Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the coronavirus disease 2019 (COVID-19). SARS-CoV-2 was first identified in Wuhan, China at the end of 2019. Since then, there has been rapid and extensive spread throughout the world, leading to a declaration of a COVID-19 pandemic by the World Health Organisation (WHO) on the 11th of March 2020.

Although SARS-CoV-2 is mainly transmitted via respiratory droplets and contact routes, viral RNA (genetic material) may also be detected in the stool of COVID-19 patients. Shedding of virus in stool has been reported even before detecting SARS-CoV-2 in respiratory samples and may continue for a duration of 5 to 35 days after respiratory samples were negative for SARS-CoV-2 RNA. Detection of viral RNA in faeces and urine samples is not an indication that the virus is infectious, but may prove useful for tracking viral spread within communities.

Wastewater-based epidemiology, a method of determining the presence of chemicals, pollutants and microbes in raw wastewater or sewage, has been used as a surveillance tool to detect the presence of certain enteric pathogens such as polioviruses. SARS-CoV-2 shedding in stool has been reported to occur in severe, mild, and asymptomatic infections. The fact that asymptomatic individuals, who are usually missed by clinical and laboratory diagnosis, shed virus in their stool and that it is impractical and expensive to screen everyone, makes water-based epidemiology an attractive tool for SARS-CoV-2 surveillance. This method will provide population-based data for effective modelling and allow determination of COVID-19 prevalence in the absence of extensive testing. SARS-CoV-2 wastewater surveillance can also serve as an early warning sign of the presence of SARS-CoV-2 in certain communities, to allow for targeted testing and interventions, and SARS-CoV-2 WBE can also be used to monitor re-emergence after a country has been declared free of SARS-CoV-2.

To date, several countries have successfully implemented WBE SARS-CoV-2 surveillance using different methods for sewage concentration and SARS-CoV-2 RNA extraction. In South Africa, proof-of-concept has been demonstrated by several laboratories, including the Centre for Vaccines and Immunology at the NICD, who has been processing wastewater samples for SARS-CoV-2. The Centre for Vaccines and Immunology is a WHO poliovirus regional reference laboratory and has previous experience detecting poliovirus from wastewater.   

Surveillance of wastewater treatment plants offers an opportunity for near–real-time outbreak data and as an early warning for resurgence of the outbreak. To date, the wastewater-based epidemiology approach has been successfully piloted in developed countries where there is wide coverage of waterborne sanitation, such as the Netherlands, France, United States of America, and more. However, given the varied water and sanitation services delivery mechanisms in South Africa, the country was in a position to pioneer the development and piloting of an all-encompassing water and sanitation-focused approach for the surveillance of COVID-19 spread in less developed communities.


The main objective of the platform is to establish a national surveillance of SARS-CoV-2 in wastewater. This will complement national initiatives by providing early warning of spread of infection, providing information on locations with emerging SARS-CoV-2 infections or fluctuations in viral circulation, and monitoring resurgences. The platform aims to offer strategic responses to curb the escalation of infections in communities, through timely responses.


From November 2020, a one-year pilot phase of a national COVID-19 environmental surveillance system is being implemented. The pilot programme prepares the country to build the logistics and networks to transition into a national programme. The pilot will organise the capacitate a network of laboratories and municipalities to perform SARS-CoV-2 surveillance. Data will be collated by the Centre for Vaccines and Immunology at the NICD using the SACCESS database. Surveillance data from the SACCESS database will be used to supplement patient testing data and identify areas requiring targeted intervention. If the pilot phase is successful, the project will be expanded to national surveillance in 2022.

Expected potential impact of knowledge outputs

Our work will provide valuable information for the management, control, and response to COVID-19 in South Africa. Such data is particularly valuable as it does not depend on health-seeking behaviour of infected individuals or testing patterns.  The information generated will be crucial in detecting a possible resurgence of infection or fluctuations, including after potential SARS-CoV-2 vaccine introduction in future.