Three-in-one test developed for COVID-19 surveillance

A new type of COVID-19 test could help streamline the process of identifying COVID-19 cases, tracking SARS-CoV-2 variants and detecting co-infecting viruses — three different diagnostic procedures that currently require separate assays and complex workflows carried out in highly specialised facilities. Researchers at the King Abdullah University of Science and Technology (KAUST) have now combined all three kinds of tests into a single procedure that should allow for point-of-care tracking of COVID-19 and its many variants, as described in the journal Med.

The test involves a briefcase-sized mini laboratory that avoids all the slow and expensive techniques that are standard for COVID-19 screening and monitoring. It takes advantage of a recent genetic method (called recombinase polymerase amplification) and a next-generation portable sequencer to quickly detect the presence of viral sequences and provide read-outs — in up to 96 patient samples at a time.

KAUST stem cell biologist Mo Li, in collaboration with researchers from Saudi Arabia, the United States and Spain, designed the test to decode five segments of the SARS-CoV-2 genome, each chosen to help guide variant tracking. They also incorporated assays for three common respiratory viruses that can cause symptoms similar to COVID-19.

Working with clinical collaborators from hospitals in Mecca, Medina and Jeddah, the team validated the technique — termed NIRVANA — using nose and throat swabs from people suspected of having SARS-CoV-2 infections. They also tested wastewater samples collected from municipal sewage at KAUST to show how the method could allow for population-level surveillance of SARS-CoV-2 and other viruses.

“NIRVANA can rapidly diagnose multiple viral infections in a high-throughput manner,” said Chongwei Bi, a PhD student in Li’s lab. What’s more, when it comes to SARS-CoV-2 monitoring, “it can simultaneously detect the virus and report its mutations,” Bi said. However, one limitation of the test is that it can only detect SARS-CoV-2 mutations in selected genomic regions — and as new variants of concern crop up, those regions might need to be updated to reflect the evolving nature of the virus.

Li described the all-in-one test, which he is continuing to refine for large-scale deployment, as “a promising integrated solution for rapid field-deployable detection and mutational surveillance of pandemic viruses”. He is now seeking to collaborate with hospitals to test the platform in the clinic.

Image ©2021 KAUST

Please follow us and share on Twitter and Facebook. You can also subscribe for FREE to our weekly newsletters and bimonthly magazine.