Testing the waters
Wastewater surveillance emerges as a critical disease-tracking tool
The Centers for Disease Control and Prevention (CDC) calls it a new frontier for public health. The National Institutes of Health (NIH) says it is a data gold mine. The UN Environment Programme calls it a sentinel for disease.
These organizations are all talking about wastewater surveillance. The process of looking for a virus in sewage gained traction in the 1940s as part of polio eradication efforts. It proved an effective method for detecting the presence or absence of polio virus in specific geographic areas or populations. In the 1980s, some scientists used it to monitor for hepatitis A virus. Then came COVID-19.
With the advent of the global pandemic, researchers quickly determined the SARS-CoV-2 virus—although it causes respiratory symptoms—was shed in feces. That meant it could be detected in wastewater, and wastewater surveillance efforts exploded in an effort to understand spatial and temporal trends of this new disease. In the past four years, researchers have discovered just how valuable a tool wastewater surveillance can be for COVID-19 and other diseases.
Analyzing wastewater from sewage treatment plants is anonymous. It is efficient: A single test can represent thousands or millions of people. It doesn’t rely on people going to the doctor, and it can detect virus shed from infected people who don’t have any symptoms. Perhaps most importantly, it’s fast. Spikes in the virus can be detected in the wastewater several days before rates of reported cases or hospitalizations started to increase.
When COVID-19 hit, Rollins was in a good spot to respond. The school has a leading Center for Global Safe Water, Sanitation, and Hygiene (CGSW). That center was one of the few academic research institutions already conducting wastewater surveillance for a typhoid fever project in India. And the school maintains strong ties with the Georgia Department of Public Health (DPH) and the CDC. As a result, Rollins emerged a leader in this relatively new and critically important surveillance strategy.
“I think that you can truthfully describe Emory as a powerhouse of innovation on wastewater surveillance both in the U.S. and internationally,” says Christine Moe, PhD, Eugene J. Gangarosa Chair in Safe Water and Sanitation and director of CGSW. “Last fall I presented at the Africa CDC workshop on environmental surveillance, and when I looked at my presentation compared to the other people that were at that workshop, we had done work in more countries with more targets than any other group.”
The Centers for Disease Control and Prevention (CDC) calls it a new frontier for public health. The National Institutes of Health (NIH) says it is a data gold mine. The UN Environment Programme calls it a sentinel for disease.
These organizations are all talking about wastewater surveillance. The process of looking for a virus in sewage gained traction in the 1940s as part of polio eradication efforts. It proved an effective method for detecting the presence or absence of polio virus in specific geographic areas or populations. In the 1980s, some scientists used it to monitor for hepatitis A virus. Then came COVID-19.
With the advent of the global pandemic, researchers quickly determined the SARS-CoV-2 virus—although it causes respiratory symptoms—was shed in feces. That meant it could be detected in wastewater, and wastewater surveillance efforts exploded in an effort to understand spatial and temporal trends of this new disease. In the past four years, researchers have discovered just how valuable a tool wastewater surveillance can be for COVID-19 and other diseases.
Analyzing wastewater from sewage treatment plants is anonymous. It is efficient: A single test can represent thousands or millions of people. It doesn’t rely on people going to the doctor, and it can detect virus shed from infected people who don’t have any symptoms. Perhaps most importantly, it’s fast. Spikes in the virus can be detected in the wastewater several days before rates of reported cases or hospitalizations started to increase.
When COVID-19 hit, Rollins was in a good spot to respond. The school has a leading Center for Global Safe Water, Sanitation, and Hygiene (CGSW). That center was one of the few academic research institutions already conducting wastewater surveillance for a typhoid fever project in India. And the school maintains strong ties with the Georgia Department of Public Health (DPH) and the CDC. As a result, Rollins emerged a leader in this relatively new and critically important surveillance strategy.
“I think that you can truthfully describe Emory as a powerhouse of innovation on wastewater surveillance both in the U.S. and internationally,” says Christine Moe, PhD, Eugene J. Gangarosa Chair in Safe Water and Sanitation and director of CGSW. “Last fall I presented at the Africa CDC workshop on environmental surveillance, and when I looked at my presentation compared to the other people that were at that workshop, we had done work in more countries with more targets than any other group.”
