda L, Carcamo J, Pontigo J, Loncoman C Viruses. 2024; 16(4).

PMID: 38675898 PMC: 11053957. DOI: 10.3390/v16040556.

Sleeping With the Enemy? The Current Knowledge of Piscine Orthoreovirus (PRV) Immune Response Elicited to Counteract Infection.

Vallejos-Vidal E, Reyes-Lopez F, Sandino A, Imarai M Front Immunol. 2022; 13:768621.

PMID: 35464421 PMC: 9019227. DOI: 10.3389/fimmu.2022.768621.

References

Adamek M, Hellmann J, Flamm A, Teitge F, Vendramin N, Fey D . Detection of piscine orthoreoviruses (PRV-1 and PRV-3) in Atlantic salmon and rainbow trout farmed in Germany. Transbound Emerg Dis. 2018; 66(1):14-21. DOI: 10.1111/tbed.13018. View

Dhamotharan K, Tengs T, Wessel O, Braaen S, Nyman I, Hansen E . Evolution of the Genome Linked to Emergence of Heart and Skeletal Muscle Inflammation in Farmed Atlantic Salmon (). Viruses. 2019; 11(5). PMC: 6563308. DOI: 10.3390/v11050465. View

Pojezdal L, Adamek M, Syrova E, Steinhagen D, Minarova H, Papezikova I . Health Surveillance of Wild Brown Trout () in the Czech Republic Revealed a Coexistence of Proliferative Kidney Disease and Infection. Pathogens. 2020; 9(8). PMC: 7460431. DOI: 10.3390/pathogens9080604. View

Purcell M, Powers R, Evered J, Kerwin J, Meyers T, Stewart B . Molecular testing of adult Pacific salmon and trout (Oncorhynchus spp.) for several RNA viruses demonstrates widespread distribution of piscine orthoreovirus in Alaska and Washington. J Fish Dis. 2017; 41(2):347-355. DOI: 10.1111/jfd.12740. View

Kuehn R, Stoeckle B, Young M, Popp L, Taeubert J, Pfaffl M . Identification of a piscine reovirus-related pathogen in proliferative darkening syndrome (PDS) infected brown trout (Salmo trutta fario) using a next-generation technology detection pipeline. PLoS One. 2018; 13(10):e0206164. PMC: 6197672. DOI: 10.1371/journal.pone.0206164. View

Lovoll M, Alarcon M, Bang Jensen B, Taksdal T, Kristoffersen A, Tengs T . Quantification of piscine reovirus (PRV) at different stages of Atlantic salmon Salmo salar production. Dis Aquat Organ. 2012; 99(1):7-12. DOI: 10.3354/dao02451. View

Madhun A, Isachsen C, Omdal L, Einen A, Maehle S, Wennevik V . Prevalence of piscine orthoreovirus and salmonid alphavirus in sea-caught returning adult Atlantic salmon (Salmo salar L.) in northern Norway. J Fish Dis. 2018; 41(5):797-803. DOI: 10.1111/jfd.12785. View

Dhamotharan K, Vendramin N, Markussen T, Wessel O, Cuenca A, Nyman I . Molecular and Antigenic Characterization of Piscine orthoreovirus (PRV) from Rainbow Trout (Oncorhynchus mykiss). Viruses. 2018; 10(4). PMC: 5923464. DOI: 10.3390/v10040170. View

Wessel O, Olsen C, Rimstad E, Dahle M . Piscine orthoreovirus (PRV) replicates in Atlantic salmon (Salmo salar L.) erythrocytes ex vivo. Vet Res. 2015; 46:26. PMC: 4350956. DOI: 10.1186/s13567-015-0154-7. View

10.

Garver K, Marty G, Cockburn S, Richard J, Hawley L, Muller A . Piscine reovirus, but not Jaundice Syndrome, was transmissible to Chinook Salmon, Oncorhynchus tshawytscha (Walbaum), Sockeye Salmon, Oncorhynchus nerka (Walbaum), and Atlantic Salmon, Salmo salar L. J Fish Dis. 2015; 39(2):117-28. DOI: 10.1111/jfd.12329. View

11.

Godoy M, Kibenge M, Wang Y, Suarez R, Leiva C, Vallejos F . First description of clinical presentation of piscine orthoreovirus (PRV) infections in salmonid aquaculture in Chile and identification of a second genotype (Genotype II) of PRV. Virol J. 2016; 13:98. PMC: 4906990. DOI: 10.1186/s12985-016-0554-y. View

12.

Ferguson H, Kongtorp R, Taksdal T, Graham D, Falk K . An outbreak of disease resembling heart and skeletal muscle inflammation in Scottish farmed salmon, Salmo salar L., with observations on myocardial regeneration. J Fish Dis. 2005; 28(2):119-23. DOI: 10.1111/j.1365-2761.2004.00602.x. View

13.

LARKIN M, Blackshields G, Brown N, Chenna R, McGettigan P, McWilliam H . Clustal W and Clustal X version 2.0. Bioinformatics. 2007; 23(21):2947-8. DOI: 10.1093/bioinformatics/btm404. View

14.

Garseth A, Fritsvold C, Opheim M, Skjerve E, Biering E . Piscine reovirus (PRV) in wild Atlantic salmon, Salmo salar L., and sea-trout, Salmo trutta L., in Norway. J Fish Dis. 2012; 36(5):483-93. DOI: 10.1111/j.1365-2761.2012.01450.x. View

15.

Madhun A, Isachsen C, Omdal L, Bardsgjaere Einen A, Bjorn P, Nilsen R . Occurrence of salmonid alphavirus (SAV) and piscine orthoreovirus (PRV) infections in wild sea trout Salmo trutta in Norway. Dis Aquat Organ. 2016; 120(2):109-13. DOI: 10.3354/dao03009. View

16.

Notredame C, Higgins D, Heringa J . T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol. 2000; 302(1):205-17. DOI: 10.1006/jmbi.2000.4042. View

17.

Wiik-Nielsen C, Lovoll M, Sandlund N, Faller R, Wiik-Nielsen J, Bang Jensen B . First detection of piscine reovirus (PRV) in marine fish species. Dis Aquat Organ. 2012; 97(3):255-8. DOI: 10.3354/dao02425. View

18.

Yu G . Using ggtree to Visualize Data on Tree-Like Structures. Curr Protoc Bioinformatics. 2020; 69(1):e96. DOI: 10.1002/cpbi.96. View

19.

Kibenge F . Emerging viruses in aquaculture. Curr Opin Virol. 2019; 34:97-103. DOI: 10.1016/j.coviro.2018.12.008. View

20.

Wessel O, Braaen S, Alarcon M, Haatveit H, Roos N, Markussen T . Infection with purified Piscine orthoreovirus demonstrates a causal relationship with heart and skeletal muscle inflammation in Atlantic salmon. PLoS One. 2017; 12(8):e0183781. PMC: 5571969. DOI: 10.1371/journal.pone.0183781. View