Riding the Wave of Public Health Laboratory Funding into the Future

A burst of emergency federal funding during the COVID-19 pandemic allowed public health laboratories to upgrade, improve and invest. Laboratories modernized equipment, hired personnel, created more efficient processes and expanded public health programs such as next-generation sequencing and wastewater surveillance.

But supplemental funding has begun to recede. The boom-and-bust cycle of public health funding is well-known to public health professionals. They’ve seen it time and time again, which spurred laboratory directors during the pandemic to think critically and sustainably about how to invest COVID-19 dollars beyond the initial pandemic response.

“With an impending fiscal cliff coming for public health laboratories, we have found that it was important to think about how capacity built during COVID-19 could be repurposed for other pressing needs within our state and any future testing needs,” said Emily Travanty, PhD, laboratory director at the Colorado Department of Public Health and Environment.

 

State, local and territorial public health laboratories receive most of their funding from the federal government, primarily through the US Centers for Disease Control and Prevention (CDC). From fiscal year (FY) 2014 to 2023, CDC’s budget increased by just six percent after adjusting for inflation, according to Trust for America’s Health.

There won’t be much growth in the coming year either. In 2023, Congress passed the debt ceiling agreement, or the Fiscal Responsibility Act of 2023, which rescinds COVID-19 relief funding and sets spending caps for two years. Under these limitations, President Biden’s fiscal year 2025 budget request includes mostly flat or tiny increases. For CDC, Biden requested $9.68 billion, a $499.2 million increase, according to the National Association of County and City Health Officials. However, there was no request for a funding increase for Public Health Emergency Preparedness (PHEP) cooperative agreements, which is where public health laboratories get most of their preparedness funding. There was also no request for increased public health infrastructure and capacity money.

Two primary areas public health laboratories invested in during the pandemic’s early days were equipment and personnel. Surge funding allowed laboratories to buy a lot of new equipment. This was necessary not only to respond to the need for COVID-19 testing and surveillance, but it often benefited multiple laboratory programs and initiatives. And for some laboratories, it was a long time coming, after years of working with older, slower and less-efficient machines.

 

Now, laboratories have faster, more efficient and modern machines, including next next-generation sequencing equipment and high-throughput molecular testing platforms. They have been able to pivot from COVID-19 testing to an expansion of their previous work, such as adding more sexually transmitted infections to their testing list.

In Colorado, the focus from the beginning was diversification to allow for sustainability. Colorado was the first state to open a drive-through COVID-19 testing site. Initially, the laboratory could test about 160 samples a day. After new equipment arrived, laboratory staff rapidly scaled up to 20,000 samples in one day, Travanty said.

 

“We had to add additional equipment in order to meet that demand, and we focused on open platforms. And that was the key to sustainability of our funding,” Travanty said. “We put our funding into separate instrumentation for extraction and amplification, so that it could, in the future, be applied to extraction and amplification to detect other pathogens.”

 

The Colorado State Public Health Laboratory also replaced its refrigerators, freezers and biosafety cabinets. The diversity of equipment helped mitigate supply chain issues and later allowed the staff to pivot to non-COVID-19 samples. “Those pieces of equipment have also been able to be used for things like the Mpox response, some Neisseria meningitidis testing, West Nile virus surveillance, and, of course, flu,” Travanty said. “We have been talking recently about ‘Are we prepared to surge if we are needed to for any future respiratory and flu-type outbreaks?’”

New equipment has also allowed laboratories to expand their wastewater surveillance programs. In September 2020, CDC launched the National Wastewater Surveillance System to detect SARS-CoV-2 in wastewater across the country and track COVID-19 prevalence. This was the first time wastewater surveillance was used as a federally supported and centralized public health tool.

Public health laboratories embraced wastewater surveillance as an early warning sign for potential outbreaks. Like many states, Delaware used COVID-19 funding to implement a wastewater surveillance program, initially to detect SARS-CoV-2, then other pathogens.

 

“We have expanded wastewater testing for not only COVID-19 but multiple respiratory viruses, as well as any emerging threats, such as fungal diseases like Candida auris, or vector-borne diseases like West Nile virus, and even food-borne diseases such as hepatitis,” said Gregory Hovan, MBA, director of the Delaware Public Health Laboratory.

Colorado already had a strong sequencing program focused on foodborne illness when COVID-19 hit four years ago. The laboratory was able to quickly pivot expertise in genomic surveillance to add wastewater testing, beginning first by looking for evidence of SARS-CoV-2 and then adding other respiratory viruses, like flu and respiratory syncytial virus (RSV).

Now, Travanty said, laboratory personnel are looking to “right-size the testing so that we get representative samples across the state and can maximize the amount of information that we can get from each sample.” The program has some of the most wide-reaching implications, she said, in terms of informing public health efforts and helping residents across the entire state of Colorado.

When COVID-19 testing launched in 2020, laboratories needed to quickly scale up personnel to respond to the demand. Many laboratories hired short-term contractors, who could be onboarded quickly. As the need for testing declined, the number of laboratory personnel went back down, too. However, some states have kept a few people, moving them into other open permanent roles and/or securing grant funding for their salaries.

Like in many states, contractors in Tennessee were hired and shifted around to different areas based on how the needs changed. Some of the contractors moved into permanent positions, but some who were supported by COVID-19 funding remain with the laboratory.

