From Drug Use to Viral Outbreaks, How Monitoring Sewage Can Save Lives

Most of us, after we flush the toilet, don’t think twice about our body waste. To us, it’s garbage. To epidemiologists, however, wastewater can provide valuable information about public health and help save lives.

History of Wastewater-Based Epidemiology

Wastewater-based epidemiology (WBE) is the analysis of wastewater to monitor public health. The term first emerged in 2001, when a study proposed the idea of analyzing wastewater in sewage-treatment facilities to determine the collective usage of illegal drugs within a community. At the time, this idea to bridge environmental and social sciences seemed radical, but there were clear advantages. Monitoring wastewater is a nonintrusive and relatively inexpensive way to obtain real-time data that accurately reflects community-wide drug usage while ensuring the anonymity of individuals.

This idea was realized in a 2005 study, in which scientists collected sewage water in major Italian cities to estimate local cocaine usage. Traditionally, cocaine usage was estimated using population surveys, consumer interviews, medical records and crime statistics, all of which can be largely biased. The data they obtained from wastewater surveillance was eye-opening, revealing a much higher level of average daily cocaine usage than previously determined. Now, wastewater is used to estimate local drug use in many countries, including cities and universities in the US.

In addition to monitoring drug use, WBE has been used for decades to monitor viral diseases. Viral genetic material can be detected in human feces for days or even weeks before the onset of patient symptoms. This makes wastewater monitoring the perfect early warning system for preventing outbreaks.

In Israel, a wastewater surveillance program to monitor polio outbreaks has been in place since 1988, which involves monthly sampling of 8–10 sewage treatment facilities in populated areas. In 2013, the polio virus suddenly reappeared in sewage water, alerting health officials to initiate a nationwide vaccination campaign. Because of the early warning, a potentially disastrous outbreak was prevented. Other recent studies demonstrated how wastewater can be used to detect various strains of norovirus and hepatitis viruses.

WBE for Tracking COVID-19

Fast forward to 2020, the COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has further propelled WBE into the spotlight. Many believe that sewage surveillance is the most practical way for long-term monitoring of SARS-CoV-2 outbreaks. This approach is more cost-effective compared to large-scale diagnostic testing and can detect the virus even before symptoms have occurred, meaning public health officials can be proactive rather than reactive when controlling outbreaks.

Several municipalities have already begun monitoring sewage for the presence of SARS-CoV-2 viral RNA. Since 2018, a group at Arizona State University has been monitoring wastewater for opioid use in the city of Tempe, Arizona, and the data is released through a public-facing dashboard that reports the levels of four common opioid drugs. This experience has allowed them to quickly respond to the pandemic by creating a COVID-19 dashboard that provides the overall infection trend of 185,000 residents in seven areas within the city. Other states, including Utah and Montana, are following suit.

The idea of using wastewater surveillance to monitor COVID-19 long-term has spread globally. In March 2021, the European Commission recommended that all member countries put in place a national wastewater surveillance system as soon as possible. This will be an important strategy to monitor the spread of SARS-CoV-2 variants and other emerging pathogens in the future. Similar efforts by the US Centers for Disease control in conjunction with state health labs has resulted in a broad effort to monitor the RNA levels of wild type SARS-CoV-2 and variants of concern across the country.

Development of Viral RNA Detection Methods

To support the global demand for wastewater testing, Promega scientists have developed a family of kits that provide labs a complete workflow solution for viral detection in wastewater. In an interview with GenomeWeb, Promega Global Commercialization Marketing Manager, Brigitta Saul, states that Promega’s “expertise on the design of nucleic acid purification systems and formulating PCR master mixes tolerant of inhibitors commonly found in environmental samples allows us to design and formulate workflow solutions that are able to cope with these kinds of samples.”

The PCR-based method commonly being used for detecting viral RNA in wastewater is very similar to what is used in clinical or research labs. However, the complexity of wastewater samples brings some additional challenges, such as the presence of PCR inhibitors. Therefore, the viral RNA purification method is crucial for successful detection. Promega now offers two new kits for viral nucleic acid concentration and extraction from wastewater: the Wizard® Enviro Total Nucleic Acid Kit and Maxwell® RSC Enviro Total Nucleic Acid Kit. Both use a unique filter-based direct capture method that can concentrate total viral nucleic acid faster than existing precipitation methods. The Wizard® Kit includes minicolumns for manual purification; the Maxwell® RSC Kit allows automated  total nucleic acid purification designed to work with Maxwell® Instruments, which can automatically process up to 48 samples at once. For labs that require higher throughput, a plate-based format is also available (please contact for more information).

With these new extraction kits, you can get from sample to purified nucleic acid in as little as two hours. The purified nucleic acid can then be used directly for amplification using the Promega RT-qPCR kits specific for SARS-CoV-2 detection in wastewater. These sets of kits include primers and probes to detect SARS-CoV-2 (N1, N2, or E targets) as well as amplification controls and PPMoV internal process controls. The RT-qPCR master mix allows sensitive detection and quantification even in the presence of reverse transcriptase inhibitors or PCR inhibitors common to wastewater samples. Primer and probe sets for SARS-CoV-2 variants of concern are also available.

As methods for detecting viral RNA in wastewater continue to advance, there is hope that WBE programs will be implemented globally to help control and prevent outbreaks of COVID-19 as well as future viral diseases.

Learn more about wastewater-based epidemiology and methods for detecting viral RNA detection in wastewater!


Coronavirus Pandemic Jumpstarts Wastewater-Based Epidemiology, GenomeWeb

Mondal, S. et al. (2021) A direct capture method for purification and detection of viral nucleic acid enables epidemiological surveillance of SARS-CoV-2. Sci Total Environ. 795:148834.

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Johanna Lee
Johanna is a Science Writer at Promega. She earned her PhD in Biomedical Sciences at Baylor College of Medicine. She was a freelance writer and full-time mom for five years before joining Promega. Johanna is from Taiwan and she believes Taiwanese food is the best in the world. She loves doing yoga, traveling and spending time with her two kids.

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