Detecting evidence of COVID-19 in wastewater

Wastewater-based epidemiology has been around for decades, used most prominently as a means of detecting the existence of the polio virus in communities. In recent months, interest in this often-overlooked field has exploded as engineers, researchers, private companies, and all levels of government turn to sewage to track trends associated with the spread of COVID-19. 

Following the onset of the pandemic, scientists quickly determined that the genetic material of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the organism that causes COVID-19, is present in the feces of infected individuals, often as much as several days to a week before such individuals begin showing symptoms and including those who never show symptoms at all. The discovery set off a rush in the United States and elsewhere to sample and test wastewater for the presence of the genetic material. This data can provide a cost-effective indicator of the presence of COVID-19 in a given community long before other methods of detection, giving the public health system more time to act.

In the United States, nearly 80 percent of households are served by municipal wastewater collection systems, according to the Centers for Disease Control and Prevention. As a result, wastewater-based epidemiology offers a potentially straightforward method for monitoring the prevalence of COVID-19 in communities across much of the country. Wastewater surveillance data can detect whether disease rates are increasing or decreasing earlier than might be indicated by the results of individualized testing. Depending on the degree to which wastewater sampling efforts can be conducted upstream in a sewer system, the results can be used to assess the prevalence of COVID-19 in ever smaller geographic areas. Such data can also inform public health officials as to whether certain medical and social interventions intended to combat the disease are having the desired effects.

“The primary advantages of this technique are that it is an extremely cost-effective way to quickly sample a large community without bias or discrimination, and it provides an early warning system for potential emerging infections because it detects signals from people regardless of whether they have symptoms or not,” says Christobel Ferguson, the chief innovation officer for the Water Research Foundation.

Wastewater-based epidemiology offers a potentially straightforward method for monitoring the prevalence of COVID-19 in communities across much of the country.

A leader in the field of wastewater-based epidemiology, the city of Tempe, Arizona, was uniquely situated to begin testing for SARS-CoV-2 genetic material in its wastewater when the COVID-19 pandemic hit the United States in the spring. Approximately two years earlier, the city had begun wastewater monitoring to check for biomarkers indicating the presence of drugs. 

The idea grew out of the city’s efforts to make better use of data as a means of improving its services, says Rosa Inchausti, Tempe’s director of strategic management and diversity. The city had developed a working group to combat the opioid epidemic. Because of the stigma associated with opioid use, the city had no way of knowing with precision where opioid use was most prevalent. As a result, it had no way to determine how best to target resources aimed at addressing opioid addiction. Nearly all of the information the city had on the subject came from its fire department, which tracked calls for service that were deemed likely to be related to opioids, and its use of medication to treat opioid overdoses. “Those are lagging indicators,” Inchausti says. 

In 2018, Inchausti met Rolf Halden, Ph.D., P.E., M.ASCE, the director of the Center for Environmental Health Engineering at the Biodesign Institute, a professor in the Ira A. Fulton School for Sustainable Engineering and the Built Environment, and a senior sustainability scientist in the Global Institute of Sustainability and Innovation at Arizona State University, which has its main campus in Tempe. Halden suggested that Tempe work with ASU to monitor the city’s wastewater as a means of obtaining more detailed information regarding illicit drug use within its jurisdiction. Because the suggestion meshed with Tempe’s goal to become more data driven, the city jumped at the idea, Inchausti says. 

ASU began analyzing wastewater samples collected by the city, and Tempe created an online dashboard displaying the results of the wastewater-based epidemiology on a regional basis. As a result, anyone with an internet connection can see at a glance generally what types of opioids are present in the city and where they are used most heavily. At the same time, the dashboard indicates the per capita average monthly mass load values for various opioid-based compounds within each of five regions, providing a quantitative as well as a qualitative assessment of opioid use.

“The city of Tempe had done something that nobody had done and still hasn’t done, and that is to take information from wastewater on a neighborhood basis and immediately share it with the public,” Halden says. With the dashboard, Tempe is “essentially taking a genuine look at the health profile, without censoring the data in any way, and making it available to all the stakeholders in the city,” he notes. “We can lay claim on having produced the first wastewater-based, epidemiology-informed dashboard in the world.”

The data also revealed the extent to which a government-imposed order for all nonessential workers to remain at home helped lower the prevalence of the disease.

