Frequent RNA virus mutations raise concerns about evolving virulent variants. The purpose of this study was to investigate genetic variation in salmonid alphavirus-3 (SAV3) over the course of an experimental infection in Atlantic salmon and brown trout. Atlantic salmon and brown trout parr were infected using a cohabitation challenge, and heart samples were collected for analysis of the SAV3 genome at 2-, 4- and 8-weeks post-challenge. PCR was used to amplify eight overlapping amplicons covering 98.8% of the SAV3 genome. The amplicons were subsequently sequenced using the Nanopore platform. Nanopore sequencing identified a multitude of single nucleotide variants (SNVs) and deletions. The variation was widespread across the SAV3 genome in samples from both species. Mostly, specific SNVs were observed in single fish at some sampling time points, but two relatively frequent (i.e., major) SNVs were observed in two out of four fish within the same experimental group. Two other, less frequent (i.e., minor) SNVs only showed an increase in frequency in brown trout. Nanopore reads were de novo clustered using a 99% sequence identity threshold. For each amplicon, a number of variant clusters were observed that were defined by relatively large deletions. Nonmetric multidimensional scaling analysis integrating the cluster data for eight amplicons indicated that late in infection, SAV3 genomes isolated from brown trout had greater variation than those from Atlantic salmon. The sequencing methods and bioinformatics pipeline presented in this study provide an approach to investigate the composition of genetic diversity during viral infections.

The Global Burden of Animal Diseases (GBADs) programme\'s key objective â€\" to provide a systematic approach to determine the burden of animal disease â€\" is as relevant to aquatic as to terrestrial animal production systems. However, to date GBADs methods have mainly been applied to terrestrial animal production systems. The challenges in applying GBADs methods, notably the Animal Health Loss Envelope (AHLE), vary considerably by production system. The authors demonstrate how the AHLE can be calculated for rainbow trout production in England and Wales and acknowledge that its application to other systems (e.g. hatchery production, polyculture and no-feed mollusc production) is more complex. For example, in small scale tropical fish production the impact of suboptimal nutrition on production would need to be addressed. Recirculating aquaculture systems have inherent high levels of biosecurity and disease control, and thus low levels of disease. Removing the capital and running costs associated with biosecurity fundamentally changes the system and invalidates the AHLE calculation. Lack of data from many systems, notably small-scale tropical finfish farming, means that expert opinion will be needed to support the application of GBADs methods. While calculation of the AHLE is the focus of this article, it should be noted that attribution to causes and value chain modelling are needed to generate data on the wider societal impact of aquatic animal diseases (and possible interventions), which governments require to support decision-making about resource allocation.
Les principaux objectifs du programme \" Impact mondial des maladies animales \" (GBADs) visent à fournir une méthode systématique pour déterminer l\'impact des maladies animales et sont pertinents aussi bien pour les systèmes de production d\'animaux terrestres que pour les systèmes aquacoles. Néanmoins, à ce jour, les méthodes du GBADs ont surtout été appliquées aux systèmes de production d\'animaux terrestres. Les difficultés d\'application des méthodes du GBADs, en particulier le calcul de l\'enveloppe des pertes sanitaires animales varient considérablement d\'un système de production à l\'autre. Les auteurs décrivent la méthode appliquée pour calculer l\'enveloppe des pertes sanitaires animales dans les élevages de truites arc-en-ciel en Angleterre et au pays de Galles, méthode dont ils reconnaissent que l\'application à d\'autres systèmes (par exemple la production en écloserie, la polyculture et la production de mollusques sans intrants de fourrage) est plus complexe. Par exemple, dans la production de poissons tropicaux à petite échelle, l\'impact d\'une nutrition sous-optimale sur la production devrait être pris en compte. Les systèmes de recirculation fermée en aquaculture garantissent intrinsèquement des niveaux élevés de biosécurité et de contrôle sanitaire qui se traduisent par un niveau faible de maladies. La suppression des coûts d\'investissement et de fonctionnement associés à la biosécurité modifie fondamentalement le système et invalide le calcul de l\'enveloppe des pertes sanitaires animales. Compte tenu de l\'absence de données disponibles concernant un grand nombre de systèmes, notamment les petits élevages de poissons tropicaux, il faudra recourir aux avis d\'experts pour étayer l\'application des méthodes du GBADs. Si l\'article aborde essentiellement le calcul de l\'enveloppe des pertes sanitaires animales, les auteurs signalent l\'importance de rechercher les causes et de modéliser les chaînes de valeur afin de générer des données représentatives de l\'impact sociétal au sens large des maladies affectant les animaux aquatiques (ainsi que des interventions envisageables), outils indispensables pour étayer les décisions gouvernementales concernant les ressources à allouer.
El objetivo principal del programa sobre el Impacto Global de las Enfermedades Animales (GBADs), a saber, proporcionar un enfoque sistemático para determinar el impacto de dichas enfermedades, es tan pertinente para los sistemas de producción de animales acuáticos como terrestres. Sin embargo, hasta la fecha, los métodos del GBADs se han aplicado principalmente a los sistemas de producción de animales terrestres. Las dificultades que plantea la aplicación de los métodos del GBADs, en particular la cartera de pérdidas en sanidad animal, varían considerablemente según el sistema de producción. Los autores demuestran cómo puede calcularse la cartera de pérdidas en sanidad animal para la producción de trucha arco iris en Inglaterra y Gales y reconocen que su aplicación en otros sistemas (por ejemplo, la producción en viveros, el policultivo y la producción de moluscos sin insumos alimentarios) es más compleja. Por ejemplo, en la producción de peces tropicales a pequeña escala habría que abordar el impacto de una nutrición subóptima en la producción. Los sistemas de recirculación en acuicultura conllevan altos niveles de bioseguridad y control de enfermedades y, por lo tanto, bajos niveles de enfermedad. Si se eliminan los costos de capital y de explotación asociados a la bioseguridad, el sistema cambia radicalmente e invalida el cálculo de la cartera de pérdidas en sanidad animal. La falta de datos de muchos sistemas, especialmente de la cría de peces tropicales a pequeña escala, implica que se necesitará la opinión de expertos para apoyar la aplicación de los métodos del GBADs. Aunque el presente artículo se centra en el cálculo de la cartera de pérdidas en sanidad animal, cabe señalar que la determinación de las causas y la modelización de la cadena de valor son necesarias para generar datos sobre el impacto social más amplio de las enfermedades de los animales acuáticos (y las posibles intervenciones), que los gobiernos necesitan para respaldar la toma de decisiones sobre la asignación de recursos.