A New Technique
Moe remembers hearing about wastewater surveillance for the first time when she was a postdoctoral fellow at the CDC in the late 1980s. Researchers in her division were excited about how effective such surveillance was for detecting polio virus circulation in different geographic regions, and she was fascinated.
Fast-forward to 2016 and the introduction of a new typhoid fever vaccine. Health authorities were pondering how to prioritize vaccine distribution. Typhoid, like polio, has very nonspecific symptoms and infections can be asymptomatic, so silent transmission could be coursing through a community with little or no detection of cases. In addition, current diagnostic tests for typhoid fever are not very sensitive or specific. As a result, reliable data on the typhoid fever burden were severely lacking.
Recalling the discussions she heard decades earlier at CDC, Moe suggested using environmental surveillance to detect typhoid in Kolkata, India. Funded by the Bill & Melinda Gates Foundation, she and her team devised a surveillance strategy in the densely populated city. They found much more typhoid in wastewater than case-based surveillance had detected. However, Moe’s work in India came to an abrupt end in 2020 when COVID-19 swept the globe.
Moe remembers hearing about wastewater surveillance for the first time when she was a postdoctoral fellow at the CDC in the late 1980s. Researchers in her division were excited about how effective such surveillance was for detecting polio virus circulation in different geographic regions, and she was fascinated.
Fast-forward to 2016 and the introduction of a new typhoid fever vaccine. Health authorities were pondering how to prioritize vaccine distribution. Typhoid, like polio, has very nonspecific symptoms and infections can be asymptomatic, so silent transmission could be coursing through a community with little or no detection of cases. In addition, current diagnostic tests for typhoid fever are not very sensitive or specific. As a result, reliable data on the typhoid fever burden were severely lacking.
Christine Moe, PhD, Eugene J. Gangarosa Chair in Safe Water and Sanitation and director of CGSW
Christine Moe, PhD, Eugene J. Gangarosa Chair in Safe Water and Sanitation and director of CGSW
Recalling the discussions she heard decades earlier at CDC, Moe suggested using environmental surveillance to detect typhoid in Kolkata, India. Funded by the Bill & Melinda Gates Foundation, she and her team devised a surveillance strategy in the densely populated city. They found much more typhoid in wastewater than case-based surveillance had detected. However, Moe’s work in India came to an abrupt end in 2020 when COVID-19 swept the globe.
Searching the Sewers
for COVID-19
Rollins’ first foray into wastewater surveillance for SARS-CoV-2 was internal. Emory’s administration asked Moe and her team to test the wastewater from the university’s dorms in an attempt to identify dorms with undetected cases. It was slow going at first. At that time, teasing results from the samples collected required days of tedious lab work—a costly delay during a fast-moving pandemic. And correlations between virus detection in the wastewater and actual student cases were spotty at first. However, when students returned to campus after their winter break in 2020/2021, Moe’s team detected a surge in SARS-CoV-2 in the wastewater several days before a wave of students tested positive for COVID-19 in February 2021.
Rollins’ wastewater surveillance work expanded when it got a contract from a company that had come up with a new, more efficient way to isolate the SARS-CoV-2 virus from wastewater samples and wanted to test it on a large scale. Moe and her team decided to concentrate their efforts on south Atlanta. “When we looked at DPH data, reported COVID-19 cases were suspiciously low in the south part of the city,” Moe says. “That area houses a poorer population who have less access to diagnostic testing.”
Thanks to a collaboration with the City of Atlanta’s Department of Watershed Management, which supplied maps of the sewer system and helped collect samples on a weekly basis, the CGSW team was able to monitor wastewater from three wastewater treatment plants in the southside of Atlanta. Each pipe that brought wastewater into a plant served a different part of the city, so the team could determine which areas had higher levels of the virus. Drilling down further, the team also collected samples from neighborhood manholes in many different communities, enabling them to refine the resolution of their research down to individual neighborhoods. They then compared the data they gathered to the geocoded case data of COVID-19 infections from DPH.
