Context: In response to the COVID-19 pandemic the South African Medical Research Council’s Wastewater Surveillance and Research Programme (SAMRC WSARP) has been tracking SARS-CoV-2 viral RNA in wastewater across wastewater treatment plants (WWTPs) across 6 Provinces of South Africa. The objective of WSARP is to conduct long-term surveillance of pathogens and contaminants of emerging concern in wastewater for pandemic preparedness and response.

Methodology: On a weekly basis, raw influent wastewater grab samples are collected at WWTPs. Samples are transported to the laboratory and processed on the same day for the extraction of RNA, after which quantitative real-time polymerase chain reaction (qRT-PCR) is conducted.

Results: The SARS-CoV-2 RNA signal detected in the wastewater has corresponded with COVID-19 cases and assisted in identifying COVID-19 hotspots and guide preparedness strategies. Additionally, the WSARP has identified new mutations within SARS-CoV-2 from WWTPs and detected the community spread of the Delta and Omicron variants in circulation in the Western Cape province driving the third and fourth wave. Cholera detection in wastewater samples was implemented to determine the geographic spread of cholera in South Africa, and gain insight into the potential of wastewater and environmental surveillance to support cholera outbreak management. The SAMRC has further expanded to include the surveillance of 24 pathogens which have been identified as pathogens of concern in and around South Africa.

Conclusions: The results emanating from the WSARP has demonstrated the utility of wastewater and environmental surveillance in South Africa to track pathogens at the community level and guide response strategies.