CEO SUMMARY: Severe shortages of supplies for COVID-19 lab testing caused one lab director in the Midwest to buy additional instruments while also validating five different COVID-19 tests to run on analyzers the lab used before the pandemic hit. While this strategy allowed the lab to bump up the number of COVID-19 tests it can perform daily, ongoing shortages of supplies, and uncertainties about when supplies will be delivered, continue to constrain the daily volume of COVID-19 tests this lab can perform, even as daily demand for tests increases.
EVEN TODAY, IN THE FIFTH MONTH OF THE COVID-19 PANDEMIC, clinical labs throughout the United States continue to report that they cannot obtain adequate supplies to fully meet the daily demand for SARS-COV-2 testing coming from the communities they serve.
Demand for COVID-19 testing supplies continues to outstrip the ability of lab vendors to manufacture and deliver enough collection supplies, viral test media, reagents, kits and personal protective equipment. Yet there is one product category in the lab supply chain that seems to be available in sufficient quantities to fill the needs of many labs.
That product category is instrumentation. Across the nation, labs tell The Dark Report that they are able to purchase and take delivery of new instruments and analyzers on a relatively speedy timeline. In fact, one of the most common strategies larger labs are using to maintain and add to the volume of COVID-19 tests they can perform daily is operate multiple analyzers from different vendors in their labs—often as many as four to six different vendors and different COVID-19 tests.
This is true for a health system in the Midwest with a large anchor hospital and several community hospitals in the system. Its laboratory added new analyzers from several vendors and now operates instruments from six different vendors.
“Despite being a customer of these vendors, supply shortages continue to limit our lab’s COVID-19 testing capacity to about 20% of optimal levels,” said the laboratory’s director, who asked to remain anonymous so that he could speak freely.
Workarounds to Get Supplies
In an interview with The Dark Report on June 9, he explained the lab’s workarounds to the shortage of SARS-CoV-2 testing supplies now in the fifth month from the day of the first diagnosed case in the U.S. (Jan. 19): buy, install, validate, and run as many new molecular-test platforms from different vendors as possible.
“After installing and validating those platforms, our lab has not solved the supply-shortage problem entirely,” he noted. “But adding new assays from different vendors allowed our lab to eke out a few hundred more coronavirus tests per day.
“By acquiring new testing platforms, we can shift testing to different analyzers when supplies for one platform run out,” he explained. The molecular tests are the reverse-transcription polymerase chain reaction (RT-PCR) assays for the SARSCoV-2 coronavirus.
During the interview, the lab director identified four lessons the lab staff learned about how to expand COVID-19 test volume while facing crippling supply shortages. They are:
- Don’t rely on one vendor for all the COVID-19 testing capacity your lab needs. Acquire and use different tests to adjust as needed.
- Assess inventory of COVID-19 test kits and supplies in order to predict which platforms will have the most supplies of reagents, test kits, specimen-collection swabs, and transport media. Having a longish run of supplies in stock, or due to arrive, is important because such durable capacity means the lab can run tests on one or two machines and possibly avoid the need to switch to other machines.
- Anticipate the need for new equipment when possible and then acquire those instruments and assays. This may be the most important lesson of the three, because the lab acquired five different SARS-CoV-2 tests since March to run on its lab instruments.
- Order a new analyzer to increase overall testing capacity if funding and administration support allow such a capital outlay.
Accurate Predictions Needed
Early in the year, clinical lab administrators and pathologists reacted to reports about how the novel coronavirus was spreading in China, Italy, New York, and Washington State by doing what they could to build up testing capacity. Although they did not know it at the time, when the federal Centers for Disease Control and Prevention (CDC) sent out the first RT-PCR test to labs in February, the delivery of that assay marked the inauspicious start of problems labs continue to face even now.
“In February, everyone was waiting for the CDC assay to test for the coronavirus,” the lab director commented. “But it did not go very well.” On Feb. 12, the CDC reported that it would pull the test and reworked it after some state laboratories got inconclusive results during quality-control review for that first test kit.
“At the end of February, our state public health lab began running the reworked CDC assay,” he recounted. “Our lab had it up and running by about March 16 or 17. Because the CDC test is a manual test, it has very low throughput. So we started doing COVID-19 testing on the Luminex MAGPIX equipment in our molecular lab.
Automating COVID-19 Testing
“We brought up that test on the Luminex MAGPIX at about the same time that we started to run the CDC’s reworked coronavirus assay. But we ran the reworked CDC test for only a short time because it never worked very well due to low throughput,” he commented. “We still use the CDC assay from time to time because we’ve had various supply constraints.
“By about April 2, we went live with Cepheid’s GeneXpert test, giving us the ability to run COVID-19 tests on three different platforms,” he explained. “While we waited for Cepheid to get its EUA, we used the Luminex test for most of our COVID-19 testing for about two weeks. Once Cepheid got its EUA, we began the steps to validate that assay so that we could use it for daily testing.
“We wanted to deploy the Cepheid test throughout our health system because we had used it for routine flu testing before COVID-19. So, our health system has it everywhere,” he commented.
“Because all our health system labs already had Cepheid instruments, we thought that if we could get everything from Cepheid—meaning test kits, reagents, and other supplies—all of our health system’s labs could use their existingCepheid instruments to perform COVID-19 tests. That would mean all our lab sites would be running a common instrument and using the same test kits.”
Unexpected Test Demand
This thinking, however, was flawed. “I think no one at Cepheid, or at any of our other vendors, understood what kind of demand our hospitals would have for COVID-19 testing,” he added. “High demand for these tests quickly exhausted our lab-test supplies.