Yuke Wang, PhD, research assistant professor
Yuke Wang, PhD, research assistant professor
“What we were seeing with the wastewater was matching up with where DPH was seeing cases on a very fine scale,” says Yuke Wang, PhD, research assistant professor, who designed the surveillance strategy for this project. “We were the first to do this, and it was proof of the concept that wastewater surveillance can be used to pinpoint high-risk neighborhoods instead of just city-wide trends.”
This demonstrated ability to pinpoint outbreak locations became even more valuable with the advent of home testing for COVID-19. With people no longer going to the doctor to be tested and often treating their symptoms at home, clinical surveillance became less reliable than wastewater surveillance for tracking the level of infections within the community.
In addition to neighborhoods, the CGSW also collected samples from a correctional facility in northwest Atlanta. Anne Spaulding, MD, associate professor of epidemiology, led the effort. Especially in the early days of the pandemic, many of the large COVID-19 outbreaks in the United States were in prisons and jails. These institutions were strapped to deal with the pandemic: They faced overcrowding, mask shortages, and limited means of quarantining and isolating infected residents of the jail.
“We knew the technology worked in college dormitories,” Spaulding says. “Jails are another setting of congregate living. If wastewater surveillance could detect SARS-CoV-2 before the onset of symptoms in inmates, it could give jails an early warning.”
Spaulding and her team collected wastewater samples from manhole sites outside of Fulton County Jail from October 2021 to May 2022. That collection strategy allowed the researchers to overcome common barriers to infectious disease screenings within jails, such as access issues and hesitancy of jail residents. Spaulding’s team found monitoring the wastewater could efficiently and accurately track trends of COVID-19 infections among residents of the jail.
“So many people pass through jails and then back into the community,” Spaulding says. “That means protecting the health of detained individuals can impact the health of the entire community.”
Rollins’ first foray into wastewater surveillance for SARS-CoV-2 was internal. Emory’s administration asked Moe and her team to test the wastewater from the university’s dorms in an attempt to identify dorms with undetected cases. It was slow going at first. At that time, teasing results from the samples collected required days of tedious lab work—a costly delay during a fast-moving pandemic. And correlations between virus detection in the wastewater and actual student cases were spotty at first. However, when students returned to campus after their winter break in 2020/2021, Moe’s team detected a surge in SARS-CoV-2 in the wastewater several days before a wave of students tested positive for COVID-19 in February 2021.
Rollins’ wastewater surveillance work expanded when it got a contract from a company that had come up with a new, more efficient way to isolate the SARS-CoV-2 virus from wastewater samples and wanted to test it on a large scale. Moe and her team decided to concentrate their efforts on south Atlanta. “When we looked at DPH data, reported COVID-19 cases were suspiciously low in the south part of the city,” Moe says. “That area houses a poorer population who have less access to diagnostic testing.”
Thanks to a collaboration with the City of Atlanta’s Department of Watershed Management, which supplied maps of the sewer system and helped collect samples on a weekly basis, the CGSW team was able to monitor wastewater from three wastewater treatment plants in the southside of Atlanta. Each pipe that brought wastewater into a plant served a different part of the city, so the team could determine which areas had higher levels of the virus. Drilling down further, the team also collected samples from neighborhood manholes in many different communities, enabling them to refine the resolution of their research down to individual neighborhoods. They then compared the data they gathered to the geocoded case data of COVID-19 infections from DPH.
Yuke Wang, PhD, research assistant professor
Yuke Wang, PhD, research assistant professor
“What we were seeing with the wastewater was matching up with where DPH was seeing cases on a very fine scale,” says Yuke Wang, PhD, research assistant professor, who designed the surveillance strategy for this project. “We were the first to do this, and it was proof of the concept that wastewater surveillance can be used to pinpoint high-risk neighborhoods instead of just city-wide trends.”
This demonstrated ability to pinpoint outbreak locations became even more valuable with the advent of home testing for COVID-19. With people no longer going to the doctor to be tested and often treating their symptoms at home, clinical surveillance became less reliable than wastewater surveillance for tracking the level of infections within the community.
