Anticipating Change in COVID-19 Test Volume

With emerging COVID-19 variants causing surges in cases and testing, clinical labs must remain nimble

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David-DexterCEO SUMMARY: New and more easily transmitted variants of SARS-CoV-2 are causing surges and declines in both the daily number of COVID-19 tests and new cases. This presents pathologists and lab administrators with two common problems: how to scale a COVID-19 testing program and how to staff that program. David Dexter, CEO at Sonora Quest Laboratories, shares his lab’s lessons learned after dealing with intense COVID-19 surges in Arizona. 

TWO YEARS INTO THE SARS-CoV-2 PUBLIC HEALTH EMERGENCY, the pandemic continues to provide lessons in how to speedily right size a clinical laboratory as testing for COVID-19 surges, retreats, and surges again. 

Even as the daily number of new COVID-19 cases and hospitalizations has declined in the past month, the pandemic continues to produce new variants that are more easily transmitted. Another factor that can directly lessen demand for SARS-CoV-2 PCR tests is the growing competition from at-home/consumer self-test COVID-19 antigen tests. 

Because of this situation, many labs are scrambling for strategies and operational approaches that allow them to swiftly right-size the lab, whether COVID-19 test volumes are increasing or decreasing. This must be done at the same time that test services for the regular volume of routine, reference, and esoteric testing referred by physicians is sustained in a timely manner. 

This is true for Sonora Quest Laboratories (SQL), which had the unique challenge of meeting the SARS-CoV-2 testing needs of its extensive lab outreach business while at the same time sustaining inpatient and outpatient care at the hospitals and clinics of its health system parent. For this reason, when it comes to managing the ups and downs of demand for COVID-19 testing in recent years, the strategies employed by SQL’s management team have something to offer for both independent clinical lab operators and hospital/health system laboratory administrators. 

SQL is a clinical laboratory joint venture between Banner Health (51% owner) and Quest Diagnostics (49% owner). It is a major provider of testing services to office-based physicians and other providers throughout Arizona and the surrounding markets it serves. 

SQL’s executive team also operates Laboratory Sciences of Arizona (LSA), owned by Banner Health. LSA employs and manages the lab staff in all the hospitals and satellite labs operated by Banner Health. Thus, LSA’s team is responsible for maintaining COVID-19 and other lab testing for the 30 hospitals operated by Banner in six states. 

In an exclusive interview with David Dexter, CEO at Sonora Quest Laboratories, he shared several innovations and business strategies that were responses to the testing waves generated by new variants of SARS-CoV-2. The strategies include:

  • Surges come and go quickly—such as from the Omicron variant—that mandate a lab be nimble about adjusting testing capacity on short notice. Doing so is essential for lab leaders who align operations to sustain service levels while at the same time working to maintain stable lab finances.
  • Clinical labs must be ready to hire workers quickly if testing volume must be quickly ramped up.

Dexter noted that, despite the prevalence of at-home rapid testing, clinical laboratories must stay vigilant about protecting communities. That includes recognizing the capabilities of different types of COVID-19 tests.

“Labs do need to maintain a PCR testing safety net,” he observed. “An antigen test is not nearly as sensitive as a PCR test, and you can’t really determine what variant it is from an antigen test.” Dexter noted that the PCR methodology does allow a genetic analysis that can identify the COVID-19 mutations of interest. 

Demand Rises and Falls

Sonora Quest tackled significant testing demands in its home state of Arizona during the early months of the pandemic in 2020. Dubbed “Operation Catapult,” Sonora Quest’s program eliminated a testing backlog at the time and taught the company how to scale testing capacity in the future. (See the sidebar below for more details.) 

Fast forward to late 2021. Like the rest of the country, Arizona experienced a sudden surge from the Omicron variant. “This second surge caused us to ramp up Operation Catapult again around Dec. 1 as it became obvious that Omicron was fueling a major surge in the daily number of new COVID-19 cases,” Dexter recalled. 

“Our lab team continues to get better at ramping up and ramping down Operation Catapult. It takes a considerable number of people to build the capacity that we need when demand calls for it,” he noted.

Highest-Ever Positivity Rate

At its height in Arizona, Omicron infected nearly half of the people who received testing. “By the time we hit the third week of January, the virus surveillance topped out at 46.5% in Arizona,” he said. “That was the PCR positivity rate, and that’s the highest ever measured in Arizona. At that point, Sonora Quest was performing 37,000 PCR tests a day. That was a substantial volume of work flowing through our labs.

“However, just as fast as Omicron rose, it dropped off a cliff on the other side,” he continued. “Now, as of late March, our positivity rate has fallen as low as 4% and we’re doing about 2,500 PCR tests daily.”

