by Ya’el Courtney
figures by MacKenzie Mauger
edited by  Yuli Lily Hsieh

January 2023 marked the third anniversary of the discovery of SARS-CoV-2, the virus responsible for the COVID-19 pandemic that halted life as we knew it. It overwhelmed hospitals worldwide, and is still infecting around 250,000 people daily across the globe in February 2023. Over these three years, many countries have struggled to monitor the rapidly changing virus. For months, a lack of publicly available testing made it difficult to track community spread. Now, in many places, regular testing is no longer in place. How can health departments keep tabs on the spread of this virus in their region without regular testing? 

Innovations in the field of wastewater surveillance have demonstrated its potential to detect and track COVID-19 levels through monitoring sewage. This technique takes advantage of the fact that SARS-CoV-2 replicates in the digestive system and can be shed in high quantities, often before symptoms appear. This provides a way to monitor infections at the population level that is cheaper and less labor-intensive than community-wide testing systems. This article will discuss the history of wastewater surveillance as a public health tool, its applications to COVID-19, and the current goals for, considerations around, and challenges facing its future implementation.

A brief history of wastewater surveillance

Scientists have looked to regional sewage for clues about disease spread since the 1850s. By the 1800s, industrialization had made London, UK the most populous city in the world. Infrastructure could not keep up with the population growth, and living conditions were squalid and unhygienic. By 1850, the city had weathered epidemics of influenza and typhoid fever, as well as two catastrophic outbreaks of a deadly disease called cholera. At this time, there was no general agreement about how diseases spread, so tracking and prevention of outbreaks was nearly impossible. When a new cholera outbreak struck, local physician Dr. John Snow was determined to track down the origin of the outbreaks and began mapping cases around the city. He noted geographical patterns that centered around specific water companies and particular water pumps in the city. He suggested that something about these pumps was spreading the disease. Dr. Snow was right—the overburdened city was failing to dispose of its population’s waste, and cholera was a disease spread through contamination of water by infected feces. This laid the foundation for the recognition of waterborne diseases and was critical in the later development of intentional wastewater monitoring strategies. 

Figure 1. Timeline of advances in wastewater surveillance. Using wastewater to monitor disease dates back to the 1850s, but modern methods were not developed until the 1990s. The COVID-19 pandemic brought wastewater surveillance to the public eye, and the CDC formed a national surveillance system in 2020. 

Although Dr. Snow identified outbreak centers, he did not quantify the presence of the disease-causing pathogen itself. After 1854, advances in the Germ Theory of disease highlighted that many diseases could be traced to the presence of microorganisms like bacteria or viruses. This prompted scientists to take a water sample and quantify the number of bacteria or viruses in it. In the 1940s, physicians and epidemiologists Dr. James Trask and Dr. John Paul from the Yale School of Medicine proposed that periodic examination of sewage might be useful for tracking outbreaks of a new epidemic in the United States: polio. The two doctors identified particles of poliovirus in wastewater samples from several locations in the United States with active polio epidemics: New York City, NY, New Haven, CT, Charleston, SC, and Detroit, MI. They showed that poliovirus was detectable during the epidemic and not detectable after the epidemic, demonstrating temporal specificity in using wastewater levels to infer active community infection. 

How do scientists detect pathogens in wastewater today? 

Scientists can only find live viruses or bacteria in sewage if they are present in a person’s digestive tract and remain alive after being expelled in solid waste products – where most only survive for a few days. For example, coronaviruses survive only 2-4 days outside the body. How can scientists detect the presence of diseases caused by these agents in a population then? Even if the pathogen isn’t alive, there may be traces of its genetic material in the wastewater. For COVID-19 monitoring, spotting viruses in sewage requires detective work to find their ribonucleic acids, more commonly referred to as RNA. This genetic material allows scientists to identify the presence and quantify the levels of virus in a wastewater sample. 

Wastewater surveillance and the COVID-19 pandemic 

In response to the COVID-19 pandemic, the Centers for Disease Control and Prevention (CDC) launched the National Wastewater Surveillance System (NWSS) in September 2020. This represented the first usage of wastewater surveillance as a federally-supported and centralized public health tool. Local scientists identify a wastewater treatment plant and the sewershed that it serves, collect wastewater samples, and test for the presence of SARS-CoV-2. Then, local testing laboratories submit data to the NWSS, with frequencies ranging from 2-5 times a week. State health departments ensure that data are collected from a site suitable for surveillance and are of the quality needed for public health interpretation. Much of the challenge of a nation-wide wastewater sampling strategy comes down to standardization of sample collection and testing, which the CDC has ensured with thorough published protocols. The CDC analyzes submitted data and reports the results to both public health experts and the public. 

