Long before patients arrive at clinics, the first signs of an outbreak may already be flowing beneath our cities. Every day, wastewater carries microscopic traces of viruses, bacteria and parasites shed by infected individuals, creating a hidden but powerful stream of public health data. Researchers at the Council for Scientific and Industrial Research (CSIR) are harnessing this resource to build wastewater surveillance systems capable of detecting disease outbreaks earlier, tracking infection trends across entire communities and strengthening South Africa’s public health response.
“Wastewater gives us a community-wide snapshot of health. Instead of testing individuals one by one, we can analyse wastewater samples and understand what is happening across thousands of people, including those who may not even know they are infected,” says CSIR senior researcher and laboratory manager, Wouter le Roux.
For decades, disease surveillance has depended largely on clinical data, with health systems tracking patients only once they seek care and receive a diagnosis. While this approach has been effective, it is inherently reactive, often identifying outbreaks only after they are already spreading. The Covid-19 pandemic exposed these limitations and accelerated the development of wastewater-based epidemiology across the globe.
CSIR senior researcher Lisa Schaefer elaborates, “During Covid-19, we saw how quickly wastewater data could signal rising infections before clinical cases increased. Early indicators can make a critical difference in how we respond to outbreaks.
The science behind wastewater surveillance is simple and powerful. When people are infected, they shed disease-causing microbes in their waste, which enters sewer systems and flows to treatment plants. This creates a pooled sample of an entire community’s health. At facilities such as the Olifantsfontein Wastewater Treatment Works, researchers collect raw wastewater samples on a regular basis; often weekly, and transport them to CSIR laboratories for analysis.
In the laboratory, CSIR microbiologists concentrate microbial material from the wastewater and use highly sensitive molecular techniques to detect even trace amounts of viruses, bacteria and parasites. “Even very small concentrations can tell us a lot. We are looking for biological signals that indicate whether a pathogen is present and how its levels are changing over time,” says le Roux.
However, detecting pathogens is only the first step. To translate these findings into meaningful public health insights, researchers apply advanced mathematical, statistical and spatial modelling. These tools allow scientists to estimate infection levels within communities based on the concentration of pathogens found in wastewater, offering a broader – and often earlier – picture than clinical testing alone.
“Wastewater does not just capture people who go to clinics; it includes asymptomatic individuals and those without access to healthcare, which makes it a much more inclusive and sensitive surveillance tool,” emphasises Schaefer.
This ability to capture diagnosed and undiagnosed infections means that rising disease levels can be detected days or even weeks before they appear in clinical data, giving health authorities valuable time to prepare and respond. During the Covid-19 pandemic, this approach proved particularly valuable in South Africa, where the CSIR collaborated with research councils, universities and public health institutions to implement wastewater surveillance programmes. The data contributed to national monitoring efforts, including systems linked to the National Institute for Communicable Diseases, helping to strengthen the country’s ability to track and respond to the virus.
Building on this foundation, CSIR researchers are now expanding wastewater surveillance beyond Covid-19 to monitor a wider range of infectious diseases, particularly those linked to water and sanitation. These include cholera, typhoid fever and infections caused by protozoan parasites that can spread rapidly in vulnerable communities where water quality and sanitation systems are under pressure.
“Water and health are deeply connected,” says le Roux. “By monitoring wastewater, we are not just tracking disease; we are gaining insight into broader environmental and public health risks.”
The work is supported by strong collaboration across disciplines and institutions, including partnerships with the University of Pretoria. By bringing together expertise in microbiology, epidemiology, environmental science and mathematical modelling, researchers are refining techniques and strengthening South Africa’s capacity for disease monitoring.
One of the greatest advantages of wastewater surveillance is its efficiency. A single sample can represent thousands of people, making it a cost-effective way to monitor entire communities in near real time. Because it does not rely on individuals seeking medical care or accessing testing, it can detect outbreaks that might otherwise go unnoticed until they become severe.
“This approach allows us to move from reacting to outbreaks to proactively anticipating them,” says Schaefer. “That shift is essential for building more resilient public health systems.”
Through ongoing research and innovation, the CSIR is transforming wastewater systems into large-scale public health monitoring networks. By turning what was once considered waste into a vital source of insight, scientists are helping reshape how South Africa detects and responds to disease. The result is a proactive surveillance tool that works quietly beneath our feet but has the potential to safeguard communities long before warning signs appear in clinics and hospitals.
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Published 7 April 2026