Characterization of ranaviruses isolated from lumpfish Cyclopterus lumpus L. in the North Atlantic area: proposal for a new ranavirus species (European North Atlantic Ranavirus).

The commercial production of lumpfish Cyclopterus lumpus L. is expanding with the increased demand for their use as cleaner fish, to control sea-lice numbers, at marine Atlantic salmon Salmo salar L. aquaculture sites throughout Northern Europe. A new ranavirus has been isolated from lumpfish at multiple locations in the North Atlantic area. First isolated in 2014 in the Faroe Islands, the virus has subsequently been found in lumpfish from Iceland in 2015 and from Scotland and Ireland in 2016. The Icelandic lumpfish ranavirus has been characterized by immunofluorescent antibody test, optimal growth conditions and transmission electron microscopy. Partial sequences of the major capsid protein gene from 12 isolates showed 99.79-100% nt identity between the lumpfish ranaviruses. Complete genome sequencing from three of the isolates and phylogenetic analysis based on the concatenated 26 iridovirus core genes suggest these lumpfish ranavirus isolates form a distinct clade with ranaviruses from cod Gadus morhua L. and turbot Scophthalmus maximus L. isolated in Denmark in 1979 and 1999, respectively. These data suggest that these viruses should be grouped together as a new ranavirus species, European North Atlantic Ranavirus, which encompasses ranaviruses isolated from marine fishes in European North Atlantic waters.

Genomic analysis of the host response to nervous necrosis virus in Atlantic cod (Gadus morhua) brain.

Genome sequencing combined with transcriptome profiling promotes exploration of defence against pathogens and discovery of immune genes. Based on sequences from the recently released genome of Atlantic cod, a genome-wide oligonucleotide microarray (ACIQ-1) was designed and used for analyses of gene expression in the brain during infection with nervous necrosis virus (NNV). A challenge experiment with NNV was performed with Atlantic cod juveniles and brain samples from virus infected and uninfected fish were used for microarray analysis. Expression of virus induced genes increased at 5 days post challenge and persisted at stable level to the last sampling at 25 days post challenge. A large fraction of the up-regulated genes (546 features) were known or expected to have immune functions and most of these have not previously been characterized in Atlantic cod. Transcriptomic changes induced by the virus involved strong activation of genes associated with interferon and tumour necrosis factor related responses and acute inflammation. Up-regulation of genes involved in adaptive immunity suggested a rapid recruitment of B and T lymphocytes to the NNV infected brain. QPCR analyses of 15 candidate genes of innate immunity showed rapid induction by poly(I:C) in Atlantic cod larvae cells suggesting an antiviral role. Earliest and greatest expression changes after poly I:C stimulation was observed for interferon regulatory factors IRF4 and IRF7. Comparative studies between teleost species provided new knowledge about the evolution of innate antiviral immunity in fish. A number of genes is present or responds to viruses only in fish. Innate immunity of Atlantic cod is characterized by selective expansion of several medium-sized multigene families with ribose binding domains. An interesting finding was the high representation of three large gene families among the early antiviral genes, including tripartite motif proteins (TRIM) and proteins with PRY-SPRY and NACHT domains. The latter two with respectively 52 and 114 members in Atlantic cod have gone through expansions in different groups of fish. These proteins most likely have ligand binding properties and their propagation could be linked to the loss of MHC class II in the Atlantic cod genome.

Dynamic expression profiles of virus-responsive and putative antimicrobial peptide-encoding transcripts during Atlantic cod (Gadus morhua) embryonic and early larval development.

