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1.
Viruses ; 14(2)2022 02 06.
Article in English | MEDLINE | ID: mdl-35215924

ABSTRACT

The production of the aquaculture industry has increased to be equal to that of the world fisheries in recent years. However, aquaculture production faces threats such as infectious diseases. Betanodaviruses induce a neurological disease that affects fish species worldwide and is caused by nervous necrosis virus (NNV). NNV has a nude capsid protecting a bipartite RNA genome that consists of molecules RNA1 and RNA2. Four NNV strains distributed worldwide are discriminated according to sequence homology of the capsid protein encoded by RNA2. Since its first description over 30 years ago, the virus has expanded and reassortant strains have appeared. Preventive treatments prioritize the RGNNV (red-spotted grouper nervous necrosis virus) strain that has the highest optimum temperature for replication and the broadest range of susceptible species. There is strong concern about the spreading of NNV in the mariculture industry through contaminated diet. To surveil natural reservoirs of NNV in the western Mediterranean Sea, we collected invertebrate species in 2015 in the Alboran Sea. We report the detection of the RGNNV strain in two species of cephalopod mollusks (Alloteuthis media and Abralia veranyi), and in one decapod crustacean (Plesionika heterocarpus). According to RNA2 sequences obtained from invertebrate species and reported to date in the Mediterranean Sea, the strain RGNNV is predominant in this semienclosed sea. Neither an ecosystem- nor host-driven distribution of RGNNV were observed in the Mediterranean basin.


Subject(s)
Decapodiformes/virology , Disease Reservoirs/veterinary , Nodaviridae/isolation & purification , Pandalidae/virology , Animals , Disease Reservoirs/virology , Fishes/classification , Fishes/virology , Genome, Viral/genetics , Mediterranean Sea , Nodaviridae/classification , Nodaviridae/genetics , Phylogeny , RNA, Viral/genetics , Shellfish/classification , Shellfish/virology
2.
Viruses ; 13(4)2021 04 08.
Article in English | MEDLINE | ID: mdl-33917662

ABSTRACT

Cross-species transmission of emerging viruses happens occasionally due to epidemiological, biological, and ecological factors, and it has caused more concern recently. Covert mortality nodavirus (CMNV) was revealed to be a unique shrimp virus that could cross species barrier to infect vertebrate fish. In the present study, CMNV reverse transcription-nested PCR (RT-nPCR)-positive samples were identified from farmed sea cucumber (Apostichopus japonicas) in the CMNV host range investigation. The amplicons of RT-nPCR from sea cucumber were sequenced, and its sequences showed 100% identity with the RNA-dependent RNA polymerase gene of the original CMNV isolate. Histopathological analysis revealed pathologic changes, including karyopyknosis and vacuolation of the epithelial cells, in the sea cucumber intestinal tissue. The extensive positive hybridization signals with CMNV probe were shown in the damaged epithelial cells in the in situ hybridization assay. Meanwhile, transmission electron microscopy analysis revealed CMNV-like virus particles in the intestine epithelium. All the results indicated that the sea cucumber, an Echinodermata, is a new host of CMNV. This study supplied further evidence of the wide host range of CMNV and also reminded us to pay close attention to its potential risk to threaten different aquaculture animal species.


Subject(s)
Host Specificity , Nodaviridae/genetics , RNA Virus Infections/veterinary , Sea Cucumbers/virology , Animals , Aquaculture , In Situ Hybridization , Nodaviridae/classification , Nodaviridae/isolation & purification , Nodaviridae/pathogenicity , Phylogeny , RNA Virus Infections/virology
3.
Viruses ; 13(1)2021 Jan 07.
Article in English | MEDLINE | ID: mdl-33430224

ABSTRACT

Nodaviruses are small bisegmented RNA viruses belonging to the family Nodaviridae. Nodaviruses have been identified in different hosts, including insects, fishes, shrimps, prawns, dogs, and bats. A novel porcine nodavirus was first identified in the United States by applying next-generation sequencing on brain tissues of pigs with neurological signs, including uncontrollable shaking. RNA1 of the porcine nodavirus had the highest nucleotide identity (51.1%) to the Flock House virus, whereas its RNA2 shared the highest nucleotide identity (48%) with the RNA2 segment of caninovirus (Canine nodavirus). Genetic characterization classified porcine nodavirus as a new species under the genus Alphanodavirus. Further studies are needed to understand the pathogenicity and clinical impacts of this virus.


