London Calling 2023: Detection and differentiation of respiratory viral pathogens using near real-time sequencing

In the recent respiratory disease season, we observed increased instances of multiple infections in single patients. Coinfection of influenza and COVID-19 can exacerbate illness severity and clinical impact. Our research aimed to develop a rapid detection and differentiation method for viral infections. We focused on detecting and characterizing co-infections, analyzing both historical and current patient samples. Our real-time Oxford Nanopore sequencing procedure enabled the detection of coexisting viral infections within hours of obtaining samples. We amplified genetic material from respiratory pathogens in collected samples and identified respiratory infections. Over 30 different pathogens were distinguished during multiplex reactions. Using a Flongle Flow Cell, 90 individuals could be analysed at a reduced cost. The ability to  distinguish so many pathogens is not achievable using classical or other molecular methods.