High throughput wild type measles quantification in settled solids using digital RT-PCR v1

We developed and validated a hydrolysis probe-based RT-qPCR assay for specific detection of wild-type measles virus RNA in wastewater that eliminates cross-reactivity with vaccine strains. The wild type measles assay targets the 3′ region of the measles N gene with redesigned probe and reverse primer sequences optimized for circulating genotypes B3 and D8. In vitro validation demonstrated no cross-reactivity against 23 common respiratory pathogens or measles vaccine strains.