By Jill Sakai, PhD, writer
On December 31, 2019, the Wuhan Municipal Health Commission in China reported a cluster of cases of pneumonia in Wuhan, Hubei Province to the World Health Organization (WHO), ringing in the new year in ominous fashion. The cause of the pneumonia, the novel coronavirus SARS-CoV-2, swept the globe. Within weeks, the United States had its first confirmed case: a traveler from Wuhan who arrived in Washington.
On March 11, WHO declared the COVID-19 outbreak a global pandemic. “We have never before seen a pandemic sparked by a coronavirus,” said WHO Director-General Tedros Adhanom Ghebreyesus, PhD, in his announcement. “And we have never before seen a pandemic that can be controlled, at the same time.”
The ensuing global response to do just that has become a defining event of 2020. The scale and duration of the pandemic and its response efforts have revealed strengths and weaknesses in health systems around the world, while also highlighting the creativity and generosity of the human spirit.
In the US, public health laboratories pivoted from regular testing and surveillance duties into emergency response mode, operating around the clock, mobilizing staff and coordinating shifts to ensure personal safety, and scrambling to keep their shelves stocked with critical testing supplies.
With a hyperfocus on testing throughout the pandemic response, US public health laboratories were thrust into the spotlight for officials, media and the public alike. As they responded with a blend of resilience and ingenuity in the face of testing snafus, crushing workloads and massive supply shortages, it has become clear that SARS-CoV-2 has changed the future course of public health.
On Sunday, January 19, Washington State Public Health Laboratory director Romesh Gautom, PhD, received a call from his microbiology director. The laboratory had received a request to pick up a specimen from a nearby community clinic for coronavirus testing. Laboratory staff and an epidemiologist collected, packaged and shipped the sample to the US Centers for Disease Control and Prevention (CDC). Then they waited.
The next evening, the Washington team got the news they had both dreaded and expected: the sample was positive for SARS-CoV-2. The US had its first confirmed case of the novel coronavirus.
That day, the Washington State Department of Health activated an Incident Management Team at the building that houses both the state public health laboratory and the communicable diseases epidemiology office. “Forty, fifty, sixty people appeared over the course of weeks,” Gautom recalled. “Our lunchroom was converted into an operation center. Conference rooms were converted into offices to accommodate everyone.”
On the national level, APHL was also mobilizing staff and resources to support members. It established its own Incident Command System on January 22 to coordinate with CDC and other federal agencies. At the end of the month, APHL established a COVID-19 Laboratory Task Force with laboratory directors from jurisdictions across the country and initiated weekly calls between public health laboratories and CDC for situational updates and briefings on testing strategies and rollout plans.
With that information, laboratories were able to start preparing even before a test was available, acquiring supplies and equipment and training staff. But as the number of specimens mounted, so did the urgency. “Every day, there was a lot of pressure to establish testing here at the lab,” Gautom said.
With many travelers from Asia arriving in southern California, the Orange County Public Health Laboratory had been prepping and shipping numerous specimens to CDC. Eager to move testing in-house, the laboratory staff were glad to finally receive the CDC testing kit on a Friday in early February.
“My staff came in on Saturday to start the validation,” recalled laboratory director Megan Crumpler, PhD, HCLD, “and I can still remember—I was at my son’s baseball practice—getting the phone call from my molecular supervisor saying, ‘Something just doesn’t look right.’”
The problems with the initial CDC test have since been well documented. With pressure building across the country to expand testing capabilities, APHL lobbied the US Food and Drug Administration (FDA) to allow public health laboratories to develop their own tests. At the end of February, those efforts were successful and CLIA-certified laboratories were able to begin testing in-house, greatly expanding testing capabilities.
As testing got underway, however, it quickly became clear that existing capacity was insufficient to meet the need. “Demand started to grow exponentially,” Gautom said. Washington added higher throughput equipment and stood up several teams for each step in the process, from accessioning through extraction and PCR to releasing results. From 15 specimens on their first day of testing, they quickly ramped up to 400 specimens per day.
In Orange County, COVID-19 testing needs translated into an all-hands-on-deck approach, as they shifted all possible instruments to extraction and PCR and cross-trained all available staff with even slightly relevant microbiological or technical expertise. With hundreds of samples arriving each day—800 on the peak day—they hired temporary staff and expanded the laboratory’s active hours, opening early and rotating through two staggered shifts to help accommodate the testing volume.