Subject(s)
Nodaviridae/genetics , Nodaviridae/isolation & purification , RNA Virus Infections/veterinary , RNA, Viral/genetics , Swine Diseases/virology , Amino Acid Sequence , Animals , Base Sequence , Capsid Proteins/genetics , Genomics , Nodaviridae/classification , Phylogeny , Swine/virology , United States
4.
Virus Res ; 286: 198092, 2020 09.
Article in English | MEDLINE | ID: mdl-32659308

ABSTRACT

The prevalence of covert mortality nodavirus (CMNV) has become one of the major threats to the shrimp farming industry in Asia and South America recently. Here, the genomic RNA1 and RNA2 of CMNV were characterized by using transcriptome sequencing and RT-PCR. Our study revealed that RNA1 is 3228 bp in length, and contains two putative Open Reading Frames (ORFs), one encoding the RNA dependent RNA polymerase (RdRp) of length 1043 amino acids and another encoding the protein B2 with a length of 132 amino acids. RNA2 is 1448 bp in length and encodes a capsid protein of 437 amino acids. CMNV shared the highest similarity of 51.78 % for RdRp with the other known nodaviruses. Phylogenetic analyses on the basis of RdRp, B2 and capsid proteins indicated that CMNV might represent a novel viral species in the family Nodaviridae. This study reported the first genome sequence of CMNV and it would be helpful for further studies of CMNV in relation to its evolution, diagnostic technique and control strategy.


Subject(s)
Genome, Viral , Nodaviridae/classification , Nodaviridae/genetics , Penaeidae/virology , Phylogeny , RNA, Viral/genetics , Animals , Aquaculture , Genomics , Nodaviridae/isolation & purification , Open Reading Frames
5.
Viruses ; 12(4)2020 04 10.
Article in English | MEDLINE | ID: mdl-32290177

ABSTRACT

Viruses are among the most abundant and diverse biological components in the marine environment. In finfish, viruses are key drivers of host diversity and population dynamics, and therefore, their effect on the marine environment is far-reaching. Viral encephalopathy and retinopathy (VER) is a disease caused by the marine nervous necrosis virus (NNV), which is recognized as one of the main infectious threats for marine aquaculture worldwide. For over 140 years, the Suez Canal has acted as a conduit for the invasion of Red Sea marine species into the Mediterranean Sea. In 2016-2017, we evaluated the prevalence of NNV in two indigenous Mediterranean species, the round sardinella (Sardinella aurita) and the white steenbras (Lithognathus mormyrus) versus two Lessepsian species, the Randall's threadfin bream (Nemipterus randalli) and the Lessepsian lizardfish (Saurida lessepsianus). A molecular method was used to detect NNV in all four fish species tested. In N. randalli, a relatively newly established invasive species in the Mediterranean Sea, the prevalence was significantly higher than in both indigenous species. In S. lessepsianus, prevalence varied considerably between years. While the factors that influence the effective establishment of invasive species are poorly understood, we suggest that the susceptibility of a given invasive fish species to locally acquired viral pathogens such as NVV may be important, in terms of both its successful establishment in its newly adopted environment and its role as a reservoir 'host' in the new area.


Subject(s)
Fish Diseases/virology , Fishes/virology , Nodaviridae/classification , Nodaviridae/physiology , Animals , Mediterranean Sea , Phylogeny , RNA, Viral
6.
J Fish Dis ; 42(12): 1773-1783, 2019 Dec.
Article in English | MEDLINE | ID: mdl-31637759

ABSTRACT

Betanodaviruses are small ssRNA viruses that cause viral encephalopathy and retinopathy, a severe neuropathological infectious disease in marine fish species worldwide. In the present study, the occurrence of betanodaviruses was investigated in wild and cultured populations of fishes and invertebrates of the Greek territorial waters. Betanodaviruses were detected in 35 species belonging to 21 families and 12 orders. To our knowledge, 23 of those are reported for the first time in Greek waters, while 11 of them are reported for the first time globally. The positive samples were subjected to sequencing and phylogenetic analysis of partial segments of RNA1 and RNA2 genes. Almost all the viruses circulating in Greece fell within RGNNV genotype, while reassortant viruses were detected in three samples, namely two inter-RGNNV and one RGNNV/SJNNV. A novel unclassified Betanodavirus sequence was also identified. Most of the Greek sequence types have a restricted geographic distribution except for two RNA1 and one RNA2 sequence types that are widespread throughout the Mediterranean basin. The results of this study indicate the range of reservoirs/hosts of betanodaviruses and also their wide spread in the Greek territorial waters and reinforce the hypothesis that wild fish species transmit the virus to cultured ones and vice versa.


