Carp edema virus (CEV), an emerging pathogen, poses a significant threat to global aquaculture, especially in China, the world's leading producer of carp. This study investigated the molecular epidemiology of carp edema virus (CEV) in China from 2013 to 2019, during which 781 samples across 21 provinces were analyzed via PCR. The results indicated a CEV positivity rate of 9.86%, with the highest prevalence noted in Henan and Jiangsu provinces. Common carp and koi are sensitive to CEV, while grass carp, Prussian carp, and goldfish are resistant, even under coculture conditions. Notably, CEV and KHV coinfections have been reported, and this study documents the first instance of CEV and SVCV coinfection in China. Phylogenetic analysis of a 357-bp fragment of the CEV P4a gene (83 Chinese strains and 45 GenBank reference sequences) identified 31 P4a sequence types (STs; unique 357-bp haplotypes). All Chinese strains clustered within genogroup II, with most STs assigned to subgenogroup IIa, suggesting multiple introductions of CEV into China, while a distinct cluster of Henan strains fell within subgenogroup IIb indicated a separate introduction. This study underscores the role of environmental temperatures, ranging from 8 degrees C to 30 degrees C, in the ecological adaptability and infection rates of CEV. The genetic relatedness of Chinese isolates to European strains points to international trade as a possible transmission route. This research advocates advanced molecular diagnostics to enhance pathogen identification, highlighting the crucial role of systematic surveillance and biosecurity measures in controlling the spread of CEV in aquaculture, a factor that complicates disease management and highlights the need for multi-pathogen surveillance.

Spring viremia of carp (SVC), caused by spring viremia of carp virus (SVCV), is a highly contagious disease that poses a serious threat to cyprinid aquaculture and international trade, and it is listed as a notifiable disease by the World Organization for Animal Health (WOAH). Effective surveillance and control of SVCV rely on accurate and highly sensitive molecular diagnostic methods. However, several previously published RT–qPCR assays contain mismatches between primer/probe sequences and viral genomes, which may lead to false-negative results and reduced diagnostic reliability. In this study, a whole-genome comparison of 24 representative SVCV strains covering all four genotypes (SVCVa–d) was conducted, and a new primer–probe set (Cefas AR) targeting a highly conserved region of the L gene was designed. Reaction conditions were optimized, and the assay was rigorously validated in accordance with the WOAH Manual of Diagnostic Tests for Aquatic Animals. The developed RT–qPCR assay exhibited excellent analytical performance, with a limit of detection of 1.28 copies/μL, diagnostic sensitivities of 100% for cell-culture isolates and 96.6% for tissue samples, and a diagnostic specificity of 100%. In addition, the assay demonstrated strong reproducibility and consistency across nine independent laboratories. In conclusion, the WOAH-validated RT–qPCR assay developed in this study provides a highly sensitive, specific, and reliable tool for rapid screening, routine surveillance, and confirmatory diagnosis of SVCV, supporting sustainable aquaculture development and international aquatic animal health management.

The haplosporidian parasites Bonamia ostreae (BO) and B. exitiosa (BE) are serious oyster pathogens. Two independent laboratories evaluated fluorescence real-time loop-mediated isothermal amplification (LAMP) assays for rapidly detecting these parasites. Specific LAMP assays were designed on the BO actin-1 and BE actin genes. A further generic assay was conceived on a conserved region of the 18S gene to detect both Bonamia species. The optimal reaction temperature varied from 65 to 67 °C depending on the test and instrument. Melting temperatures were 89.8–90.2 °C, 87.0–87.6 °C, and 86.2–86.6 °C for each of the BO, BE, and generic assays. The analytical sensitivity of these assays was 50 copies/µL in a 30 min run. The BO and BE test sensitivity was ~1 log lower than a real-time PCR, while the generic test sensitivity was similar to the real-time PCR. Both the BO and BE assays were shown to be specific; however, the generic assay potentially cross-reacts with Haplosporidium costale. The performance of the LAMP assays evaluated on samples of known status detected positives within 7–20 min with a test accuracy of 100% for the BO and generic tests and a 95.8% accuracy for BE. The ease of use, rapidity and affordability of these tests allow for field deployment.

