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.
Highlights
Six PCR amplicons spanning the salmonid alphavirus (SAV) genome were sequenced in SAV-infected heart tissue from 94 Atlantic salmon individuals (Figures 1 and 2) on the ONT MinION platform
While these sequences share 97.9% nucleotide identity, almost all mapping was to MH708652 (Figure 3A), which is expected as Norwegian SAV2 genomes are more closely related to this sequence than
Mapping depth represents the number of times the base pairs in the genome are covered by the mapped narepresents the number of times the base pairs in the SAV genome are covered by the mapped nopore reads. (B) Frequency histogram depicting the number of samples showing genome-wide nanopore reads. (B) Frequency histogram depicting the number of samples showing genome-wide coverage against the same reference genomes
Summary
Fuelled by recent advances in second and third-generation sequencing, including portable devices such as the MinION platform (Oxford Nanopore Technologies, ONT), genomic sequencing and surveillance programs have gained prominence as tools for monitoring human viral diseases [2,3]. Such efforts are best illustrated by global-scale initiatives to sequence hundreds of thousands of SARSCoV-2 genomes in human populations, which have been instrumental in characterizing genetic diversity and COVID-19 transmission routes [4,5]
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