Unknown virus in ‘throwaway’ DNA discovered
A chance discovery has opened up a new method of finding unknown viruses
Next-Generation Sequencing has revolutionised genomics research and is currently used to study and understand genetic material. It allows scientists to gather vast amounts of data, from a single piece of DNA, which is then collated into huge, online, genome databases that are publically accessible.
Dr Aris Katzourakis, an Associate Professor, and Dr Amr Aswad, Research Associate at Oxford’s Department of Zoology, initially discovered the new use for the database, by chance. While looking for an ancient herpes virus in primates, they found evidence of two new undocumented viruses.
The viral data collected, that may otherwise be discarded as a nuisance, is a unique resource for looking for both pathogenic and benign viruses that would otherwise have remained undiscovered.
Spurred by their accidental discovery, 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 recognisable viral DNA. Sure enough, 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 that the viral evidence was not simply a fluke, or a data processing error, they tested additional samples from a local supermarket and sushi restaurant. The same viral fragments were found in the bought samples.
Study author Dr Aris Katzourakis, from Oxford University’s Department of Zoology, said: ‘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.’
The key to the success of this research is in its inter-disciplinary approach, combining techniques from two fields: evolutionary biology and genomics. Together, these are at the core of the new field of paleovirology – the study of ancient viruses that have integrated their DNA into that of their hosts, sometimes millions of years ago. Each technique used has been developed to analyse huge quantities of DNA sequence data.
Co-author and Research Associate at Oxford’s Department of Zoology and St. Hilda’s College, Dr Amr Aswad, said: ‘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.’
Finding new viruses has historically not been an easy process. Cells do not grow on their own, so must be cultured in a laboratory before they can be analysed, which involves months of work. But the Oxford research represents a massive opportunity for the future.
Beyond this study, the approach could be used to identify viruses in a range of different species, particularly those known to harbour transmissible disease. Bats and rodents, for example, are notorious carriers of infectious disease that they are seemingly immune to. Insects such as mosquitoes are also carriers of viral diseases that harm humans, such as Zika. If applied effectively the method could uncover other viruses before an outbreak even happens.
Dr Katzourakis added: ‘One of the real strengths of this technique, as compared to more traditional virology approaches, is the speed of discovery, and the lack of reliance on identifying a diseased individual. The viral data collected, that may otherwise be discarded as a nuisance, is a unique resource for looking for both pathogenic and benign viruses that would otherwise have remained undiscovered.’
The team will next begin to identify the impact of the viruses and whether they have any long term implications for disease, or commercial fish-farming. While an infectious virus may not cause disease in its natural host - in this case, fish. there is a risk of cross-species transmission to either farmed fish or wild populations. However, the risk to humans is minimal. Dr Aris Katzourakis said: ‘Put it this way, I’m not going to stop eating sashimi.’
Other news from the department science
Start-up Colossal Biosciences Joins Biorescue In Its Mission To Save The Northern White Rhino From Extinction
Colossal will assist the rescue mission by leveraging genome sequencing and gene editing methods to save the endangered species
"For the first time, we have systematically measured the size and abundance of cells across all major tissues and organs"
What's that smell? New gut microbe produces smelly toxic gas but protects against pathogens
Taurine-degrading bacteria influence intestinal microbiome
Wastewater treatment plants as drivers for the energy transition
Technical add-on module can, in principle, turn any wastewater treatment plant into a CO2 sink and decentralized methane production plant
At which age we are at our happiest
An evaluation of over 400 samples shows how subjective well-being develops over the course of a lifespan
New approach to testing for long Covid
Blood vessels in the eye altered with persistent coronavirus symptoms
Researchers create pioneering approaches for the detection of viral antigens
Sybodies: a revolution in biological recognition
New SARS-CoV-2 variant Eris on the rise
SARS-CoV-2 lineage EG.5.1 has an advantage at evading neutralizing antibodies
Does the human brain have an Achilles heel that ultimately leads to Autism?