Background Patagonian toothfish ( Dissostichus eleginoides ) is an economically and ecologically important fish species in the family Nototheniidae. Juveniles occupy progressively deeper waters as they mature and grow, and adults have been caught as deep as 2500 m, living on or in just above the southern shelves and slopes around the sub-Antarctic islands of the Southern Ocean. As apex predators, they are a key part of the food web, feeding on a variety of prey, including krill, squid, and other fish. Despite its importance, genomic sequence data, which could be used for more accurate dating of the divergence between Patagonian and Antarctic toothfish, or establish whether it shares adaptations to temperature with fish living in more polar or equatorial climes, has so far been limited. Results A high-quality D. eleginoides genome was generated using a combination of Illumina, PacBio and Omni-C sequencing technologies. To aid the genome annotation, the transcriptome derived from a variety of toothfish tissues was also generated using both short and long read sequencing methods. The final genome assembly was 797.8 Mb with a N50 scaffold length of 3.5 Mb. Approximately 31.7% of the genome consisted of repetitive elements. A total of 35,543 putative protein-coding regions were identified, of which 50% have been functionally annotated. Transcriptomics analysis showed that approximately 64% of the predicted genes (22,617 genes) were found to be expressed in the tissues sampled. Comparative genomics analysis revealed that the anti-freeze glycoprotein (AFGP) locus of D. eleginoides does not contain any AFGP proteins compared to the same locus in the Antarctic toothfish ( Dissostichus mawsoni ). This is in agreement with previously published results looking at hybridization signals and confirms that Patagonian toothfish do not possess AFGP coding sequences in their genome. Conclusions We have assembled and annotated the Patagonian toothfish genome, which will provide a valuable genetic resource for ecological and evolutionary studies on this and other closely related species.

Spring viraemia of carp (SVC) is an infectious disease responsible for severe economic losses for various cyprinid species, particularly common carp (Cyprinus carpio carpio). The causative agent is the Rhabdovirus carpio or SVC virus (SVCV), a member of the Sprivivirus genus, within the Rhabdoviridae family. Phylogenetically, SVCV is divided into four genogroups (SVCV a, SVCV b, SVCV c and SVCV d), which have a reasonable correlation with the geographical distribution of the virus. In the late twentieth century, the disease was widespread in Serbian aquaculture and caused massive deaths in common carp. This study aimed to molecularly characterize the circulating SVCV isolates in Serbia over a 17-year period. The genetic relationships between 21 SVCV isolates from common carp and rainbow trout in Serbia between 1992 and 2009 were determined based on the partial nucleotide sequence of the glycoprotein gene (G gene). The phylogenetic analysis showed that the dominant SVCV isolates in Serbia belong to the SVCV d genogroup, with only one isolate belonging to genogroup SVCV b. The SVCV strains circulating in Serbia exhibited high homogeneity, as several isolates shared 100% similarity within these genogroups. Most Serbian isolates belonged to SVCV d1 and d2 subgroups, with one isolate notably different and included in a new subgroup SVCV d5. Understanding the SVCV genetic variants circulating in Serbia would be helpful in future epizootic investigations.

Lumpfish are used routinely as cleaner fish to delouse farmed Atlantic salmon ( Salmo salar ) and are often translocated globally. In September 2021, an aquaculture production business in Dorset, England experienced considerable mortalities in consignments of lumpfish ( Cyclopterus lumpus ) imported from Norway. Following suspicion of infection with Cyclopterus lumpus virus (CLuV) by a veterinarian, commercial testing provided presumptive confirmation of a CLuV infection using reverse-transcription real-time polymerase chain reaction (RT-rPCR). Affected fish were later resampled by the Centre of Environment, Fisheries, and Aquaculture Science, Fish Health Inspectorate for screening of CLuV by RT-rPCR, and confirmation by conventional RT-PCR and sequence analysis. Additional samples were tested using isolation of viruses on cell cultures, bacteriology, histopathology, and PCR/rPCR techniques to investigate whether other pathogens of concern to the salmon aquaculture industry were also present. All samples tested negative for the presence of viral haemorrhagic septicaemia virus, infectious haematopoietic necrosis virus , nervous necrosis virus, infectious pancreatic necrosis virus , infectious salmon anaemia virus , ranavirus, and salmonid alphavirus. Four pools of ten samples tested positive by RT-rPCR for CLuV (Ct values between 19 and 29) and was confirmed using conventional RT-PCR. Sequence analysis showed that amplicons shared a 99.63 % match with the published sequences for CLuV. The CLuV has only recently been reported in aquatic animals and its full impact is not yet known. To the best of our knowledge this is the first report of CLuV in England.