Early in 2020, as it became clear that COVID-19 was becoming a worldwide problem, ASU and Tempe decided to begin testing for the virus’s genetic material as well. “We were very well positioned to take on monitoring of the SARS-CoV-2,” Halden says. “With the help of ASU virus experts, we immediately retooled our monitoring system to measure COVID-19 by way of SARS-CoV-2 particles in wastewater using reverse transcriptase quantitative (polymerase chain reaction),” he says, referring to a common laboratory method for quantifying the viral RNA load present in wastewater.

Just as it did for opioid use, the city of Tempe created a publicly accessible dashboard to display data regarding levels of the virus in wastewater samples from six collection areas in the city as well as the adjacent town of Guadalupe. (One of the collection areas later was divided in two, so the dashboard now displays data for seven areas within Tempe.) Posted results represent the weekly average of SARS-CoV-2 genome copies per liter of wastewater collected as part of three 24-hour composite samples from each of the areas. 

Begun in March, the new dashboard was “very successful at providing us with an early view” of the spread of COVID-19 locally, Halden says. “We have a very fine-resolution information database” that shows “how much of the virus is where at what point in time.”

The data also revealed the extent to which a government-imposed order for all nonessential workers to remain at home helped lower the prevalence of the disease. “We saw that the lockdown was very efficient in driving the virus numbers down,” Halden notes. Meanwhile, the data also indicated an uptick in the virus load when the economy began to reopen. “With loosening of the lockdowns, we saw an increase in virus particles,” he says. Similarly, a subsequent mask ordinance “really made a difference” in terms of the viral load in the wastewater, “driving numbers down below the detection limit for various areas,” Halden says. 

The city of Tempe is spending roughly $300,000 to $400,000 annually on sampling related to its wastewater-based epidemiology program. It is money well spent, Inchausti says. “Part of the utility of using this data has been the outreach in the community,” she says. Such efforts include multilingual education and communication about city-provided services, the delivery of masks, and COVID-19 saliva-based testing for individuals in areas shown to be hot spots for the disease. “The city is really invested,” she says. “They’ve seen the benefits of using wastewater [testing] and utilizing it to deploy different strategies.”

The city is also looking to use the results of the wastewater testing as a means to combat COVID-19 as cost-effectively as possible. “We need to be more efficient in how we deploy resources,” Inchausti says. For example, the city does not have the wherewithal to routinely clean each of its many parks to limit the spread of the virus. However, targeting only those parks that are located in areas shown by the wastewater testing to be COVID-19 hot spots would require significantly fewer resources on the part of the city while still protecting public health adequately, she maintains. In the event that the wastewater testing shows the virus to be significantly more prevalent in one area, the city would have the option to close only those parks in that area rather than having to shut down every park in the city.

ASU has enjoyed such success with its wastewater monitoring efforts that it created two separate entities in 2019 to handle the workload, Halden says. A for-profit venture that licensed the wastewater sampling and testing process developed by ASU — AquaVitas LLC — offers various consultation services pertaining to wastewater-based epidemiology for municipalities and private organizations. Halden is the chief business development officer for AquaVitas.

The university also formed the nonprofit organization OneWaterOneHealth, which uses wastewater-based epidemiology as a means of improving health outcomes, primarily in marginalized or underserved communities. When OneWater­OneHealth began last year, “we weren’t quite sure which step was best to take forward at that point,” says Devin Bowes, a nutritional epidemiologist and one of the co-founders of OneWaterOneHealth, along with Halden and Nivedita Biyani, a graduate research assistant at ASU. Upon the arrival of the COVID-19 pandemic, Bowes says, “we knew exactly how we could help.” Since then, OneWaterOneHealth has worked with communities that “may not get the clinical testing access that they need in order to make some sound decisions within their community,” she says. 

Boise, Idaho, is another city that has begun using a publicly accessible internet dashboard to display the results of its testing for the presence of SARS-CoV-2 genetic material in its wastewater. Since late May, the city has been sampling and testing influent daily at the heads of its two water renewal facilities, says Kyle Patterson, a city data strategist for Boise. The two facilities treat, in addition to wastewater from Boise, wastewater from the Idaho towns of Garden City and Eagle. For the purposes of testing for SARS-CoV-2 in its wastewater, Boise sends its 24-hour composite samples to the University of Missouri for analysis by means of quantitative polymerase chain reaction testing, a method of quickly making millions of copies of genetic material.

