New test ‘fishes’ for multiple respiratory viruses using DNA as ‘bait’

A brand new test that ‘fishes’ for multiple respiratory viruses directly using single strands of DNA as ‘bait’, and offers extremely correct ends in below an hour, has been developed by Cambridge researchers.

The test makes use of DNA ‘nanobait’ to detect the most typical respiratory viruses – together with influenza, rhinovirus, RSV and COVID-19 – on the identical time. In comparability, PCR (polymerase chain response) exams, whereas extremely particular and extremely correct, can solely test for a single virus at a time and take a number of hours to return a end result.

While many frequent respiratory viruses have related signs, they require totally different therapies. By testing for multiple viruses directly, the researchers say their test will guarantee sufferers get the proper remedy shortly and will additionally cut back the unwarranted use of antibiotics.

In addition, the exams can be utilized in any setting, and may be simply modified to detect totally different micro organism and viruses, together with potential new variants of SARS-CoV-2, the virus which causes COVID-19. The outcomes are reported within the journal Nature Nanotechnology.

The winter chilly, flu and RSV season has arrived within the northern hemisphere, and healthcare staff should make fast choices about remedy when sufferers present up of their hospital or clinic.

Many respiratory viruses have related signs however require totally different therapies: we wished to see if we might search for multiple viruses in parallel. According to the World Health Organization, respiratory viruses are the reason for loss of life for 20% of kids who die below the age of 5. If you might provide you with a test that might detect multiple viruses shortly and precisely, it might make an enormous distinction.”

Filip Bošković, paper’s first creator from Cambridge’s Cavendish Laboratory

For Bošković, the analysis can also be private: as a younger little one, he was in hospital for virtually a month with a excessive fever. Doctors couldn’t work out the reason for his sickness till a PCR machine turned obtainable.

“Good diagnostics are the key to good treatments,” stated Bošković, who’s a PhD pupil at St John’s College, Cambridge. “People show up at hospital in need of treatment and they might be carrying multiple different viruses, but unless you can discriminate between different viruses, there is a risk patients could receive incorrect treatment.”

PCR exams are highly effective, delicate and correct, however they require a chunk of genome to be copied thousands and thousands of instances, which takes a number of hours.

The Cambridge researchers wished to develop a test that makes use of RNA to detect viruses instantly, with out the necessity to copy the genome, however with excessive sufficient sensitivity to be helpful in a healthcare setting.

“For patients, we know that rapid diagnosis improves their outcome, so being able to detect the infectious agent quickly could save their life,” stated co-author Professor Stephen Baker, from the Cambridge Institute of Therapeutic Immunology and Infectious Disease. “For healthcare workers, such a test could be used anywhere, in the UK or in any low- or middle-income setting, which helps ensure patients get the correct treatment quickly and reduce the use of unwarranted antibiotics.”

The researchers primarily based their test on buildings constructed from double strands of DNA with overhanging single strands. These single strands are the ‘bait’: they’re programmed to ‘fish’ for particular areas within the RNA of goal viruses. The nanobaits are then handed by means of very tiny holes referred to as nanopores. Nanopore sensing is sort of a ticker tape reader that transforms molecular buildings into digital info in milliseconds. The construction of every nanobait reveals the goal virus or its variant.

The researchers confirmed that the test can simply be reprogrammed to discriminate between viral variants, together with variants of the virus that causes COVID-19. The strategy permits close to 100% specificity as a result of precision of the programmable nanobait buildings.

“This work elegantly uses new technology to solve multiple current limitations in one go,” stated Baker. “One of the things we struggle with most is the rapid and accurate identification of the organisms causing the infection. This technology is a potential game-changer; a rapid, low-cost diagnostic platform that is simple and can be used anywhere on any sample.”

A patent on the expertise has been filed by Cambridge Enterprise, the University’s commercialization arm, and co-author Professor Ulrich Keyser has co-founded an organization, Cambridge Nucleomics, centered on RNA detection with single-molecule precision.

“Nanobait is based on DNA nanotechnology and will allow for many more exciting applications in the future,” stated Keyser, who relies on the Cavendish Laboratory. “For commercial applications and roll-out to the public we will have to convert our nanopore platform into a hand-held device.”

“Bringing together researchers from medicine, physics, engineering and chemistry helped us come up with a truly meaningful solution to a difficult problem,” stated Bošković, who acquired a 2022 PhD award from Cambridge Society for Applied Research for this work.

The analysis was supported partly by the European Research Council, the Winton Programme for the Physics of Sustainability, St John’s College, UK Research and Innovation (UKRI), Wellcome, and the National Institute for Health and Care Research (NIHR) Cambridge Biomedical Research Centre.


Journal reference:

Bošković, F., et al. (2023) Simultaneous identification of viruses and viral variants with programmable DNA nanobait. Nature Nanotechnology.

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