Molecular epidemiological study on Infectious Pancreatic Necrosis Virus isolates from aquafarms in Scotland over three decades

• Main Author: Ulrich, Kristina
• Other Authors: Weidmann, Manfred, Bekaert, Michael
• Format: Doctoral or Postdoctoral Thesis
• Language: English
• Published: University of Stirling 2018
• Subjects: Infectious Pancreatic Necrosis Virus; IPNV; Codon Adaptation Index; CAI; Virus; Evolution; Next Generation Sequencing; NGS; MinION; Atlantic salmon; Rainbow trout; RNA viruses; Salmo salar
• Online Access: http://hdl.handle.net/1893/28340; http://dspace.stir.ac.uk/bitstream/1893/28340/1/Kristina_Ulrich_PhD_thesis_04112018.pdf; http://dspace.stir.ac.uk/bitstream/1893/28340/2/Kristina_Ulrich_PhD_thesis_04112018_appendix_scripts.pdf

Introduction RNA viruses are economically important pathogens of fish, and among these viruses, infectious pancreatic necrosis virus (IPNV) is of particular concern for the aquaculture industry, especially for farmed rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar). This non-enveloped aquatic virus, which was first isolated in the UK in 1971, belongs to the family of Birnaviridae and has a bi-segmented dsRNA genome of about 6kb. IPNV is classified in 6 genogroups with correspondence to 10 known serotypes and an additional proposed genogroup of marine aquabirnaviruses (MABV). IPNV causes high mortality in fry and a reduced mortality in adult fish, respectively. Fish, which survive, can become carriers and this can lead to a clinical outbreak by releasing infective material into water or by vertical transmission via oocytes, milt and seminal fluids. Methods This project aimed at determining the phylogeny and genomic changes of IPNV in Scotland by whole genome sequence analysis of IPNV isolates (diagnostic TCID50 supernatants) spanning 3 decades since 1982, using next generation sequencing technology. Viral RNA of IPNV culture supernatant (CHSE-214 and TO cell culture) was processed for next generation sequencing on an Illumina MiSeq platform. Library preparation was performed using the Nextera XT DNA Library Kit, prior to sequencing according to the manufacturer’s MiSeq Reagent Kit v3 (150cycles) protocol. To optimize whole genome next generation sequencing for IPNV, we compared two RNA processing protocols, the Glasgow (GLAP) and the Goettingen protocol (GOEP) with focus on missing terminal nucleotides after a de novo genome assembly. Sequences were used to determine the phylogeny and selection pressure on the genome as well as a possible virus-host adaptation. Results The results showed that both protocols were able to give full length genomes as well as genomes with missing terminal nucleotides. The phylogenetic analysis of 57 sequenced IPVN isolates shows that 78.95 % of the isolates group ...