Subject(s)
Fishes/virology , Invertebrates/virology , Nodaviridae/classification , Animals , Fish Diseases/virology , Genotype , Greece , Phylogeny , RNA Virus Infections/veterinary , RNA Virus Infections/virology , RNA, Viral/genetics , Reassortant Viruses
7.
J Virol ; 93(21)2019 11 01.
Article in English | MEDLINE | ID: mdl-31434736

ABSTRACT

Three RNA viruses related to nodaviruses were previously described to naturally infect the nematode Caenorhabditis elegans and its relative, Caenorhabditis briggsae Here, we report on a collection of more than 50 viral variants from wild-caught Caenorhabditis. We describe the discovery of a new related virus, the Melník virus, infecting C. briggsae, which similarly infects intestinal cells. In France, a frequent pattern of coinfection of C. briggsae by the Santeuil virus and Le Blanc virus was observed at the level of an individual nematode and even a single cell. We do not find evidence of reassortment between the RNA1 and RNA2 molecules of Santeuil and Le Blanc viruses. However, by studying patterns of evolution of each virus, reassortments of RNA1 and RNA2 among variants of each virus were identified. We develop assays to test the relative infectivity and competitive ability of the viral variants and detect an interaction between host genotype and Santeuil virus genotype, such that the result depends on the host strain.IMPORTANCE The roundworm Caenorhabditis elegans is a laboratory model organism in biology. We study natural populations of this small animal and its relative, C. briggsae, and the viruses that infect them. We previously discovered three RNA viruses related to nodaviruses and here describe a fourth one, called the Melník virus. These viruses have a genome composed of two RNA molecules. We find that two viruses may infect the same animal and the same cell. The two RNA molecules may be exchanged between variants of a given viral species. We study the diversity of each viral species and devise an assay of their infectivity and competitive ability. Using this assay, we show that the outcome of the competition also depends on the host.


Subject(s)
Caenorhabditis/virology , Genetic Speciation , Genetic Variation , Nodaviridae/classification , Nodaviridae/pathogenicity , RNA Virus Infections/virology , Sympatry , Animals , Caenorhabditis/classification , Genome, Viral , Host-Pathogen Interactions , Phylogeny , Species Specificity
8.
Fish Shellfish Immunol ; 85: 85-89, 2019 Feb.
Article in English | MEDLINE | ID: mdl-29056488

ABSTRACT

Viral encephalopathy and retinopathy (VER) is a severe infective disease characterized by neuropathological changes in several fish species associated with high mortality. The etiological agent is a virus belonging to the Nodaviridae family, genus Betanodavirus. To date, four different betanodavirus species have been officially recognized by International Committee on Taxonomy of Viruses (ICTV), namely the red-spotted grouper- (RGNNV), the striped jack- (SJNNV), the barfin flounder- (BFNNV) and the tiger puffer nervous necrosis virus (TPNNV). Moreover, two reassortants RGNNV/SJNNV and SJNNV/RGNNV have been described. Betanodaviruses can be classified into three different serotypes (A, B and C) that are antigenically different, so none (between serotype A and C) or partial (between serotype B and C) cross-immunoreactivity has been detected in vitro. In this study we investigated the in vivo cross-protection of the two main betanodavirus species (RGNNV and SJNNV), which belong to distinct serotype, by immunizing intraperitoneally (IP) juvenile sea bass with formalin inactivated RGNNV and SJNNV vaccines, followed by a challenge with RGNNV. Fish IP vaccinated with inactivated RGNNV showed a high protection value (85%). Serological analyses highlighted a great specific anti-NNV immunoglobulin M (IgM) production against the homologous virus, while a good seroconversion with low neutralization property was highlighted against the heterologous virus. In fish IP vaccinated with inactivated SJNNV the protection recorded was equal to 25%, significantly lower respect to the one provided by RGNNV IP vaccine. ELISA test detected good IgM production against the homologous virus, and a lower, but still detectable IgM production against the heterologous one. By contrast, serum neutralization test highlighted a poorly detectable antibody production unable to neutralize either the homologous or the heterologous virus. These results confirm that the two serotypes are not cross-protective in vivo. According to these findings, the production of multivalent formulation, or at least the provision of different types of vaccines based on both fish and virus species requirement, should be recommended in order to broaden the range of protection.


