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When I entered public service in 1991 as a research scientist with the Environmental Protection Agency, its attention was focused on the impact of pesticides and industrial chemicals on humans and wildlife.

A breakthrough came eight years later with an article I wrote with my colleague Thomas Ternes describing what would eventually become known as the exposome — the totality of exposure over time to all stressors, chemical and nonchemical alike. We showed that a far larger spectrum of chemicals not normally found in the human body that can elicit subtle or profound effects on health enter the environment via sewage treatment plants. These include pharmaceuticals, personal care products, their breakdown products, and more.

That led me to envision sewage treatment plants as a tool for not only tracking an emerging class of pollutants but also for monitoring the overall status of community-wide health or disease. This concept has become known as wastewater-based epidemiology (WBE).


WBE initially gained attention in Europe for tracking illicit drug use, and continues to be advanced and refined for a variety of uses by an international consortium of scientists. In the U.S., however, it has not been embraced at any level of government.

The Covid-19 pandemic could — and should — change that.


Using wastewater-based epidemiology for early warning of the emergence and spread of local Covid-19 infections could afford health care providers more time to anticipate case loads, allow public health officials to better target mitigation and control measures, and conserve diagnostic resources.

Scientists worldwide are applying wastewater-based epidemiology to the pandemic, with coordination by organizations such as the Water Research Foundation and the Covid-19 WBE Collaborative. But its implementation in the U.S. has been limited mainly to local pilot studies with little collaboration across states. Significantly absent has been leadership and coordination from the federal government, which slows the transfer of knowledge and hinders improvement of this vital tool.

The U.S. urgently needs a national strategic plan for wastewater-based epidemiology. President-elect Biden’s Covid-19 task force could lead this effort, perhaps by creating a standing expert panel devoted to wastewater-based epidemiology applications that interfaces with the Centers for Disease Control and Prevention and the EPA. It could champion the advancement of WBE, ensure the steady availability of federal resources via competitive grants and contracts, and coordinate and foster the nationwide implementation of a wastewater-based epidemiology network.

It is in the nation’s interest that this tool become a workhorse in epidemiological investigations.

Importance of federal R&D leadership

The federal government needs to take the lead in coordinating the development of wastewater-based epidemiology and shepherding further development, refinement, standardization, and nationwide implementation of a networked WBE capability. The CDC’s progress with the National Wastewater Surveillance System is a first step.

Urgently needed is a unified national approach in which wastewater-based epidemiology is closely integrated into national surveillance programs for testing individuals. These two arms of testing — individuals and communities — need to work seamlessly together as an integrated whole, with wastewater-based testing promoting and guiding the intelligent use of diagnostic testing, thereby conserving time and resources.

Research and development efforts on wastewater-based epidemiology also need to be coordinated with the World Health Organization. Much can be learned — and duplication of effort can be spared — by collaborating with like-minded scientists in other countries who are making headway applying WBE to Covid-19.

Protecting national security with wastewater-based epidemiology

Wastewater-based epidemiology can play an important role in monitoring confined living quarters, such as those aboard naval vessels or at U.S. military bases. The U.S. military must develop approaches for deploying WBE to avoid outbreaks such as the ones that incapacitated the crews of the U.S.S. Theodore Roosevelt, the U.S.S. Michael Murphy, and dozens of other ships. Outbreaks have also been recorded at military bases. Control of Covid-19 aboard Navy vessels and at military bases is critical to ensure national security by maintaining normal operations (including training exercises) and force readiness.

Need for alternative viral detection methods

The application of wastewater-based epidemiology to Covid-19 has primarily relied on the use of costly, time-consuming polymerase chain reaction (PCR) technology to detect and quantify viral RNA in sewage. Less costly and simpler detection methods are needed, especially for rural and poorer locales. Examples include biosensors, paper-based nucleic acid techniques, and detection of viral antigens.

Extensive research will also be needed before WBE can be calibrated to permit the reliable quantitation of the actual number of Covid-19 cases in a community. This partly involves correlating levels of viral RNA copies in sewage at a particular treatment plant to the prevalence of Covid-19 cases in the community it serves. Doing so would unlock the full potential of WBE by enabling direct comparisons across different communities of real-time, quantitative case data, such as the magnitude and trends in infected case rates.

Adopting Covid-19 biomarkers

Much could be gained by measuring biomarkers of Covid-19 infection in sewage along with markers of the virus itself. PCR-based wastewater epidemiology can’t currently estimate the number of active Covid-19 infections in a community, nor can it distinguish the severity of infections, which range from asymptomatic to life-threatening.

In contrast, measuring complementary biomarkers in sewage (originating from urinary or fecal excretion) could greatly enhance the information value of WBE data and improve its calibration. Examples of potential alternative biomarkers that could be elevated during SARS-CoV-2 infection include isoprostanes or neopterin (markers of systemic inflammation), calprotectin (a marker of gut inflammation), and zonulin (a marker of gut dysfunction due to excessive permeability); biomarkers excreted from the critical integrated stress response could be particularly useful for complementing Covid-19 monitoring. The urinary proteome is a rich, underappreciated source of countless underexplored proteins that could serve as potential biomarkers.

Using wastewater-based epidemiology to improve public trust

A complex array of factors has bred public distrust in messaging from the federal government regarding the seriousness of Covid-19. By encouraging local authorities to implement WBE programs, the public might be more inclined to trust the data and their interpretation, especially if made available in real time on locally maintained digital dashboards.

This may be a tough sell, however, because local officials themselves sometimes resist the implementation of WBE, often because of concerns surrounding individuals’ privacy or “tarnishing” a city’s image.

Data generated by local authorities might better immunize the public against rampant misinformation, skepticism, and Covid-19 denialism, serving to depoliticize the disease and help blunt pandemic fatigue. This approach might foster collective community consciousness leading to better engagement and willingness to abide by simple control measures.

Finally, by monitoring for biomarkers of persistent, long-term disease, such as experienced by individuals with post-Covid-19 morbidity — the “long-haulers” — rather than for direct markers of the virus itself, those who discount the severity of Covid-19 might take more notice.

Preparing for future pandemics

Even if wastewater-based epidemiology can’t become fully operationalized during Covid-19, investing in a permanent, national wastewater-based epidemiology network could prove vital in preparing for faster and more effective control of the inevitable next pandemic. It could also play a key role in revealing health disparities and vulnerabilities among communities by monitoring for biomarkers of noncontagious diseases, a key issue for public health in the years to come.

Christian Daughton is an environmental scientist, now retired from the U.S. Environmental Protection Agency’s Office of Research and Development.

  • Great article. I have heard that there is a lot of COVID testing of wastewater going on now. But we do need a WBE program to coordinate the testing and use of results. Biden’s COVID team should consider this of utmost importance.

  • WBE is an excellent efficient approach to faster and more targeted localizing of Covid occurrence. Areas or zone not showing infection do not need further investigation, and more testing efforts can be directed to the areas or zones that are. This intelligent application of individual testing would save millions of tests and the massive efforts around that. The fear of area “labelling” is far less important than eliminating Covid spread. The writer and others in this important field should seriously bring this to Biden’s Covid czar’s attention.

  • Let’s hope there will be some looking ahead and preparation for whatever is next! We lost far too much time on our current bout with a virus.

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