Wastewater surveillance, the monitoring of wastewater for contaminants or pathogens, emerged as a critical tool to track the spread of SARS-CoV-2 in the United States during the height of the COVID-19 pandemic. It now has expanded to monitor other pathogens, such as avian influenza H5N1, respiratory syncytial virus (RSV), mpox, and more. These systems track emerging health threats and detect changes in the levels of pathogens within a community, thus providing data critical to public health decision-making at local, regional, and national levels.
National Wastewater Surveillance: Current US Landscape
Governments, commercial entities, and academic lab groups operate wastewater monitoring programs, ranging from individual-level facilities, that is, a single wastewater treatment plant, to national networks that include multiple plants across the country. Two of the most prominent wastewater surveillance programs in the US include the Centers for Disease Control and Prevention’s National Wastewater Surveillance System (CDC NWSS) and a collaboration between Stanford and Emory Universities known as WastewaterSCAN. While a variety of organizations conduct wastewater surveillance in the US, only CDC NWSS and WastewaterSCAN publicly share data at the national level.
CDC NWSS was developed in 2020 to help monitor levels of COVID-19. Through support and coordination of state, local, tribal, and territorial (STLT) health departments, the system collates independent wastewater monitoring efforts into a national platform that now covers more than 45% of the US population. NWSS receives data on SARS-CoV-2, mpox (clades I and II), RSV, influenza A, and influenza A(H5). The CDC prioritizes monitored pathogens based on several factors, including scientific feasibility, that is, the ability for resulting data to inform public health action, and the need for additional situational awareness for pathogens that pose immediate public health risks.
Complementing this federal effort is WastewaterSCAN, a collaboration between Stanford and Emory Universities. While covering a smaller population (about 12% of the US), WastewaterSCAN provides consistent, frequent monitoring across the country for SARS-CoV-2, mpox (clades Ib and II), influenza A, influenza A(H1), influenza A(H3), influenza A(H5), influenza B, RSV, Human Metapneumovirus (HPMV), Enterovirus D68 (EVD68), Norovirus, Candida auris, and Hepatitis A. WastewaterSCAN selects monitored pathogens by consulting public health decision-makers to understand their needs and priorities, while also considering the research potential of a pathogen. This includes asking questions like: Can monitoring this pathogen answer significant research questions? Is it possible to track this pathogen through wastewater surveillance? In contrast to CDC NWSS, which primarily focuses on the public health implications of its targets, WastewaterSCAN balances this focus with a commitment to research meant to advance the field of wastewater surveillance. WastewaterSCAN says a key goal of their organization is to encourage and support the CDC in broadening the range of pathogens monitored through wastewater surveillance.
Complementary Approaches, Different Structures
The current NWSS surveillance infrastructure involves a diverse, integrated network of organizations, including utilities, public health laboratories, academic/private partners, health departments, and environmental health groups, who collect and process samples at a defined frequency. Data may then be sent to the CDC and are made publicly available through CDC’s wastewater surveillance dashboards. NWSS data is provided by state and local public health departments–which make up about 75% of NWSS sites–and sites covered through a CDC national testing contract with Verily Life Sciences, an independent subsidiary of Alphabet Inc, previously known as Google Life Sciences. NWSS also receives voluntary data submissions from other programs, such as WastewaterSCAN, as well as from states that partner with academic or private laboratories for testing. While WastewaterSCAN tracks 12 pathogens, only data for pathogens included on the CDC NWSS dashboard is shared with the CDC. This reflects how each implementing partner, whether government or private, may monitor different priority pathogens, some of which may not be publicly shared on CDC dashboards. This allows communities to monitor for diseases that are priorities at their local level. Because CDC NWSS data come from a variety of implementers, sampling frequency and methods vary across sites, which can make it difficult to compare data consistently over time. As a result, informatics and normalization efforts, such as the Wastewater Viral Activity Levels (WVALs), are important for data aggregation, interpretation, and trending over time.
WastewaterSCAN coordinates sample retrieval two to seven times a week from each collection site and sends samples to Verily Life Sciences’ labs. Each sample is processed and analyzed the same way, which aids in sample comparison across sites and time. Once samples arrive at a Verily lab, data are publicly shared within 48 hours, a faster turnaround time than CDC NWSS. Additionally, as a private and academic initiative, WastewaterSCAN has greater flexibility to begin tracking new pathogens.
National Wastewater Surveillance Coverage
National wastewater surveillance efforts reach a significant portion of the US population, with the most extensive coverage coming through CDC NWSS’ network of 1,539 active sites spanning all 50 states, six territories, and some tribal lands, though the specific pathogens tracked vary by location. Of the active NWSS sites on public dashboards, 324 are tracking H5, 389 are tracking mpox, and 598 are tracking RSV. The differences in coverage result from the decentralized structure of NWSS, as each site independently selects the pathogens it monitors. While the CDC offers strong recommendations and at times provides funding to support tracking certain pathogens, individual jurisdictions retain discretion in their monitoring choices, though most funded sites must report data on specific pathogens like SARS-CoV-2. Sites participating in the NWSS testing contract, have a set number of pathogens that are monitored.