We have investigated the changes in the microbial communities on the surface of trout eggs and the skin of adult trout in relation to the presence of Saprolegnia parasitica. This pathogen causes saprolegniosis, a disease responsible for significant losses in salmonid farms and hatcheries. It is known from other disease systems that the host-associated microbiome plays a crucial role in the defence against pathogens, but if the pathogen predominates, this can lead to dysbiosis. However, analyses of the effects of S. parasitica on the diversity, composition, and function of microbial communities on fish skin and eggs are scarce. Thus, we have collected skin swabs from injured and healthy trout (N = 12), which differed in S. parasitica load, from three different fish farms in Croatia (Kostanjevac, Radovan, and Solin), while trout egg samples (N = 12) were infected with S. parasitica in the laboratory. Illumina sequencing of the V4 region of the 16S rRNA marker gene showed that infection with S. parasitica reduced the microbial diversity on the surface of the eggs, as evidenced by decreased Pielou\'s evenness and Shannon\'s indices. We further determined whether the bacterial genera with a relative abundance of >5.0% in the egg/skin samples were present at significantly different abundances in relation to the presence of S. parasitica. The results have shown that some genera, such as Pseudomonas and Flavobacterium, decreased significantly in the presence of the pathogen on the egg surface. On the other hand, some bacterial taxa, such as Acinetobacter and Janthinobacterium, as well as Aeromonas, were more abundant on the diseased eggs and the injured trout skin, respectively. Finally, beta diversity analyses (weighted UniFrac, unweighted UniFrac, Bray-Curtis) have shown that the sampling location (i.e., fish farm), along with S. parasitica infection status, also has a significant influence on the microbial communities\' composition on the trout skin and eggs, demonstrating the strong influence of the environment on the shaping of the host surface microbiome. Overall, we have shown that the presence of S. parasitica was associated with changes in the diversity and structure of the trout skin/egg microbiome. The results obtained could support the development of new strategies for the management of saprolegniosis in aquaculture.

