Researchers have discovered that next-generation sequencing and its associated online DNA databases can be used in viral discovery. They created algorithms that detect DNA from viruses in fish blood or tissue samples, and that could be used to identify viruses in a range of different species.
Drs. Aris Katzourakis and Amr Aswad, research associates at the University of Oxford, initially discovered the new use for the database by accident. While looking for an ancient herpes virus in primates, they found evidence of two new undocumented viruses. They set out to see if they could intentionally achieve the same result. In a separate project to find new fish-infecting herpes viruses, they used the technique to examine more than 50 fish genomes for recognizable viral DNA. In addition to the herpes viruses they were expecting to find, the researchers identified a distant lineage of unusual viruses that may even be a new viral family. The traits were found scattered in fragments of 15 different species of fish, including the Atlantic salmon and rainbow trout. To confirm their findings, they tested additional samples from a local supermarket and sushi restaurant. The same viral fragments were found in the purchased samples.
According to Dr. Katzourakis, “In the salmon genome we found what seems to be a complete and independent viral genome, as well as dozens of fragments of viral DNA that had integrated into the fish DNA. We know from recent studies that viruses are able to integrate into the genome of their host, sometimes remaining there for millions of years. In this case, it looks like the virus may have acquired the ability to integrate by stealing a gene from the salmon itself, which explains how it has become so widespread in the salmon genome.”
“Discovering new viruses has historically been biased towards people and animals that exhibit symptoms of disease. But, our research shows how useful next-generation DNA sequencing can be in viral identification. To many, viral DNA in say, chimp or falcon data is a nuisance, and a rogue contaminant that needs to be filtered from results. But we consider these an opportunity waiting to be exploited, as they could include novel viruses that are worth studying—as we have found in our research. We could be throwing away very valuable data,” noted Dr. Aswad.