In addition to neighborhoods, the CGSW also collected samples from a correctional facility in northwest Atlanta. Anne Spaulding, MD, associate professor of epidemiology, led the effort. Especially in the early days of the pandemic, many of the large COVID-19 outbreaks in the United States were in prisons and jails. These institutions were strapped to deal with the pandemic: They faced overcrowding, mask shortages, and limited means of quarantining and isolating infected residents of the jail.
Anne Spaulding, MD, associate professor of epidemiology
Anne Spaulding, MD, associate professor of epidemiology
“We knew the technology worked in college dormitories,” Spaulding says. “Jails are another setting of congregate living. If wastewater surveillance could detect SARS-CoV-2 before the onset of symptoms in inmates, it could give jails an early warning.”
Spaulding and her team collected wastewater samples from manhole sites outside of Fulton County Jail from October 2021 to May 2022. That collection strategy allowed the researchers to overcome common barriers to infectious disease screenings within jails, such as access issues and hesitancy of jail residents. Spaulding’s team found monitoring the wastewater could efficiently and accurately track trends of COVID-19 infections among residents of the jail.
“So many people pass through jails and then back into the community,” Spaulding says. “That means protecting the health of detained individuals can impact the health of the entire community.”
National Surveillance
Moe and her team worked with the CDC to support its National Wastewater Surveillance System (NWSS) and the DPH’s Georgia National Wastewater Surveillance System (GA NWSS). Led by Rollins alum Amy Kirby, NWSS now includes data from more than 1,200 sampling sites covering an estimated 37% of the U.S. population.
Rollins alum Amy Kirby
Rollins alum Amy Kirby
“We worked closely with the Georgia Department of Public Health to support the startup of their system,” says Marlene Wolfe, PhD, assistant professor of environmental health. “We ran samples for them for a while
in the lab at Emory, and then we transferred our protocols over to them and helped train their lab staff. It’s been a great transfer of knowledge that has happened throughout the pandemic.”
Wolfe co-leads a separate national wastewater surveillance network, this one funded entirely by a philanthropy and run out of Stanford University in partnership with Emory. The network, called WastewaterSCAN, grew out
of a pilot program Wolfe worked on while she was a postdoc at Stanford that collected wastewater samples around the Bay Area and posted the results on a public dashboard.
Marlene Wolfe, PhD, assistant professor of environmental health
Marlene Wolfe, PhD, assistant professor of environmental health
Now in its third year, WastewaterSCAN collects three samples per week from 150 sites in 40 states and tests those samples for 10 pathogens, including influenza, respiratory virus, rotavirus, and, of course, COVID-19. Because it’s not a tax-funded government program, WastewaterSCAN is more nimble and able to respond quickly to emerging threats. It was the first group to monitor wastewater for the mpox (formerly monkeypox) virus, beginning just two weeks after the first case of mpox was reported in the United States in 2022 and expanding nationwide within six weeks. It began testing for highly pathogenic avian influenza A (H5N1) virus very quickly after the first case of avian flu in cattle was reported in March 2024.
“We are not trying to be the CDC,” Wolfe says. “Our goal is to support the CDC and state programs. Because we are made up of academics, we can do research, develop and test new tools, and put them in practice much more quickly than the wheels of government can typically move. It’s a unique platform that gives us the opportunity to do research in real time and translate it to have immediate impact.”
Moe and her team worked with the CDC to support its National Wastewater Surveillance System (NWSS) and the DPH’s Georgia National Wastewater Surveillance System (GA NWSS). Led by Rollins alum Amy Kirby, NWSS now includes data from more than 1,200 sampling sites covering an estimated 37% of the U.S. population.
Rollins alum Amy Kirby
Rollins alum Amy Kirby
“We worked closely with the Georgia Department of Public Health to support the startup of their system,” says Marlene Wolfe, PhD, assistant professor of environmental health. “We ran samples for them for a while
in the lab at Emory, and then we transferred our protocols over to them and helped train their lab staff. It’s been a great transfer of knowledge that has happened throughout the pandemic.”
Wolfe co-leads a separate national wastewater surveillance network, this one funded entirely by a philanthropy and run out of Stanford University in partnership with Emory. The network, called WastewaterSCAN, grew out
of a pilot program Wolfe worked on while she was a postdoc at Stanford that collected wastewater samples around the Bay Area and posted the results on a public dashboard.
