Genomic Characterization and Phylogenetic Position of Two New Species in Rhabdoviridae Infecting the Parasitic Copepod, Salmon Louse (Lepeophtheirus salmonis)

Abstract

Several new viruses have emerged during farming of salmonids in the North Atlantic causing large losses to the industry. Still the blood feeding copepod parasite, Lepeophtheirus salmonis, remains the major challenge for the industry. Histological examinations of this parasite have revealed the presence of several virus-like particles including some with morphologies similar to rhabdoviruses. This study is the first description of the genome and target tissues of two new species of rhabdoviruses associated with pathology in the salmon louse. Salmon lice were collected at different Atlantic salmon (Salmo salar) farming sites on the west coast of Norway and prepared for histology, transmission electron microscopy and Illumina sequencing of the complete RNA extracted from these lice. The nearly complete genomes, around 11 600 nucleotides encoding the five typical rhabdovirus genes N, P, M, G and L, of two new species were obtained. The genome sequences, the putative protein sequences, and predicted transcription strategies for the two viruses are presented. Phylogenetic analyses of the putative N and L proteins indicated closest similarity to the Sigmavirus/Dimarhabdoviruses cluster, however, the genomes of both new viruses are significantly diverged with no close affinity to any of the existing rhabdovirus genera. In situ hybridization, targeting the N protein genes, showed that the viruses were present in the same glandular tissues as the observed rhabdovirus-like particles. Both viruses were present in all developmental stages of the salmon louse, and associated with necrosis of glandular tissues in adult lice. As the two viruses were present in eggs and free-living planktonic stages of the salmon louse vertical, transmission of the viruses are suggested. The tissues of the lice host, Atlantic salmon, with the exception of skin at the attachment site for the salmon louse chalimi stages, were negative for these two viruses.

Comparative paleovirological analysis of crustaceans identifies multiple widespread viral groups

“…4 ), suggesting that the two types of sequences originated from two distinct viral lineages. It is also noteworthy that the L. salmonis sequence clusters tightly with the two sequences of exogenous Rhabdoviruses reported in this same host species by Okland et al [ 19 ] (bootstrap value = 80), suggesting that it must result from a relatively recent endogenization event.…”

“…These viruses are relatively easy to detect because of the iridescent blue or red color of infected individuals [ 35 – 37 ]. Dunlap et al [ 38 ] also described a circovirus infecting two ecologically important copepod species, and two new species of rhabdoviruses were recently characterized in the salmon louse [ 19 ].…”

Taxonomy of the order Mononegavirales: update 2019

“…Genus Caligrhavirus was created to include three new species, Caligus caligrhavirus, Lepeophtheirus caligrhavirus, and Salmonlouse caligrhavirus for Caligus rogercresseyi rhabdovirus (CRoRV) detected in a copepod (Caligus rogercresseyi) [19], Lepeophtheirus salmonis rhabdovirus 127 (LSalRV-127), and Lepeophtheirus salmonis rhabdovirus 9 (LSalRV-9), both identified in salmon lice (Lepeophtheirus salmonis) [18], respectively (2018.002M.A.v1.Caligrhavirus). The genus Dichorhavirus was expanded by three species: Citrus chlorotic spot dichorhavirus, Citrus leprosis N dichorhavirus, and Clerodendrum chlorotic spot dichorhavirus for citrus chlorotic spot virus (CiCSV) discovered in sweet orange trees [7], citrus leprosis virus N (CiLV-N) also found in sweet orange trees [24], and Clerodendrum chlorotic spot virus (ClCSV) discovered in an ornamental plant (Clerodendrum sp.)…”

Effects of the vertically transmitted microsporidian Facilispora margolisi and the parasiticide emamectin benzoate on salmon lice (Lepeophtheirus salmonis)

“…However, the non-additive effects from combinations of microsporidia infection and parasiticide treatment merit further study. In addition to microsporidia, the salmon louse also hosts viruses [ 58 ] and bacteria [ 59 ] and the present observations indicate a need to better understand the possible influence of hyperparasitism with respect to copepod sensitivity to parasiticides as well as the confounding effects these infections may have on transcriptomic studies.…”