Because Boise conducts its sampling at its water renewal facilities and not further upstream, as Tempe does, its dashboard does not display results on the local level. Instead, Boise’s dashboard shows a single daily result comprising the average virus quantity in the samples from its two facilities. This average is weighted on the basis of flow and adjusted on the basis of a control test. 

Boise opted to share the data online because “people are really hungry for information related to COVID-19,” Patterson says. “We wanted to do our part to help provide that publicly.” The city also wanted to share its data with Central District Health, one of seven public health districts within the state of Idaho. Central District Health serves the counties of Ada, Boise, Elmore, and Valley; the city of Boise is in Ada County. “We want to do our part to help our public health experts here locally in their fight against COVID-19,” Patterson says.

For its part, the Central District Health is “still working on the best way to incorporate this data into our decision-making processes and how it may be used to identify potential increases or decreases in illnesses within our communities,” says Brandon Atkins, a public information specialist for the district. “Our hope is that this information will provide us an additional tool to help provide effective mitigation strategies within our communities.”

Like Tempe, other U.S. cities and states have begun teaming with academic institutions to test samples for the presence of the virus’s genetic material.

Like Tempe, other U.S. cities and states have begun teaming with academic institutions to test samples for the presence of the virus’s genetic material. For example, in August, the state of Colorado announced that it was developing a partnership to conduct wastewater-based epidemiology using samples from 17 wastewater utilities that, combined, serve as much as 65 percent of the state’s population. As part of the $520,000 project, each utility will provide two samples per week taken from the influent of its wastewater treatment facilities. Analytical testing will be conducted primarily by Colorado State University, with assistance from Metropolitan State University of Denver. 

“Knowing whether we’ll have an increase in cases allows health officials to adapt and shift resources to those communities so they are ready for the outbreak,” said Nicole Rowan, the clean water program manager for the Colorado Department of Public Health and Environment, in an Aug. 12 news release. “And if we see a potential decrease in cases, then it can be one tool in the toolbox to help inform whether to ease up on restrictions.” 

The effort is slated to continue through August 2021, says MaryAnn Nason, a spokesperson for the Colorado Department of Public Health and Environment. “If the pilot is successful and the need continues, we hope to expand it so more utilities can participate,” Nason says. “We will share this data with local public health agencies, and we anticipate we will have enough data after several months to launch a public dashboard.”

In August, New York state announced that it was launching a $500,000 pilot program to test wastewater for the presence of SARS-CoV-2 in Onondaga County and the cities of Albany, Newburgh, and Buffalo.

Also in August, New York state announced that it was launching a $500,000 pilot program to test wastewater for the presence of SARS-CoV-2 in Onondaga County and the cities of Albany, Newburgh, and Buffalo. An Aug. 14 news release from the office of Democratic Gov. Andrew Cuomo explained, “The wastewater pilot will be used to assess the feasibility of a statewide initiative to utilize wastewater as a leading indicator of the prevalence of COVID-19 in the population, usefulness in predicting diagnostic testing and contact tracing needs, as well as potential mitigation measures such as hospital preparedness, the need to reinforce Executive Orders or reevaluate reopening plans.” 

The pilot project involves the New York State Department of Health, the New York State Department of Environmental Conservation, Syracuse University, the State University of New York College of Environmental Science and Forestry, the State University of New York Upstate Medical University, the diagnostics company Quadrant Biosciences Inc., and the engineering consulting firm Arcadis. 

Onondaga County, Albany, Newburgh, and Buffalo were selected for the pilot because they “have features and areas that will allow for specific monitoring of smaller geographic areas such as residential, industrial, commercial and/or resort areas,” according to the governor’s release. “The relationship between wastewater virus data and COVID-19 cases within the corresponding area will be analyzed. The pilot study will also provide for an in-depth daily sampling program at up to 10 locations of high concern or special interest.”

For the pilot, Arcadis will identify sampling locations and collect wastewater samples. “We’re sampling two to three days per week, depending on the location,” says Darcy Sachs, a project manager for Arcadis. “That allows us to gain a better understanding of the variability” of the genetic material of the virus in the wastewater,” Sachs says. “In each of these cities, we have up to 15 locations we’re sampling. So we can get a fair bit of resolution on the virus presence in those areas.”

