Can wastewater surveillance reveal hidden disease trends and strengthen public health in South Africa?

Infectious diseases caused by viral and bacterial pathogens remain a major public health concern. Traditional surveillance systems, which rely on laboratory-confirmed cases, can be affected by socioeconomic factors, delayed healthcare-seeking, and under-reporting. These challenges can obscure the true burden of disease and the patterns of transmission within communities, limiting timely public health responses.

Wastewater and environmental surveillance (WES) offers a complementary approach by providing population-level data independent of clinical testing. Historically used to monitor diseases such as cholera and polio, WES has more recently played a key role during the COVID-19 pandemic and the mpox multi-country outbreak.

By detecting and quantifying viral and bacterial genetic material in wastewater, WES captures a non-invasive, community-wide snapshot of disease circulation, helping to identify emerging trends and unreported infections.

In South Africa, the National Institute for Communicable Diseases manages a national WES sentinel surveillance network, with sampling sites at 28 wastewater treatment plants across all nine provinces and selected border transit points, as well as 19 community sampling sites located within the catchment areas of three large treatment plants in Gauteng.

During 2024, samples were analysed for measles, rubella, hepatitis A and E, influenza A and B, mpox, SARS-CoV-2, and Mycobacterium tuberculosis, with detected levels compared to available clinical data to understand trends over time and across locations.

The following report describes the application of WES for infectious disease surveillance, including measles, rubella, influenza, hepatitis A and E, mpox, and tuberculosis, and describe method development and results for surveillance programmes over 2024. We also reflect on emerging interpretive strategies and on the way forward for WES in South Africa and beyond.

Materials and Methods

During 2024, wastewater samples from sentinel sites across South Africa were analysed for SARS-CoV-2, measles, rubella, influenza A and B, hepatitis A and E, mpox, and Mycobacterium tuberculosis. Samples were concentrated using ultrafiltration or bead-based methods, with rubella processed separately, and total nucleic acids were extracted for analysis. 

Digital PCR was used for quantification, with primers validated against clinical assays and positive controls. Assays were run in multiplex formats, and genome copy numbers were calculated to estimate pathogen levels, providing a standardised dataset for comparison with clinical surveillance.

Results

Between 1 January and 30 November 2024, wastewater samples from national sentinel and community sites across South Africa were analysed for multiple infectious agents. SARS-CoV-2 was detected in 56% of samples, while hepatitis A and E were found in 34% and 16%, respectively. Influenza A was detected slightly more frequently than influenza B (10% vs 6%). Measles and rubella were the least frequently detected pathogens at 7% and 6%.

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