Nanopore sequencing of the infectious pancreatic necrosis virus (IPNV) vp2 gene from Andean trout cultures in Peru reveals genogroups 1 and 5. This insight aids in understanding strain diversity and pathogenicity, vital for effective disease surveillance, and control measures in aquaculture.

The mechanosensory lateral line (LL) system of salmonid fishes has been the focus of comparative morphological studies and behavioral and physiological analyses of flow sensing capabilities, but its morphology and development have not been studied in detail in any one species. Here, we describe the post-embryonic development of the cranial LL system in Brook Trout, Salvelinus fontinalis, using vital fluorescent staining (4-Di-2-ASP), scanning electron microscopy, µCT, and clearing and staining to visualize neuromasts and the process of cranial LL canal morphogenesis. We examined the relationship between the timing of LL development, the prolonged life history of salmonids, and potential ecological implications. The LL system is composed of seven canals containing canal neuromasts (CNs) and four lines of superficial neuromasts (SNs) on the skin. CNs and SNs increase in number and size during the alevin (larval) stage. CN number stabilizes as canal morphogenesis commences, but SN number increases well into the parr (juvenile) stage. CNs become larger and more elongated than SNs, but the relative area occupied by sensory hair cells decreases during ontogeny in both types of neuromasts. Neuromast-centered canal morphogenesis starts in alevins (yolk sac larvae), as they swim up into the water column from their gravel nests (~4 months post-fertilization), after which yolk sac absorption is completed and exogenous feeding begins. Canal morphogenesis proceeds asynchronously within and among canal series and is not complete until ~8 months post-fertilization (the parr stage). Three characters in the LL system and associated dermal bones were used to identify their homologs in other actinopterygians and to consider the evolution of LL canal reduction, thus demonstrating the value of salmonids for the study of LL evolution. The prolonged life history of Brook Trout and the onset of canal morphogenesis at swim-up are predicted to have implications for neuromast function at these critical behavioral and ecological transitions.

The evolutionary histories of adaptive radiations can be marked by dramatic demographic fluctuations. However, the demographic histories of ecologically-linked co-diversifying lineages remain understudied. The Laurentian Great Lakes provide a unique system of two such radiations that are dispersed across depth gradients with a predator-prey relationship. We show that the North American Coregonus species complex (\"ciscoes\") radiated rapidly prior to the Last Glacial Maximum (80-90 kya), a globally warm period, followed by rapid expansion in population size. Similar patterns of demographic expansion were observed in the predator species, Lake Charr (Salvelinus namaycush), following a brief time lag, which we hypothesize was driven by predator-prey dynamics. Diversification of prey into deep water created ecological opportunities for the predators, facilitating their demographic expansion, which is consistent with an upward adaptive radiation cascade. This study provides a new timeline and environmental context for the origin of the Laurentian Great Lakes fish fauna, and firmly establishes this system as drivers of ecological diversification and rapid speciation through cyclical glaciation.

Climate change, with its profound effects on stream sediment, hydrological, and temperature dynamics, will exacerbate impacts on habitat conditions for many species, particularly those with vulnerable early life stages relying on the hyporheic zone, such as gravel-spawning fishes. Due to the complex and interactive nature of multiple stressor effects, we employed large-scale outdoor mesocosms to systemically test how the reproductive success of three gravel-spawning fish species brown trout (Salmo trutta), nase, (Chrondrostoma nasus) and Danube salmon (Hucho hucho) was affected by individual and combined effects of warming (+3-4 °C), fine sediment (increase in <0.85 mm by 22 %) and low-flow (eightfold discharge-reduction). Fine sediment had the most detrimental effect on emergence rate and fry length in all three species, reducing the emergence rate to zero in brown trout, 9 % in nase, and 4 % in Danube salmon. The emergence mortality caused by fine sediment surpassed that of hatching distinctly, suggesting that negative effects due to hypoxia were considerably exacerbated by entombment. Warming had only minor effects as a single stressor, but low flow reduced emergence rates of the spring spawning species nase and Danube salmon by 8 and 50 %, respectively. In combined treatments including fine sediment, however, the emergence success of all three species responded strongly negatively, even in the cyprinid species nase, which showed little interactive effects between stressors regarding hatching success. Warming and fine sediment also led to the earlier emergence of fry, implying a risk of asynchrony with available food resources. This study dramatically shows that climate change can have deleterious impacts on the reproductive success of gravel-spawning fish species, irrespective of taxonomic or ecological traits.

