Explore the vast range of titles available.

Cyprinid herpesvirus 2 (CyHV-2), which infects goldfish and crucian carp causing high mortality, is an emerging viral pathogen worldwide. The genome of CyHV-2 is large and comprises double-stranded DNA, including several genes similar to cyprinid herpesvirus 1, ictalurid herpesvirus-1, cyprinid herpesvirus 3, and ranid herpesvirus-1. Genes of DNA viruses are expressed in three temporal phases: immediate-early (IE), early (E), and late (L) genes. Viral IE genes initiate transcription as soon as the virus enters the host, without viral DNA replication. IE gene products enable the efficient expression of E and L genes or regulate the host to initiate virus replication. In the present study, five IE genes of CyHV-2 were identified, including open reading frame (ORF)54, ORF121, ORF141, ORF147, and ORF155. Time course analysis and reverse transcription polymerase chain reaction confirmed five IE genes, thirty-four E genes, and thirty-nine L genes. In addition, all 150 ORFs identified in the CyHV-2 genome are transcribed, and are expressed in chronological order, similar to other herpesviruses. This study is the first to identify the IE genes of CyHV-2, which will provide more information for viral molecular characterization.

The study was conducted at the Greater Zab River at Aski-Kalak City in three stations during the period from November 2020 to October 2021.The lowest water temperature value was 9.2°C at January while the highest value was 30 °C during July 2021. Salinity values ranged between 0.21 at January to 0.49 g/l during July 2021. Dissolve oxygen was high which range between 12.5 and 5.2 mg/l during December 2020 and July 2021 respectively. A total of 2368 specimens with a total weight of 848.97Kg were collected. These fishes were represented by 28 fish species belong to 7 families.The dominance commercial fishes (15 species) were recorded with a total weight of 775.56 kg formed 91.35% of a total fish catches. While, non – commercial fishes (13 species) were recorded with a total weight of 73.41kg represent 8.65% of total fishes catches. Fish species of Chondrostoma regium were occurred to be dominating of fish number and represented by 11.9% followed by Capoeta trutta (11.8%) and Arabibarbus grypus (11.1%) of total fish caches. Also, fish species of Luciobarbus kersin come at the first of total weight of fish catches and formed 18.15%,  then followed by Arabibarbus grypus (16.12%) and Cyprinus carpio (7.95%). Finally, fishes of Alburnu spallidus formed the lowest in fish number within 0.2% and in fish total weight was Garrarufa within 0.01% of total fish catches. Thepresent study concluded that Greater Zab River within freshwater, good airing and a favorable habitat for different fish species, more of that, there was considerable stock of commercial Iraqi fishes.

The number of olfactory receptor genes (ORs), which are responsible for detecting diverse odor molecules varies extensively among mammals as a result of frequent gene gains and losses that contribute to olfactory specialization. However, how OR expansions/contractions in fish are influenced by habitat and feeding habit and which OR subfamilies are important in each ecological niche is unknown. Here, we report a major OR expansion in a freshwater herbivorous fish, Megalobrama amblycephala, using a highly contiguous, chromosome-level assembly. We evaluate the possible contribution of OR expansion to habitat and feeding specialization by comparing the OR repertoire in 28 phylogenetically and ecologically diverse teleosts. In total, we analyzed > 4,000 ORs including 3,253 intact, 122 truncated, and 913 pseudogenes. The number of intact ORs is highly variable ranging from 20 to 279. We estimate that the most recent common ancestor of Osteichthyes had 62 intact ORs, which declined in most lineages except the freshwater Otophysa clade that has a substantial expansion in subfamily β and ε ORs. Across teleosts, we found a strong association between duplications of β and ε ORs and freshwater habitat. Nearly, all ORs were expressed in the olfactory epithelium (OE) in three tested fish species. Specifically, all the expanded β and ε ORs were highly expressed in OE of M. amblycephala. Together, we provide molecular and functional evidence for how OR repertoires in fish have undergone gain and loss with respect to ecological factors and highlight the role of β and ε OR in freshwater adaptation.

