A dual-duplex RT-dPCR surveillance strategy for discriminating avian and seasonal influenza viruses in wastewater

Abstract The highly pathogenic avian influenza (HPAI) A(H5Nx) viruses, specifically those of clade 2.3.4.4b, remain a major concern for global animal and public health. The current epidemiological situation in Europe and beyond reveal an alarming increase in spread and occurrence of these viruses, underscoring the need for enhanced surveillance and proactive intervention measures. We propose a dual duplex strategy (combining CDC Flu SC2 multiplex and JRC HA-JRC MP duplex assays) for discriminating avian and seasonal influenza viruses in wastewater, supporting rapid strain-specific environmental monitoring.