Genomic Epidemiology of Salmonid Alphavirus in Norwegian Aquaculture Reveals Recent Subtype-2 Transmission Dynamics and Novel Subtype-3 Lineages

Abstract

Viral disease poses a major barrier to sustainable aquaculture, with outbreaks causing large economic losses and growing concerns for fish welfare. Genomic epidemiology can support disease control by providing rapid inferences on viral evolution and disease transmission. In this study, genomic epidemiology was used to investigate salmonid alphavirus (SAV), the causative agent of pancreas disease (PD) in Atlantic salmon. Our aim was to reconstruct SAV subtype-2 (SAV2) diversity and transmission dynamics in recent Norwegian aquaculture, including the origin of SAV2 in regions where this subtype is not tolerated under current legislation. Using nanopore sequencing, we captured ~90% of the SAV2 genome for n = 68 field isolates from 10 aquaculture production regions sampled between 2018 and 2020. Using time-calibrated phylogenetics, we infer that, following its introduction to Norway around 2010, SAV2 split into two clades (SAV2a and 2b) around 2013. While co-present at the same sites near the boundary of Møre og Romsdal and Trøndelag, SAV2a and 2b were generally detected in non-overlapping locations at more Southern and Northern latitudes, respectively. We provide evidence for recent SAV2 transmission over large distances, revealing a strong connection between Møre og Romsdal and SAV2 detected in 2019/20 in Rogaland. We also demonstrate separate introductions of SAV2a and 2b outside the SAV2 zone in Sognefjorden (Vestland), connected to samples from Møre og Romsdal and Trøndelag, respectively, and a likely 100 km Northward transmission of SAV2b within Trøndelag. Finally, we recovered genomes of SAV2a and SAV3 co-infecting single fish in Rogaland, involving novel SAV3 lineages that diverged from previously characterized strains >25 years ago. Overall, this study demonstrates useful applications of genomic epidemiology for tracking viral disease spread in aquaculture.

Emerging technologies revolutionising disease diagnosis and monitoring in aquatic animal health

“…Nanopore sequencing is a promising tool for aquaculture to sequence genomes of various fish species 99–101 and pathogens affecting aquaculture, including novel pathogens. Nanopore sequencing was successfully utilised to sequence the novel subtype‐3 lineage of salmon alphavirus, identifying a previously unrecognised strain within the alphavirus family 102 . It can detect pathogens easily without requiring the samples to be taken to a laboratory.…”

“…Rapid and accurate identification of viral pathogens can help with prompt planning and management to prevent future outbreaks. Nanopore technology has been shown to accurately identify Salmon alphavirus (SAV) and infectious salmon anaemia virus (ISAV), which cause significant economic losses for farmers in aquaculture 37,102 . Another group of researchers has also employed Oxford nanopore sequencing technology to enhance Tilapia Lake virus (TiLV) detection with similarity between Oxford nanopore sequencing and other sequencing methods, such as Illumina and Sanger, was found to be around 99%–100% 103 .…”

“…Nanopore sequencing was successfully utilised to sequence the novel subtype-3 lineage of salmon alphavirus, identifying a previously unrecognised strain within the alphavirus family. 102 It can detect pathogens easily without requiring the samples to be taken to a laboratory. Rapid and accurate identification of viral pathogens can help with prompt planning and management to prevent future outbreaks.…”

“…Nanopore technology has been shown to accurately identify Salmon alphavirus (SAV) and infectious salmon anaemia virus (ISAV), which cause significant economic losses for farmers in aquaculture. 37,102 Another group of researchers has also employed Oxford nanopore sequencing technology to enhance Tilapia Lake virus (TiLV) detection with similarity between Oxford nanopore sequencing and other sequencing methods, such as Illumina and Sanger, was found to be around 99%-100%. 103 In addition to viral disease diagnostics, nanopore sequencing has been implemented in other pathogenic bacteria and parasites.…”

Whole Genome Sequencing and Pan-Genomic Analysis of Multidrug-Resistant Vibrio cholerae VC01 Isolated from a Clinical Sample

“…The fast5 data from MinKNOW were converted to fastq format using the Guppy base caller in fast mode on a MinIT device (Oxford Nanopore, Oxford, UK). The fastq reads were demultiplexed using qcat v1.0.1.3 [ 17 ]. All short-read sequences were first considered to detect the contamination of the other organisms.…”