The Washington team knew from past outbreaks that data handling could pose a large stumbling block. From the earliest days of their response, they were building a specimen dashboard to facilitate data entry and result reporting for specimens coming into their lab.
“The system largely eliminated the need for manual communication between the laboratory and epidemiology staff,” Gautom said.
Crumpler noted that other routine testing needs dropped, with fewer people going into clinics for non-COVID-related reasons. “That worked to our advantage because our other departments were slower. I think it was our saving grace,” she said.
The South Dakota Public Health Laboratory has also seen non-COVID-19 testing drop, especially for sexually transmitted diseases. The lower volume has been helpful for managing the crisis, said laboratory director Tim Southern, PhD. But he’s concerned about what these “disturbing trends” mean for the future.
“We’re trying to find ways to support our provider community so that we don’t create other public health issues in the future by not providing care that our populations need,” Southern said.
Many laboratories worked to build regional and statewide capacity in parallel with their own. In Washington, laboratory staff devoted significant time and effort to develop testing capacity at clinical, private, academic and veterinary laboratories throughout the state, helping laboratories obtain CLIA certification and validate their methods. The state had around 20 active testing sites by late March and more than 40 in June, bringing statewide capacity to around 25,000 to 30,000 samples a day, of which only around 1,000 are handled at the state public health laboratory.
With a relatively small team of seven medical microbiologists, South Dakota prioritized enhancing a robust statewide infrastructure encompassing public and clinical laboratories, biomedical supply manufacturers, healthcare providers, tribal organizations, government agencies and other partners. Public health laboratory staff helped two of the principal healthcare systems in the state develop their own RT-PCR capabilities and assisted clinical laboratories with acquiring collection supplies. A strong partnership with Hologic helped them get an instrument to provide high throughput testing capability for the western half of the state, where such capacity had not existed.
“We have built in South Dakota a level of relationship, communication and partnership with our clinical laboratories that I’ve never seen before,” Southern noted. “We’ve got lasting relationships and partnerships that I think we’re going to be able to leverage in the future, not just for COVID but for other things.”
Linking New Supply Chains
Those relationships helped when South Dakota faced one of the most defining challenges of the COVID-19 response: limited availability of critical supplies.
Despite planning ahead, there were issues acquiring supplies from vendors and manufacturers. The entire US public health infrastructure was vying for the same supplies with all of the laboratories around the globe—at the exact same time. “We could see that they were doing all that they could,” Southern said. “The market couldn’t bear it any longer.”
At one point, after exhausting its supplies of extraction reagents, South Dakota was forced to halt testing. Staff raised alarms about the fragility of their supply chains with manufacturers, state leaders and federal officials. Southern credits South Dakota Governor Kristi Noem and APHL staff with advocating at the highest levels of the federal response team. The laboratory was able to resume testing after a shutdown of about 48 hours.
“Almost every item needed for testing has been a limiting factor at one point,” Gautom agreed, noting that the Washington state laboratory was within hours of running out of supplies on more than one occasion. And in Orange County, Crumpler said there were several times when the laboratory gave out their last nasopharyngeal swab specimen collection kit without knowing exactly where the next supply would come from.
“We have resorted to making our own viral transport media and saline. That’s been really helpful. But, you know, that’s more staff work,” she said.
For extraction, the Orange County team ping-ponged between different manufacturers and platforms to cobble together whatever capacity they could manage. That diversification—and communications with APHL and a network of colleagues to track down information and supplies—allowed them to keep going, Crumpler said, but “it is really difficult to plan when you don’t have a steady supply of reagents.”
Many laboratories found help through partnerships, some familiar and others unexpected: regional laboratory networks, companies, government entities, universities and foundations.
“There was overwhelming support from several local companies as they stepped up to provide resources,” Gautom said, ranging from swabs and personal protective equipment to technical assistance with streamlining methods. The University of Washington provided testing capacity. The state patrol even helped shuttle supplies between laboratories. Washington, because of its location in Seattle, is fortunate to have so many tech companies and other giants in the area. The Bill and Melinda Gates Foundation helped secure supplies, and Microsoft worked with the state laboratory to build a specimen submission portal that standardized and automated data entry for samples sent to the lab, reducing staff work and errors.
