The effects and genetic diversity of salmon gill poxvirus in freshwater Atlantic salmon in Scotland

Abstract

Salmon gill poxvirus (SGPV) is an emerging pathogen causing significant losses in the Scottish Atlantic salmon farming industry. Clinical presentation varies widely, from sub-clinical infection to severe clinical signs and gill pathology. Understanding the causes for this variation in clinical presentation and mortality is key to mitigating the significant economic losses caused by this virus. To date, little research has been done in Scotland on the effects of SGPV infection, and why disease presentation is so unpredictable. In this thesis, a natural outbreak of SGPV disease in an enclosed freshwater system was studied. A range of SGPV positive samples from geographically distinct detections were sequenced to explore the genetic diversity of SGPV in Scotland. During the naturally-occurring outbreak, histological findings showed the gills to be the primary target organ, with severe pathology correlating with high viral loads. Common pathologies associated with SGPV disease (SGPVD) were found in the gills, including severe hyperplasia, hypertrophy and widespread inflammation. However, epithelial apoptosis, described in many published studies as the pathognomonic clinical sign of SGPV infection, was only found in low levels during this study. Downregulation of anti-viral immune markers MDA-5 and Mx was observed in clinically diseased fish, when compared with sub-clinically infected fish, which suggests that the host antiviral immune response is being differentially modulated. Samples positive for SGPV were collected from outbreaks and incidental detections across six geographically distinct sites in Scotland and used for whole-genome sequencing and phylogenetic analysis. Genetic diversity was found to be limited between these cases, with sequence similarity of >85% in near-complete genomes. Some areas of nucleotide variation were also identified, possibly representing targets for phylogenetic studies. This work provides an insight into the pathogenesis of a natural outbreak that will aid the control and monitoring of SGPVD on freshwater Atlantic salmon farms.