At peak capacity, Sonora Quest has eight COVID-19 diagnostic lines available. During times of low community infection, several lines are not running. To bring a dormant line back on takes time, so it’s important for the company to monitor increases in infection rates.

“If a line is not up, it takes a week, possibly as much as two weeks, to get one to two lines up and running at full capacity,” Dexter explained. “Our operations people have done a great job with that. As of late March, we’re doing about 2,500 tests per day. If we get another surge from the BA.2 variant [a lineage of Omicron], it will take us about a month to ramp up to that full capacity of 37,000.”

Sonora Quest has also been able to fine-tune the testing process on the lines to reduce errors, such as quality control lapses or mix-ups with specimens.

“We’ve got the number of failures down to less than 1%,” Dexter said. “When we first started with those SARS-CoV-2 lines, our failure rate went up to about 15%. 

“However, with our culture of Lean, Six Sigma, and Quality Management, we knew our medical lab team had the operational and the technical expertise to continuously identify and reduce the sources of failure. That’s essentially what we’ve done over time.” 

Hiring Follows More Capacity

Dealing with that ebb and flow of heightened testing capacity requires clinical laboratories to quickly hire staff members—and just as quickly reduce labor if necessary. Each of the eight COVID-19 testing lines that Sonora Quest runs employs six people.

“It takes a significant number of full-time equivalents. We’ve used a lot of temporary workers and that’s required us to be effective at training them quickly and thoroughly,” Dexter noted. “As each wave of COVID-19 test volumes dropped, it was necessary for us to reduce the number of temporaries we employed in specimen processing as well as in molecular.”

Finding temporary workers quickly presents difficulties for any lab that experiences a rapid surge in test volume that requires a significant increase in the lab’s testing. 

“This is a challenge, particularly in a tight market for lab labor, but our lab has managed to be successful at recruiting and hiring the needed staff,” Dexter noted. 

Lab hiring managers must be aware of what’s needed for COVID-19 testing procedures. For some duties, such as accession, it’s possible to quickly train temp workers with little clinical experience. 

However, analyzing COVID-19 PCR test results and entering them into medical records requires the skills of certified medical technologists (MT). During a surge of COVID-19 testing, hiring those people on a temporary basis may not happen as rapidly because the labor pool of MTs is limited. 

Clinical laboratories can avoid those problems, by establishing networks ahead of time with health systems and med tech school programs.

Future of the Pandemic 

Seen from the perspective of a social need, Dexter considers lab-based COVID-19 testing to be a cornerstone that protects communities as the pandemic inevitably becomes endemic. 

“It’s concerning that the current administration is flooding the market with hundreds of millions of antigen tests,” Dexter commented. “One reason is because the sensitivity of these consumer self-test kits is not comparable to a PCR test done in a CLIA-accredited laboratory. 

“A second reason is that few people who receive a positive result from an antigen test are going to call the state and report they got a positive result. That means the public health data reported daily may under-report the true number of positive COVID-19 cases.”

Dexter added that it is impossible to track variants from at-home antigen tests while clinical laboratories are set up to provide PCR specimens to determine variants.

“Working closely with the state of Arizona, and also with health systems in Arizona, SQL tracks the variants very closely,” he explained. “We take the positives from our PCR tests and we share them with the TGen—the Translational Genomics Research Institute. 

“TGen determines what variant is there. This ongoing surveillance allows our lab and the public health officials in Arizona to determine what SARS-CoV-2 variants exist county by county.”

However, Dexter noted, “I think we’re going to be handicapped going forward if we have another surge. Use of antigen test means we’re not going be able to track new variants as effectively,” he added.

In Early Days of Pandemic, Arizona State Officials Wanted 60,000 Tests/Day from Sonora Quest

AS WITH MANY CLINICAL LABORATORIES IN THE U.S., at the start of the pandemic the need to expand testing volume for SARS-CoV-2 was a pressing problem at Sonora Quest Laboratories in Phoenix. 

In June 2020, Sonora Quest CEO David Dexter met with officials from both the state of Arizona and Banner Health. Sonora Quest’s labs were maxed out at about 10,000 PCR tests daily and the backlog at the moment was more than 67,000 tests.

State officials and executives from Banner Health, the largest health system in Arizona, threw a surprise at Dexter—Arizona needed 60,000 tests run per day from Sonora Quest. 

“At the time, I didn’t see a way to go from 10,000 COVID-19 PCR tests each day to 60,000,” Dexter recalled. “It would be fair to say I was a bit shell-shocked when I walked out of that room.”

COVID-19 cases slammed Arizona in the spring and summer of 2020. Maricopa County—home to Phoenix—saw more than 2,000 cases per day in late June. The problem was compounded by a dearth of testing in the state. Arizona was near the bottom of the 50 states in per capita testing, the Arizona Republic reported on May 17, 2020.