Early life stage mortality is one of the problems faced by Atlantic cod aquaculture. However, our understanding of immunity in early life stage fish is still incomplete, and the information available is restricted to a few species. In the present work we investigated the expression of immune-relevant transcripts in Atlantic cod during early development. The transcripts subjected to QPCR analysis in the present study were previously identified as putative anti-viral or anti-bacterial genes in Atlantic cod using suppression subtractive hybridization (SSH) libraries, QPCR, and/or microarrays. Of the 11 genes involved in this study, only atf3, cxc chemokine and gaduscidin-1 were not detected at the transcript level in all developmental stages investigated from unfertilized egg to early larval stage. Adam22, hamp, il8, irf1, irf7, lgp2, sacsin, and stat1 transcripts were detected in unfertilized egg and 7h post-fertilization (~2-cell stage) embryos, showing maternal contribution of these immune-relevant transcripts to the early embryonic transcriptome. The Atlantic cod genes included in this study presented diverse transcript expression profiles throughout embryonic and early larval development. For example, adam22 and sacsin transcripts rose abruptly during blastula/gastrula stage and were then expressed at relatively high levels through subsequent embryonic and early larval developmental stages. A peak in irf1 and irf7 transcript expression during early segmentation suggests that these interferon pathway genes play developmental stage-specific roles during cod embryogenesis. Stat1 had increasing transcript expression throughout blastula/gastrula, segmentation, and early larval developmental stages. Atf3, cxc chemokine, gaduscidin-1, and il8 transcripts rose approximately 2-3 fold during hatching, supporting the hypothesis that there is preparation at the immune-relevant transcript expression level to deal with environmental pathogens that may be encountered during early larval development. The specific roles that interferon pathway and other immune-relevant genes play in early life stage cod, and the potential impact of their dynamic transcript expression on immune competence of Atlantic cod embryos and larvae, remain unclear and warrant further study.

Characterization of a novel alloherpesvirus from Atlantic cod (Gadus morhua).

Alloherpesviruses affect freshwater and marine fish species. The aim of the current study was to characterize a novel alloherpesvirus in Atlantic cod (Gadus morhua). Samples were processed for histopathology, transmission electron microscopy (TEM), virus isolation, molecular characterization, and in situ hybridization (ISH). Histopathology revealed that the infection was restricted to the gills and that it induced cytomegaly in infected cells. By TEM, numerous viral particles with morphology compatible with a herpesvirus were observed inside the cytomegalic cells. To characterize this new agent, polymerase chain reaction amplified regions of the ATPase subunit of the terminase, and DNA polymerase genes were sequenced. Phylogenetic analysis revealed strongest similarity with alloherpesviruses belonging to the genus Ictalurivirus and Salmonivirus. The ISH showed specific labeling of nuclear inclusions in the cytomegalic cells. While virus isolation was unsuccessful, the results obtained through different diagnostic tests in the present study confirm the discovery of a new alloherpesvirus affecting Atlantic cod. The authors propose the formal species designation Gadid herpesvirus 1 (GaHV-1) to be considered for approval by the International Committee on the Taxonomy of Viruses.

Comparative study of ranavirus isolates from cod (Gadus morhua) and turbot (Psetta maxima) with reference to other ranaviruses.

Two iridovirus isolates recovered from cod (Gadus morhua) and turbot (Psetta maxima) in Denmark were examined in parallel with a panel of other ranaviruses including frog virus 3 (FV3), the reference strain for the genus Ranavirus. The isolates were assessed according to their reactivity in immunofluoresent antibody tests (IFAT) using both homologous and heterologous antisera and their amplification in PCR using primers targeting five genomic regions. The corresponding PCR fragments were sequenced, and the sequences obtained were used in phylogenetic analysis. In addition, the pathogenicity to rainbow trout under experimental challenge conditions was investigated. The viruses were serologically and genetically closely related to highly pathogenic ranaviruses such as European catfish iridovirus (ECV), European sheatfish iridovirus (ESV) and epizootic haematopoietic necrosis virus (EHNV). The challenge trials indicate that rainbow trout fry cultured at 15 degrees C are not target species for the virus isolates in the present panel. We suggest that the two isolates belong in the genus Ranavirus and propose the name Ranavirus maxima (Rmax) for the turbot isolate.

Impact of asymptomatic nodavirus carrier state and intraperitoneal viral mimic injection on brain transcript expression in Atlantic cod (Gadus morhua).

