Highly Accurate Test "Fishes" For Respiratory Viruses Using DNA as Bait

Following the arrival of the winter cold, flu and RSV season in the northern hemisphere, healthcare workers are required to take quick decisions about the treatment to be given to patients presenting themselves at hospitals or clinics. PCR (polymerase chain reaction) tests are highly specific and accurate, but are capable of testing for only a single virus at a time and return results after several hours. Now, a new test uses single strands of DNA as ‘bait’ to ‘fish’ for multiple respiratory viruses at once and delivers accurate results in less than an hour.

The new test developed by researchers at University of Cambridge (Cambridge, UK) uses DNA ‘nanobait’ to detect common respiratory viruses – including influenza, rhinovirus, RSV and COVID-19 – simultaneously. Many of the common respiratory viruses have similar symptoms, but need different treatments. The new approach tests for multiple viruses at once, allowing the right treatment to be administered quickly to the patients and minimizing the unwarranted use of antibiotics. Additionally, it is possible for healthcare workers to use the test in any setting, and it can also be easily modified to detect different bacteria and viruses, including future SARS-CoV-2 variants.

While PCR tests are powerful, sensitive and accurate, they require a piece of genome to be copied millions of times – a process that can take several hours. The researchers set out to develop a test that uses RNA to detect viruses directly without the need for copying the genome, but had sufficiently high sensitivity for use in a healthcare setting. The team developed the test based on structures built from double strands of DNA with overhanging single strands. These single strands act as the ‘bait’ meaning they are programmed to ‘fish’ for specific regions in the RNA of target viruses. The nanobaits are then passed through very tiny holes called nanopores. Nanopore sensing is similar to a ticker tape reader that transforms molecular structures into digital information within milliseconds. Each nanobait’s structure reveals the target virus or its variant. The researchers demonstrated that it is possible to easily reprogram the test to allow it to discriminate between viral variants, including SARS-CoV-2 variants. The precision of the programmable nanobait structures allows the approach to offer almost 100% specificity.

“Good diagnostics are the key to good treatments,” said Filip Bošković from Cambridge’s Cavendish Laboratory. “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.”

“For patients, we know that rapid diagnosis improves their outcome, so being able to detect the infectious agent quickly could save their life,” said 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.”

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