Revisiting the Classification of Percid Perhabdoviruses Using New Full-Length Genomes

Abstract

Perhabdoviruses are a threat to some freshwater fish species raised in aquaculture farms in Europe. Although the genetic diversity of these viruses is suspected to be high, the classification of isolates is still in its infancy, with just one full-length genome available and only partial sequences for a limited number of others. Here, we characterized a series of viruses isolated from percids in France from 1999 to 2009 by sequencing the nucleoprotein (N) gene. Four main clusters were distinguished, all related at varying levels of similarity to one of the two already-recognized species, namely Perch perhabdovirus and Sea trout perhabdovirus. Furthermore, we obtained the complete genome of five isolates, including one belonging to Sea trout rhabdovirus. The analysis of the complete L genes and the concatenated open reading frames confirmed the existence of four main genetic clusters, sharing 69 to 74% similarity. We propose the assignation of all these viral isolates into four species, including two new ones: Perch perhabdovirus 1, Perch perhabdovirus 2, Sea trout perhabdovirus 1 and Sea trout perhabdovirus 2. In addition, we developed new primers to readily amplify specific portions of the N gene of any isolate of each species by conventional PCR. The presence of such genetically diverse viruses in France is likely due to divergent viral populations maintained in the wild and then introduced to experimental facilities or farms, as well as via trade between farms across the European continent. It is now urgent to improve the identification tools for this large group of viruses to prevent their unchecked dissemination.

A New Lineage of Perch Rhabdovirus Associated with Mortalities of Farmed Perch

“…The present genetic data as well as amplification methods can contribute to the rapid and accurate identification of any new isolate in order to compare it with known isolates, which is crucial for tracing outbreaks. Due to the general lack of active surveillance in Europe, it is likely that known, and yet unknown, genotypes and species will emerge in the next decade [12]. Furthermore, given the host-switching capacity of these viruses and their frequent geographic translocations, the emergence of any of these viruses will likely affect various hosts-not only those already recognized (percids and non-percids), but also possibly new freshwater hosts that are increasingly farmed worldwide, such as tilapias.…”

“…In summary, using primers amplifying different regions of perhabdoviruses, a total of seven amplicons were obtained whose sequences led to the complete N and G ORFs. [12]. Note the different sizes of the amplicons for viruses 18-193 and 18-211 compared to virus 20-43.…”

“…For some viruses, additional small open reading frames (ORFs) are encoded, but there are no experimental data illustrating their expression or role in the molecular biology of the virus. The genus Perhabdovirus includes four viral species recognized by the International Committee on Taxonomy of Viruses (ICTV): Perhabdovirus anguilla represented by viruses infecting eels only (i.e., EVEX), Perhabdovirus perca (formerly Perch perhabdovirus) and Perhabdovirus trutta (formerly Sea trout perhabdovirus), both represented by diverse viruses infecting percids as well as a few other fish species (i.e., Sea trout rhabdovirus and virus R6146), and Perhabdovirus leman (including Leman rhabdovirus (LeRV)), described as virus 18-193 [12]. Genomic data have demonstrated the existence of four main genogroups infecting percids.…”

“…Considering this genetic diversity, four sets of primers have previously been designed, each one able to amplify a specific portion of the N gene of all the members of a given genogroup [12]. Although the specificity of these assays is not high enough for diagnostic tests, because they occasionally produce non-specific products, they are useful as an Nbased identification tool for any new isolate produced in cell culture or directly from infected fish.…”

Characterization of Novel Rhabdoviruses in Chinese Bats

“…The genome sequences of the six new rhabdoviruses (isolates 958, 1127, 1017, D170001, D170022, and D170190) were determined by next generation sequencing (NGS), as previously described [ 43 , 51 ]. Host rRNA depletion was carried out with the kit Terminator 5′-Phosphate-Dependent Exonuclease (Epicentre Biotechnologies, Madison, Wi, USA).…”