Spatially Informed Wastewater Differentiation among Locations during an Ongoing Measles Outbreak in Texas, USA

Though reverse transcription-quantitative polymerase chain reaction (RT-qPCR), RT digital PCR (RT-dPCR), and RT digital droplet PCR (RT-ddPCR) are commonly used for wastewater-based epidemiology and surveillance (WBE/WBS), differences among the platforms exist. While RT-ddPCR has been suggested as an ideal approach to use globally for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) monitoring, access to RT-qPCR instrumentation is more widely available in many regions, and it is more economical. Subsequently, a larger number of studies have used RT-qPCR for SARS-CoV-2 wastewater monitoring, along with additional pathogens that can be detected with WBS. In this study, we employed RT-qPCR and RT-dPCR platforms for the comparative detection of vaccine (A genotype Edmonston) and wild-type (D8 genotype) measles RNA from wastewater in nearby cities separated by <50 km during an ongoing measles outbreak in Texas, USA, in addition to several other locations up to 30–1400 km from the outbreak location. The limit of detection (LOD) for each methodology was evaluated using a synthetic gBlock DNA gene fragment of known concentrations, with comparable LODs identified for both the RT-dPCR (∼0.5 gc/μL) and RT-qPCR (∼0.4 gc/μL) platforms. Using composite supernatant-solid wastewater samples, RNA aliquots were analyzed on each platform in parallel. The RT-qPCR platform demonstrated a higher detection rate than RT-dPCR for the vaccine strain quantified in wastewater samples, with equivalent detections for the wild-type strain in both platforms, and notable differences in the gene copies quantified in wastewater based on the platform. Our study identifies that regardless of PCR methodology employed, WBS is a particularly valuable approach for the spatially informed differentiation of measles during rapid response to an active outbreak.