Testing the System -- Clinical Labs During COVID-19

TESTING THE SYSTEM

by WHITNEY J. PALMER and SUSAN REEVES

IT’S BEEN A WHIRLWIND YEAR FOR DUKE CLINICAL LABORATORIES with no precedent or road map for guidance. In 2020 the group moved from being behind the scenes to being front-and-center in North Carolina’s fight against the COVID-19 pandemic. “It’s been an amazing journey,” summarized Christopher Polage, MD, Director of Clinical Microbiology, who along with Michael Datto, MD PhD, Medical Director and Associate Vice President, Duke Health Clinical Laboratories, recounted the tale of the roller coaster ride through COVID-19.

From interviews on March 4, 2021 and December 2020

Nelea Roscot, Medical Lab Scientist, handles tubes with COVID specimens for testing in the COBAS 6800 instrument.

The Early Days

News of the first case in the United States, identified in Washington state, hit on January 19, 2020. It wasn’t long before the virus spread nationally, with North Carolina identifying its first patient on March 3. Duke’s clinical lab leaders knew they needed to prepare, but they had no way of knowing the avalanche of testing that would soon inundate them, starting with Duke’s first case on March 13.

Fortunately, the Clinical Labs were part of the planning from the start. Datto explains, “Our senior laboratory leaders were part of Duke Health’s COVID incident response team and were helping create Duke’s strategy to manage the COVID pandemic. Labs were not just involved, but in many ways we were driving the discussion with key pieces of information around infection rates, testing capacity and testing strategies.Very early in the pandemic, our labs understood that testing was going to be one of the main mechanisms used to get the pandemic under control,” he said. “Within weeks, our hospitals shut down to all but the sickest patients with the most urgent needs. Elective care was put on hold and our clinics, ORs, and the University were closed to routine business. All research had stopped. We were out of PPE and we required patients to have a negative COVID test to receive care that could put them or their providers at risk. In short, restarting the health system was completely dependent on our ability to start testing patients.”

Just a little pressure.

The Labs started planning for in-house testing in January 2020, while sending the first tests to the NC Department of Health and Human Services State Lab and Viracor. “The first month was a giant puzzle with a number of different possible solutions and no one clear best answer. Unfortunately our sendout partners quickly became overwhelmed with testing requests and could no longer support our Duke patients,” Datto said. The first in-house test was offered March 23, but this was a highly manual CDC assay, and the need for higher volume testing became evident.

Polage says the number of samples the lab could process on any given day was too low, between 66 and 150 tests. “In hindsight, it was ridiculously few.”

Michael Datto, MD PhD, Medical Director and Associate Vice President Duke Health Clinical Laboratories

A Team-Based Effort

Test supplies were low and hard to come by, lab staff were being pushed to capacity, and at any given point, they were within 24 hours of being unable to handle any more samples. So they created the Clinical Labs COVID Response Team on March 19, 2020, bringing together all the laboratory expertise Duke had to offer. (See List of Team Members below.)

The team connected every day over Zoom to touch base, identify needs, and brainstorm solutions. They divided responsibilities, reducing the pressure on Polage’s team and allowing individual members and their teams to focus on their specific areas of expertise and delegated responsibility. This allowed Polage and the Clinical Microbiology Laboratory the time to focus on bringing new test platforms on line and operationally running the tests.

“Each person involved with the crisis management team had a role. With each call, we went around the virtual room—how were our swab supplies,our transport, our kit supplies?” Polage explained. “We tracked each test platform on a daily basis. We set up communication chains to monitor the testing volume we had to get done each day and we reviewed it multiple times during the day. It became a strategy to help us manage our workload.”

“There was a time when we literally had just a few hundred nasopharyngeal collection swabs left for all of Duke Health and that was it,” remembers Datto. “In an attempt to address supply chain issues, we diversified our testing options and validated every platform we could. This provided us with the ability to fully meet Duke’s needs.”