Marlene Wolfe, PhD, assistant professor of environmental health
Marlene Wolfe, PhD, assistant professor of environmental health
Now in its third year, WastewaterSCAN collects three samples per week from 150 sites in 40 states and tests those samples for 10 pathogens, including influenza, respiratory virus, rotavirus, and, of course, COVID-19. Because it’s not a tax-funded government program, WastewaterSCAN is more nimble and able to respond quickly to emerging threats. It was the first group to monitor wastewater for the mpox (formerly monkeypox) virus, beginning just two weeks after the first case of mpox was reported in the United States in 2022 and expanding nationwide within six weeks. It began testing for highly pathogenic avian influenza A (H5N1) virus very quickly after the first case of avian flu in cattle was reported in March 2024.
“We are not trying to be the CDC,” Wolfe says. “Our goal is to support the CDC and state programs. Because we are made up of academics, we can do research, develop and test new tools, and put them in practice much more quickly than the wheels of government can typically move. It’s a unique platform that gives us the opportunity to do research in real time and translate it to have immediate impact.”
Predicting the Future
Since the start of the pandemic, wastewater surveillance has cemented itself as a crucial public health tool. However, most of the funding to establish these surveillance programs has come out of COVID-19 funds. That leaves researchers worried funding may dry up as the pandemic wanes.
“We have learned a lot since the beginning of the pandemic,” says Pengbo Liu, PhD, research associate professor of global health. “We have developed better, very sensitive methods for detecting the presence of pathogens in the wastewater. But we need to keep these surveillance systems up and running. If there
is a new epidemic, we can detect the pathogen one to two weeks before the disease arises in the general population. That means we can give an early warning to the government to help prevent the spread of the disease.”
And that might prevent the next epidemic from becoming another pandemic.
Story by Martha Nolan
Designed by Linda Dobson
Illustration by Marcin Wolski
Photography by Jenni Girtman
Since the start of the pandemic, wastewater surveillance has cemented itself as a crucial public health tool. However, most of the funding to establish these surveillance programs has come out of COVID-19 funds. That leaves researchers worried funding may dry up as the pandemic wanes.
Pengbo Liu, PhD, research associate professor of global health
Pengbo Liu, PhD, research associate professor of global health
“We have learned a lot since the beginning of the pandemic,” says Pengbo Liu, PhD, research associate professor of global health. “We have developed better, very sensitive methods for detecting the presence of pathogens in the wastewater. But we need to keep these surveillance systems up and running. If there
is a new epidemic, we can detect the pathogen one to two weeks before the disease arises in the general population. That means we can give an early warning to the government to help prevent the spread of the disease.”
And that might prevent the next epidemic from becoming another pandemic.
Story by Martha Nolan
Designed by Linda Dobson
Illustration by Marcin Wolski
Photography by Jenni Girtman
Antibiotic-Resistant Pathogens
Maya Nadimpalli, PhD, assistant professor of environmental health, is taking wastewater surveillance in a new direction, trying to use it to detect bacteria—specifically antibiotic-resistant bacteria—instead of viruses. She is hoping this technique will give her insights into the relationship between social determinants of health and antibiotic resistance.
In researching this topic in the past, Nadimpalli was stumped by the necessity of relying on patient medical records. “Patient medical records are a nightmare to deal with,” she says. “It’s really hard to use records from single health care systems to get a comprehensive look at a specific city or region. And they are not representative—uninsured or underinsured people are less likely to go to the doctor.”
So she began to wonder if she might be able to get a more representative snapshot of the kinds of antibiotic-resistant bacteria people are harboring or infected with in particular geographic areas by looking in the sewer. Atlanta was a perfect location for her study.
“Atlanta is so diverse,” Nadimpalli says. “And it’s not just diverse. As a result of segregation and redlining and gentrification, it’s also very segregated. The populations served by different wastewater treatment plants are very, very different from each other.”