Subject(s)
Bass , Cross Protection/immunology , Fish Diseases/prevention & control , Nodaviridae/immunology , RNA Virus Infections/veterinary , Vaccination/veterinary , Animals , Fish Diseases/immunology , Fish Diseases/virology , Injections, Intraperitoneal/veterinary , Nodaviridae/classification , RNA Virus Infections/immunology , RNA Virus Infections/prevention & control , RNA Virus Infections/virology
9.
J Gen Virol ; 100(2): 166-175, 2019 02.
Article in English | MEDLINE | ID: mdl-30461374

ABSTRACT

Interspecies transmission of viruses, where a pathogen crosses species barriers and jumps from its original host into a novel species, has been receiving increasing attention. Viral covert mortality disease, caused by covert mortality nodavirus (CMNV), is an emerging disease that has recently had a substantial impact on shrimp aquaculture in Southeast Asia and Latin America. While investigating the host range of CMNV, we found that this virus is also capable of infecting populations of the farmed Japanese flounder Paralichthys olivaceus, a vertebrate host. The infected fish were being raised in aquaculture facilities that were also producing marine shrimp. Through RT-nPCR, targeting the RNA-dependent RNA polymerase (RdRp) gene of CMNV, we found that 29 % of the fish sampled were positive. The amplicons were sequenced and aligned to the RdRp gene of shrimp CMNV and were found to have 98 % identity. Histopathological examination indicated that CMNV-positive fish showed vacuolation of nervous tissue in the eye and brain, as well as extensive necrosis of cardiac muscle. In situ hybridization showed positive reactions in tissues of the eye, brain, heart, liver, spleen and kidney of infected fish. Transmission electron microscopy showed the presence of CMNV-like particles in all of the above-mentioned tissues, except for brain. The novel finding of a shrimp alphanodavirus that can also infect farmed P. olivaceus indicates that this virus is capable of naturally crossing the species barrier and infecting another vertebrate. This finding will contribute to the development of efficient strategies for disease management in aquaculture.


Subject(s)
Fish Diseases/virology , Flounder/virology , Nodaviridae/isolation & purification , RNA Virus Infections/veterinary , Animal Structures/pathology , Animal Structures/virology , Animals , Aquaculture , Asia, Southeastern , Histocytochemistry , Host Specificity , Latin America , Nodaviridae/classification , Nodaviridae/genetics , Nodaviridae/growth & development , Penaeidae/virology , RNA Virus Infections/virology , RNA, Viral/genetics , Sequence Analysis, DNA , Sequence Homology
10.
J Gen Virol ; 100(1): 3-4, 2019 01.
Article in English | MEDLINE | ID: mdl-30431412

ABSTRACT

The family Nodaviridae includes two genera, Alphanodavirus and Betanodavirus. The family name derives from the Japanese village of Nodamura where Nodamura virus was first isolated from Culex tritaeniorhynchus mosquitoes. Virions are non-enveloped and spherical in shape with icosahedral symmetry (T=3) and diameters ranging from 25 to 33 nm. The genome consists of two molecules of single-stranded positive-sense RNA: RNA1 and RNA2. The virion capsid consists of 180 protein subunits arranged on a T=3 surface lattice. Alphanodaviruses infect insects, whereas betanodaviruses are pathogens of fish. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Nodaviridae, which is available at www.ictv.global/report/nodaviridae.


