Gene Expression and Epidemiology
Mordecai, G.J. et al. "Aquaculture mediates global transmission of a viral pathogen to wild salmon." Science Advances (2021)
Objective: illuminate the epidemiology of piscine orthoreovirus-1 (PRV-1) in wild fish populations, particularly in endangered wild Pacific salmon
Utilization of Standard BioTools™ products: • Biomark™ HD system
• IFC Controller HX
• 96.96 Dynamic Array™ IFCs Conclusions: • Atlantic salmon aquaculture may have facilitated PRV-1 spread from Europe to the North and Southeast Pacific
• PRV-1 in endangered wild Pacific salmon may be fueled by aquacultural transmission, based on phylogeographic analyses and rtPCR surveillance
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SALMON CASE STUDY
Objective: The objective of this study was to measure gene expression levels of Hemocyte immune response genes when exposed to White Spot Syndrome Virus (WSSV) and Fusarium solani (fungal) in order to understand the molecular mechanisms driving shrimp-pathogen interactions to develop strategies to control disease outbreaks in shrimp production systems with L. vannamei. Utilization of Standard BioTools products: Biomark System NanoFlex 4-IFC Controller 96.96 dynamic arrays Real-Time PCR Analysis Software Conclusions: Genes that were monitored showed up regulation and down regulation over the time course study. Results reported can serve as immunomarkers for mortality events and could help reduce the loss in shrimp production systems
Results
• Origin of PRV-1 in the NE Pacific suggested to have diverged from a strain in the Atlantic in 1989
• PRV-1 prevalence in wild Chinook salmon was closely tied to farm proximity, suggesting transmission from farm to wild
• Phylogenetic reconstruction showed that wild and farmed salmon shared clades, indicating PRV-1 transmission
Conclusions
• Freshwater hatcheries are a source of PRV transmission to wild salmon populations
• Standard BioTools IFCs enabled high-throughput pathogen detection in thousands of samples, providing a fast, cost- effective solution over traditional qPCR and sequencing methods
Results and conclusions
Methods
• Data was collected using the 96.96 GE IFC on Biomark HD to quantify the presence and relative load of viral PRV RNA (Chinook n=6,791, coho n=2,165, sockeye n=4,140)
• Samples were sequenced with NGS
• Phylogenetic analyses were performed to track the evolution of PRV-1 in wild and aquaculture groups
• PRV epidemiological modeling performed to track PRV prevalence in aquaculture and describe the distance between wild salmon vs. aquaculture
Background
• PRV causes moderate to severe pathological changes in salmon, endangering wild populations and resulting in downstream effects in the ecosystem
• The introduction and origin of PRV-1 into wild salmon populations is unclear, thought to potentially be from farmed fish/aquaculture
• The authors analyzed viral genomes to help determine the evolutionary history of PRV and quantify transmission dynamics between farm and wild salmon populations
