In Michigan, Short Supplies Constrain COVID Test Capacity

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

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‚Äôs 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. ‚ÄúHospital 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,‚ÄĚ 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

‚ÄúDue 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 ‚Äėnormal‚Äô testing levels,‚ÄĚhe explained. ‚ÄúManufacturers are in the¬†same boat, in that demand for reagents and¬†consumables far exceeded ‚Äėnormal‚Äô testing¬†patterns because the novel coronavirus hasbeen anything but normal. In other words,¬†the system totally failed.‚ÄĚ

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.

‚ÄúWhen we went live with testing¬†for COVID-19 we were one of the first¬†health systems to do so in Michigan,‚Ä̬†said Ducatman, Professor and Chair of¬†Pathology at Oakland University at the¬†William Beaumont School of Medicine.¬†‚ÄúWe are testing in three different ways.¬†We have the CDC‚Äôs assay and tests from¬†Luminex and Cepheid. But on all platforms,¬†we‚Äôve been severely limited.‚ÄĚ

As of April 23, the Beaumont Hospital¬†lab was running about 500 tests per day.¬†‚ÄúAt that time, we were extremely limited¬†by the number of extraction reagents we¬†could get for the Cepheid machines,‚ÄĚ she¬†explained. ‚ÄúThe people at Cepheid told¬†me they‚Äôve 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

‚ÄúSince 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,‚ÄĚ 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.

‚ÄúIn 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,‚Ä̬†Ducatman reported. ‚ÄúTherefore, we have¬†limited COVID-19 testing to only our¬†emergency room patients, hospital inpatients,¬†and labor and delivery.

‚ÄúSometimes we would give second¬†tests to people who have a strong pretest¬†probability of having COVID-19, but¬†who tested negative,‚ÄĚ she added. ‚ÄúAlso,¬†we were sending some tests out, but those¬†tests were mostly for our employees who¬†were returning to work.‚ÄĚ

By the end of April, the lab started¬†serology testing for all 38,000 employees¬†of Beaumont Health. ‚ÄúThat testing is¬†voluntary,‚ÄĚ noted Ducatman. ‚ÄúFor the¬†employee testing, we‚Äôre using Perkin¬†Elmer and the EUROIMMUN system,¬†but that‚Äôs only if we can get the reagents¬†for those tests.

‚ÄúObtaining supplies has been a continual¬†problem,‚ÄĚ Ducatman commented.¬†‚ÄúEvery day is like the Wild West‚ÄĒnot¬†only in our attempts to get reagents but¬†to get other essential lab supplies as well.‚ÄĚ

During the pandemic, Ducatman has¬†filled two jobs: Chief Medical Officer for¬†Beaumont Hospital, the largest facility in¬†the Beaumont system, and the system‚Äôs¬†Lab Director. ‚ÄúThere are nine labs in our¬†eight hospitals and one in our free-standing¬†emergency center,‚ÄĚ she noted.

‚ÄúEvery day there is a shortage of something¬†our laboratory desperately needs¬†for testing,‚ÄĚ she added. ‚ÄúNothing we do¬†seems to get us the reagents we need. We¬†would love to run 3,000 tests per day and¬†it‚Äôs 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,‚Ä̬†Ducatman explained. ‚ÄúEarly in April I was on the phone with FEMA, and their comment to me was to send the tests¬†that we couldn‚Äôt do to LabCorp and to¬†Quest Diagnostics because they had the¬†reagents that we didn‚Äôt have.

‚ÄúAt that time, Beaumont Health¬†had the largest share of COVID-positive¬†patients in Michigan,‚ÄĚ she said.¬†‚ÄúTherefore, sending those tests to other¬†labs didn‚Äôt make a whole lot of sense.‚ÄĚ

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.¬†‚ÄúWe‚Äôve validated four different platforms:¬†Abbott, Cepheid, DiaSorin, and¬†Thermo Fisher,‚ÄĚshe said.

Dahl, who is the¬†Associate Director for MLabs‚Äô outreach¬†and reference testing programs, also serves¬†as Assistant Professor, Gastrointestinal¬†and Hepatobiliary Pathology at Michigan¬†Medicine. ‚ÄúWe 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,‚ÄĚ 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. ‚ÄúOur lab is eager¬†to test more patients, but we couldn‚Äôt run¬†that many tests because we didn‚Äôt have¬†enough reagents, swabs, or viral transport¬†media,‚ÄĚ explained Dahl. ‚ÄúWe have tested¬†dry swabs, but those are not ideal. We‚Äôve¬†been negotiating for swabs from our supply¬†chain, but doing that through our¬†normal channels has been challenging.

‚ÄúThe 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,‚ÄĚ she added. ‚ÄúIt appears that¬†we have more capacity to test COVID-19¬†patients than we have demand for testing¬†because we‚Äôve restricted who can get¬†tested‚ÄĒat least for the moment. We expect¬†that to change in the coming weeks.

‚ÄúWe 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,‚ÄĚ sheexplained. ‚ÄúIn early April, we reached out¬†to them to discuss how we could develop¬†a plan for COVID-19 testing in those¬†congregate environments.

‚ÄúThen, we rolled out that testing over¬†the next few weeks to provide services to¬†those four nursing homes and to several¬†skilled nursing facilities,‚ÄĚ she said. ‚ÄúWe 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

‚ÄúIn an ideal world, we may eventually have¬†an effective point-of-care test for COVID-19, but we don‚Äôt have that now, at least not¬†one we can use in a lot of different settings,‚Ä̬†said Dahl. ‚ÄúPersonally, 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.