A carp disease with clinical signs of acute gill rot (AGR) has frequently occurred in Henan province of China since 2013, leading to substantial economic losses. However, the causative agent of virus-related carp AGR (CAGR) disease has been controversial. Our study showed that carp edema virus (CEV), specifically the sub-genogroup IIa, might be the primary agent causing virus-related CAGR that is endemic to Henan, China. This conclusion is based on a cohabitation experiment using isolates from an outbreak in 2019 and a retrospective analysis of CAGR samples collected between 2013 and 2015 in Henan, China. In the cohabitation experiment, the clinical development and pathological changes of CEV disease were observed. The pathological alterations in the fish brain were first noticed to be strongly associated with clinical signs of being sleepy, suggesting that pathological alterations in the fish brain may be a critical differential characteristic of CEV. Another important finding in our study was that the mortality in common carp and koi carp was strongly associated by a temperature change and less correlated to the viral loads in organs. Considering the frequent outbreaks of virus-related CAGR disease in Henan (China), effective prevention, good environmental stress management, and efficient diagnosis are needed. Based on comparing the qPCR and the nested PCR designed at the CEFAS Weymouth Laboratory, we recommend using the qPCR method on gills to identify this pathogen because of the assay's sensitivity and the viral load in gill tissues.

Aquatic non-indigenous species (NIS) threaten biodiversity, ecosystem functions, and the economy worldwide. Monitoring NIS is of immediate concern to identify newly arriving species, assess the efficacy of mitigation measures, and report long-term indicators of introduction, spread, and impacts. The challenges associated with conventional methods of specimen collection and morphological identification have led to the development of alternative methods, such as DNA-based methods, which could offer rapid and cost-effective detection of NIS. Depending on whether a few (targeted monitoring) or many species (passive monitoring) are being monitored, environmental DNA (eDNA) can infer presence-absence and relative abundances, enabling informed decisions and actions to be made based on patterns of detection. Compared to more conventional methods, eDNA tools can increase the levels of detection and sensitivity for rare and elusive species, which is even more noticeable for some taxa when using targeted monitoring. The use of DNA-based tools not only minimizes the onus on taxonomic expertise and reduces resource demands but can also be more sensitive and cost-efficient in detecting NIS, thus proving its value as an early warning tool. As nucleic acid (DNA/RNA) methods advance rapidly for NIS detection, there must be a balance between method sensitivity, logistical requirements, and associated costs, which must be factored into future management decisions. While there are many complementary reviews available, our aim is to emphasize the importance of incorporating eDNA tools into NIS surveys and to highlight the available opportunities in this field.

Intricate links between aquatic animals and their environment expose them to chemical and pathogenic hazards, which can disrupt seafood supply. Here we outline a risk schema for assessing potential impacts of chemical and microbial hazards on discrete subsectors of aquaculture—and control measures that may protect supply. As national governments develop strategies to achieve volumetric expansion in seafood production from aquaculture to meet increasing demand, we propose an urgent need for simultaneous focus on controlling those hazards that limit its production, harvesting, processing, trade and safe consumption. Policies aligning national and international water quality control measures for minimizing interaction with, and impact of, hazards on seafood supply will be critical as consumers increasingly rely on the aquaculture sector to supply safe, nutritious and healthy diets.

In March 2021, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by four families (Aliusviridae, Crepuscuviridae, Myriaviridae, and Natareviridae), three subfamilies (Alpharhabdovirinae, Betarhabdovirinae, and Gammarhabdovirinae), 42 genera, and 200 species. Thirty-nine species were renamed and/or moved and seven species were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.

Many of the most significant viral pathogens of fish are members of three genera within the family Rhabdoviridae. Fish rhabdoviruses collectively infect a broad range of fish host species in the Northern hemisphere and cause disease outbreaks in fish reared in aquaculture, as well as wild fish populations. While many of the best known fish rhabdoviruses are associated with acute disease and high mortality, others are isolated from chronic or asymptomatic infections.

