Like countless public health laboratory professionals, Martin Shafer, PhD, watched with concern as a new pandemic began to unfold in late 2019 and early 2020. A senior scientist and research lead at the Wisconsin State Laboratory of Hygiene (WSLH), Shafer had some familiarity with environmental microbiology and a taste for innovative research projects. Knowing that wastewater testing had shown some value in the U.S. and abroad for monitoring disease agents—notably polio—he and other scientists from the laboratory proposed developing a wastewater surveillance program for the state of Wisconsin.

In March 2020, the WSLH team received a green light to move forward. With support from the state health department, they built out the necessary infrastructure and validated methods to quantify SARS-CoV-2 from wastewater. They drew on their existing relationships with wastewater treatment facilities across the state and adapted molecular methodologies from environmental microbiology and virology. By September 2020, 73 wastewater treatment facilities in the state had agreed to participate in the program.

In the years since, the Wisconsin Wastewater Surveillance Program has expanded and evolved, adding pathogens and engaging epidemiologists, data scientists and others to refine collection, help interpret the data and implement public health mitigation strategies. It now monitors about 66% of the sewered population in the state.

As an early foray into wastewater surveillance, the effort benefited greatly from the involvement of the WSLH and its existing networks and expertise, Shafer said. “This was kind of homegrown in the public health laboratory, with a strong collaboration with the state Department of Health Services.”

APHL and its member laboratories have consistently been at the forefront of laboratory science, positioned to quickly identify and respond to new public health threats. Drawing on this tradition of innovation, many groups are leveraging new techniques and technologies to expand the reach and influence of public health laboratory science.

Monitoring Disease Through Wastewater

With the rise of at-home and point of care testing, wastewater surveillance is now being recognized as more valuable for SARS-CoV-2 monitoring than traditional clinical testing. “Wastewater can actually provide a more accurate and representative picture of the viral load in the community,” Shafer said. It captures asymptomatic cases, as well as populations that may be underrepresented in clinical data due to lack of access to health care or other reasons.

Wastewater surveillance has driven a tremendous amount of innovation among both academic and commercial partners, he said. The program has spurred development of several new wastewater-focused chemistries and technologies, including novel methods for isolating viruses, probes for measuring pathogen nucleic acids and wastewater-specific automation tools.

“Wastewater can actually provide a more accurate and representative picture of the viral load in the community.”


– Martin Shafer, PhD, Wisconsin State Laboratory of Hygiene.

The effort has also forged partnerships across academic institutions, state agencies, wastewater treatment facilities, public health labs, environmental regulators and more. “It showed that we can accomplish some really great public health goals by working together. And that continues,” Shafer said. “The wastewater treatment facilities, which are participating voluntarily, are absolutely key to this program.”

With the infrastructure now in place, the team members are building out validations and methods for other pathogens. Routine monitoring of influenza, RSV and norovirus are now in place, with methods for Candida auris and a suite of antibiotic resistance genes soon to follow. This is especially important as at-home testing becomes available for more agents, such as influenza, he notes.

The goal is “a more pathogen-agnostic approach, where we can use the tools to capture as many pathogens as possible, kind of an all-in-one sample collection,” Shafer said. Such an approach would enable faster identification and response to emerging threats—as successfully shown during the recent mpox outbreak—as well as the use of broad metagenomic tools to better detect unknown entities.

Named a National Center of Excellence within CDC’s National Wastewater Surveillance System in 2023, the Wisconsin program is now developing a nationwide performance testing program, with the goal of improving the overall quality and comparability of wastewater-based pathogen data across the whole system.

Spurring Global Innovation

Wastewater testing is showing promise as a catalyst of innovation globally as well. With support from the Global Fund, APHL is conducting a wastewater sampling pilot project in Maputo, Mozambique, for PCR testing for SARS-CoV-2 early detection in communities.

The project, building off an expansion of Mozambique’s public health laboratory system during the pandemic, has tested new methods of collecting and concentrating wastewater samples developed by the National Institutes for Health (NIH).

We were successfully able to prove that concept here,” said Solon Kidane, APHL’s in-country director. “The NIH in Mozambique now has a national strategy to expand the wastewater testing to five regions in the country.”

As in other parts of the world, the Mozambique project aims to evaluate the use of wastewater data as clinical reporting drops. Sampling in Maputo wrapped up in December 2023 and the team has completed its primary analysis of wastewater positivity rates. Getting clinical data for comparison has been more difficult, Kidane said, but work is ongoing.