‚ÄúThere 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,‚ÄĚ 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.

‚ÄúAlso, rapid detection COVID-19 tests¬†can be used for employees who become¬†febrile at work,‚ÄĚ said Dahl. ‚ÄúThen, 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.‚ÄĚ

At McLaren Health, the lab has been¬†doing molecular testing for the SARSCoV-¬†2 virus since April, ‚Äúdespite not¬†having enough reagents,‚ÄĚ said Barton P.Buxton, EdD, McLaren‚Äôs 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

‚ÄúIn our corporate laboratory, we have the¬†Roche 6800 platform and the Cepheid¬†Infinity GeneXpert analyzer,‚ÄĚ he reported.¬†‚ÄúAll 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.

‚ÄúOur 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,‚ÄĚ he added.¬†‚ÄúOur COVID-19 testing is limited only by¬†supplies we can acquire; meaning swabs¬†and VTM. If we can‚Äôt get the supplies we¬†need, we have validated our equipment to¬†run on specimens transported in saline if¬†necessary.‚ÄĚ

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.

‚ÄúBut our total systemwide capacity is¬†2,500 tests a day, meaning we‚Äôre below¬†total capacity,‚ÄĚ said Buxton. ‚ÄúWe 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‚Äôt 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

‚ÄúWhen our laboratory started testing,¬†we tested for the coronavirus in acute¬†patients who were in our hospitals,‚ÄĚ he¬†explained. ‚ÄúAs 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.

‚ÄúIn the hospital, we take the position¬†that we treat the patient, not the test¬†result,‚ÄĚ he commented. ‚ÄúBut in the nursing¬†homes, once we test, then they want¬†to separate those patients as best they can.¬†‚ÄúSome nursing homes in our area¬†were hit hard by COVID-19, because¬†people there are closely located,‚ÄĚ he said.

‚ÄúThis is also true in prisons,‚ÄĚ Buxton¬†added, ‚Äúwhere social distancing isn‚Äôt¬†always possible unless prisoners are independent¬†in their cells.‚ÄĚ

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. ‚ÄúBut for our Cepheid and Abbott machines,¬†we‚Äôve had no reagents,‚ÄĚ he noted. ‚ÄúSo, 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.‚ÄĚ

Need to Do Extractions

As of April 23, Memorial was testing¬†270 patients a day problem-free on the¬†Thermo Fisher equipment. ‚ÄúOne 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,‚ÄĚ he explained. ‚ÄúWhile that process¬†cuts into the number of tests our¬†laboratory can do, we can still perform¬†about 500 tests a day without any issues.‚ÄĚ

Memorial may be able to provide¬†COVID-19 PCR tests for some of the¬†Ascension hospitals in Michigan, he¬†reported. ‚ÄúAscension 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.‚ÄĚ

Decker also contacted nursing homes in¬†Memorial‚Äôs service area between Flint and¬†Lansing, offering to test their residents for¬†the novel coronavirus. ‚ÄúThey were sending¬†tests to LabCorp and Quest, but those labs¬†had a 10-day turnaround time,‚ÄĚ he said.¬†‚ÄúIt doesn‚Äôt do those nursing homes¬†any good to test all their residents and¬†then wait almost two weeks to get the¬†results,‚ÄĚ he commented. ‚ÄúThat kind of¬†delay means those nursing homes would¬†have to test everybody all over again.

That‚Äôs 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.‚ÄĚ

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. ‚ÄúState 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,‚ÄĚ said Decker.¬†‚ÄúThat idea is interesting because that lab¬†normally does genetics testing.‚ÄĚ

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.¬†‚ÄúThe 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,‚ÄĚ 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.

‚ÄúAt the site, we collected almost 9,000¬†tests,‚ÄĚ said Isabel Gauss, MT (ASCP),¬†Regional Lab Operations Director for Saint¬†Joseph Mercy Health System, an affiliate¬†of Trinity Health, one of the nation‚Äôs largest¬†Catholic health systems. ‚ÄúBy 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,‚ÄĚ 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‚Äôs requisition for¬†testing. One lesson Gauss learned was the¬†importance of explaining to hospital administrators¬†that using the term ‚Äúdrive-up¬†testing sites‚ÄĚ was misleading.

‚ÄúWe had to be very specific with our¬†medical leadership about drive-up and¬†curbside collections,‚ÄĚ noted Gauss. ‚ÄúMany¬†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‚Äôs not the case, because those tests are¬†not designed to produce rapid results.‚ÄĚ

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.

‚ÄúOur allocation of the reagents we¬†need for COVID-19 testing has been¬†quite limited,‚ÄĚ she commented. ‚ÄúSo, we¬†do what we can to preserve reagents. We¬†also work with multiple different vendors¬†to get the supplies we need,‚ÄĚ she noted.

‚ÄúIn addition, we have multiple different¬†collection sites‚ÄĒsuch 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.

‚ÄúCurrently, we are working on developing¬†plans to open up our operating¬†rooms and to do COVID-19 testing in our¬†nursing homes,‚ÄĚ she commented. ‚ÄúOur¬†mission is to facilitate COVID-19 testing¬†in both settings.‚ÄĚ

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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