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12 Feb 2024

Sequencing from COVID-19 rapid antigen devices possible paradigm shifter in respiratory infection surveillance

People with respiratory symptoms may use a COVID-19 rapid antigen test (RAT) to check for the SARS-CoV-2 virus, before discarding the test. Although a test may be negative for COVID-19, these individuals may have a different viral infection, such as influenza or Respiratory Syncytial Virus (RSV).

Using Polymerase Chain Reaction (PCR) and whole genome sequencing on used RAT devices, Doherty Institute scientists identified the presence of non-SARS-CoV-2 viruses in the test samples. The findings of this study suggest that these RATs could potentially serve as a valuable tool for detecting various respiratory viruses, thus enhancing global surveillance efforts.

COVID-19 RATs have become commonplace in community and healthcare settings such as emergency departments, aged care facilities, schools and regional centres, offering a cost-effective and quick alternative to more time-consuming gene-based tests.

University of Melbourne’s Dr Michael Moso, an infectious diseases physician and clinical PhD student at the Doherty Institute, also co-first author of the paper published in Lancet Microbe, explained how the innovative method they developed leverages COVID-19 RAT devices through further analysis of the samples present on the test strips.

“In our study, we showed that COVID-19 RATs could be further employed to detect other respiratory viruses. After collecting and transporting the tests to the lab, we conducted PCR testing and performed genome sequencing to identify other potential respiratory pathogens,” said Dr Moso.

The scientists used a technique developed by the Victorian Infectious Diseases Reference Laboratory (VIDRL) to sequence viruses from the devices containing the deposited sample. About two-thirds of archival samples used in the study tested positive for respiratory viruses in RATs, with varying detection rates for different viruses, while some samples collected from the Royal Melbourne Hospital’s emergency department tested positive for various respiratory viruses. Sequencing efforts successfully assembled most viral genomes, demonstrating the effectiveness of the methods used in the study in detecting a range of respiratory viruses.

“With this technique, we were able to detect various respiratory viruses from the tests, including influenza A and B, human metapneumovirus (hMPV), rhinovirus, adenovirus, parainfluenza and other seasonal coronaviruses,” added Dr Moso.

University of Melbourne’s Professor Deborah Williamson, Honorary Professorial Fellow in Infectious Diseases at the Doherty Institute and senior author, said the research highlights the important role this method can play in public health and pandemic preparedness.

“Being able to analyse COVID-19 RAT samples for other viruses is a game changer for widespread surveillance of respiratory viruses, especially in areas not easily captured by current methods of testing. It could also facilitate the rapid expansion of pathogen tracking capabilities during outbreak situations,” said Professor Williamson.

“More broadly, the methods developed and used in this study are extremely valuable in the context of pandemic preparedness and highlights the need to have ‘off the shelf’ innovative tools ready to deploy.”

Respiratory viruses such as COVID-19, Influenza and RSV often affect the nose, throat, bronchi and, occasionally, lungs. Pregnant women, children under five (5), the elderly and individuals with chronic medical conditions are at higher risk of infection and complications from infection. An estimated one billion cases of seasonal influenza are detected annually, and more than half result in severe illness. The costly process of accurately detecting the various respiratory viruses has hampered a clear picture and knowledge of disease prevalence across communities, a situation that the current ease of access to RATs can change. 

The researchers posit that additional research will be needed to optimise storage and transport conditions, and ensure maximal recovery of genetic information in the future. Additionally, there is a need to conduct the study in wider clinical and public health settings and with more samples. 

Peer review: Moso M, et al. Non-SARS-CoV-2 respiratory viral detection and whole genome sequencing from COVID-19 rapid antigen test devices: A laboratory evaluation study. Lancet Microbe (2024). DOI: 10.1016/S2666-5247(23)00375-0

Funding: Australian Government Medical Research Future Fund, Australian National Health and Medical Research Council.