“This bolus of funding has been incredibly helpful, but as it recedes, we’re looking at alternative ways to create that revenue for the laboratory and fill in the gaps that we anticipate they’re going to leave,” said Kara Levinson, PhD, MPH, D(ABMM), director of the Tennessee Public Health Laboratory.

The laboratory’s funding for personnel ends in 2026 and 2027, Levinson said. “We’ve got a little bit of time, but we’re thinking about it now. We’ve tried to be strategic all along, but this is really where we’re starting to plan and find alternative ways to fund those gaps,” she said. That includes looking for grant funding and analyzing the laboratory’s fees-for-service.

When the pandemic began, Delaware’s public health laboratory had about 50 full-time positions. That number doubled in response to the pandemic. Now, the laboratory has about 60 full-time positions. Some of those roles are now supported by ongoing grants, including PHEP and Epidemiology and Laboratory Capacity.

“So, we have options,” Hovan said. “We’re working with our division partners to utilize the best resources and determining how the positions are going to be utilized in the future.”

Some states were able to use funding—and garner support from state lawmakers—to renovate or expand their space or even build a new public health laboratory.

Delaware’s laboratory, which opened its current building in 1990, is undergoing a $35 million expansion. The addition will nearly double the current 26,000-square-foot space, which will allow the laboratory to expand its programs. In addition, the infectious disease epidemiology team will relocate to the laboratory.

Tennessee will have a brand-new public health laboratory in a couple of years, thanks to the surge in federal funding. “We’re very excited about that,” Levinson said. “We’re finishing up the programming and design and about to move into construction.”

The current building was originally a TB hospital that was retrofitted into a laboratory in the 1980s. The new building, which will be built behind the old one, will increase space by about 30 percent. “It’s also going to be set up much more efficiently for laboratory processes and workflows,” Levinson said.

As COVID-19 funding recedes, modern equipment, new staff and building renovations will stay. However, laboratory directors are concerned about stagnant federal funding and ongoing costs. One challenge that comes with the new equipment is the annual maintenance agreements.

“We have so many new instruments,” explained Lixia Liu, PhD, MP(ASCP), D(ABMM), director of the Indiana State Public Health Laboratory. “Currently, we can afford maintenance because of the funding. However, after that, that is a huge expense. So, being able to keep up that will be a challenge for us.”

Leslie Wolf, PhD, HCLD(ABB), director of the Louisville Metro Public Health and Wellness Laboratory in Kentucky, said she cannot justify keeping the maintenance agreements on all the new equipment now that the COVID-19 testing demand is so low. “We’ve kept it on the ones that we know we’ll use for other purposes,” she said. That includes the new automated high-throughput nucleic acid purification machines that they use to test mosquitoes for diseases.

But other equipment is not being used. In addition, Wolf has learned some manufacturers are replacing equipment with newer versions. And even equipment that is state-of-the-art today might be antiquated or obsolete when needed for the next outbreak or pandemic. “I thought I was planning for sustainability and future use, but it didn’t quite go that way,” she said.

Wolf has seen this boom-and-bust cycle plenty of times, unfortunately. “I’ve been in the field of public health, primarily in infectious diseases, since 1997, and I’ve seen it happen so many times, that a lot of money is thrown at the disease of the day,” she said. “It seems that for many of our governing bodies, the memories are short. I saw us go through that with TB in the ’80s: ‘Oh, we’ve solved TB; it’s not a problem.’ And so, funding was severely cut and then cases started coming back.”

Wolf can name several other infectious diseases where she saw this cycle of successful public health initiatives, then funding cuts, then disease return: syphilis, HIV, West Nile virus, Zika.

When the pandemic started, public health laboratories received the brightest spotlight in years. Many in the public never even thought of laboratories before, let alone wondered what they did. If ever there was a time to advocate for public health funds, this was it.

In Indiana, Liu is thankful for the support public health receives from state lawmakers. Republican Governor Eric Holcomb created a Public Health Commission in 2021 to study Indiana’s public health challenges and successes. In 2023, Holcomb rallied support in the Republican-led Legislature to increase funding to local health departments in Indiana by 1,500 percent, according to a 2023 Politico article.

To keep the funding coming, it will be important for public health leaders to explain their successes and needs. While Liu was not a member of the Commission, she said she is not shy about telling health department leaders what the laboratory needs. In 2023, Liu’s team gave a laboratory tour to the governor and his cabinet members. “He was so impressed by what we do in the laboratory, and he also had the staff in his office come in for another tour.”

Word got around, and in March 2024, the health department’s executive board—which includes physicians, hospital administrators, a veterinarian, a nurse, a dentist and a pharmacist—came in for a tour.

“A lot of people outside of a public health laboratory really do not know much about it,” Liu said. “I think it is our responsibility to let people know what we are doing. So when they were coming into our laboratory, we took the opportunity to showcase all different aspects of our public health laboratory services.”

As the team explained the functions of the six laboratory divisions, Liu said it was important that they illustrated how those services could help improve the health of Hoosiers across the state. “We try to use real-life stories to connect our testing to the health of the community,” she said.

Even as federal funding recedes, laboratories have stories and data and evidence that they can use to advocate for sustained state and federal public health funding.

“COVID-19 enabled us to demonstrate what we can do when those funding barriers are removed,” said Levinson in Tennessee. “You can throw money at a problem, and we can show you what we can do with it. And, we can do a lot; we can make significant progress in a short amount of time and really show what it takes to make a public health laboratory even more effective.”