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In Michigan, Short Supplies Constrain COVID Test Capacity - The Dark Intelligence Group

In Michigan, Short Supplies Constrain COVID Test Capacity

JVHL labs say lack of supplies limits COVID-19 testing to just 40% of capacity

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CEO SUMMARY: Because of a severe shortage of supplies, members of Michigan’s two hospital laboratory networks have been stymied in their ability to respond to the pandemic and operate their SARS-CoV-2 analyzers at full capacity. The lack of primers, reagents, specimen-collection swabs, test kits, and viral transport media resulted from directives federal officials imposed in the supply chain in favor of unnamed preferred laboratories, unusually strong demand for testing after years of payment cuts, and disruption in traditional relationships with vendors, lab directors reported.

TESTING SUPPLIES SUCH AS REAGENTS, SWABS, AND TRANSPORT MEDIA HAVE BEEN SO SCARCE that members of two hospital laboratory networks in Michigan have been running tests for the novel coronavirus  at only about 40% of full capacity.

If the members of the Joint-Venture Hospital Laboratory (JVHL) and the Great Lakes Laboratory Network (GLLN) could get all of the supplies they need to perform coronavirus testing at full capacity, they could run more than 20,000 tests per day for the SARS-CoV-2 virus that causes the COVID-19 illness, said JVHL CEO John Kolozsvary. But a shortage of specimen-collection swabs, viral-transport media (VTM), and reagents limited the daily number of tests the labs could run to 6,500 per day, or about 40% of full volume.

What’s more, the hospital labs have been extremely cautious in their use of supplies by limiting the average number of virus tests performed to about 5,000 per day, Kolozsvary said. “Hospital labs do not want to take the chance of running out of reagents, swabs, or VTM in anticipation of a delivery that might turn out to be a 50% cut of their supplies or a complete diversion of supplies from the hospital,” he added.

To understand the scope of the problems now choking the clinical laboratory virus-testing supply chain in the United States, The Dark Report interviewed seven Michigan lab directors on April 23. Those lab directors represent more than 30 hospitals in the Detroit metropolitan area and statewide. Other lab executives, including Kolozsvary of JVHL and Mike Hiltunen MBA, MT (ASCP), CLC (AMT), Executive Director of GLLN, were on the call as well.

Since then, the lab directors provided data on the number of tests they were running as of the last week in May. This article includes comments from lab directors at Beaumont Hospital, McLaren Health, Memorial Health Care, Michigan Medicine Labs, and the Saint Joseph Mercy Health System. In a coming issue, our coverage will include comments from other JVHL-member lab directors.

Three Supply Choke Points

During the call with hospital and health system lab directors, the participants explained that a variety of factors cut into their normal supply sources, limiting test volume. Among the most important of the factors were these three:

1) Federal redistribution of the supply chain contributed to an unequal distribution of supplies that favored unnamed commercial and other preferred labs over hospital laboratories. One lab director on the call reported that her lab ran short because the Federal Emergency Management Agency (FEMA) had requisitioned substantial volumes of reagents, swabs, and transport media, taking about half of all the supplies from the lab’s regular supply vendor. That vendor has been unable to fulfill her lab’s normal supply orders, she said.

2) Choke points in the supply chain. Traditionally, labs acquire all the materials and supplies they need through their relationships with a variety of vendors, including the manufacturers of their installed analyzers. But during the pandemic, those traditional vendors ran short, forcing one lab to acquire a new analyzer from Thermo Fisher, and then get the machine installed and validated so that the lab could run at least some of the tests needed to meet the rising patient demand while the other analyzers ran routine assays.

3) Strong demand for testing after years of lab payment cuts. Over several years, commercial and federal payers have made deep reductions in payment for lab testing. That now hampers the ability of all labs to prepare for a huge surge in testing during the pandemic, said Hiltunen.