Fluorescence real-time LAMP assays were designed for the orf43 gene of CyHV-3 European genotype and the p4a gene of the CEV genogroup I. A third LAMP assay to detect the ef1a gene of the host common carp was designed as an internal control. The limit of detection was 102 and 103 viral copies under 25 min for CyHV-3 and CEV, respectively. The specificity of the CyHV-3 LAMP assay was 95.6% of 72 fish herpesviruses tested. Sixty-three non-lethal common carp mucus swabs were collected across 16 sites during disease investigations. DNA extractions were performed in under 10 min using the QuickExtract™ digestion buffer. The LAMP amplification of CyHV-3 DNA in mucus swabs from clinical cases was detected from 4 to 13 min in 13 sites, while a co-infection of CyHV-3 and CEV was confirmed by LAMP in a single site. The LAMP results agreed with the results of the reference laboratory. The common carp ef1a was amplified only in 61% of the mucus swabs collected, preventing its use as a robust internal control to distinguish false negatives from invalid tests. After further optimization, these tests could be implemented for border inspection posts surveillance and decentralizing testing during disease outbreaks.

In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. At the genus rank, 20 new genera were added, two were deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted, ten were moved and renamed, and 30 species were renamed. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.

This is the first record of a fish nidovirus isolated from a consignment of goldfish at the United Kingdom (UK) border. The full-length viral genome was 25,985 nt, sharing a 97.9% nucleotide identity with the Chinook salmon bafinivirus (CSBV) NIDO with two deletions of 537 and 480 nt on the ORF Ia protein. To assess the potential impact on UK fish species, Atlantic salmon, common carp and goldfish were exposed to the virus via an intraperitoneal (IP) injection and bath challenge. Moribundity was recorded in only 8% of IP-injected goldfish. A high viral load, ≈107 of the CSBV PpIa gene, was measured in the kidney of moribund goldfish. Mild histopathological changes were observed in the kidneys of challenged carps. Ultrastructural observations in renal tubule epithelial cells of goldfish showed cylindrical tubes (≈15 nm in diameter) and tubular structures budding spherical virions (≈200 nm in diameter) with external spike-like structures. Negative staining showed both circular and bacilliform virions. Seroconversion was measured in common carp and goldfish but not in Atlantic salmon. This study reinforces the potential risk of novel and emerging pathogens being introduced to recipient countries via the international ornamental fish trade and the importance of regular full health screens at the border inspection posts to reduce this risk.

In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylumNegarnaviricotawas amended and emended. At the genus rank, 20 new genera were added, two were deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted, ten were moved and renamed, and 30 species were renamed. This article presents the updated taxonomy ofNegarnaviricotaas now accepted by the ICTV.

Although native to eastern Canada and the USA, American lobsters (Homarus americanus) have been reported from British coastal waters in recent years. The introduction of most have been as escapees from holding facilities or releases by members of the public for animal welfare or religious reasons. Life-history traits ofH. americanusput them at a potential competitive advantage over and hybridisation with the European lobster (Homarus gammarus), the 5th most valuable seafood to the UK. While yearly reported numbers ofH. americanusfound in British waters have been low, a mass release of 361H. americanusinto the English Channel off Brighton, southern England, took place in June 2015. This review identified 162 records ofH. americanusin British waters between 2012 and 2018, with specimens caught mainly in or around Brighton, although additionalH. americanusreleased may have gone undetected. While this evidence suggests a growing potential for establishment of the species, further information is provided evidencing hybridisation between releasedH. americanusand nativeH. gammarusvia genetic analysis. This review highlights the need for a more robust means of detectingH. americanusand other non-native species in British waters.

The family Rhabdoviridae includes 20 genera and 144 species of viruses with negative-sense, single-stranded RNA genomes of approximately 10–16 kb (Table 1.Rhabdoviridae). Virions are typically enveloped with bullet-shaped or bacilliform morphology but nonenveloped filamentous virions have also been reported. The genomes are usually (but not always) single RNA molecules with partially complementary termini. Almost all rhabdovirus genomes have 5 genes encoding the structural proteins (N, P, M, G and L); however, many rhabdovirus genomes encode other proteins in additional genes or in alternative open reading frames (ORFs) within the structural protein genes. The family is ecologically diverse with members infecting plants or animals including mammals, birds, reptiles or fish. Rhabdoviruses are also detected in invertebrates, including arthropods some of which may serve as unique hosts or may act as biological vectors for transmission to other animals or plants. Rhabdoviruses include important pathogens of humans, livestock, fish or agricultural crops.

