How accessible genome sequencing supports sustainable aquaculture

New, affordable technologies are changing the speed and cost at which full-genome sequences can be produced for diverse applications.

For just one example, these advances are aiding the studies of the research group led by Dan Macqueen, professor at the Roslin Institute, looking at viruses affecting aquaculture.

“Sequencing of viral pathogens affecting aquaculture has mainly been done using Sanger sequencing, which is very low throughput. This provides valuable information, typically which viral strain (subtype) you have in a sample. However, it’s not very fine-grained data and takes a lot of time to process a lot of samples,” Macqueen explained.

Portable power

Pointing to how things have changed, he noted a recent project focused on salmonid alphavirus1 infections on Atlantic salmon farms in Norway, which used a technology called a nanopore sequencer.

“It’s a portable sequencer, about the size of a big USB stick, that plugs into a laptop. In one single sequencing experiment, which took a few hours, we sequenced 96 different samples and obtained most of the virus genome back in each. This is transformative compared to how things have been commonly done until now,” he said.

“Such technologies are changing how we can monitor the evolution and spread of pathogens in farmed animals, because this work can be done very cost effectively, at a much greater scale than traditional methods.”

Tracking pathogens over time

A recent project on salmonid alphavirus mapped the spread of a subtype of the virus known as SAV2 between salmon farming regions using genomics — much the same as what was done with Covid-19, when there was an initial rush to establish transmission routes, he explained.

Sequencing, as seen in the pandemic, can also track how viruses change over time. This has helped establish what was behind recent outbreaks of infectious pancreatic necrosis (IPN) in salmon that have been vaccinated and bred for resistance to the IPN virus.

“The work that brought about genetic resistance of farmed salmon to IPN2 is a great example of applying genomic technologies to reduce disease outbreaks through breeding. But two studies3,4 sequenced IPN virus following recent disease outbreaks, revealing the virus is evolving to overcome human interventions that have been controlling it,” he said.

Wider impact requires collaboration

Bringing sequencing into the mainstream for disease surveillance may require “technology transfer” from academic to commercial and regulatory settings, Macqueen suggested. As part of this, a new PhD project led by Macqueen and co-funded by the Sustainable Aquaculture Innovation Centre and PHARMAQ is set to begin later this year.

The project will look to establish databases of virus sequences based on a regular supply of samples from Norway and Scotland, looking at different pathogens including salmonid alphavirus, IPN virus and piscine orthoreovirus. Enabled by affordable, high-throughput technologies, it will be the largest effort of its kind for these pathogens.

“I’m particularly interested in using genomic technologies to support the sustainability of aquaculture in this project to gain new information on recent pathogen spread and evolution, which can be used in future disease-mitigation measures,” he stressed.

“To be effective, such work requires collaboration and cooperation between different producers and regulators. We’re working in open water, so everybody has a stake in controlling the spread of transmissible diseases.”

1 Macqueen DJ, Eve O, Gundappa MK, Daniels RR, Gallagher MD, Alexandersen S, Karlsen M. Genomic epidemiology of salmonid alphavirus in Norwegian aquaculture reveals recent subtype-2 transmission dynamics and novel subtype-3 lineages. Viruses 2021;13(12):2549.

2 Houston RD, Bean TP, Macqueen DJ, Gundappa MK, Jin YH, Jenkins TL, Selly SLC, Martin SA, Stevens JR, Santos EM. Harnessing genomics to fast-track genetic improvement in aquaculture. Nat Rev Genet. 2020;21(7):389-409.

3 Benkaroun J, Muir KF, Allshire R, Tamer C, Weidmann M. Isolation of a new infectious pancreatic necrosis virus (IPNV) variant from a fish farm in Scotland. Viruses 2021;13(3):385.

4 Hillestad B, Johannessen S, Melingen GO, Moghadam HK. Identification of a new infectious pancreatic necrosis virus (IPNV) variant in Atlantic salmon (salmo salar L.) that can cause high mortality even in genetically resistant fish. Front Genet. 2021;12:635185.