Inadequate Lab Supplies

“Due to declining reimbursements over the last several years, the laboratories have gotten very good at just-in-time ordering and other Lean activities that keep supplies at what we might consider to be ‘normal’ testing levels,”he explained. “Manufacturers are in the same boat, in that demand for reagents and consumables far exceeded ‘normal’ testing patterns because the novel coronavirus hasbeen anything but normal. In other words, the system totally failed.”

Among the labs’ biggest need is for reagents to run their high-speed reverse-transcription polymerase chain reaction (RT-PCR) analyzers. After reagents, the labs also need specimen-collection swabs and VTM.

On May 25, the Association for Molecular Pathology (AMP) released results of a survey of lab professionals from academic medical centers, commercial reference laboratories, and community hospitals, all based in the United States, that offer SARS-CoV-2 tests. The survey confirmed what the Michigan lab directors reported to TDR.

The lab directors explained the problems they faced in obtaining the requisite supplies to increase virus testing volume in their laboratories, and outlined the plans they have to collect specimens in the state’s nursing homes and other congregate facilities and to serve other high-risk populations.

Beaumont Hospital

Barbara S. Ducatman, MD, Lab Director at Beaumont Hospital, Royal Oak, said the lab introduced its first COVID-19 test on March 17, but since then has yet to run at full testing capacity due to supply contraints. Beaumont has 1,109 beds and serves Detroit and its suburbs as a level 1 trauma center and as a major teaching hospital. The Beaumont system has nine clinical labs.

“When we went live with testing for COVID-19 we were one of the first health systems to do so in Michigan,” said Ducatman, Professor and Chair of Pathology at Oakland University at the William Beaumont School of Medicine. “We are testing in three different ways. We have the CDC’s assay and tests from Luminex and Cepheid. But on all platforms, we’ve been severely limited.”

As of April 23, the Beaumont Hospital lab was running about 500 tests per day. “At that time, we were extremely limited by the number of extraction reagents we could get for the Cepheid machines,” she explained. “The people at Cepheid told me they’ve been constrained by FEMA in how many reagents they could send out because they had to give FEMA about half of their supply.

FEMA’s Directives, Control

“Since FEMA began directing where those supplies go, we were unable to get those reagents, even though Michigan was a hotspot at that time and still is to some extent,” Ducatman said.

At that time, Michigan had 2,812 deaths (third highest among the 50 states behind only New York and New Jersey) and 33,929 cases (seventh highest among states in the number of cases per 100,000 residents), according to data from the American Heart Association Health Metrics and Evaluation. On May 29, Michigan ranked eighth in the number of cases, and fifth in number of deaths, AHA data show.

“In late April, we were doing only about 500 tests a day, and into May we still do 500 tests a day because we are unable to obtain the supplies needed to support our total capacity of 3,000 tests,” Ducatman reported. “Therefore, we have limited COVID-19 testing to only our emergency room patients, hospital inpatients, and labor and delivery.

“Sometimes we would give second tests to people who have a strong pretest probability of having COVID-19, but who tested negative,” she added. “Also, we were sending some tests out, but those tests were mostly for our employees who were returning to work.”

By the end of April, the lab started serology testing for all 38,000 employees of Beaumont Health. “That testing is voluntary,” noted Ducatman. “For the employee testing, we’re using Perkin Elmer and the EUROIMMUN system, but that’s only if we can get the reagents for those tests.

“Obtaining supplies has been a continual problem,” Ducatman commented. “Every day is like the Wild West—not only in our attempts to get reagents but to get other essential lab supplies as well.”

During the pandemic, Ducatman has filled two jobs: Chief Medical Officer for Beaumont Hospital, the largest facility in the Beaumont system, and the system’s Lab Director. “There are nine labs in our eight hospitals and one in our free-standing emergency center,” she noted.

“Every day there is a shortage of something our laboratory desperately needs for testing,” she added. “Nothing we do seems to get us the reagents we need. We would love to run 3,000 tests per day and it’s very frustrating not to do so.