Nodaviruses and other RNA viruses have a profoundly negative impact on the global aquaculture industry. Nodaviruses target nervous tissue causing viral nervous necrosis, a disease characterized by neurological damage, swimming abnormalities, and morbidity. This study used functional genomic techniques to study the Atlantic cod (Gadus morhua) brain transcript expression responses to asymptomatic high nodavirus carrier state and intraperitoneal injection of polyriboinosinic polyribocytidylic acid (pIC). Reciprocal suppression subtractive hybridization (SSH) cDNA libraries enriched for virus-responsive brain transcripts were constructed and characterized. We generated 1,938 expressed sequence tags (ESTs) from a forward brain SSH library (enriched for transcripts upregulated by nodavirus and/or pIC) and 1,980 ESTs from a reverse brain SSH library (enriched for transcripts downregulated by nodavirus and/or pIC). To examine the effect of nodavirus carrier state on individual brain gene expression in asymptomatic cod, 27 transcripts of interest were selected for quantitative reverse transcription-polymerase chain reaction (QPCR) studies. Transcripts found to be >10-fold upregulated in individuals with a high nodavirus carrier state relative to those in a no/low nodavirus carrier state were identified as ISG15, IL8, DHX58 (alias LGP2), ZNFX1, RSAD2 (alias viperin), and SACS (sacsin, alias spastic ataxia of Charlevoix-Saguenay). These and other SSH-identified transcripts were also found by QPCR to be significantly (P < 0.05) upregulated by pIC compared with saline-injected controls within 72 h of injection. Several transcripts identified in the reverse SSH library, including two putative ubiquitination pathway members (HERC4 and SUMO2), were found to be significantly (P < 0.05) downregulated in individuals with a high nodavirus carrier state. Our data shows that Atlantic cod brains have a strong interferon pathway response to asymptomatic high nodavirus carrier state and that many interferon pathway and other immune relevant transcripts are significantly induced in brain by both nodavirus and pIC.

Characterization and expression analyses of anti-apoptotic Bcl-2-like genes NR-13, Mcl-1, Bcl-X1, and Bcl-X2 in Atlantic cod (Gadus morhua).

NR-13, Mcl-1, and BCL-X(L), are conserved anti-apoptotic proteins that belong to the anti-apoptotic Bcl-2 sub-family, which inhibits cell death by preventing mitochondrial membrane permeabilization (MMP). Given the anti-apoptotic functions of these proteins in vertebrates (e.g. human, mouse, and zebrafish) and the involvement of apoptotic regulation in immune responses, we studied the sequences of these genes and their transcript expression in Atlantic cod (Gadus morhua) during innate immune responses to viral and bacterial stimuli. Based on previously generated Atlantic cod expressed sequence tags (ESTs), we identified partial cDNA sequences of putative orthologues of Atlantic cod NR-13, Mcl-1, and Bcl-X, and obtained the full-length cDNA, genomic, and promoter region sequences for these genes. The analyses of Atlantic cod cDNA sequences, and comparisons of the cod deduced amino acid sequences to putative orthologues in other species, revealed the presence of highly conserved Bcl-2 homology (BH) and transmembrane (TM) domains in the Atlantic cod sequences. Analysis of gene structure revealed conserved intron/exon boundaries within the coding regions of human and Atlantic cod putative orthologues. We found that an intron/exon boundary immediately following the codon for the 8th residue (tryptophan) of the BH2 domain exists in all anti-apoptotic Bcl-2 sub-family genes regardless of vast evolutionary distance. We also identified a non-coding exon in the Atlantic cod NR-13-like gene, which appears to be absent in its putative mammalian orthologues. Quantitative reverse transcription-polymerase chain reaction (QPCR) was used to study constitutive gene expression in six tissues (blood, brain, gill, head kidney, pyloric caecum, and spleen) of non-stressed juvenile cod; NR-13 and Bcl-X2 were most highly expressed in gill, whereas Mcl-1 and Bcl-X1 were most highly expressed in blood. In cod challenged with intraperitoneal (IP) injections of the viral mimic polyriboinosinic polyribocytidylic acid (pIC), (1) NR-13 mRNA expression was significantly up-regulated (compared to both 0h pre-injection and timed saline injected controls) in spleen at 6h post-injection and in head kidney at both 6 and 24h post-injection (HPI), and (2) both Mcl-1 and Bcl-X2 were significantly up-regulated (compared to both 0h pre-injection and timed saline injected controls) in spleen at 6 HPI. QPCR was used to show that, in cod challenged with IP injections of formalin-killed, atypical Aeromonas salmonicida (ASAL), only NR-13 appeared to be responsive (significantly up-regulated in spleen at 6 HPI compared to 0h pre-injection controls). Interestingly, QPCR showed that saline injection had a mild (less than 3-fold) but significant inductive effect (compared to 0h pre-injection controls) on both NR-13 and Mcl-1 transcript expression in spleen at 2 HPI. Although we only obtained partial cDNA and genomic sequences for Bcl-X2, sufficient evidence was accumulated to show that two Bcl-X paralogues exist in Atlantic cod, possibly due to the teleost-specific genome duplication event. Promoter regions for NR-13, Mcl-1, and Bcl-X1 were obtained and analyzed for the first time in fish, and potential regulatory sites (e.g. putative NF-kappaB binding sites) that were found in the promoter regions of NR-13 and Mcl-1 may account for their transcriptional activation by pIC.