Subject(s)
Nodaviridae/classification , RNA, Viral/genetics , Viral Proteins/analysis , Virion/ultrastructure , Animals , Fishes/virology , Insecta/virology , Nodaviridae/genetics , Nodaviridae/isolation & purification , Nodaviridae/ultrastructure
11.
PLoS Biol ; 16(10): e3000038, 2018 10.
Article in English | MEDLINE | ID: mdl-30346944

ABSTRACT

Macrobrachium rosenbergii nodavirus (MrNV) is a pathogen of freshwater prawns that poses a threat to food security and causes significant economic losses in the aquaculture industries of many developing nations. A detailed understanding of the MrNV virion structure will inform the development of strategies to control outbreaks. The MrNV capsid has also been engineered to display heterologous antigens, and thus knowledge of its atomic resolution structure will benefit efforts to develop tools based on this platform. Here, we present an atomic-resolution model of the MrNV capsid protein (CP), calculated by cryogenic electron microscopy (cryoEM) of MrNV virus-like particles (VLPs) produced in insect cells, and three-dimensional (3D) image reconstruction at 3.3 Å resolution. CryoEM of MrNV virions purified from infected freshwater prawn post-larvae yielded a 6.6 Å resolution structure, confirming the biological relevance of the VLP structure. Our data revealed that unlike other known nodavirus structures, which have been shown to assemble capsids having trimeric spikes, MrNV assembles a T = 3 capsid with dimeric spikes. We also found a number of surprising similarities between the MrNV capsid structure and that of the Tombusviridae: 1) an extensive network of N-terminal arms (NTAs) lines the capsid interior, forming long-range interactions to lace together asymmetric units; 2) the capsid shell is stabilised by 3 pairs of Ca2+ ions in each asymmetric unit; 3) the protruding spike domain exhibits a very similar fold to that seen in the spikes of the tombusviruses. These structural similarities raise questions concerning the taxonomic classification of MrNV.


Subject(s)
Nodaviridae/ultrastructure , Palaemonidae/virology , Animals , Capsid Proteins/chemistry , Capsid Proteins/genetics , Capsid Proteins/ultrastructure , Cryoelectron Microscopy , Imaging, Three-Dimensional , Models, Molecular , Nodaviridae/classification , Nodaviridae/pathogenicity , Protein Interaction Domains and Motifs , Protein Structure, Quaternary , Species Specificity , Tombusviridae/classification , Tombusviridae/ultrastructure , Virion/ultrastructure , Virus Assembly
12.
J Fish Dis ; 41(2): 233-246, 2018 Feb.
Article in English | MEDLINE | ID: mdl-29027679

ABSTRACT

Using two serially executed PCRs, the discriminative multiplex two-step RT-PCR (DMT-2 RT-PCR) following the detection seminested two-step RT-PCR (DSN-2 RT-PCR), we found a high frequency presence of BFNNV genotype as well as RGNNV in various domestic and imported shellfish. This was definitely different from the previous reports of outbreaks and asymptomatic infection only by the RGNNV genotype in cultured finfish in Korea. Cultivation of NNV entrapped in shellfish was performed successfully by a blind passage. Thus, in an attempt to elucidate the epidemiology of betanodavirus, experiments conducted on 969 shellfish samples concluded that (i) distribution of NNV genotype, especially BFNNV, in shellfish is clearly different from that found in finfish of the world; (ii) unlike RGNNV, which showed a high rate in summer, BFNNV showed no seasonal variation and this result suggests BFNNVs in the marine environment remain fairly constant throughout the year; and (iii) the entrapped virus in shellfish was alive and culturable in vitro. These results are the first report of high level prevalence of in vitro culturable NNV in shellfish, for both BFNNV and RGNNV, which may present a potential risk in transmitting nodaviruses to host species in a marine environment.


Subject(s)
Bivalvia/virology , Nodaviridae/physiology , Animals , Nodaviridae/classification , Nodaviridae/genetics , Phylogeny , RNA, Viral , Republic of Korea
13.
J Fish Dis ; 41(4): 603-611, 2018 Apr.
Article in English | MEDLINE | ID: mdl-29205402