To ensure that the resulting data are as useful as possible, Arcadis developed sampling plans that are “very customized” to the individual communities participating in the pilot, Sachs says,  “knowing the sewer system is crucial to coming up with a plan that will work.” To this end, Arcadis staff accounted for such factors within the collection systems as high flow rates, combined sewer overflows, sewer depths, the existence of offline or in-line stormwater collection and holding, the use of disinfecting chemicals for odor control, and disinfection. To varying degrees, each variable “can impact the measurability of the viral RNA,” Sachs says.

Armed with the data from the pilot, epidemiologists from Syracuse University will “develop models to predict case transmissions” within each of the participating communities, Sachs says. “We hope that this becomes a springboard for a New York statewide platform.” By providing advance data regarding the actual rates of COVID-19 transmission, the pilot project is intended to facilitate better, more informed decision-making on the part of the state government. “We are hoping that this allows the New York State Department of Health to make decisions quickly and snuff out any significant transmission of the virus in a given community,” Sachs says.

By providing advance data regarding the actual rates of COVID-19 transmission, the pilot project is intended to facilitate better, more informed decision-making on the part of the state government.

The pilot project offers a vital way for civil engineers to work with scientists and other technical professionals to further the cause of public health, says John McCarthy, P.E., the water business line president for Arcadis. “It’s exciting to be on the front line of the COVID-19 challenges,” McCarthy says. “For civil engineers to be there and to be protecting public health, I think that’s a big deal. It’s very much in line with our overall mission, which is improving quality of life. Here we’re protecting the quality of life.”

Looking to work with health agencies, wastewater treatment agencies, and others to address the COVID-19 threat, the engineering firm GHD announced in early September that it was initiating a wastewater-based epidemiology service with the support of the bioanalytical testing company Eurofins Scientific. In a press release issued Sept. 9, Peter Capponi, the North American industrial and manufacturing sector leader at GHD, stated, “The launch of this service translates to one more weapon in the fight against the pandemic. The testing technology has the potential to offer scientific evidence to a wide range of organizations to support their decision-making.” 

While demand for sampling grows, the jury is still out on which techniques are best. “Currently, there is no federal (Environmental Protection Agency)-approved methodology for sampling, but for the most part, health departments and utilities across the country have the same approach — sampling either at the intake of the wastewater treatment plant or upstream throughout the collection system at possible hot spot locations,” says Emily Remmel, a director of regulatory affairs for the National Association of Clean Water Agencies. And hot spots can include hospitals, long-term health care facilities, prisons, and schools and universities.

Determining where to sample “should not be a decision made by the wastewater utility single-handedly,” Remmel points out. “This type of epidemiological surveillance is outside the traditional role of a wastewater treatment plant and should be made in tandem with direction from local and state health departments,” she says. 

That said, sampling at a wastewater treatment facility offers a straightforward approach that can take advantage of existing equipment. “Most utilities are getting good results by sampling primary effluent at the wastewater treatment plant,” says Ferguson of the Water Research Foundation. “There is some indication that primary settled sewage may be the most reliable/representative sample to collect and test to represent an overall community.”

Much still remains unclear about exactly how to interpret SARS-CoV-2 signals detected in wastewater. Unknown factors include the extent to which rainwater, industrial effluent, and other constituents present in collection systems might affect the RNA signal from the virus.

The question of sampling frequency also is undetermined. “We are learning more and more about sampling wastewater for COVID-19 RNA and the usefulness of the data,” Remmel says. “Ideally, a wastewater sample would be collected at least weekly. But as our learning has evolved on this issue, increasing sampling can improve trend outputs. Therefore, sampling three times a week, although more costly, can give us a more refined picture of RNA prevalence in a given community.”

In June, the Water Research Foundation published a paper, titled Wastewater Surveillance of the COVID-19 Genetic Signal in Sewersheds, summarizing the findings of an international panel it convened in April to assess the known state of wastewater-based epidemiology as it pertains to SARS-CoV-2. The paper includes a best practices section that addresses safety, equipment and preliminary activities, sample collection, documentation, and transport, storage, and preservation. (Visit tinyurl.com/wwaterCOVID for the full report.)