“It turned out that we didn’t have enough supply of COVID-19 tests to use the Cepheid equipment in all of our hospitals,” he explained. “Instead, we deployed it to only two hospitals. Eventually, Cepheid sent us more test kits, which allowed us to test on this platform throughout our entire system.
“We use Cepheid’s COVID-19 tests strategically,” he noted. “That test helps us manage inpatients because we can use it to assess them quickly. Since it’s not a batch test, we can put each patient specimen right on the machine and get an answer in about an hour.
“With that kind of turnaround time, we use it to triage emergency room patients,” explained the lab director. “A fairly rapid result allows the hospital staff to determine where those patients should go. If the result is positive, they’re cohorted to the COVID-positive units. Or, if it’s negative, these patients will go to a COVID-negative unit. Sending patients to different units helps with infection control, which is obviously important for patient care.”
A Daily Juggling Act
During April, the health system juggled supplies and ran coronavirus tests on Cepheid and Luminex equipment. When needed, the lab used the CDC’s COVID-19 assay as well. “By about the end of April or the beginning of May we added the Thermo Fisher test kit in our molecular lab,” he said. On March 13, the FDA announced an EUA for that test, the TaqPath COVID-19 Combo Kit.
“Then, during the first week in May we added the BD BioGX test from Becton Dickinson, which runs on the BD MAX, a molecular instrument that our lab was using for a different line of testing,” he noted. “After BD got an EUA for their new coronavirus test in March, we added that platform too.”
Even after adding tests from Thermo Fisher and BD, the lab still operated at less than maximum capacity, he said. So, by the end of May, the lab was working to acquire another analyzer, the Roche cobas 6800 instrument. On March 13, Roche announced that the FDA had issued an EUA for the cobas SARS-CoV-2 Test.
“We currently have five testing platforms (the CDC assay, Luminex, Cepheid, Thermo Fisher, and BD Max), and we’re working on bringing in the Roche cobas 6800, which would give us six in total,” explained the lab director. “With all of these different vendors’ analyzers, we can run COVID-19 tests in as little as one hour, or as much as eight hours depending on the platform.”
While the strategy of acquiring multiple tests for the new coronavirus allows the laboratory to manage the shortage of supplies more efficiently than it did previously, there is a drawback to this strategy. Changing from one instrument and test to another takes time, slowing production. “There are technical challenges when changing out from one instrument to another because multiple steps are required before we can run specimens on some of the platforms,” he explained. “That’s why we prefer to use the platforms where there’s no extraction needed, such as the Cepheid GeneXpert and the BD MAX.
“Our lab can run those tests faster and both instruments offer much faster turnaround time than the other molecular tests that are batched and perform 48 or 96 tests at a time,” he added. “While these molecular tests enable better throughput, they’re still technically challenging for staff to operate.”
High Demand Continues
Minimizing technical challenges is important because demand for testing for the new coronavirus remains high and is expected to rise still further in the coming weeks. “In terms of testing volume, we predict we’ll see demand like what we’ve seen for the last couple of weeks,” he concluded. “Nothing’s changed. We still have the same supply constraints and we still have the same demand for tests.”
To date, the lab has been testing symptomatic patients, but soon expects to test people who are asymptomatic. “As we open up the economy, we’ll be testing into a new phase,” he commented. “That means there’ll be a need to test individuals for surgeries, for chemotherapy, and for women going into labor and delivery.”
Toughest Challenge of COVID-19 Testing is How to Increase the Daily Number of Tests Performed
ONE CLINICAL LABORATORY DIRECTOR at a large health system in the Midwest faces difficult questions every day about how to increase the daily volume of tests for SARS-CoV-2, the coronavirus that causes the COVID-19 illness.
To date, he has had answers for most of these questions, but the continuing lack of adequate supplies means the health system’s labs have unused capacity to run many more COVID-19 tests daily. “The questions about increasing COVID-19 test volume to meet the needs in our community have been continuous,” said the lab director, who asked not to be named.
“Each day, we ask: How much testing are we doing and how can we do more? Where are the problems we need to solve? What do we need to do to maintain our testing capacity and supplies in the system?
“In a perfect world, we could test thousands of people daily for COVID-19, but that’s only if our lab gets all the supplies needed to run our existing instruments at their full capacity,” he added. “That’s our goal, and we’re doing creative things to get there.
“As it stands now, our lab has capacity to safely do COVID-19 tests for at least 3,000 patients a day if we were unconstrained,” he noted. “Unconstrained would mean we had no supply chain issues, no swabbing issues, no reagent issues. If we had to do more, we would probably be closer to 4,000 COVID-19 tests per day.
“But we’re not even hitting the 1,000 mark,” he continued. “Instead, our lab runs somewhere between 500 and 700 SARS-CoV-2 tests daily because we have so many constraints—even to this day.”
If the average number of tests run per day for the new coronavirus is 600, and the unconstrained safest level of testing is 3,000 daily tests, then the shortage of lab testing supplies means the lab limps along each day at just 20% of full capacity.
“For our lab to run COVID-19 testing at our full capacity requires a consistent supply chain,” he noted. “Problems come when a test-supply vendor says its own supplies will run out at some date in the future. They might tell us that in 30 days they’ll be unable to supply what we need. Then what do we do?
“Our molecular lab has tried to figure out the best combination to get us the most durable capacity—meaning from a single vendor that we could keep long term,” he explained. “But it’s technically challenging, because we want something that everybody can be trained on and that all shifts could operate. If only our most specialized individuals can do it for one eight-hour or 12-hour shift, that doesn’t help our lab if we need 24-hour capacity for COVID-19 testing.”