ABSTRACT

Betanodaviruses are small ssRNA viruses responsible for viral encephalopathy and retinopathy, otherwise known as viral nervous necrosis, in marine fish worldwide. These viruses can be either horizontally or vertically transmitted and have been sporadically detected in invertebrates, which seem to be one of the possible viral sources. Twenty-eight new betanodavirus strains were retrieved in three molluscs species collected from different European countries between 2008 and 2015. The phylogenetic analyses revealed that strains retrieved from bivalve molluscs are closely related to viruses detected in finfish in Southern Europe in the period 2000-2009. Nevertheless, a new betanodavirus strain, markedly different from the other members of the RGNNV genotype, was detected. Such a massive and varied presence of betanodaviruses in bivalve molluscs greatly stresses the risks of transmission previously feared for other invertebrates. Bivalve molluscs reared in the same area as farmed and wild finfish could act as a reservoir of the virus. Furthermore, current European regulations allow relaying activities and the sale of live bivalve molluscs, which could pose a real risk of spreading betanodaviruses across different geographic regions. To our knowledge, this is the first study, which focuses on the detection and genetic characterization of betanodaviruses in bivalve molluscs.


Subject(s)
Bivalvia/virology , Nodaviridae/physiology , Animals , Crassostrea/virology , Europe , Mytilus/virology , Nodaviridae/classification , Nodaviridae/genetics , Phylogeny , Sequence Analysis, RNA
14.
Sci Rep ; 7(1): 10658, 2017 09 06.
Article in English | MEDLINE | ID: mdl-28878324

ABSTRACT

Grouper aquaculture around Asia is impacted by the nervous necrosis virus (NNV) and, in response, host resistance to this infection is being considered as a trait for selection. However efficient selection may be confounded if there are different genetic strains of NNV within and between regions and over years. This study uses statistical approaches and assessment of "characteristic attributes" (i.e. nucleotide positions that discriminate among strains) to assess whether published and new NNV RNA2 cds sequences show genetic differentiation over geography, host species and years. Rather clear evidence was found for regional strains of NNV. Interestingly, most of the geographic defining "characteristic attributes" were in codon position three, and not translated into differences for the protein capsid (i.e. they were synonymous variations), suggesting that while NNV strains were geographically isolated and had diverged in different regions for RNA sequences, selection had largely conserved the protein sequences among regions. The apparent selection constraint on the capsid protein may mitigate the risk that despite geographic subdivision, NNV strain variability will confound genetic selection for host resistance. The existence of regional Asian NNV strains may suggest that hatcheries are at risk from NNV not only from imported material but also from endemic reservoirs.


Subject(s)
Genetic Variation , Nodaviridae/genetics , Animals , Evolution, Molecular , Female , Fish Diseases/virology , Genome, Viral , Male , Nodaviridae/classification , Phylogeny , RNA Virus Infections/virology , RNA, Viral , Selection, Genetic , Sequence Analysis, RNA
15.
Sci Rep ; 7(1): 2083, 2017 05 18.
Article in English | MEDLINE | ID: mdl-28522842

ABSTRACT

White tail disease in the giant freshwater prawn Macrobrachium rosenbergii causes significant economic losses in shrimp farms and hatcheries and poses a threat to food-security in many developing countries. Outbreaks of Macrobrachium rosenbergii nodavirus (MrNV), the causative agent of white tail disease (WTD) are associated with up to 100% mortality rates. There are no interventions available to treat or prevent MrNV disease however. Here we show the structure of MrNV virus-like particles (VLPs) produced by recombinant expression of the capsid protein, using cryogenic electron microscopy. Our data show that MrNV VLPs package nucleic acids in a manner reminiscent of other known nodavirus structures. The structure of the capsid however shows striking differences from insect and fish infecting nodaviruses, which have been shown to assemble trimer-clustered T = 3 icosahedral virus particles. MrNV particles have pronounced dimeric blade-shaped spikes extending up to 6 nm from the outer surface of the capsid shell. Our structural analysis supports the assertion that MrNV may belong to a new genus of the Nodaviridae. Moreover, our study provides the first structural view of an important pathogen affecting aquaculture industries across the world.


