Moldal, T. | bioRxiv Science

bioRxiv2026

: A standardized bath challenge of Atlantic salmon reveals distinct infection dynamics and mortality across ten HPR-deleted infectious salmon anaemia virus isolates.

Infectious salmon anaemia virus with highly polymorphic region deletions (ISAV-HPR{Delta}) is classified as pathogenic, yet field outbreaks display wide variation in disease severity. To determine the extent of inherent virulence differences among ISAV-HPR{Delta} isolates, we conducted a standardized freshwater bath challenge in Atlantic salmon using ten isolates, including the high-virulent reference strain NO/Glesvaer/2/90 and nine recent Norwegian field isolates. Cumulative mortality, infection kinetics, tissue viral loads, shedding, and pathological changes were characterised through RT-qPCR, histopathology, immunohistochemistry, and flow cytometry. All isolates established systemic infection, but exhibited pronounced differences in infection dynamics, virus shedding, clinical signs, and pathological outcomes. Cumulative mortality ranged from 15% to 100%, allowing separation of isolates into high- ([≥]90%), moderate- (40-50%), and low-mortality (<20%) categories. Isolates with high mortality showed rapid systemic spread, extensive endothelial infection, and significant pathology compatible with infectious salmon anaemia. Shedding profiles of virus to water differed substantially and were not clearly correlated with cumulative mortality, viral RNA load in tissues or mortality. High ISAV RNA was detected in water for the H16 isolate with [~]10 - 100-fold higher viral RNA than H20 and [A]. VA and S, although giving high mortality (>90%), had much lower (shedding (highest RNA range 1.1 - 3.6^102). Segment 5 and 6 sequencing confirmed that all isolates carried genetic mutations typical of pathogenic ISAV except [A], that have an atypical mutation in the putative protease cleavage site on segment 5. However, these mutations alone did not account for the wide biological continuum of mortality.

microbiology↗

bioRxiv2025

Whole genome sequencing reveals a novel Renibacterium salmoninarum lineage and suggests geographic endemism combined with anthropogenic spread in the North-East Atlantic area

Renibacterium salmoninarum is the causative agent of bacterial kidney disease (BKD) and has been isolated from northern European salmonid farms since the 1960s. The bacterium has been detected only sporadically in Norway during the last decades, but the country experienced several geographically spread outbreaks since December 2022. The phylogenomic relationships of R. salmoninarum isolates associated with the epizootics ongoing on the West Coast and in Mid-Norway were explored using a whole genome sequencing approach. A broad overview of the phylogeography of this pathogen was gained through sequencing and analysis of a collection of isolates from Norway (n=67), Iceland (n=12), Denmark (n=12), and the Faroe Islands (n=1), along with a collection of 109 publicly available sequences. We identified two distinct contemporary clades of R. salmoninarum causing BKD in Norway in the period 2022-2024. Both clades belong to the expanding, aquaculture-associated Lineage 1. The epidemiological picture appears consistent with contemporary aquaculture operations, raising questions on the effectiveness or practice of current biosecurity practices towards R. salmoninarum. Our work also describes a hitherto undescribed lineage (Lineage 3), predominantly from Iceland, where BKD is considered endemic. The detection of endemic reservoirs of R. salmoninarum in European water systems underscores the potential for ongoing pathogen circulation independent of acute outbreaks. This finding emphasizes the importance of further investigation of the mechanisms of pathogen persistence, particularly within environments related to aquaculture, where chronic infection reservoirs could compromise disease management and biosecurity. IMPORTANCERenibacterium salmoninarum, the causative agent of bacterial kidney disease (BKD), is a chronic salmonid pathogen that often presents subclinically, complicating detection and control. Effective management of BKD is therefore crucial for sustainable aquaculture and wild fish conservation. Recognizing the need for comprehensive sampling, previous studies have underscored the importance of a global isolate collection to better understand the epidemiology of the pathogen. While the slow genetic evolution and highly conserved genome of the bacterium have reduced the resolution of conventional typing methods in the past, applying whole genome sequencing has enabled its molecular tracing at the outbreak level. Here, we present the largest phylogenomic analysis of R. salmoninarum to date, including sequences from Denmark, Iceland, and the Faroe Islands for the first time. This expanded dataset elucidates past and present movements of the pathogen in European waters, providing actionable insights to support development of targeted BKD management and biosecurity strategies.

genomics↗