Steps to Increased Volume

Dexter and his lab team had to find new ways to increase COVID-19 PCR testing volume. Three steps were taken to eventually bring Sonora Quest’s capacity to 60,000 tests per day. 

The first step was financial: He pushed to spend $10 million for additional equipment and reagents, roughly 10 times over his spending authority at the time. Soon after, Sonora Quest Laboratories launched “Operation Catapult” to meet the goal that Arizona and Banner Health set.

Once the funding was in place, SQL’s second step was to reach out to large purchasers of equipment and supplies in Europe in hopes of grabbing additional stock of needed resources.

“We knew that the supply of reagents and other supplies was tight at the time because every lab in the United States was short of equipment and supplies,” he explained.

Opening a 24/7 COVID Lab

Once equipment arrived, Sonora Quest’s third step was to open a new 24/7 clinical laboratory that the company had been planning to open for some time. 

The company hired about 300 employees for Operation Catapult to work in this new 250,000-square-foot facility. The larger labor force and added equipment helped Sonora Quest aggressively tackle its backlog while keeping turnaround times for new COVID-19 PCR tests in the 12- to 24-hour range.

“Shipments of test kits and supplies arrived the weekend of July 4, and by August 3, the backlog of 67,000 tests was eliminated. And this new inventory extended our testing capacity going forward,” Dexter said. The company also hit the goal of 60,000 tests daily.

By mid-August 2020, COVID-19 cases dropped 75% in Arizona, thanks to a combination of mask mandates, community education, and increased testing, the Washington Post reported on Nov. 2, 2020.

“The rates of infection had calmed down a bit, so some of that capacity was taken down,” Dexter noted. “Then, we got hit with a second wave around November that lasted into the early days of 2021. But we were able to accommodate high levels of testing again, which meant Operation Catapult was still paying dividends.”

Intelligent Use of COVID-19 Pooled Testing Helps Clinical Lab Serve Schools in Arizona

SONORA QUEST LABORATORIES USED ITS COVID-19 TESTING CAPACITY to aid schools in Arizona with pooled testing as students returned to in-person learning. 

Initially in early 2021, there was little funding for such surveillance testing, said David Dexter, CEO at Sonora Quest. But he got introduced to the National COVID-19 Testing Action Plan (NTAP), a program run by philanthropic organization Rockefeller Foundation in New York. NTAP worked collaboratively with federal agencies and the White House to seek funding sources for the safe return to classrooms for K through 12 students. 

Use of Pooled COVID Testing

One key to school-based pool testing is the ability to scale pool sizes based on infection rates in a community or the occurrence of a surge. 

Research from the University of Nebraska Medical Center and the University of Nebraska-Lincoln conducted in 2020 showed that five specimens was the ideal number to batch in a COVID-19 testing pool. Researchers also said pooled testing works best in areas with an infection rate below 10%. (See TDR, “COVID-19 Pooled Testing: Good for Labs? Not for IVDs?” July 13, 2020). 

“When the incidence rate of SARS-CoV-2 infection is 10% or less, group testing will result in the saving of reagents and personnel time with an overall increase in testing capability of at least 69%,” researchers wrote in the June 2020 edition of the American Journal of Clinical Pathology.

“Our lab did validations of pooled samples of five, 10, 15, 20, and 25 specimens at a time,” Dexter explained. “We understood that we would need a range of pools, depending on the prevailing infection rate. If that rate is high, the size of the pool of specimens being tested in batch will need to be smaller.

“The goal was to ensure that we weren’t diluting the sensitivity of our PCR tests so much that we wouldn’t pick up any infections,” he explained. “What we got was virtually the same result in all those different validations. We also wanted to make sure that we had levels of pools, depending on the size of the classroom or what the school or local school district wanted.”

To handle logistical issues—such as parent opt-out activities—the Arizona Department of Health Services hired Ginkgo Bioworks, a biotech company in Boston. DHS contracts with Ginkgo and Ginkgo pays Sonora Quest.

Using Ginkgo on Front End

The objective was to simplify the entire collection process. 

“This included how parents could opt out, and effective ways to explain to teachers and administrators how the collection process would work,” Dexter noted. “Ginkgo has done all of that on the front end. Frankly, that’s not the core competency of Sonora Quest. We specialize in testing and reporting results.

“We signed an agreement with Ginkgo which did not include the Arizona Department of Health Services,” he continued. “Ginkgo has a sole-source contract with the Arizona DHS for the $219 million that the state will spend on in-school testing.

“That contract has worked very well for our lab,” Dexter added. “Under this contract, SQL is allowed to do COVID-19 testing in 500 of the state’s 1,200 K through 12 schools. We’ve adjusted our testing capacity and we now have ability to do the COVID-19 testing in all 1,200 schools in Arizona.”

Contact David Dexter at Dave.Dexter@sonoraquest.com.

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