Following a request from the European Commission, EFSA was asked to deliver a scientific opinion on red carotenoid-rich Paracoccus carotinifaciens NITE SD 00017 for salmon and trout (category: sensory additives; functional group: colourants; substances which when fed to animals add colours to food of animal origin) for the renewal of its authorisation. The applicant provided evidence that the additive complies with the conditions of the authorisation. The Panel concludes that the use of the additive in salmon and trout remains safe for the target species, the consumer and the environment under the authorised conditions of use. When assessing consumer exposure to canthaxanthin and adonirubin at the level of the existing maximum residue limits (MRL) for poultry and the proposed MRL for trout/salmon (5 mg/kg muscle), the exposure of consumers exceeds the acceptable daily intake (ADI) in the population classes toddlers and other children. The Panel considers that there is no need to restrict the use of the additive to fish older than 6 months or of more than 50 g. Red carotenoid-rich Paracoccus carotinifaciens NITE SD 00017 is not irritant to the skin, but is irritant to the eyes. It is considered a dermal and respiratory sensitiser and any exposure via skin or the respiratory tract is a risk.

Current procedures to establish vertebral column regionalization (e.g., histology) in fish are time consuming and difficult to apply. The aim of this study was to develop a more rapid and accurate radiology-based method for Atlantic salmon (Salmo salar). A detailed analysis of 90 animals (4 kg) led to the establishment of region-specific radiographic hallmarks. To elucidate its transferability to other salmonid species, radiography was carried out in brown trout (Salmo trutta), Arctic char (Salvelinus alpinus), rainbow trout (Oncorhynchus mykiss), pink salmon (Oncorhynchus gorbuscha), and Chinook salmon (Oncorhynchus tshawytscha). This method was also evaluated for whole ungutted fish. The vertebral column of Atlantic salmon can be subdivided into five regions (R1-R5) based on anatomy: postcranial (R1, V1, and V2), abdominal (R2, V3-V26), transitional (R3, V27-V36), caudal (R4, V37-V53), and ural (R5, V54-V59). The following specific radiographic hallmarks allow the identification of regions: (i) lack of ribs in R1, (ii) modified parapophysis of the first vertebra of R3, (iii) prominent hemal spine of the first vertebra of R4, and (iv) the separated hemal spine of the most cranial pre-ural vertebra of R5. These hallmarks were all transferable to the other salmonid species assessed. The results include a further description of various region-specific characteristics in Atlantic salmon. The method was found applicable for sedated/whole ungutted fish, verifying it as quick and easy compared to other regionalization methods. The regions defined by radiology in this study agree with the vertebral column regions recently defined for Chinook salmon (O. tshawytscha). Thus, and considering the results of this study on various salmonid species, the currently developed regionalization protocol can be generally used for salmonids.

In Japan, stocked chum salmon (Oncorhynchus keta) fry may have become the perfect prey for non-native brown trout (Salmo trutta), which are popular targets of anglers. If this is the case, fry stocking which is intended to boost commercial fishing may be helping to sustain the populations of an invasive predator. We used dietary and biochemical analyses to examine whether brown trout quickly restore their nutritional status following wintertime declines by preying upon chum salmon fry that are stocked in spring. We targeted six rivers in Hokkaido, Japan, three with fry stocking and three without. Changes in brown trout condition factor, triglyceride contents in muscle and serum, serum insulin-like growth factor-1 (IGF-1; an indicator of short-term growth), and docosahexaenoic acid (DHA; an essential fatty acid abundant in fish) content in muscle were examined between before stocking and during the stocking period in the six rivers. Dietary analysis showed that brown trout preyed on fry during the stocking period in all stocked rivers. Their nutritional status tended to be higher during the stocking period than before stocking in stocked rivers, but not in unstocked rivers. These results suggest that the massive stocking of chum salmon fry provides brown trout with the perfect prey to quickly restore their nutritional status and fuel increased growth; this may therefore be a controversial issue among stakeholders.