The Australian Government is considering Cyprinid herpesvirus 3 (CyHV-3) for biocontrol of invasive common carp (Cyprinus carpio L.). We review the evidence-base for its potential ecological risks, benefits and effectiveness. Lower carp abundance may boost native fish biomass and improve water clarity, but there is little evidence available to suggest that the virus, alone or used in combination with other methods, can deliver effective or safe biocontrol. Further, the virus may already be present in Australia. Overseas, the virus has caused sporadic and localized mortalities of carp in lakes and rivers, but has generally had no long-term measurable effect on wild carp or native fish populations. The temperature range of disease (18–28 °C), unknown co-factors causing outbreaks, and predictable re-colonization and recruitment boom of immune and virus-resistant carp, following a biocontrol release, remain formidable and unmitigated barriers to success. CyHV-3 infection trials on Australian biota have unexplained high mortality rates of recreationally-important and threatened fishes, and the role of asymptomatic carriers remains uncertain. Finally, Australia has national and international obligations to ensure that there are no perverse outcomes from biocontrol actions. Despite political pressure, there is no environmental justification to rush the release of this virus. To achieve the Government goals of restoring native biodiversity we advocate that key uncertainties, risks and efficacy barriers first need to be addressed. It is only then that viral biocontrol could be considered a viable tool to complement broader ecological restoration strategies for Australia’s waterways.

Background The grass carp has great economic value and occupies an important evolutionary position. Genomic information regarding this species could help better understand its rapid growth rate as well as its unique body plan and environmental adaptation. Results We assembled the chromosome-level grass carp genome using the PacBio sequencing and chromosome structure capture technique. The final genome assembly has a total length of 893.2 Mb with a contig N50 of 19.3 Mb and a scaffold N50 of 35.7 Mb. About 99.85% of the assembled contigs were anchored into 24 chromosomes. Based on the prediction, this genome contained 30,342 protein-coding genes and 43.26% repetitive sequences. Furthermore, we determined that the large genome size can be attributed to the DNA-mediated transposable elements which accounted for 58.9% of the repetitive sequences in grass carp. We identified that the grass carp has only 24 pairs of chromosomes due to the fusion of two ancestral chromosomes. Enrichment analyses of significantly expanded and positively selected genes reflected evolutionary adaptation of grass carp to the feeding habits. We also detected the loss of conserved non-coding regulatory elements associated with the development of the immune system, nervous system, and digestive system, which may be critical for grass carp herbivorous traits. Conclusions The high-quality reference genome reported here provides a valuable resource for the genetic improvement and molecular-guided breeding of the grass carp.

Cyprinid herpesvirus 2 (CyHV-2) is the etiological agent of herpesviral hematopoietic necrosis disease (HVHND), which causes severe mortality in ornamental goldfish (Carassius auratus), crucian carp (Carassius auratus), and gibel/prussian carp (Carassius gibelio). Quick and hassle-free point-of-care detection of CyHV-2 is vital for the maintenance of ornamental fish health. In this manuscript, we describe the development of a rapid and sensitive RPA (recombinase polymerase amplification) assay, coupled with lateral flow dipsticks (LFD), that can achieve sensitive diagnosis of CyHV-2 in goldfish within 20 min at 36 °C with the satisfactory detection limit of 102 gene copies per reaction. This is the first report wherein major capsid protein (MCP) of CyHV-2 was targeted for RPA-LFD assay development. The assay did not show any cross-reactivity with other viral pathogens like cyprinid herpesvirus 3 (CyHV-3), spring viremia of carp virus (SVCV), infectious spleen and kidney necrosis virus (ISKNV), and viral nervous necrosis virus (VNNV). Furthermore, screening of CyHV-2 infection in CyHV-2-infected goldfish did not yield any false positive/negative results. In short, the RPA-LFD assay developed in this study presents a simple, rapid, and sensitive method for point-of-care diagnosis of CyHV-2, especially under resource-limited conditions.

The Bulago Lucustrine Protected Area (LPA) was established on Lake Victoria, Uganda, as a sanctuary for severely depleted fish stocks, a breeding and spawning ground and a biodiversity conservation zone. Despite its ecological importance, no studies have been conducted on the Bulago LPA since its creation in 2010. This study assessed the total fish catch, fishing effort and catch per unit effort (CPUE) within the LPA, as well as at 33 fish landing sites along the fishing line outside the LPA in Mukono District. Five‐year quarterly data were used to analyse trends across silver cyprinid, Nile tilapia and Nile perch. Results indicated an initial rise in catch outside the LPA for all fish species, followed by a decline linked to increasing fishing effort, with Southern sites experiencing a more consistent drop in CPUE compared to the Northern ones. Within the LPA, catch and effort remained consistently low, and CPUE was generally higher for both Nile perch and Nile tilapia. CPUE in the Southern sites showed no influence on CPUE within the LPA, while a positive correlation was observed between CPUE in the Northern and Southern areas. These findings suggest LPAs in freshwater ecosystems can contribute to species conservation and may facilitate a potential spillover effect from protected to adjacent fishing grounds, although confirming spillover remains challenging. The study recommends further research to understand species life histories, movement patterns, home ranges and broader ecosystem dynamics within and outside LPA, as well as regular collaborative monitoring and surveillance of fishing activities.