Susceptibility of Atlantic cod Gadus morhua juveniles to different routes of experimental challenge with infectious pancreatic necrosis virus (IPNV).

Atlantic cod Gadus morhua L. juveniles weighing 40 g were challenged with infectious pancreatic necrosis virus (IPNV) by intraperitoneal (i.p.) or intramuscular (i.m.) injection or by bath. The amount of infectious virus was determined over 6 wk in head kidney, heart and pylorus tissues. No mortality or clinical signs were observed in either of the challenged groups. However, 6 wk after challenge virus was still present in the fish, which shows that IPNV can persist asymptomatically in cod. I.p. and i.m. injections were the most efficient routes of challenge giving the highest virus recovery. The prevalence of individuals with a viral titre > or = 500 infectious units g(-1) tissue was lower in the group of fish challenged by bath; thus bath was a less efficient route of challenge than injection. Our data also show that pylorus and head kidney are target organs for IPNV in cod, and levels of virus recovery were not considerably different between these 2 organs. Challenged by injection, the cod heart is also a target organ for IPNV. Compared to head kidney and pylorus, the heart seems to have a minor role in virus multiplication. Virus was also recovered from cohabiting fish, demonstrating that covertly infected cod may represent a reservoir of infectious IPNV for surrounding fish populations. Expression analysis of selected cod immune genes showed that i.p. injection of IPNV induced gene expression of ISG15 and LGP2, markers for the innate antiviral defence, while expression of markers for the inflammatory response (interleukins IL-1 beta, IL-8, IL-10) was not significantly increased.

Experimental study of the susceptibility of Atlantic cod, Gadus morhua (L.), to infection with an IPNV strain pathogenic for Atlantic salmon, Salmo salar L.

Intraperitoneal (IP) injection, cohabitation and immersion routes of infection were used to determine if Atlantic cod, Gadus morhua (L.), of 1 and 3 g are susceptible to infectious pancreatic necrosis (IPN). Mortalities of cod injected IP were significantly higher when challenged with infectious pancreatic necrosis virus (IPNV) than with phosphate buffered saline. This is the first report of Atlantic cod mortalities caused by IPNV. Fish challenged by cohabitation had significantly higher mortalities than the controls, but mortalities of Atlantic cod challenged with IPNV by immersion were not significantly different from controls. Titres of IPNV in the tissues of infected fish were sometimes very high (range 10(2)-10(10) infectious units per gram of tissue) suggesting virus replication and titres of fish that died were generally higher than those of fish which survived. However, the relatively low mortality rates when challenged by cohabitation and immersion (20% and 17%, respectively), compared to the IP injection challenge (100%) suggest that 1 and 3 g cod have low susceptibility to IPN when challenged by more natural routes. These data strongly suggest that the cause of death of experimentally challenged cod was IPNV and further histological evidence for this came from 1 g cod challenged IP with IPNV in which the pancreas showed severe necrosis and heavy immunostaining for IPNV coincidentally with the peak of mortalities.

Induction of Mx protein in Atlantic cod with poly I:C: immuno-cross reactive studies of antibodies to Atlantic salmon Mx with Atlantic cod.

A polyclonal rabbit antiserum directed against the conserved region of the Atlantic salmon antiviral Mx1 protein was used to detect the putative Atlantic cod Mx protein using Western and dot blotting. A doublet band at about 75 kDa and 65 kDa was detected by Western blotting in kidney and spleen extracts of cod 3 and 4 days after i.p. injection with poly I:C but not in control fish injected with PBS. In blood leucocyte lysates, similar immunostaining could also be detected in Atlantic cod weakly after injection with PBS and more intensely after injection with poly I:C, suggesting some constitutive expression of Mx protein by leucocytes. Dot blot analysis showed that the Mx protein level was significantly higher in spleen, kidney, liver and gill of cod at least up to 4 days after injection with poly I:C when compared with the PBS-injected controls.