Throughout the summer the lab brought more assays and platforms online. With the second test, processing volume doubled to 300 samples a day, and by the time seven assays were up and running at the height of the first wave last summer, the lab was routinely handling up to 1600 COVID tests daily. The maximum processing capacity was even higher, though. In March 2021, with 10 platforms, and more than 5distinct types of covid test orders, the lab could analyze more than 3000 specimens daily if needed.

Christopher Polage, MD, Director of Clinical Microbiology

TEAM MEMBERS

In addition to Datto, Polage and Lobaugh, other key members of the Response Team include:

Chad McCall, Director, Hematology Laboratory Services

Corrie Simons, Manager, Clinical Microbiology

Diana Cardona, Associate Director, Duke Health Laboratories

Diane Butler, Administrative Specialist

Judy Fleming, Director, Quality Management

Kari Ryan, Director, Business Operations

Kathryn Winston, Manager, Referral Laboratory, Client Services

Kathy Grant, Mary Smith - Global Operations, Operations Director AP/ Operations Director CP

Mark Lee, Associate Director, Clinical Microbiology, Lead for COVID Assay Development

Nancy Henshaw, Associate Director, Clinical Microbiology

Penda Jones, Supervisor, Referral Laboratory

Raj Dash, Director, Laboratory Information Systems

Rita Winsor, Chief of Laboratory HR

Tyler Welch, Diagnostic Services Lead, Performance Services

“Also essential to our success have been the members of the Microbiology Laboratory, Molecular Diagnostics Laboratory, Referral Laboratory, Specimen Management, Phlebotomy, Couriers, and every tech who stood at the bench and did the work to keep our health system open and to care for our patients in the face of the fear and uncertainty of the raging pandemic.”

Mark Lee, PhD, Assistant Director of Clinical Microbiology, was the lead for COVID assay development.

Lab Technician Darius Smith receives cartridges from the pneumatic tube system, which is connected throughout the clinics to transport samples for testing.

The lab’s workload increased enormously. Prior to the pandemic, the Clinical Microbiology Laboratory ran approximately 500,000 tests on roughly 350,000 samples each year. With the pandemic, test volume ballooned by 50 percent—and every additional case was a COVID test. As of March 2021, the lab was receiving between 600-1000 tests for the virus daily and processing 5000-6000 cases weekly with three high-throughput pieces of equipment which can each handle more than 1000 tests in a 24-hour period. “We basically created a COVID-19 test factory to allow us to manage the daily tsunami of testing,” Polage said.

Duke Health’s Point of Care Testing (POCT) Program also played a major role. Under the direction of Dr. Bruce Lobaugh, Administrative Director of Duke Health Labs and Director of the DUHS POCT, the Program developed a comprehensive POCT solution for Duke patients. Lobaugh and his team managed the supply chain and distribution of hundreds of tests daily to multiple locations across Duke Health, to enable real-time decisions based on the result of a COVID test. Approximately one-third of all COVID tests performed at Duke were performed using tests supplied by the POCT Program.

Datto’s role as the liaison between the lab and Health System leaders and providers contributed to the success of our laboratory response. He listened to Health System requests, managed their expectations, and brought their concerns back to the team. It was often a delicate dance and negotiation, but it kept everyone informed of the Health System’s needs and what the laboratories could do to meet them.

Beyond Duke

The team’s immediate concern was helping and managing Duke patients, but infections were rampant in the surrounding region, popping up in community clinics, skilled nursing facilities, prisons, and other hospitals without local testing resources. The virus was rapidly blanketing the population, and tests were needed everywhere.

Duke’s leaders rose to the occasion. Instead of restricting testing to Duke patients or people who were sick enough to seek care at Duke, they reached out to community partners and offered assistance. “Very early on, we had capacity, and we were helping out with investigations of skilled nursing facilities,” Datto said. That aid soon extended to both the Duke County Public Health Department and the prison in Butner, NC. To streamline those efforts, the COVID Response Team turned to testing kit assembly. Team members shared the responsibilities of ordering and tracking supplies, as well as putting together ready-to-use tests that could make it easier to identify infected individuals who were not coming to the hospital. “Every day we would report out on how the team was doing on assembling these kits that would go out to the clinics, ready for a nurse or medical assistant to pull them out of the box,” Polage said. “Often representatives from these groups would come by the Lab, and I would give them boxes of COVID swab collection kits or carry them out to a car in the round-about [of the hospital].”

