Characterization of a Novel Orthomyxo-like Virus Causing Mass Die-Offs of Tilapia

Abstract

Tilapia are an important global food source due to their omnivorous diet, tolerance for high-density aquaculture, and relative disease resistance. Since 2009, tilapia aquaculture has been threatened by mass die-offs in farmed fish in Israel and Ecuador. Here we report evidence implicating a novel orthomyxo-like virus in these outbreaks. The tilapia lake virus (TiLV) has a 10-segment, negative-sense RNA genome. The largest segment, segment 1, contains an open reading frame with weak sequence homology to the influenza C virus PB1 subunit. The other nine segments showed no homology to other viruses but have conserved, complementary sequences at their 5′ and 3′ termini, consistent with the genome organization found in other orthomyxoviruses. In situ hybridization indicates TiLV replication and transcription at sites of pathology in the liver and central nervous system of tilapia with disease.

Detection of Tilapia Lake Virus in Clinical Samples by Culturing and Nested Reverse Transcription-PCR

“…This analysis revealed high sequence homology between the Israeli and Ecuadorian samples across the TiLV genome (4), and thus, all TiLV segments can be used as templates in RT-PCRs. The four primers used in our protocol are derived from segment 3 of the Israeli isolate of TiLV (4,10). Three primers (Nested ext-1, Nested ext-2, and ME1) fully match the sequences of TiLV obtained from 12 Ecuadorian samples.…”

“…Tilapia mortality, suspected of having a viral etiology, has also been described in Ecuador (11,12). Although variations in pathological presentation have been described (where lesions were focused in the central nervous system or in the liver, in Israel or Ecuador, respectively), sequencing the whole genome of TiLV revealed that tilapia in the two countries were infected with almost identical viruses (4). This analysis also revealed that this pathogen is a novel orthomyxo-like virus with a 10-segment negative-sense RNA genome (4).…”

“…Although variations in pathological presentation have been described (where lesions were focused in the central nervous system or in the liver, in Israel or Ecuador, respectively), sequencing the whole genome of TiLV revealed that tilapia in the two countries were infected with almost identical viruses (4). This analysis also revealed that this pathogen is a novel orthomyxo-like virus with a 10-segment negative-sense RNA genome (4). Segment 1 contains an open reading frame (ORF) with weak sequence homology to the polymerase subunit (PB1) of influenza C virus, while the other nine segments showed no homology to other viruses.…”

“…These assets render them most suitable for farming; indeed, tilapines are one of the most significant groups of farmed fish worldwide and serve as an important protein source, especially in developing countries (1)(2)(3)(4)(5)(6). Common ectoparasites and the few bacterial pathogens of tilapines are well controlled by pharmacotherapy.…”

Contribution of Next-Generation Sequencing to Aquatic and Fish Virology

“…Moreover, many studies have also targeted aquatic viruses essentially because of their devastating economic effects on aquaculture [13,14,15,16,17]. Indeed, the impact on the worldwide trade of some infected species, such as fishes or shrimps, has resulted in estimated losses of billions of US dollars [13,18]. Nevertheless, viruses also play a central role in ecological niches, in terms of the variety of infected hosts and nutrient/carbon cycling, further fostering research in this group.…”