Subject(s)
Capsid/ultrastructure , Nodaviridae/ultrastructure , Animals , Nodaviridae/classification , Palaemonidae/virology
16.
Sci Rep ; 7: 46755, 2017 05 02.
Article in English | MEDLINE | ID: mdl-28462930

ABSTRACT

Viral nervous necrosis (VNN) certainly represents the biggest challenge for the sustainability and the development of aquaculture. A large number of economically relevant fish species have proven to be susceptible to the disease. Conversely, gilthead sea bream has generally been considered resistant to VNN, although it has been possible to isolate the virus from apparently healthy sea bream and sporadically from affected larvae and postlarvae. Unexpectedly, in 2014-2016 an increasing number of hatcheries in Europe have experienced mass mortalities in sea bream larvae. Two clinical outbreaks were monitored over this time span and findings are reported in this paper. Despite showing no specific clinical signs, the affected fish displayed high mortality and histological lesions typical of VNN. Fish tested positive for betanodavirus by different laboratory techniques. The isolates were all genetically characterized as being reassortant strains RGNNV/SJNNV. A genetic characterization of all sea bream betanodaviruses which had been isolated in the past had revealed that the majority of the strains infecting sea bream are actually RGNNV/SJNNV. Taken together, this information strongly suggests that RGNNV/SJNNV betanodavirus possesses a particular tropism to sea bream, which can pose a new and unexpected threat to the Mediterranean aquaculture.


Subject(s)
Fish Diseases/virology , Nodaviridae/physiology , RNA Virus Infections/virology , Reassortant Viruses/physiology , Sea Bream/virology , Animals , Aquaculture , Female , Genotype , Host-Pathogen Interactions , Larva/virology , Male , Mediterranean Region , Nodaviridae/classification , Nodaviridae/genetics , Phylogeny , RNA, Viral/genetics , Reassortant Viruses/classification , Reassortant Viruses/genetics
17.
Arch Virol ; 162(8): 2315-2328, 2017 Aug.
Article in English | MEDLINE | ID: mdl-28451901

ABSTRACT

A real-time genotype-specific polymerase chain reaction (PCR) assay combined with high-resolution melting (HRM) analysis was developed to assess the most common genotypes of nervous necrosis viruses or nodaviruses. Nodaviruses are the causal agents of viral nervous necrosis infections, which have been wreaking havoc in the aquaculture industry worldwide, with fish mortality up to 100%. The four different genotypes of nodaviruses correlate with differences in viral pathogenicity. Therefore, rational development of effective vaccines and diagnostics requires analysis of genetic variation among viruses. The aim of the present study was to develop a real-time tetra-primer genotype-specific PCR assay for genotype identification. Four primers were utilized for simultaneous amplification of nodavirus genotype-specific products in a single closed-tube PCR after a reverse-transcription reaction using RNA isolated from fish samples. For high-throughput sample analysis, SYBR Green-based real-time PCR was used in combination with HRM analysis. The assay was evaluated in terms of specificity and sensitivity. The analysis resulted in melting curves that were indicative of each genotype. The detection limit when using reference plasmids was 100 ag/µL for both genotypes, while the sensitivity of the assays when testing a complex mixture was 10 fg/µL for red-spotted grouper nervous necrosis virus (RGNNV) and 100 fg/µL for striped jack nervous necrosis virus (SJNNV). To test the capability of this method under real-world conditions, 58 samples were examined. All samples belonged to the RGNNV genotype, which was fully validated. The results were in full agreement with genotyping by reference methods. The proposed methodology provides a rapid, sensitive, specific, robust and automatable assay for nodavirus genotyping, making it a useful tool for diagnosis and screening for epidemiological studies.


Subject(s)
Bass/virology , Fish Diseases/diagnosis , Nodaviridae/isolation & purification , RNA Virus Infections/veterinary , Real-Time Polymerase Chain Reaction/methods , Animals , DNA Primers , Fish Diseases/virology , Genotype , Molecular Diagnostic Techniques/methods , Molecular Diagnostic Techniques/veterinary , Nodaviridae/classification , RNA Virus Infections/diagnosis , RNA, Viral/isolation & purification , Real-Time Polymerase Chain Reaction/veterinary
18.
Virus Res ; 233: 113-119, 2017 04 02.
Article in English | MEDLINE | ID: mdl-28330752

