​Summer 2022

​Public health laboratories across the US were consumed by COVID-19 diagnostic testing in the pandemic’s early months. But after clinical laboratories began to do most of the testing, and as more people tested themselves at home with rapid antigen tests, public health laboratories shifted back to surveillance testing. Now, public health laboratories are developing new surveillance systems, taking advantage of new equipment and staff, and improving programs based on lessons learned from the pandemic.

by Melanie Padgett Powers, writer

About a week before the first COVID-19 positive case was identified in Minnesota in March 2020, Myra Kunas, MS, was sitting in a conference room with about 12 other people trying to budget for the testing that was about to hit her laboratory division. No one was wearing masks or social distancing yet, as the team huddled over their laptops and brainstormed on how many samples the laboratory might receive.

Kunas was assistant laboratory director of the Minnesota Public Health Laboratory Division at the time, but she would be promoted to director two months into the pandemic, after her director retired.

“So, we were up there discussing budgets, and we estimated we would have to test for a month, 300 samples per week, and then 200 after that, and then 100 probably for another six months. And then that’s it,” Kunas said. “And we got 1,000 in one day about one week after our first positive case.”

State public health laboratories across the United States were consumed by COVID-19 diagnostic testing in the pandemic’s early months. Many laboratories didn’t have enough staff, enough equipment or even enough space to manage and test all of the samples. They were overwhelmed with work—while also trying to stay safe from the virus. But after clinical laboratories began to do most of the testing, and as more people tested themselves at home with rapid antigen tests, testing at public health laboratories shifted from diagnostic to surveillance.

Nearly two and a half years into the pandemic, public health laboratories are developing new surveillance systems, taking advantage of new equipment and staff, and improving programs based on lessons learned from COVID-19.

“We’re not buried under specimens at the moment,” said Edward Desmond, PhD, laboratory director and administrator of the Hawaii Laboratories Division. Instead, Hawaii is using whole genome sequencing (WGS) to investigate the spread of COVID-19 and to detect new variants in communities. WGS showed that in the vast majority of cases the virus was spread by state residents, not tourists as some had assumed. “What that means is we need to have community mitigation because we can’t blame it all on the tourists,” Desmond said.

The ability to detect new variants helps show the community when renewed mitigation measures might be recommended, he said. And, it allows the laboratories division to know what mutations exist in the state, which can help guide treatment.

Establishing Wastewater Surveillance Systems

Several states, including Hawaii, have implemented new wastewater surveillance testing, which can detect early signs of diseases beyond COVID-19 through viral RNA that infected people shed in fecal matter. In Hawaii, Priscilla Seabourn, MS, PhD, established the wastewater surveillance infrastructure—one of several COVID-19 projects she worked on during the pandemic in Hawaii, first as an APHL-CDC COVID-19 Laboratory Associate and then as an APHL-CDC Antimicrobial Resistance Fellow.

During her nine-month fellowship, Seabourn researched and ordered the proper equipment, optimized protocols and established collaborations with wastewater treatment plants. The new system has the potential to detect new COVID-19 variants, as well as markers for antimicrobial resistance and other diseases such as influenza and norovirus.

“We’re thinking beyond COVID-19: How can we use wastewater surveillance as a mechanism of pandemic preparedness? And we’re looking at other types of pathogens that might have health importance,” Seabourn said.

Seabourn established collaborations with 12 wastewater treatment plants in Hawaii that will regularly gather and send wastewater samples to the laboratories division for surveillance. The facilities were also enrolled in the National Wastewater Surveillance System, which the US Centers for Disease Control and Prevention launched in September 2020 in response to the pandemic.

Colorado’s state laboratory division has also implemented wastewater surveillance. “Before the pandemic, we were doing sequence analysis for foodborne pathogens. We capitalized on that knowledge to quickly pivot to doing [WGS] on clinical samples for COVID-19,” said Emily Travanty, PhD, laboratory director of the Colorado Department of Public Health and Environment. “And then the wastewater surveillance piece came into play, so we added capacity for that type of digital droplet PCR.”

With the clinical sequencing workflow already set up, the state laboratory was able to easily “slide the water samples that were positive for COVID-19 into those same sorts of pathways,” Travanty explained.

“I’m certain that it is going to go a long way,” she continued. “It is a pillar of our ongoing surveillance that we’re going to continue in Colorado to ensure that we understand the ongoing impact that COVID-19 has in our state, as well as use the same samples and the same network of samples to expand what we’re testing for in wastewater.”

Learning About Congregate Settings

Colorado also learned how to test in congregate settings, but one unique to the US West: fire camps. August 2020 was the start of the worst fire season in Colorado history. Because of the magnitude of the fires, fire crews poured in from other states and lived together in camps, creating “ripe conditions” for COVID-19 spread, Travanty said.

At the time, PCR test results were not quick enough to learn who was infectious and who should quarantine. But the laboratory did track the data to see how COVID-19 moved through the camps. The Cameron Peak Fires lasted for five months, and fire crews from multiple states were deployed every two weeks. Firefighters were tested before they arrived and encouraged to practice social distancing.

On-site tests showed 78 firefighters tested positive for COVID-19. WGS was performed on 42 positive cases, identifying five sequence types. The types were not in clusters, which suggests COVID-19 spread among the crews, according to the APHL 2021 poster abstract “The Use of Whole Genome Sequencing (WGS) to Investigate the Spread of COVID-19 in Fire Camps During the Cameron Peak Fires (August 2020) in Larimer County, Colorado.”

