A federally funded project at Washington State University’s College of Veterinary Medicine could be a valuable tool in detecting any new viruses that may emerge and threaten important and at-risk aquatic species like salmon.
Throughout the spring and summer months, the college’s Washington Animal Disease Diagnostic Laboratory plays an important role in screening and diagnosing marine and freshwater fish, including during salmon runs on Northwest waterways. Most diseases detected are among those already classified, but the funding has allowed for the establishment of a testing “pipeline” designed to rapidly detect new and emerging diseases that could pose a threat to human and animal populations.
Spearheaded by veterinary pathologist Chrissy Eckstrand, the pipeline – which uses metagenomics and other advanced techniques – has in just the past year led to the detection of a handful of new viruses, including one associated with a potentially fatal disease in farmed coho salmon and a second that is devastating superworm colonies, which are a common food source for birds, reptiles and amphibians in zoos and private collections.
“We have demonstrated our methods work for samples with unknown infections, and now we have more confidence this can be used in real-world disease investigations,” Eckstrand said.
Metagenomics allows entire communities of microorganisms – including viruses – to be studied at the genomic level directly from a single sample, whereas traditional sequencing reads the genetic code of just one targeted organism at a time. The method allows for discovery of viruses by casting a wider net than traditional targeted techniques.
“Metagenomics is not widely used or even available as a diagnostic test by veterinary diagnostic labs,” Eckstrand said, “but its use and other next-generation sequencing modalities are growing and can allow us to perform this work much more rapidly.”
Eckstrand initially received funding in 2019 from the USDA to start up the project at WADDL, which serves as a member of the United States Department of Agriculture’s National Animal Health Laboratory Network (NAHLN), a group of animal disease diagnostic laboratories that provide animal disease surveillance and help respond to outbreaks. Early efforts focused on developing the pipeline, or infrastructure and processes. She was awarded a second grant in 2022 totaling $350,000 to improve the methods and make them more cost-effective and deployable in real-world situations.
“The first grant allowed us to develop the capability, and we demonstrated that it worked the way we wanted it to,” Eckstrand said. “The more recent grant has allowed us to troubleshoot all the parts to make it rapidly deployable for disease detection.”
In the case of the diseased fish, pathologists at WADDL initially suspected the coho salmon were infected with piscine reovirus-1, a virus commonly seen in farmed salmon. Referred to as PRV-1, the virus is associated with heart and skeletal muscle inflammation, or HSMI, which can be fatal to fish.
“One of our lead pathologists looked at the case and said this looks like it should PRV-1, but our usual tests were coming up negative for the virus,” Eckstrand said.
Samples were forwarded to WADDL’s research lab, and using the processes put in place, the team identified a new virus related to PRV-1 that they were able to associate with the disease shown in the fish.
“From that, we can now develop a PCR test for quick and easy diagnosis if we see the same thing and we don’t have to go through the entire process,” Eckstrand said.
Her team also detected a new densovirus after receiving samples of superworms from colonies that were experiencing high morbidity and mortality. Densoviruses infect insects and can cause serious disease in their hosts. Their findings were presented at the American College of Veterinary Pathologists annual conference in November.
“Superworms are a massive food source for a lot of different animals, so the loss of colonies can be catastrophic for the industry and those who rely upon them to feed their animals,” Eckstrand said.