New scalable approach for the diagnosis of multiple respiratory viruses

Cambridge scientists have created a novel test that “fishes” for many respiratory viruses at once using single strands of DNA as “bait” and provides extremely accurate results in under an hour.

The test employs DNA “nanobait” to identify multiple respiratory viruses at the same time, including influenza, rhinovirus, RSV, and COVID-19. In comparison, while PCR (polymerase chain reaction) tests are highly specific and reliable, they can only test for a single virus at a time and take several hours to provide a result.

While many common respiratory viruses cause symptoms that are similar, they demand different treatments. The experts claim that by checking for numerous viruses at once, their test will assure that patients receive the appropriate treatment as soon as possible and may help prevent the unnecessary use of antibiotics.

Furthermore, the tests can be utilized in any setting and simply adjusted to detect various bacteria and viruses, including possibly novel variants of SARS-CoV-2, the virus that causes COVID-19. The findings were published in the journal Nature Nanotechnology.

The winter cold, flu, and RSV season have begun in the northern hemisphere, and healthcare workers must make treatment decisions quickly when patients arrive at their hospitals or clinic.

Many respiratory viruses have similar symptoms but require different treatments: we wanted to see if we could search for multiple viruses in parallel. According to the World Health Organization, respiratory viruses are the cause of death for 20% of children who die under the age of five. If you could come up with a test that could detect multiple viruses quickly and accurately, it could make a huge difference.”

Filip Bošković, Study First Author, Cavendish Laboratory, University of Cambridge

For Bošković, the study is particularly personal: as a child, he spent nearly a month in the hospital with a high fever. Doctors were unable to determine the reason for his disease until a PCR machine became available.

Bošković, who is a PhD student at St John’s College, Cambridge adds, “Good diagnostics are the key to good treatments. 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 tests are robust, sensitive, and precise, but they demand millions of copies of the genome, which takes several hours.

Cambridge scientists aimed to create a test that detects viruses directly using RNA, without the need to clone the genome, but with a high enough sensitivity to be beneficial 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. 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.”

Stephen Baker, Study Co-Author and Professor, Cambridge Institute of Therapeutic Immunology and Infectious Disease

The investigators’ experiment was based on constructs made of double strands of DNA with overhanging single strands. These single strands serve as “bait,” as they are engineered to “fish” for certain regions of target viruses’ RNA.

The nanobaits are then transmitted through nanopores, which are extremely small holes. Nanopore sensing functions similar to a ticker tape reader, converting chemical structures into digital information in milliseconds. Each nanobait’s structure discloses the target virus or its variant.

The researchers demonstrated that the test may be simply reprogrammed to distinguish different viral variants, including COVID-19 virus variants. Because of the accuracy of the programmable nanobait structures, the technique achieves nearly 100% specificity.

This work elegantly uses new technology to solve multiple current limitations in one go. 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.”

Stephen Baker, Study Co-Author and Professor, Cambridge Institute of Therapeutic Immunology and Infectious Disease

Cambridge Enterprise, the University’s commercialization arm, has filed a patent on the technique, and co-author Professor Ulrich Keyser has co-founded Cambridge Nucleomics, a firm focused on RNA detection with single-molecule precision.

Keyser who is based at the Cavendish Laboratory states, “Nanobait is based on DNA nanotechnology and will allow for many more exciting applications in the future. 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,” concludes Bošković, who received a 2022 PhD award from the Cambridge Society for Applied Research for this research.