Tracking wild-type measles virus in wastewater using multiplex RT-dPCR, A novel tool for measles surveillance

A multiplex digital RT-PCR (RT-dPCR) assay targeting three distinct regions of the measles virus genome was developed for wastewater surveillance. This method was applied to 40 mL samples collected at the inlets of two French wastewater treatment plants located in urban areas where clinical measles cases involving genotypes B3 and D8 had been reported. Detection was performed retrospectively on weekly samples collected between January and July 2024 as part of the routine national SARS CoV-2 wastewater surveillance network. Positive results were obtained in 27.3 % and 66.7 % of samples, with viral concentrations ranging between 5.8 × 10² gc/L – 4.6 × 10³ gc/L and 1.8 × 10³ gc/L – 2.2 × 10⁴ gc/L, respectively. A complementary RT-dPCR, specifically targeting vaccine strain genomes, confirmed that detected signals originated from wild-type viruses and not from recent vaccination. These results confirm that the developed multiplex RT-dPCR assay can reliably detect measles virus in wastewater, even in areas with a low number of reported cases. Wastewater surveillance therefore represents a promising complementary tool for monitoring measles circulation at the community level and could support disease elimination efforts by detecting low-level residual circulation that may go undetected by clinical surveillance.