ABSTRACT

An emerging covert mortality nodavirus (CMNV) was proved to be the infectious agent of shrimp viral covert mortality disease (VCMD). Prevalence and distribution of CMNV were investigated by using the methods of reverse transcription loop-mediated isothermal amplification (RT-LAMP), nested reverse transcription PCR, gene sequencing, histopathology, in situ RNA hybridization (ISH) and transmission electron microscope (TEM) in this study. RT-LAMP results showed that CMNV positive samples appeared in the cultured crustaceans including Litopenaeus vannamei, Fenneropenaeus chinensis, Marsupenaeus japonicus, Penaeus monodon, and Macrobrachium rosenbergii, and mostly distributed the coastal provinces in China. The prevalence rates of CMNV among the collected samples in 2013, 2014 and 2015 were 45.93% (130/283), 27.91% (84/301) and 20.85% (54/259), respectively. CMNV infection in M. japonicas and P. monodon was verified by ISH. The presence of CMNV particles were confirmed by TEM analysis in the CMNV positive samples diagnosed by RT-LAMP. The high prevalence and wide epidemic distribution of CMNV in this investigation revealed that it was necessary to pay close attention to the high risk of CMNV transmission in farmed crustaceans.


Subject(s)
Nodaviridae/genetics , Palaemonidae/virology , Penaeidae/virology , Phylogeny , Animals , Aquaculture , China , Humans , In Situ Hybridization , Nodaviridae/classification , Nodaviridae/ultrastructure , Palaemonidae/ultrastructure , Penaeidae/ultrastructure , Polymerase Chain Reaction , Sequence Analysis, DNA
19.
Arch Virol ; 162(5): 1319-1324, 2017 May.
Article in English | MEDLINE | ID: mdl-28155196

ABSTRACT

Plasmopara halstedii virus (PhV) is one of the few characterized oomycete viruses. Although it is fully sequenced and well-studied in its genetic diversity, the exact classification and phylogenetic relationships of PhV remain uncertain. The only known virus with characteristics similar to PhV is the Sclerophthora macrospora Virus A (SmV-A). Both viruses infect obligate biotrophic oomycetes. While RNA-dependent RNA polymerases (RdRp) of oomycetes viruses have high similarity to the corresponding enzymes from viruses classified in the family Nodaviridae, the coat proteins (CP) seem to be completely different from those of other viruses of this family. In contrast, the coat proteins of PhV and SmV-A have high similarity to viruses classified in the Tombusviridae, Circoviridae and a new group of hybrid DNA-RNA viruses (so-called chimeric viruses or cruciviruses). Because phylogenetic analyses based on the sequences of either RdRp or CP result in different affinities, an alternative, genome-based approach combining the sequences of both proteins was used. This analysis placed the two oomycete viruses together with Tombunodavirus UC1 in a new, independent group between families Nodaviridae and Tombusviridae.


Subject(s)
Capsid Proteins/genetics , Genome, Viral/genetics , Nodaviridae/genetics , Oomycetes/virology , RNA, Viral/genetics , RNA-Dependent RNA Polymerase/genetics , Tombusviridae/genetics , Amino Acid Sequence , Base Sequence , Genetic Variation , Nodaviridae/classification , Sequence Alignment , Sequence Analysis, RNA , Tombusviridae/classification
20.
J Fish Dis ; 40(5): 717-742, 2017 May.
Article in English | MEDLINE | ID: mdl-27633881

ABSTRACT

Viral encephalopathy and retinopathy (VER), otherwise known as viral nervous necrosis (VNN), is a major devastating threat for aquatic animals. Betanodaviruses have been isolated in at least 70 aquatic animal species in marine and in freshwater environments throughout the world, with the notable exception of South America. In this review, the main features of betanodavirus, including its diversity, its distribution and its transmission modes in fish, are firstly presented. Then, the existing diagnosis and detection methods, as well as the different control procedures of this disease, are reviewed. Finally, the potential of selective breeding, including both conventional and genomic selection, as an opportunity to obtain resistant commercial populations, is examined.


Subject(s)
Brain Diseases/veterinary , Fish Diseases , Nodaviridae/physiology , RNA Virus Infections/veterinary , Retinal Diseases/veterinary , Animals , Aquaculture , Brain Diseases/diagnosis , Brain Diseases/prevention & control , Brain Diseases/virology , Fish Diseases/diagnosis , Fish Diseases/prevention & control , Fish Diseases/transmission , Fish Diseases/virology , Nodaviridae/classification , RNA Virus Infections/diagnosis , RNA Virus Infections/prevention & control , RNA Virus Infections/transmission , Retinal Diseases/diagnosis , Retinal Diseases/prevention & control , Retinal Diseases/virology
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