Diane Butler, PACE, (Supply Chain and Administrative Support) ordered and received a total of 294,100 swab kits in 2020. Per Dr. Datto, shewas “the master of the nasopharyngeal swab supply chain. There was nevera nose without a swab when needed.“

The team also provided training for point-of-care testers on how to correctly collect, handle, and test the swabs, as well as how to keep themselves safe from infection.

And in April, Datto was called on to co-chair Governor Cooper’s COVID-19 Testing Surge Working Group for the state of North Carolina.

The Clinical Labs were also part of the success of Duke University’s Fall Semester, which was held on campus. Members of the Molecular Diagnostics Lab team ran the M2000 platform along with Tom Denny’s group at the Human Vaccine Institute (DHVI). “Our labs did the confirmatory testing for the positive pools. DHVI did the pooled testing in their CLIA laboratory. They are a fantastic team and one good outcome from the pandemic was bringing our groups together,” Datto said. “We are fortunate that the positivity rate on campus was very low last semester. The students were good about being safe and the testing ensured rapid quarantine of anyone who became positive.”

Finding a Rhythm

Managing the COVID workload alongside the normal clinical workload has been challenging. But, in partnership with Duke’s Informatics group, the clinical team developed a prioritization system that categorizes tests into multiple population buckets. The system pinpoints the reason for the test and a due date, helping them process the most urgent cases first.

For example, if a patient needs a negative COVID test to be cleared for surgery, that cases rises to the top of the list. “This has allowed us to manage our workload. It’s like looking at homework with your kids—this homework is due tomorrow, this on Thursday, and this in two weeks,” Polage said. “In the beginning, we were blind. We didn’t know what homework was due tomorrow and what was due later. We only knew we had a mountain of homework, and if we didn’t get it done, we were in trouble.”

Now, though, it’s much easier to divide the case load into daily digestible bites, and the workflow is streamlined. And that’s critical because there’s a strong indication that COVID isn’t going anywhere and could be seasonal much like the flu. As of March ’21, the lab had processed 223,303 tests. Fortunately, the positivity rate has been a fraction of that amount: 22,897 (roughly 10%) have returned a positive COVID diagnosis. And thanks to proper safety protocols and personal protective equipment, there have been no COVID outbreaks among lab staff. Duke’s Clinical Labs and staff are now well equipped to not only meet the needs of patients with active disease, but to also help keep the wheels of the community turning.

“We were used to a situation where every sample came from a sick patient, and we were trying to diagnose that sick patient. Now, we were testing people so we could get things open, employees back to work, patients into surgeries. It was a different job than we were used to,” Polage said. “It’s been an amazing journey.”

Jodine Zane, MLS works with specimen testing for infections on the GeneXpert

Duke Clinical Laboratory - Clinical Research Center

During the pandemic, the Clinical Labs established a Clinical Research Center (CRC) to enable and lead in COVID research. “The Duke Clinical Laboratory CRC’s mission is to leverage our scientific and medical knowledge, state of the art operations, and millions of clinical lab specimens to deliver tomorrow’s health care today,” states Datto. “This center banked over 14,000 COVID specimens in the first six months of operation (serum for understanding antibody responses, whole blood to understand genomics indicators of outcome, and the virus itself). I truly believe that these are the specimens that hold the key to fully understanding the virus and how it effects patients—why some do better and some do worse or die. With this understanding will come better outcomes and saved lives for this and future pandemics. Our ability to change the way we practice laboratory medicine is ultimately why we choose to practice in an academic environment. We are driven by our desire to help thousands of patients each day take their next step on the path to being healthy.“

Yelena Timmons, Medical Lab Scientist (MLS) aliquoting (splitting ) COVID19 samples