In late 2018, unusual patterns of very high mortality (>50% production) were reported in intensive tilapia cage culture systems across Lake Volta in Ghana. Samples of fish and fry were collected and analysed from two affected farms between October 2018 and February 2019. Affected fish showed darkening, erratic swimming and abdominal distension with associated ascites. Histopathological observations of tissues taken from moribund fish at different farms revealed lesions indicative of viral infection. These included haematopoietic cell nuclear and cytoplasmic pleomorphism with marginalization of chromatin and fine granulation. Transmission electron microscopy showed cells containing conspicuous virions with typical iridovirus morphology, that is enveloped, with icosahedral and/or polyhedral geometries and with a diameter c.160 nm. PCR confirmation and DNA sequencing identified the virions as infectious spleen and kidney necrosis virus (ISKNV). Samples of fry and older animals were all strongly positive for the presence of the virus by qPCR. All samples tested negative for TiLV and nodavirus by qPCR. All samples collected from farms prior to the mortality event were negative for ISKNV. Follow-up testing of fish and fry sampled from 5 additional sites in July 2019 showed all farms had fish that were PCR-positive for ISKNV, whether there was active disease on the farm or not, demonstrating the disease was endemic to farms all over Lake Volta by that point. The results suggest that ISKNV was the cause of disease on the investigated farms and likely had a primary role in the mortality events. A common observation of coinfections with Streptococcus agalactiae and other tilapia bacterial pathogens further suggests that these may interact to cause severe pathology, particularly in larger fish. Results demonstrate that there are a range of potential threats to the sustainability of tilapia aquaculture that need to be guarded against.

Carp edema virus (CEV) was initially detected in Japan in the 1970s as the causative agent of koi sleepy disease (KSD) in koi and common carp (Cyprinus carpio L.) populations. CEV has spread all over the world mainly by trading of asymptomatic carrier fish. In Germany KSD was detected for the first time in spring 2009 from samples collected from imported Japanese koi at water temperatures below 10 degrees C. In 2014 large outbreaks of KSD in common carp and koi became evident in Germany. Several unsuccessful investigations were carried out to isolate the agent in permanently growing fish derived cell cultures. For diagnosis, the clinical signs of KSD were difficult to differentiate from the clinical signs related with koi herpesvirus disease (KHVD), except during the advanced stage of disease, when the fish started to lie down ("sleep") on the bottom of the tank. The only successful and reliable diagnostic methods were PCRs and qPCR. However, virus sequences obtained from diseased specimens demonstrated high geographical diversity. Therefore, the original primer pairs, published from Japan in the 1990s, gave negative or uncertain results in detection of CEV in samples from carp and koi in Europe, and new primers and probes had to be designed for PCR and nested PCR as well as for TaqMan and SYBR green based qPCRs. While some of them recognised CEV obtained from koi samples only, a decision was made to use only PCR and qPCR assays that detect all variants of CEV for diagnostic testing. Three molecular assays were chosen to conduct a laboratory comparison test with 10 Animal Health Laboratories all over Germany. The aim was to evaluate and standardise CEV detection with defined samples, thereby making the results directly comparable. The results show that even though all laboratories used different PCR kits and cycler systems, they were able to identify CEV in samples from koi and common carp with given primers and a probe. Only in samples diluted above 1:1000, were the results negative by PCR and qPCR in a few laboratories. Some participating laboratories also identified CEV from koi and carp samples by sequence analysis. These results confirm that accurate and reproducible CEV diagnostic results can be achieved resulting in both an improved control strategy, and the implementation of more effective biosecurity practices, for koi and carp farms. Additionally, it was shown that primers and the probe designed for PCR, nested PCR and qPCR are very sensitive and specific to CEV. The results were reproducible across multiple laboratories that utilised different manufacturers of both PCR kits and machines as well as varying assay conditions.