“Our purchasing department has been told that our vendors have allocated reagents for us, but they also said that the federal government is directing our vendors where to send those reagents,” Ducatman explained. “Early in April I was on the phone with FEMA, and their comment to me was to send the tests that we couldn’t do to LabCorp and to Quest Diagnostics because they had the reagents that we didn’t have.

“At that time, Beaumont Health had the largest share of COVID-positive patients in Michigan,” she said. “Therefore, sending those tests to other labs didn’t make a whole lot of sense.”

Michigan Medicine Labs

The Michigan Medicine Laboratories, known as MLabs, went live with its first COVID-19 tests on March 20. Based in AnnArbor, the labs are part of the University of Michigan Health System, said Julia Dahl, MD, Associate Director of MLabs. “We’ve validated four different platforms: Abbott, Cepheid, DiaSorin, and Thermo Fisher,”she said.

Dahl, who is the Associate Director for MLabs’ outreach and reference testing programs, also serves as Assistant Professor, Gastrointestinal and Hepatobiliary Pathology at Michigan Medicine. “We use the DiaSorin as a rapid test for emergency room patients. That rapid test is useful for making admitting decisions for emergency room patients because it has the fastest turnaround time,” she noted.

On April 23, MLabs, a reference laboratory, was running 500 to 600 daily coronavirus tests, but it had the capacity to do about 2,000 tests per day. “Our lab is eager to test more patients, but we couldn’t run that many tests because we didn’t have enough reagents, swabs, or viral transport media,” explained Dahl. “We have tested dry swabs, but those are not ideal. We’ve been negotiating for swabs from our supply chain, but doing that through our normal channels has been challenging.

“The supplies we need most are swabs. Less so reagents because we have four platforms, which allows us to spread out which platforms are meeting our demand for these tests,” she added. “It appears that we have more capacity to test COVID-19 patients than we have demand for testing because we’ve restricted who can get tested—at least for the moment. We expect that to change in the coming weeks.

“We are working with four nursing homes because those facilities are of strategic interest to Michigan Medicine and because state officials made it a priority to provide testing in those facilities,” sheexplained. “In early April, we reached out to them to discuss how we could develop a plan for COVID-19 testing in those congregate environments.

“Then, we rolled out that testing over the next few weeks to provide services to those four nursing homes and to several skilled nursing facilities,” she said. “We are developing a COVID-19 testing strategy in those facilities to determine universal versus symptomatic and how frequently we will test patients in these facilities given changing census and risks of new exposures.

Lower Threshold of Detection

“In an ideal world, we may eventually have an effective point-of-care test for COVID-19, but we don’t have that now, at least not one we can use in a lot of different settings,” said Dahl. “Personally, I would not place point-of-care serologic testing in a nursing home, because the immunologic response to infections of people over age 60 leaves them on the lower threshold of detection.

Therefore, I would be cautious about putting point-of-care testing for serologic assays in a nursing home.

“There may be a use-case scenario to consider for point-of-care PCR testing or point-of-care rapid-result testing for the SARS-CoV-2 virus,” she added. The BioFire assay is an example of a rapid-result test. These COVID-19 tests could be used in nursing homes to guide which patients should be isolated.

“Also, rapid detection COVID-19 tests can be used for employees who become febrile at work,” said Dahl. “Then, they could be sent home if they test positive so as to protect the vulnerable population in those facilities who have a much higher rate of death from COVID-19.”

At McLaren Health, the lab has been doing molecular testing for the SARSCoV- 2 virus since April, “despite not having enough reagents,” said Barton P.Buxton, EdD, McLaren’s President and CEO of McLaren Health Management Group. MHMG provides home health, palliative, and hospice care, as well as home infusion, pharmacy, and laboratory services in more than 30 counties throughout Michigan.