In addition, individuals may not have suspected they had COVID-19 because of the bad air quality—if someone is coughing is that because of the smoke or COVID-19? In future fire seasons, Travanty said, it will be important to have stronger fire camp guidelines for testing, including additional use of over-the-counter rapid tests (which were not widely available during previous fire seasons), quarantining, social distancing and use of personal protective equipment.

“If we have fires this summer, we will definitely be able to deploy,” she said. “We have teams that can deploy rapid tests, as well as teams that can go into the field now and respond and swab people for PCR testing.”

For congregate settings in Hawaii, laboratory workers learned it was necessary and possible to quickly create training materials. When point-of-care tests were distributed to congregate facilities in 2020, it was apparent that staff, such as those at prisons and nursing homes, needed test-specific training.

Seabourn quickly created a couple of slide presentations teaching people how to administer the tests, complete with embedded videos of Seabourn showing the step-by-step process. She shot the videos using only her iPhone with the help of a postdoctoral fellow.

“Everyone was just hitting the ground running, considering the pandemic,” she said. “I basically took two weeks to get updated on the literature, made sure I was very familiar with the protocol and all the different specifications, and then I just quickly made the videos.”

Creating a professionally shot and edited video would have taken longer and cost more. “I think sometimes you have to ask yourself, ‘What is the need?’ And if it’s something that you can just quickly do, it’s better to just have it out in the public and ready for everyone.”

Conducting Whole Genome Sequencing

To better track and understand COVID-19 outbreaks in Minnesota, the state public health laboratory, in partnership with universities and clinical laboratories, created the Minnesota Molecular Surveillance of SARS-CoV-2 (MN-SOS) system to conduct whole genome sequencing to detect variants of concern.

Beginning in December 2020, the public health laboratory began receiving 50 specimens a week from each of its clinical partners, according to the 2021 APHL poster abstract “Minnesota Molecular Surveillance of SARS-CoV-2.” This new system led to the discovery and investigation of the first identified case of the P.1 variant in the US, from someone who had traveled to Brazil. (A second P.1 case was positive in that person’s travel partner or household contact.)

"It was just by chance that we found that case,” Kunas said. “We received it as part of the 50 samples per week that we were getting from clinical labs. … The importance of the P.1 case was to detect and identify cases quickly and to reduce potential spread. Our partners and epidemiologists did a lot of case investigation and contact tracing to identify close contacts.”

Other investigations focused on the first case of the B.1.1.7 variant in Minnesota and the second Omicron case in the US, according to Kunas. A more recent challenge that Kunas and her team problem-solved was the overwhelming number of samples they were receiving from clinical laboratories for sequencing during the Omicron surge. They requested 50 samples a week from laboratories but were sometimes getting up to 500. Kunas admitted the backlog wasn’t truly addressed until the public health laboratory had around 11,000 samples in the queue. She pulled in staff from other areas and they worked through the samples over five weeks to eliminate the backlog.

That included identifying laboratories that were submitting too many samples, reducing how many samples were being sent from all laboratories and working with epidemiologist partners to truly prioritize their needs. This meant “going through freezers to identify how many samples there were, what they were, where they were coming from, and then working with our epis to have a real sit-down like, ‘We can’t do all of these, so let’s figure out what makes sense.’”

Next, a project manager created a dashboard to quickly visualize the samples that were arriving each day and to monitor capacity.

"It’s helped everyone with tracking so that we could focus on testing and supporting the team through that challenge,” Kunas said. “The lesson learned there is when a team is struggling, they might not have the resources or the capacity to even ask for help until it’s a much bigger problem.” Now, laboratory professionals know to check in and trust the newly-developed dashboard, and leadership knows to support staff differently when they’re getting overwhelmed, she said.

Recognition from Lawmakers

Another change at most public health laboratories since the pandemic started is how they are viewed by state and federal lawmakers.

“Historically, I likened our laboratory to poor church mice looking for crumbs and largely ignored,” Desmond said. “That’s not the case now. Federal funds have come in, and we also have a great deal of support from the state.”

In fact, his division in Hawaii has received federal funding to turn its biosafety level 3 (BSL-3) laboratory into a BSL-3+ laboratory, providing a higher level of precautions. “We think this is important because of concerns about future pandemics,” Desmond said. “If the pandemic is caused by the worst virus you can imagine, and you had an accident in one of the laboratory rooms, the virus could be discharged through the exhaust ventilation, and we don’t want that to happen.”

Hawaii has also received funding to purchase new equipment, refurbish one of the laboratory suites into a molecular biology suite, and hire new staff, including a bioinformatics specialist and a molecular biologist who together created a bioinformatics pipeline. Several state legislators have also introduced a bill that would fund public health laboratory upgrades. (As of March 2022, House Bill 2515 was with Hawaii’s House Ways and Means Committee.)

Minnesota also received federal dollars that covered new staff, COVID-19 testing and sequencing, infrastructure enhancements, updates to information technology systems and interoperability, Kunas said. And though the laboratory building is only 16 years old, Kunas said there have been significant problems through the years, including a major flood in 2014. There has been ongoing work to repair valves and corroded duct work. The laboratory had requested state money several times for repairs and additions, but it wasn’t until October 2020 that a large amount was provided: $20 million for building repairs and upgrades.

“I have to admit that I do think that COVID-19 played a role in us getting those funds,” Kunas said. “I think there’s been significant understanding from the Legislature that when you say monitoring of contaminants, that doesn’t mean you collect a sample and you get a result. There needs to be this testing infrastructure in place in order to make that all happen. … So, I do think that there’s a lot more acknowledgement of the importance of labs throughout the country.”