CHOOSEn fate: one brain organoid’s tale on Autism
Co-crystal improves the water-solubility of ASA
This could benefit patients diagnosed with suspected acute myocardial infarction
Observing nanoparticles with unprecedented precision
Illuminated: Researchers investigate new physical phenomena on the nanoscale with microstructured fibers
Falling Walls announces Science Breakthrough of the Year 2023 laureates
“These outstanding breakthroughs will change the face of the world and impressively prove what ingenuity, curiosity and courage can achieve”
Most read news
Cells with an ear for music release insulin
For the first time, researchers are using music, including Queen's global hit "We will rock you," to stimulate insulin release from cells
"Anti-obesity drugs" normalises brain in obesity
Anti-obesity drug improves associative learning in people with obesity
Microbe of the Year 2023: Bacillus subtilis – for health and technology
Already, Bacillus subtilis is indispensable in many industries, and many more innovations are expected
Younger generation gets sick earlier and more often than older generation
In spite of their advanced age, they are in the middle of life, healthy, active and mentally alert – they are referred to as the “young old”
How sleep deprivation can harm the brain
Sleep deprivation decreases the amount of a factor that protects neurons
A whole new order of bacteria could hold the key to improving biogas production
The discovery was made by researchers from Germany, Spain and the Netherlands
How to inactivate common cold viruses
In the cold season, cold viruses are everywhere. But we can do something about it
How minimal genetic differences can turn healthy food into a deadly danger
You are what you eat - this old saying could take on a new dimension according to latest research results
New approach to testing for long Covid
Blood vessels in the eye altered with persistent coronavirus symptoms
More news from our other portals
Major breakthrough in the development of electric vehicle batteries
New study finds ways to suppress lithium plating in automotive batteries for faster charging electric vehicles
Blender Bites launches at Walmart USA
The products are to be introduced in about 1,600 stores across the country
Benchtop NMR spectroscopy can accurately analyse pyrolysis oils
More accessible analysis could help develop the potential of bio-oils as an alternative to fossil fuels
Green methanol for shipping and industry: € 10.4 Mio. for the "Leuna100" project
A consortium of two Fraunhofer institutes, DBI-Gastechnologisches Institut Freiberg, Technical University of Berlin and C1 makes industrial history at the Leuna site
Clean water from fog
A property known as photocatalytic memory ensures that this also functions when skies are overcast and at night
Green, sweet and crisp - New apple variety Pia41 approved
The apple bred at the Julius Kühn Institute receives variety protection
Research shows table salt could be the secret ingredient for better chemical recycling
Table salt as the key to the plastics recycling revolution?
Sugar: Small increase in production despite record prices
EU sugar market more than in need of reform to keep medium-sized processing companies competitive
Graphene discovery could help generate hydrogen cheaply and sustainably
Microscopic insights into electrochemical interfaces
Stanford study shows how the meat and dairy sector resists competition from alternative animal products
Scientists use quantum device to slow down simulated chemical reaction 100 billion times
What happens in femtoseconds in nature can now be observed in milliseconds in the lab
New battery holds promise for green energy
Redox-flow battery eliminates costly and inefficient membrane
Fondant under the magnifying glass
New insights into the properties of sweet coating: The results could be used to optimize the industrial production process in the future
Leipzig-based start-up converts CO₂ into green chemicals with patented plasma catalysis
CO₂ recycling as a useful complement to carbon capture and storage
A microchip for Parmigiano Reggiano cheese
Consorzio del Parmigiano Reggiano, p-Chip Corporation, and Kaasmerk Matec Partner to Launch Breakthrough in Food-Safe Digital Tracking Technology
Cleaning water with ‘smart rust’ and magnets
New method for pollutants such as crude oil, glyphosate, microplastics and hormones
A Second Life for Electric Car Batteries
Scientists develop a decision model for retired lithium-ion batteries