Much still remains unclear about exactly how to interpret SARS-CoV-2 signals detected in wastewater. Unknown factors include the extent to which rainwater, industrial effluent, and other constituents present in collection systems might affect the RNA signal from the virus. “There are many confounding issues that we are not entirely clear on, such as how dilution/volume may affect the COVID-19 RNA genetic signal,” Remmel says. 

“Duration, temperature, and volume are a few of the concerns that could impact signal strength,” she notes. “In addition, other constituents — for example, pH, ammonia, total suspended solids, et cetera — may impact the genetic signal.” 

Another concern has to do with whether current testing methods are capable of detecting low levels of infection in a community. In an Aug. 17 news release, the CDC stated that the “lower limits of detection (i.e., the smallest number of people shedding the virus in stool that can still be detected by current testing methods) for sewage surveillance are not yet well understood. More data on fecal shedding by infected individuals over the course of (the) disease are needed to better understand the limits of detection.”

Another glaring question mark involves how closely virus levels in wastewater correlate to the numbers of individuals having the disease. “The trends are predicted by the levels in wastewater, but we do not have sufficient knowledge yet of other information needed to translate the signal into an estimate of the number of individuals infected,” Ferguson says. “A key piece of missing information is the amount of virus RNA shed in fecal material from asymptomatic cases.” 

Another glaring question mark involves how closely virus levels in wastewater correlate to the numbers of individuals having the disease.

The CDC is clear on this point. Currently, “it is not possible to reliably and accurately predict the number of infected individuals in a community based on sewage testing,” according to information on the agency’s website. 

That said, at least one company maintains that it has the ability to estimate closely the number of individuals in an area having COVID-19 based on the results of wastewater sampling. In late July, the Israeli wastewater management technology firm Kando announced the completion of a pilot project to detect SARS-CoV-2 in wastewater from the collection system of the city of Ashkelon, Israel. 

Working with researchers from Ben Gurion University and Technion — Israel Institute of Technology, Kando staff “were able to accurately measure concentrations of the virus remnants and determine the approximate number of those suffering from infection by factoring in the necessary data, including industrial effluent, which destroys the virus, and sewage flow, which dilutes the virus’s concentration,” according to a July 30 news release from the company. 

For the pilot, Kando collected two types of data pertaining to Ashkelon’s wastewater network — continuous sensor data and physical water samples, says Yaniv Shoshan, the company’s vice president of product and marketing. The sensor data are transmitted from Kando’s Internet of Things units to a cloud service that analyzes the wastewater behavior, Shoshan says. Collected by automatic samplers, the physical samples were analyzed in a virology lab. “The lab results (were) then integrated into a mathematical model that ingests the lab results, network properties, population properties, and actual sensor reading to estimate the infected population size,” he explains.

Back in the United States, the CDC and the U.S. Department of Health and Human Services are looking to compile and integrate the results of the many disparate efforts around the country to test wastewater for the presence of SARS-CoV-2. To that end, the CDC is developing a national database that it calls the National Wastewater Surveillance System. “The data generated by NWSS will help public health officials to better understand the extent of COVID-19 infections in communities,” the CDC said in its news release. “CDC is currently developing a portal for state, tribal, local, and territorial health departments to submit wastewater testing data into a national database for use in summarizing and interpreting data for public health action.”

The CDC and the U.S. Department of Health and Human Services are looking to compile and integrate the results of the many disparate efforts around the country to test wastewater for the presence of SARS-CoV-2.

As the ongoing COVID-19 pandemic continues to unfold, it remains highly likely that wastewater-based epidemiology will feature prominently in efforts to study and understand the transmission of the virus within an increasing number of communities. “What we have is a radar,” says Halden of ASU. “We can look and identify problems early on, find geospatial clusters, and then have a more synchronized and informed intervention, going to the places where help is needed, rather than testing everyone willy-nilly. That can be done quite inexpensively.”

At the same time, the newly reenergized field of wastewater-based epidemiology offers a means of addressing other public health threats well into the future, Halden says. “This should not be just a fad,” he says. “We want to build a public health monitoring and protection tool for the
ages.”

Inchausti, from the city of Tempe, agrees. Wastewater-based epidemiology offers “a way to save lives,” she says. But Inchausti does not stop there. “If done right nationally,” she says, “this will eradicate pandemics.”

This article first appeared in the October 2020 issue of Civil Engineering.