Orange County found a powerful ally in a National Guard civil support team (CST) based in southern California. The laboratory has maintained a relationship with the team since a bioterrorism testing exercise two years ago. When the pandemic hit the area, one of the CST members reached out to offer aid. Since then, they have been invaluable partners, Crumpler said. Both team members already met federal CLIA requirements for laboratory testing, so they trained in extraction and PCR and each took on two shifts a week in the lab. But perhaps even more important has been their ability to obtain testing kits and reagents. “I’ve been able to connect them with laboratories in California that were having trouble getting Cepheid GeneXpert kits, and the National Guard has been able to supply them,” she said. “We’re able to get some—not all that we need, but at least it’s a consistent shipment of kits.”
The Washington state laboratory helped validate members of its local National Guard CST to take on-site laboratory testing capability into more rural areas of the state, such as agricultural and meatpacking operations where clusters of cases may occur far from a testing facility. The mobile laboratory can submit testing and results electronically that feed directly into the laboratory information management system at the state laboratory.
Ensuring Critical Data Gets Its Due
APHL has also forged several informatics partnerships that have helped support the pandemic response on a national level. Building on the network established through the APHL Informatics Messaging Services (AIMS) platform, APHL was able to get up and running quickly. They standardized vocabulary and coding for COVID-19 and repurposed a feed in the public health laboratory interoperability project typically used for influenza, adapting and scaling it up to handle coronavirus test result data.
Within weeks, dozens of laboratories were already using the feed to validate their test messages. The volume has been staggering, said Michelle Meigs, APHL’s deputy director of Informatics. In May 2020, this single feed handled more than 625,000 messages—roughly an 8,000 percent increase in volume over last May. AIMS is also handling electronic laboratory reporting information, electronic test order and reporting data, county-level testing data and more, shunting millions of data messages among testing facilities, public health jurisdictions and federal agencies.
A COVID-19 module for electronic test ordering and results within the existing Lab Web Portal on AIMS was built to facilitate communication among laboratory staff, epidemiologists and healthcare providers without requiring local technical support. In addition, APHL has been working with third-party developers to host applications, such as the Sara Alert™ symptom tracking app created by the MITRE Foundation, and are working with CDC to connect new point of care testing sites—pharmacies, grocery stores, clinics and others—to a centralized test data routing portal on AIMS. “This has just been a monumental effort,” Meigs said. “We were able to not only reuse existing infrastructure, but also leverage our relationships and trust to play a large role in the response efforts.”
The pandemic has also brought heightened awareness of how data quality affects decision making and response management on both local and national levels. Patient-specific information is needed for case management, follow-up and contact tracing for individuals, while deidentified data is critical for analyzing national trends and statistics.
Detailed information about testing capacity is essential to know where it is, how it is being used, and whether it is sufficient. “This is the first time that informatics and data exchange and management have been at the forefront of discussions,” Meigs said. “It’s brought to everybody’s attention the need for good quality data and interconnected public health data streams.”
While daily routines are still upended by challenging schedules and unstable supply chains, and laboratories continue to work multiple shifts to keep up with a new spike in cases, many laboratories have carved out some energy for longer-range planning. Washington has been applying for both state and federal funds to help restore some of the routine testing that has been displaced by the pandemic, and South Dakota is diversifying to avoid future supply chain breakdowns. It now has three different testing platforms in place, but diversification brings its own challenges.
“If any one or even two of those supply chains becomes fragile again, we can migrate. For pandemic response, that’s an advantage. But for normal laboratory work, it can become a nightmare,” Southern said. “We’re have to find long-term financial means to support this really well-developed infrastructure.”
In Orange County, Crumpler is working to leverage support to build out longer lasting infrastructure. “We’re trying to buy equipment that’s usable now but will also be very beneficial for us in the future,” she said, such as high throughput equipment for whole genome sequencing, where she expects her laboratory will play an important role in the COVID-19 response moving forward. She also emphasizes the need to include surge capacity in planning and budgeting efforts and is seeking support for a better laboratory web portal to allow the laboratory to electronically receive specimens from outside submitters.
“I’ve been in the public health laboratory field for 11 years now, and never have I seen such a focus on laboratory testing. … People are really taking an interest in understanding what we’re doing,” Crumpler said. “Public health is getting a lot of support right now. So we need to use that support to plan for the future and work even more effectively.”