The zebrafish (Danio rerio) represents an increasingly important model organism in virology. We evaluated its utility in the study of economically important viruses from the genus Cyprinivirus (anguillid herpesvirus 1, cyprinid herpesvirus 2 and cyprinid herpesvirus 3 (CyHV-3)). This revealed that zebrafish larvae were not susceptible to these viruses after immersion in contaminated water, but that infections could be established using artificial infection models in vitro (zebrafish cell lines) and in vivo (microinjection of larvae). However, infections were transient, with rapid viral clearance associated with apoptosis-like death of infected cells. Transcriptomic analysis of CyHV-3-infected larvae revealed upregulation of interferon-stimulated genes, in particular those encoding nucleic acid sensors, mediators of programmed cell death and related genes. It was notable that uncharacterized non-coding RNA genes and retrotransposons were also among those most upregulated. CRISPR/Cas9 knockout of the zebrafish gene encoding protein kinase R (PKR) and a related gene encoding a protein kinase containing Z-DNA binding domains (PKZ) had no impact on CyHV-3 clearance in larvae. Our study strongly supports the importance of innate immunity-virus interactions in the adaptation of cypriniviruses to their natural hosts. It also highlights the potential of the CyHV-3-zebrafish model, versus the CyHV-3-carp model, for study of these interactions.

The taxonomy of herpesviruses has been updated by the International Committee on Taxonomy of Viruses (ICTV). The former family Herpesviridae has been split into three families, which have been incorporated into the new order Herpesvirales . The revised family Herpesviridae retains the mammal, bird and reptile viruses, the new family Alloherpesviridae incorporates the fish and frog viruses, and the new family Malacoherpesviridae contains a bivalve virus. Three new genera have been created in the family Herpesviridae , namely Proboscivirus in the subfamily Betaherpesvirinae and Macavirus and Percavirus in the subfamily Gammaherpesvirinae . These genera have been formed by the transfer of species from established genera and the erection of new species, and other new species have been added to some of the established genera. In addition, the names of some nonhuman primate virus species have been changed. The family Alloherpesviridae has been populated by transfer of the genus Ictalurivirus and addition of the new species Cyprinid herpesvirus 3 . The family Malacoherpesviridae incorporates the new genus Ostreavirus containing the new species Ostreid herpesvirus 1 .

The aquaculture industry in Iran contributed to about 1% of the world’s aquaculture production in 2020 with a volume of 0.7 million tons. A targeted approach was used to identify positive samples by collecting samples from 342 suspected carp farms showing signs of disease. The carp species was considered as the host for the viruses under investigation and Khuzestan, Mazandaran and Gilan provinces were selected for sampling. A total of 251 farms in Gilan, 68 farms in Mazandaran, and 23 farms in Khuzestan provinces were sampled. Cyprinid herpesvirus 3 (CyHV-3) was characterized by a combination of sequence analysis and duplex PCR. Genetic analyzes and phylogenetic tree construction were performed using MEGA7 software. Of the 342 farms sampled, 85 were infected with koi herpes virus (KHV). Asian 1 and Asian 2 genotypes were identified by sequence analysis of the Sph I-5 and TK gene regions. One of the positive samples showed a match in all motif positions within the TK gene, specifically genotype A1, except for positions 814 − 813 where they had the sequence AT, which was a rare exception. Duplex PCR analysis of two variable marker regions between ORF29 and ORF30 (marker I) and ORF133 and its upstream region (marker II) revealed viruses of genotype J (I ++ II + ), an intermediate genotype (I ++ II - ), and a new genotype, I ++ II -* , identified in viruses from different farms. This new genotype retains the I ++ allele of marker I and has a 5-bp deletion in the marker II. The global distribution of CyHV-3 genotypes is not yet fully elucidated. Results indicate the high degree of diversification of CyHV-3 in the West Asian regions, where at least three different genotypes (I ++ II + , I ++ II - , and I ++ II -Δ ) currently appear to circulate.