Testing for Area Hospitals

“In our corporate laboratory, we have the Roche 6800 platform and the Cepheid Infinity GeneXpert analyzer,” he reported. “All of our hospitals are outfitted with the Abbott IDNow platforms. In about mid-April, we started testing for hospitals outside of the McLaren system, and we are now testing specimens for several nursing homes in our service area. We have ample capacity, both within our lab and if we need to pivot. We also have the ability to send out COVID-19 tests.

“Our goal is to do as many tests as we can in-house, and we could do so in up to six runs each day if needed,” he added. “Our COVID-19 testing is limited only by supplies we can acquire; meaning swabs and VTM. If we can’t get the supplies we need, we have validated our equipment to run on specimens transported in saline if necessary.”

In late April, McLaren was running about 400 to 500 tests per day on the Roche machines and 300 per day on the Cepheid equipment in the core laboratory. McLaren’s hospital labs have been running about 50 tests per day.

“But our total systemwide capacity is 2,500 tests a day, meaning we’re below total capacity,” said Buxton. “We have a shortage of swabs and viral-transport media, and those are probably the two most-limiting factors. We can use dry swabs, but we don’t like to do that because the specimens collected with those swabs are not ideal for running tests on our high- or medium-throughput machines. The Abbott machines take the dry swabs, which has been helpful.

Testing in Nursing Homes

“When our laboratory started testing, we tested for the coronavirus in acute patients who were in our hospitals,” he explained. “As we tested more of those patients, we started seeing cases in nursing homes. Where we can get into nursing homes, we are offering them COVID-19 testing.

“In the hospital, we take the position that we treat the patient, not the test result,” he commented. “But in the nursing homes, once we test, then they want to separate those patients as best they can. “Some nursing homes in our area were hit hard by COVID-19, because people there are closely located,” he said.

“This is also true in prisons,” Buxton added, “where social distancing isn’t always possible unless prisoners are independent in their cells.”

Nicholas Decker, MLS (ASCP), Lab Director for Memorial Healthcare in Owosso, Mich., said his lab was prepared to test for COVID-19 since March 25. “But for our Cepheid and Abbott machines, we’ve had no reagents,” he noted. “So, I bought a Thermo Fisher RT-PCR platformand had it installed, validated, and got an emergency use authorization fromthe FDA. We did all that before either of those other two companies would return a call from us or give us any indication about when we would get reagents.”

Need to Do Extractions

As of April 23, Memorial was testing 270 patients a day problem-free on the Thermo Fisher equipment. “One of our limiting factors is a labor issue, because we have to do the extractions before we load the tests onto the Thermo Fisher platform,” he explained. “While that process cuts into the number of tests our laboratory can do, we can still perform about 500 tests a day without any issues.”

Memorial may be able to provide COVID-19 PCR tests for some of the Ascension hospitals in Michigan, he reported. “Ascension has had a challenge using the commercial labs, and so some of its smaller outlying hospitals have sent COVID-19 specimens to us since about the beginning of April. That turned out to be a short-term need.”

Decker also contacted nursing homes in Memorial’s service area between Flint and Lansing, offering to test their residents for the novel coronavirus. “They were sending tests to LabCorp and Quest, but those labs had a 10-day turnaround time,” he said. “It doesn’t do those nursing homes any good to test all their residents and then wait almost two weeks to get the results,” he commented. “That kind of delay means those nursing homes would have to test everybody all over again.

That’s why some lab directors say that testing individuals with a PCR test that takes 10 days to two weeks for results causes more problems than it solves.”

Next-Gen Testing Labs

One way to address the problems of testing shortages in Michigan is to use the capacity in next-generation sequencing labs. “State officials have suggested sending COVID-19 tests to NxGen MDx in Grand Rapids, a private, next-generation sequencing lab that has reagents and some idle equipment,” said Decker. “That idea is interesting because that lab normally does genetics testing.”

