Wastewater testing during the South African 2022-2023 measles outbreak demonstrates the potential of environmental surveillance to support measles elimination

Abstract Background Surveillance is a key component of the WHO 2030 measles elimination strategy. Wastewater and environmental surveillance (WES) has successfully supported polio surveillance, however, it has not been applied to measles control. Aim We developed a measles virus (MeV) digital-PCR (dPCR) assay using WHO recommended clinical primer-probes and applied it to retained wastewater samples from national SARS-CoV-2 wastewater sentinel surveillance sites. We compared results with national clinical measles surveillance data. Setting Wastewater concentrates were collected from 47 SARS-CoV-2 wastewater surveillance sites across South Africa. Methods We determined the limit of detection using the assay on serial dilutions of MeV positive controls. Subsequently we conducted batch testing on wastewater concentrates retained at -20°C for up to 15 months and compared wastewater results with national laboratory-confirmed measles case data by district and epidemiological week. Results Our assay identified 43/2149 (2%) samples containing MeV RNA in concentrations ranging from 1.97 – 165.8 genome copies/mL. Amongst 27 week-district instances where at least one MeV positive wastewater sample was detected, no clinical cases were detected in 13 (48%) of these. Conclusion Despite likely RNA degradation, it was possible to detect MeV in wastewater samples in districts where clinical surveillance failed to identify cases. Contribution WES has evident potential to strengthen surveillance in support of the measles elimination agenda. With immediate processing and improved wastewater RNA concentration methods, WES sensitivity will likely increase. Funding This work was funded by BMGF (INV-049271)