New clade of betanodaviruses detected in wild and farmed cod (Gadus morhua) in Norway.

Betanodaviruses have been isolated and detected in both farmed and wild fish species worldwide. They are classified in five clusters, and all are connected to mortalities in farmed fish. The clusters do not represent specific geographical areas or host species, but one cluster, barfin flounder nervous necrosis virus (BFNNV), is mainly associated with cold water fish species. This study presents the first species-specific clade within the BFNNV cluster. This clade consists of six isolates from wild and farmed Atlantic cod in Norway and is genetically distinct from other betanodaviruses in the North Atlantic. Screening of farmed and wild cod in Norway shows that betanodaviruses are present in wild fish on the west coast of Norway, including migratory cod, but so far we have not detected any betanodavirus-positive wild cod in northern Norway. The presence of significant amounts of betanodaviruses in wild cod represents a serious challenge for the management of viral nervous necrosis in farmed cod in Norway. Betanodavirus-positive farmed cod were present both in western and northern Norway. Mortalities in three cod farms were suspected to be caused by betanodaviruses; however, in two of these, other pathogens may have been responsible for or strongly contributed to the mortalities.

Characterisation and expression analysis of the interleukin genes, IL-1beta, IL-8 and IL-10, in Atlantic cod (Gadus morhua L.).

The mammalian interleukins IL-1beta and IL-8 are important pro-inflammatory cytokines often used as markers of an activated inflammatory response, while IL-10 is regarded as an anti-inflammatory cytokine and plays a crucial role in the regulation of inflammation. Few cytokines from gadoid fish have been described, and herein the sequence and expression of these interleukin genes are studied in Atlantic cod (Gadus morhua L.). IL-1beta, IL-8 and IL-10 from cod show similarities in gene organisation and predicted protein sequences, compared to counterpart genes in other teleosts. Gene expression was studied using quantitative real time PCR in response to several treatments both in vitro and in vivo. In adherent head kidney cells, infectious pancreatic necrosis virus (IPNV) and lipopolysaccharide (LPS) significantly stimulated gene expression of IL-1beta. The expression of IL-1beta was not increased after treatment with a viral imitator (poly I:C), and neither IL-8 nor IL-10 responded to any of these agents in vitro. However, in vivo administrated poly I:C and formalin-killed Vibrio anguillarum (In-V.ang) induced interleukin expression, varying in intensity between different organs. IL-1beta and IL-10 gene expression profiles showed an opposite induction pattern in the in vivo experiments. Injection of In-V.ang highly induced IL-1beta expression, while a low induction was evident for IL-10, whereas the opposite was observed after injection of poly I:C. This pattern was particularly marked in spleen, where also IL-8 followed the expression pattern of IL-1beta. The opposite expression profiles indicate a suppressive role for IL-10 on the transcription of IL-1beta, and to a lesser extent on IL-8 transcription. Along with the identification of important promoter regulatory motives, these results provide tools for studying inflammatory responses in cod.

Nodavirus in farmed Atlantic cod Gadus morhua in Norway.

Viral encephalopathy and retinopathy (VER) was diagnosed in 5 to 24 g sized farmed Atlantic cod Gadus morhua kept in sea cages at Parisvatn, Hordaland county, on the west coast of Norway. Moderate mortality (10 to 15%) was observed, along with anorexia and abnormal swimming behaviour, such as looping or spiral swimming and reduced coordination. Nodavirus was detected by 2 different real-time RT-PCR assays, and this was later confirmed by immunohistochemistry. This is the first report of an outbreak of VER in farmed cod in Norway, and the first report that VER affect cod exceeding 5 g in size.

Studies on uptake and intracellular processing of infectious pancreatic necrosis virus by Atlantic cod scavenger endothelial cells.