In its report on supply shortages issued last Thursday, the Association for Molecular Pathology (AMP) confirmed what the Michigan lab directors were experiencing. The supply shortages affected RNA extraction kits, primers, probes, enzymes, specimen collection swabs, and VTM, reported the AMP.

The lab professionals who responded to the survey reported needing to validate at least three diagnostic testing methods in case reagents or other materials for one method ran short. Also, survey results showed that 60% to 70% of labs responding from academic medical centers and hospitals had serious supply shortages, while only 13% of commercial labs surveyed reported supply shortages.

Supply Allocations

In its report, AMP recommended that federal, state, and local governments set priorities for supply allocations based on clinical testing needs, and that they should recognize these needs could change over time. “The need for testing supplies designed for acute care, surveillance, high-throughput, and other clinical needs should be monitored widely to provide real-time feedback to agencies to support data-driven supply allocations,” said the AMP.

Local Health Systems Contribute to Detroit’s Effort to Operate a Drive-Up Specimen-Collection Site

IN LATE MARCH, Detroit Mayor Mike Duggan called on multiple health systems to develop a drive-up site to collect specimens from patients concerned they had the novel coronavirus.

Following that request, Duggan and Public Safety Health Director Robert Dunne, MD, announced a partnership with Henry Ford Health System, the Detroit Medical Center, and Trinity Health in Detroit to establish the site at the Joe Dumars Fieldhouse at the former Michigan State Fairgrounds.

“At the site, we collected almost 9,000 tests,” said Isabel Gauss, MT (ASCP), Regional Lab Operations Director for Saint Joseph Mercy Health System, an affiliate of Trinity Health, one of the nation’s largest Catholic health systems. “By doing that, we helped to decompress a lot of the patient testing volume that was coming in through the emergency rooms in hospitals and health systems,” she explained.

The program began at the end of March and a closing date has yet to be set. At the drive-up site, the health systems collected more than 400 specimens per day for Detroit residents. Each patient needed an appointment and a doctor’s requisition for testing. One lesson Gauss learned was the importance of explaining to hospital administrators that using the term “drive-up testing sites” was misleading.

“We had to be very specific with our medical leadership about drive-up and curbside collections,” noted Gauss. “Many of our patients thought they would drive up, get a specimen collected with a nose swab, and have a moment of pain. But then they expected to get a COVID-19 test result. That’s not the case, because those tests are not designed to produce rapid results.”

To increase testing for the novel coronavirus, the health system’s labs have run Cepheid and Abbott instruments and recently acquired one of the new BioFire platforms, Gauss said.

“Our allocation of the reagents we need for COVID-19 testing has been quite limited,” she commented. “So, we do what we can to preserve reagents. We also work with multiple different vendors to get the supplies we need,” she noted.

“In addition, we have multiple different collection sites—such as curbside and drive-through collections. We transport those samples to our community hospital labs and also use our primary reference lab, Warde Medical Laboratory.

“Currently, we are working on developing plans to open up our operating rooms and to do COVID-19 testing in our nursing homes,” she commented. “Our mission is to facilitate COVID-19 testing in both settings.”

CAP Survey Shows Supply Shortage

ON MAY 6, THE COLLEGE OF AMERICAN PATHOLOGISTS (CAP) reported that pathologists continued to face shortages of critical testing supplies for COVID-19. A CAP survey of accredited laboratories showed that more than 60% of laboratory directors who responded report difficulties getting test kits (69%), nasopharyngeal swabs (66%), and viral or universal transport media (62%).

Nearly 80% of the laboratories providing COVID-19 tests reported that they had the capacity to do more COVID-19 testing than they were doing when the survey was conducted from April 23 to 30. And, laboratory directors expected their COVID-19 testing volume to increase by about 40% by the middle of May.

Nearly all labs surveyed reported substantial losses in revenues and the need to furlough employees in some cases.

Contact John Kolozsvary at 313-271-3692 ext. 231 or jkolozsvary@jvhl.org.

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