WastewaterSCAN receives samples from 147 sites that cover more than 40 states. While its coverage is more limited geographically, the collaboration maintains consistent pathogen monitoring across its sites.
Despite these efforts, significant gaps remain in our national surveillance picture. Both systems primarily operate in urban counties with lower Social Vulnerability Index scores, which is a metric of a county’s vulnerability to hazards and stressors, including disease outbreaks. This urban focus reflects the practical limitations of the two monitoring networks, which exclusively collect samples from centralized wastewater systems, excluding areas with decentralized systems like septic tanks. Privacy concerns play a role in the discrepancy. For example, WastewaterSCAN requires participating wastewater facilities to serve at least 10,000 people to ensure that the data cannot be traced back to individuals. NWSS is working to expand coverage to wider geographic areas.
H5N1 Wastewater Surveillance
Wastewater testing has enhanced data collection for influenza A(H5) in 46 states and Washington DC. Since testing for H5N1 is not widely available, wastewater surveillance can clue us into where the virus is spreading in people or animals. For example, a biomarker for H5N1 was found in a Texas wastewater treatment plant more than a month before confirmation of the first case of H5N1 in dairy cattle. Although current testing methods cannot tell whether the virus detected in wastewater comes from an animal or a human, they allow public health officials to initiate testing in nearby facilities and alert health care providers to look for increases in potential symptoms, such as conjunctivitis, in humans.
Limitations
While wastewater monitoring is an important source of passive disease surveillance, it does have limitations. A primary challenge lies in pathogen source attribution. Wastewater data alone cannot identify whether detections or increases of pathogens, like H5N1, are coming from humans, an animal product (like milk from an infected cow), or an animal (like a bird). Some sewer systems are more open to environmental input than others, and this can impact detections and efforts to determine pathogen sources.
Another significant constraint is that wastewater data cannot estimate the number of infected individuals in a community due to varied inputs and unknown pathogen characteristics. Data such as the pathogen’s density in stool, stool production rate, and more are needed to make a conversion. Some researchers have attempted to estimate the number of infected individuals contributing to wastewater treatment plants, but a large-scale model that can be used by a national wastewater surveillance system is not yet available. The CDC recommends that wastewater surveillance data should not be used to make point estimates of community infection and is most useful for indicating trends.
A funding cliff is looming
Wastewater surveillance in the US faces critical funding uncertainties that could affect long-term sustainability. Federal funding to support CDC NWSS’ mission was initially provided through the 2020 Coronavirus Aid, Relief, and Economic Security (CARES) Act to support eight pilot sites. Over time, the program expanded its scope and scale. Currently, CDC NWSS is funded solely through supplemental funding through FY2025, leaving its future and partnerships uncertain.
Before these funding challenges arose, wastewater surveillance played a pivotal role in guiding public health decisions during the pandemic, as highlighted in a National Academies of Sciences, Engineering, and Medicine report. In Ohio, a sharp increase in SARS-CoV-2 wastewater levels led to the state offering local health departments testing, vaccination, and contract tracing support. In Utah, SARS-CoV-2 wastewater levels were used alongside other metrics to rank the state’s local municipalities. Decision makers then used this ranking and other considerations to prioritize where to allocate resources. In Virginia, public health officials used SARS-CoV-2 wastewater levels to target vaccination campaigns in high-prevalence areas. These examples reinforce the value of wastewater surveillance in enhancing public health response efforts.
The current funding landscape reflects the broader challenges of transitioning wastewater surveillance from an emergency response tool into more permanent public health infrastructure. Most STLT health departments rely on CDC funding for wastewater surveillance through the Epidemiology and Laboratory Capacity for Prevention and Control of Emerging Infectious Diseases Cooperative Agreement, though a small number of states receive funding from local governments. This dependence on federal funding makes the system vulnerable to funding gaps.
Even privately supported initiatives face funding challenges. Despite philanthropic funding from the Sergey Brin Family Foundation and Bloomberg Philanthropies, WastewaterSCAN recently stopped partnering with several wastewater sites and is not currently enrolling new sites due to funding constraints.
Looking Ahead
Wastewater surveillance represents one of the most significant public health innovations to emerge from the COVID-19 pandemic. Its ability to provide early warning signals for disease outbreaks and track pathogen spread has proven invaluable for public health decision-making. The technology has already demonstrated its versatility by expanding beyond SARS-CoV-2 to monitor multiple pathogens, from H5N1 to norovirus. However, the full potential of this tool remains untapped. Uncertain long-term funding in the US poses a significant challenge to its sustainability and growth. For wastewater surveillance to truly become a key part of public health infrastructure, we need ongoing investment and greater testing capacity.
Temi Ibitoye is a Visiting Fellow at the Brown University Pandemic Center. Nellie Bristol is an analyst, writer, and editor specializing in global health policy.