Since the late 1930s, scientists have known that infectious poliovirus was present in the sewage of cities experiencing outbreaks1. As a result, wastewater surveillance has played an important part in the polio-eradication campaign2. Building from the work on poliovirus, data from wastewater have complemented clinical surveillance during the COVID-19 pandemic by offering a comprehensive view of infection burden and transmission — both symptomatic and asymptomatic — and information on which SARS-CoV-2 variants are circulating in a community3,4 (including so-called cryptic variants that have never been detected in clinical samples5). Yet despite the established value of wastewater surveillance for monitoring poliovirus and its emerging importance during the COVID-19 pandemic, most global public health surveillance systems still rely heavily on medically attended case data6. This needs to change to enable effective pandemic preparedness and response.

Sewage science

Wastewater monitoring involves the collection of pooled samples from community- or institution-level sewage systems. For community-level surveillance, the sewers are a catch-all, aggregating human waste into centralized locations. However, sampling can be done at much more localized scales and in communities that lack centralized sewage collection and treatment systems. Sampling from centralized locations can provide rich insight into pathogenic viruses, bacteria and protozoa present in the community7 (Fig. 1). Of these, pathogens that are stable in wastewater and/or are consistently shed in fecal material or urine are strong candidates for wastewater monitoring.

Fig. 1: Wastewater-monitoring pathway.
figure 1

After SARS-CoV-2 is shed in human feces, the sewage may travel to centralized locations, such as wastewater treatment plants. Depending on the goals and resources for wastewater monitoring, a variety of methods can be used to collect samples of the sewage, which is routinely done between twice weekly and once monthly. The samples are first processed in a lab to concentrate and amplify genetic evidence (RNA or DNA, depending on the pathogen). Genetic material is then tested to detect and quantify pathogens of interest, with PCR-based methods or NGS used for variant detection. Results are then reported to public health departments to improve situational awareness and inform action.

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From a public health perspective, diseases that are under-reported by traditional surveillance systems and lead to widespread poor health outcomes should be prioritized in wastewater-monitoring programs. These include diseases with nonspecific symptoms, such as polio, influenza and viral gastroenteritis, or those for which patients do not seek care until symptoms are serious. There is also a strong use case for conducting wastewater monitoring for diseases for which current diagnostic tests are inadequate, have limited accessibility and/or are expensive and for which the data could help guide vaccine campaigns or other interventions that can improve health outcomes.

Among the wide range of biomarkers and chemicals that can be measured in sewage to assess health and well-being8, one of the most promising has been viruses. Additionally, a growing body of evidence indicates that wastewater may be an ideal environment for the detection of antimicrobial-resistant pathogens — a rising global public health threat9. Other applications include assessing community use of illicit and therapeutic drugs10; monitoring consumption of everyday compounds, including caffeine, nicotine and alcohol11; and measuring exposure to environmental contaminants such as pesticides and plasticizers12.

Numerous studies over the past 30 years have shown that wastewater testing provides an accurate population-level view of disease13, and recent research has shown that trends in wastewater concentrations of SARS-CoV-2 are strongly predictive of clinical case counts14,15. Although the lead time may diminish as the pandemic progresses27, suggests a continuing need for technological advancements to keep pace with these changes and provide relevant surveillance28. A global, adaptive early-warning system that includes wastewater variant monitoring will be critical for protecting the public and easing the strain on the healthcare system when the next novel threat emerges.