However, monitoring bacteria in wastewater is an entirely different ballgame than tracking viruses. When a virus enters the sewer system, it doesn’t replicate or change in any way. Not so bacteria, which are champions of metamorphosis. Also, an entire microbial community lives in the sewer system that has nothing to do with what is coming from toilets or sinks. In fact, according to Nadimpalli, if you look at sewage at a treatment plant, only about 10% of the bacteria present are from humans. The rest is environmental.
The effective and proven test to detect viral RNA in sewage samples—digital PCR, or polymerase chain reaction technology—is not feasible for identifying antibiotic-resistant bacteria. Instead, Nadimpalli has to use culture-based methods, which are a lot less sensitive and more time consuming.
“We also have a lot less confidence that what we’re measuring at the point of the treatment plant is actually what was excreted by humans in the first place,” Nadimpalli says. “That’s just the nature of bacteria. They’re able to survive and thrive in sewer systems in a way that viruses can’t.”
Nevertheless, Nadimpalli and her team found sewer sheds that received wastewater from areas with a higher percentage of crowded households also had higher concentrations of drug-resistant bacteria in their wastewater.
“You would never have been able to draw that conclusion from patient medical records,” she says. “Doctors don’t ask how many people you live with or how crowded your housing is. So this work provides proof of principle that wastewater sampling can be a way to identify characteristics of how people live or where they live that could be associated with their risk of harboring drug-resistant bacteria. It’s technologically less ambitious than what people are trying to do with viruses, but I think wastewater surveillance for antibiotic-resistant bacteria can be helpful in filling critical knowledge gaps.”
Antibiotic-Resistant Pathogens
Maya Nadimpalli, PhD, assistant professor of environmental health, is taking wastewater surveillance in a new direction, trying to use it to detect bacteria—specifically antibiotic-resistant bacteria—instead of viruses. She is hoping this technique will give her insights into the relationship between social determinants of health and antibiotic resistance.
In researching this topic in the past, Nadimpalli was stumped by the necessity of relying on patient medical records. “Patient medical records are a nightmare to deal with,” she says. “It’s really hard to use records from single health care systems to get a comprehensive look at a specific city or region. And they are not representative—uninsured or underinsured people are less likely to go to the doctor.”
So she began to wonder if she might be able to get a more representative snapshot of the kinds of antibiotic-resistant bacteria people are harboring or infected with in particular geographic areas by looking in the sewer. Atlanta was a perfect location for her study.
“Atlanta is so diverse,” Nadimpalli says. “And it’s not just diverse. As a result of segregation and redlining and gentrification, it’s also very segregated. The populations served by different wastewater treatment plants are very, very different from each other.”
However, monitoring bacteria in wastewater is an entirely different ballgame than tracking viruses. When a virus enters the sewer system, it doesn’t replicate or change in any way. Not so bacteria, which are champions of metamorphosis. Also, an entire microbial community lives in the sewer system that has nothing to do with what is coming from toilets or sinks. In fact, according to Nadimpalli, if you look at sewage at a treatment plant, only about 10% of the bacteria present are from humans. The rest is environmental.
The effective and proven test to detect viral RNA in sewage samples—digital PCR, or polymerase chain reaction technology—is not feasible for identifying antibiotic-resistant bacteria. Instead, Nadimpalli has to use culture-based methods, which are a lot less sensitive and more time consuming.
“We also have a lot less confidence that what we’re measuring at the point of the treatment plant is actually what was excreted by humans in the first place,” Nadimpalli says. “That’s just the nature of bacteria. They’re able to survive and thrive in sewer systems in a way that viruses can’t.”
Nevertheless, Nadimpalli and her team found sewer sheds that received wastewater from areas with a higher percentage of crowded households also had higher concentrations of drug-resistant bacteria in their wastewater.
“You would never have been able to draw that conclusion from patient medical records,” she says. “Doctors don’t ask how many people you live with or how crowded your housing is. So this work provides proof of principle that wastewater sampling can be a way to identify characteristics of how people live or where they live that could be associated with their risk of harboring drug-resistant bacteria. It’s technologically less ambitious than what people are trying to do with viruses, but I think wastewater surveillance for antibiotic-resistant bacteria can be helpful in filling critical knowledge gaps.”
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