The new sample collection and concentration methods were designed to be relatively simple and require minimal resources so they can be adapted to work throughout the country. In addition to expanding regionally, the NIH strategy also includes testing for other pathogens, including cholera, polio and influenza.

The APHL project is also helping the laboratories explore the use of next-generation sequencing (NGS) of wastewater samples. “APHL has procured some reagents and we’ve done some training,” Kidane said. “As a gold standard, next-generation sequencing is a goal here.”

Sequencing in Newborn Screening

Sequencing is also expanding possibilities in newborn screening. Historically, public health laboratories have relied primarily on biochemical biomarkers for the disorders on the Recommended Uniform Screening Panel for newborns. As the panel expands to include more complex conditions, however, laboratories are increasingly turning to genetic sequencing as a powerful supplemental detection method.

“Not all conditions have informative biochemical biomarkers expressed in the newborn period,” said Amy Gaviglio, MS, a genetics consultant for APHL. “DNA sequencing affords us the potential to expand our screening for a lot more diseases, relatively quickly.”

“Second-tier testing
result in a higher
positive predictive
value than a
first-tier screen”


– Guisou Zarbalian, MS, MPH
Manager, Newborn Screening and Genetics, APHL.

Some programs are now exploring second-tier testing using NGS. A program at the Utah Public Health Laboratory is looking to use NGS to examine the whole exome, or the portion of the genome that is expressed. And the Texas Department of State Health Services Laboratory is exploring the use of whole-genome sequencing as a second-tier testing option in newborn screening.

“Second-tier testing using technologies like NGS can be more sensitive and specific, which can result in a higher positive predictive value than a first-tier screen,” said Guisou Zarbalian, MS, MPH, APHL’s manager of newborn screening and genetics.

With greater access to data comes greater responsibility for protecting that data, and APHL continues to be active around issues of genetic privacy, Zarbalian adds. “We are working on ways to address concerns that families have with what is being done with their baby’s residual specimen and their baby’s data.”

Through a legislative affairs subcommittee, APHL has projects underway to develop policy language that states can adopt or adapt regarding how to securely store and protect data and samples from newborn screening.

Overdose Biosurveillance

Amy Miles, state toxicologist at the WSLH, has seen the potential of data to save lives in a very different context: overdose monitoring and surveillance.

A few years ago, while working on overdose testing for the forensics program, she had some cases for an individual with two separate impaired driving offenses. Then a post-mortem case came in—for the same person. “Had there been earlier intervention during those impaired driving cases,” Miles said, “potentially, the post mortem could have been avoided.”

The experience brought home the importance of using data to drive early and targeted intervention, she said. “The more we can inform not only the community, but ourselves, the better we can be at putting effective intervention programs in place.”

photo of laboratory techniciansAPHL’s Overdose Biosurveillance Task Force, started in 2019 and which Miles now co-chairs, is creating resources to help public health laboratories create testing programs and collect data for non-fatal overdose surveillance. A model biosurveillance strategy offers guidance for monitoring non-fatal overdose admissions to emergency departments and neonatal abstinence syndrome cases. Epidemiologists and other local officials can use such data to identify areas in need of targeted education, prevention or other intervention efforts.


A handful of state laboratories across the country currently have overdose biosurveillance programs—including Rhode Island, Minnesota and South Carolina as well as Wisconsin—and an influx of funding through the CDC’s Overdose to Action (OD2A) grant is expanding interest. Public health laboratories are well positioned to leverage the tools and connections already in place through the Laboratory Response Network to support non-fatal overdose surveillance, Miles said.


Most overdose testing can detect thousands of drugs of abuse. The task force’s goal is to get everybody to look at the same scope of compounds to make reported data more comparable across different labs and states.


“When we first started, we really focused on opioids. But we knew that’s not the full picture,” Miles said. And new opioids and other compounds are constantly being introduced into the drug supply.


The task force released new guidance in October 2023 to highlight the challenges presented by the prevalence of polysubstance use. Building on its previous model, the expanded strategy helps laboratories adapt to shifting trends and devise ways to pivot their testing to accommodate new compounds. It also provides guidance for labs that are now adopting high-resolution mass spectrometry as a more robust testing technology.


“With each iteration of the task force, we’re bringing in new people to get a mix of ideas and perspectives,” Miles said. “Everyone is very passionate and it’s been such an incredible group to work with.”



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