Previous work in our group has identified the scavenger endothelial cells (SECs) of heart endocardium in cod, Gadus morhua L., as the major site for elimination of both physiological and foreign macromolecular waste from the circulation. The present study was undertaken to establish the role of cod SECs in the clearance of virus. We focused on infectious pancreatic necrosis virus (IPNV) as it is a well-known virus with a broad host range, and causes significant economic losses in the salmon industry. Our results showed that cod SEC cultures infected by the IPNV produce high titres of new virus. Ligand-receptor inhibition experiments suggested that the virus did not enter the cells through any of the major endocytosis receptors of cod SECs. Yet, the infection lowered the capacity of the cells to endocytose ligands via the scavenger receptor. Inhibitors of receptor recycling and vesicle acidification did not affect virus infectivity. The finding that SEC cultures prepared from 25% of the cod produced high titres of IPNV without being infected in the laboratory, suggests that SECs of cod may serve as reservoirs for IPNV in persistently infected cod.

Expression kinetics of ISG15 and viral major capsid protein (VP2) in Atlantic cod (Gadus morhua L.) fry following infection with infectious pancreatic necrosis virus (IPNV).

Atlantic cod fry (1g) were infected by intraperitoneal injection with IPNV and samples of liver were taken every second day from four fish up to day 21. Samples were analysed for levels of viral transcripts by real time RT-PCR and the induction of expression of interferon stimulated gene 15 (ISG15) transcripts were estimated by conventional RT-PCR relative to beta-actin. Mortality of over 40% occurred in infected groups between day 6 and 12 after infection. Levels of viral transcripts were low on day 1, rose on day 3, peaked on day 5 remaining high till day 13, and thereafter declined to low levels by day 21. The highest levels of viral transcripts, therefore, coincided with the onset and duration of mortality, but low levels persisted in surviving fish. ISG15 transcripts in control fish were detectable at low levels. Following infection with IPNV there was a marked increase in transcripts on day 3 and this level persisted up to day 21. This is the first report that IPNV induces the expression of the ISG15 gene in Atlantic cod.

Infectious salmon anaemia virus (ISAV) in experimentally challenged Atlantic cod (Gadus morhua).

Juvenile Atlantic cod, Gadus morhua, (6 g) were challenged with infectious salmon anaemia virus (ISAV) either by intraperitoneal (i.p.) injection or by cohabitation with ISA-diseased Atlantic salmon (Salmo salar). Samplings of cod were performed over a period of 45 days and various tissue samples were collected. The presence of ISAV RNA (segment 8) in samples was assessed by both conventional RT-PCR and a competitive quantitative real-time RT-PCR. In the i.p.-challenged group, ISAV RNA was detected in fish from all samplings, i.e. at days 7, 15, 21, 30 and 45 post-challenge. At day 7 post-challenge, all individual fish were positive, and so were the vast majority of individual tissue samples. At later samplings, the fraction of positive brain samples remained high (approximately 75%). In contrast, the positive fraction of other tissues/organs declined during the experiment. Analysis of positive brain samples by a quantitative real-time RT-PCR analysis showed that the level of ISAV RNA increased significantly (approximately 20 times) between days 7 and 30 post-challenge and remained high at day 45, indicating that a replication of ISAV had taken place. ISAV RNA was not detected in any control or cohabitation-challenged fish. No abnormal behaviour, clinical disease or, most notably, mortality was observed in any of the challenge or control groups.

Infectious pancreatic necrosis virus establishes an asymptomatic carrier state in kidney leucocytes of juvenile Atlantic cod, Gadus morhua L.

Juvenile Atlantic cod (10 g) were infected with infectious pancreatic necrosis virus (IPNV) by intraperitoneal injection and cohabitation. Fish showed no signs of disease but IPNV could be re-isolated from kidney tissue for up to 12 weeks. On weeks 2, 5, 8, 10, 11 and 12 following infection, kidney leucocytes were fractionated on Percoll gradients, and cells separated into plastic adherent and non-adherent cell populations after overnight incubation. IPNV was detectable in lysates of both cell populations and in supernatants by culture in CHSE-214 cells. Wells containing 10(5)-10(6) macrophages had an IPNV TCID(50) of about 10(3)/well and in serially diluted macrophages the minimum number of cells required to detect virus ranged from 10(1) to 10(4). These data indicate that about one in 10(4) macrophages were infected and the mean number of virus/infected cell was about 10. Replication of IPNV in the macrophages was low as the titre of the virus in macrophage lysates did not increase between days 1 and 3 of culturing the macrophages, but virus was released into the supernatant over this time.