COVID-19 wastewater surveillance data are used to: (1) monitor the presence of infection in a community; (2) track infection trends in a community; and (3) screen for infections at a targeted site to trigger additional individual testing or mitigation measures. These data were made available as early as 2020 to identify localized spikes in communities experiencing a surge of infection. Based on this information, states implemented mobile testing and vaccination sites to communities experiencing a spike and coordinated efforts to amplify communication about masking and vaccination. These data were also used to determine the effectiveness of transmission-reduction strategies at targeted sites like universities and correctional facilities

As the COVID-19 pandemic progressed, scientists and public health agencies expanded the use of wastewater surveillance to detect the distribution of SARS-CoV-2 variants within different communities. A variant is a version of the virus that has undergone changes in its genetic code. Some variants have increased transmissibility, cause more severe diseases, or are less preventable by current vaccines. Wastewater surveillance of the omicron variant suggested to researchers that it was more transmissible than any of the variants that preceded it based on the rapidity with which it replaced the delta variant as the dominant variant infecting communities around the globe. This prompted researchers to start studying what made this strain more problematic. In addition, the CDC can now reach out and give hospitals advanced warning when a surge is expected in their area, so that the hospital can prepare sufficient equipment, treatments, and staffing levels. 

Figure 2. Graphic summary of wastewater surveillance theory, process, results, and current challenges. 

What’s next for wastewater? Future applications, advantages, and challenges.

The significant expansion and centralization of wastewater surveillance infrastructure in the United States, catalyzed by COVID-19, has applications to other diseases as well. Near-term goals for wastewater surveillance include using the same wastewater sample to test for multiple diseases. There has been a boom of scientific publications in the last couple of years demonstrating methods to monitor levels of other viruses like influenza, respiratory syncytial virus (RSV), and monkeypox. There is also enthusiasm for using wastewater surveillance to monitor foodborne pathogens like E. coli and norovirus, and researchers are even looking into tracking antibiotic resistance.

Wastewater surveillance offers several advantages over other public health monitoring tools. It does not require any direct patient interaction or invasive procedures. It can be applied to communities or diseases even if people are not going to the doctor and getting diagnosed. The presence of viruses or bacteria in sewage also precedes the heaviest disease or symptom load in a community, so it can give a 4-6 day lead time on increases or decreases in COVID-19 cases, allowing doctors and hospitals more time to prepare. 

Wastewater surveillance has the potential to help local officials overcome access and affordability issues associated with diagnostic testing, and provide action-oriented information about where to focus public health resources. However, it is important to consider the shortcomings of wastewater surveillance, especially when these shortcomings apply to how this technique can benefit communities in an equitable way. Black, Hispanic, and American Indian or Alaska Native populations have experienced disproportionate negative health outcomes during the COVID-19 pandemic relative to their White counterparts. Likewise, rural Americans have died from COVID-19 at twice the rate of urban Americans. In these underserved communities, the impact of COVID-19 has been exacerbated by limited health care access, a higher prevalence of underlying conditions associated with severe COVID-19, and inequitable access to reliable and convenient COVID-19 testing. So far, wastewater surveillance has almost exclusively been implemented in regions with well-maintained sewage systems. This is problematic, as 20 percent of households in the United States—including many tribal and rural communities—are not connected to a sewer line. These households, along with poorer communities with failing sewer infrastructure, have been largely overlooked by state and national wastewater monitoring efforts.

Further, even after sampling infrastructure may be in place, it is critical that researchers partner with disadvantaged communities to effect positive change. This applies to communities with a strong sense of self-determination and systems of governance, like indigenous and tribal communities, but also to underrepresented or poorer communities around the country. Ultimately, it is up to the governing body of any given community to decide how they can use wastewater surveillance data to push for change—whether that be more resources for diagnostic testing, messaging, or vaccination. Community leaders and public health experts will need to have active conversations about  how to interpret wastewater surveillance data and what it means about local risk. 

Wastewater surveillance has recently gained significant momentum in the United States in terms of federal funding, expansion into new diseases, and public health implementation. It has the exciting potential to allow us to monitor a variety of public health threats. As progress continues, it will be important to pay special attention to the following considerations to ensure that this technique brings the greatest benefit possible to communities across the nation in an equitable way: 

  • Development and funding of state laboratories with the capacity to process wastewater samples in rural communities 
  • Increasing partnership with American tribal communities, of whom only 100 out of 574 are currently represented in wastewater surveillance data
  • Intentional education and outreach by researchers to community leaders about how to interpret data and implement protective strategies
  • More thorough mapping of the 20% of Americans not connected to a sewage system and efforts to implement alternative testing methods that can estimate the scope of outbreaks in these regions

Ya’el Courtney is a fourth year PhD candidate in the Neuroscience program at Harvard University. You can find her on Twitter as @ScienceYael. 

MacKenzie Mauger is a fourth year PhD candidate in the Biological and Biomedical Sciences program at Harvard Medical School. You can find her on Twitter as @MacKenzieMauger.

Yuli Lily Hsieh is a fourth year PhD candidate in the Health Policy (Decision Sciences) program at Harvard University. 

Cover image by kubinger from Pixabay

For More Information:

  • To watch a webinar hosted by the National Academies’ Committee on community wastewater-based infectious disease surveillance, click here.
  • To learn more about the CDC Waterborne Disease & Outbreak Surveillance Reporting System, click here.
  • Click here to see an interactive, real-time time-series of Covid-19 wastewater monitoring in the U.S. and  here to see a map of U.S. sewage treatment facilities.

One thought on “Something in the Sewage: What watching our wastewater can tell us about infectious diseases

  1. Climate change is also posing challenges for wastewater treatment, as extreme weather events can disrupt operations and increase pollution.

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