NEW YORK – The SARS-CoV-2 testing supply chain has dominated most discussions of laboratory shortages during the pandemic, but facilities have also struggled to secure supplies for more routine testing.
Labs have taken a number of steps to compensate, including outsourcing some testing, shifting back to older technologies, and, in some cases temporarily removing some tests from their test menus, said several laboratory heads.
"If you would have told me a year ago that major suppliers would be running out of the simplest, most basic things as far as lab supplies go, I would have said you were out of your mind," said Gregory Tsongalis, a professor of pathology and laboratory medicine, and director of clinical genomics and advanced technology at Dartmouth College's Geisel School of Medicine.
He cited pipette tips, specimen tubes, 96-well plates, and DNA extraction reagents as among the biggest challenges.
Pipette tip shortages, Tsongalis said, have proved particularly vexing because different automated molecular systems often use different kinds of tips, which means that if one supplier is out, labs can't necessarily use tips from another instrument or supplier.
Pipettes for "the big, automated instruments where they have a specific size tip for that particular instrument have been tough to get, and whether you are doing COVID-19 testing or not, those are supplies you need to run those instruments," he said.
Tsongalis said that generic pipette tips for these instruments are available, but they don't always work well, and labs could run into issues with their warranties or service contracts if they had problems with an instrument due to the use of generic equipment.
Christina Wojewoda, a pathologist and director of microbiology at the University of Vermont Medical Center, likewise, said that pipette tips and supplies of other plastics are a major issue both for COVID-19 and non-COVID-19 testing.
Efforts to ramp up SARS-CoV-2 testing has impacted the availability of microbiology supplies broadly, she said. "A lot of microbiology supplies are on back order or in short supply because test manufacturers are, rightly, focusing their attention on COVID."
For instance, her lab recently ran out of PCR cartridges for testing for MRSA. Reagents needed for molecular testing of Varicella-Zoster Virus (which causes chickenpox and shingles) are on back order, as are test kits for molecular stool testing.
"COVID is the big issue right now, but I'm concerned that while everyone is focused on COVID we are going to have other public health issues because we are not able to do the appropriate testing that we would normally do because those supplies are short," she said.
The shortages have been "pretty significant," said Nathan Ledeboer, medical director of clinical microbiology and molecular diagnostics at Froedtert Hospital and the Medical College of Wisconsin. "It's more a question of what isn't being affected at the moment."
He cited testing for sexual transmitted infections (STIs) as an area where shortages are particularly acute, noting that one of his lab's main vendors for such testing is able to supply tests at the same level of last year but isn't able to keep up with growing demand. In the case of rapid STI testing supplies, the lab is "very short of what we need," Ledeboer said, noting that it is getting roughly a tenth of its normal supply of these tests.
He said the lab typically uses these rapid tests for two purposes — in the emergency department and as a confirmatory test, particularly in situations where child abuse is suspected, and two independent tests are required for legal purposes.
In the case of the confirmatory testing, the lab has been sending this work out to a reference lab due to the shortages that Ledeboer described.
In the case of the ED, "we just have to say, we don't have the ability to offer [rapid testing] to you right now, we have to do it as a routine batch test," he said.
Like Wojewoda, Ledeboer, also cited a lack of molecular stool pathogen panels. This has led both facilities to return to culture-based methods for stool pathogen detection.
Ledeboer said that as one of the few facilities in its area to continue offering culture-based testing, Froedtert-MCW has received many inquiries from other providers in the area about doing culture-based testing.
Culturing is subject to its own supply constraints, though, he said. "We've run into problems because media is in limited supply and being able to get enough media to do those selective cultures has been a bit of a problem."
He said the lab has had to explore alternate types of media and different vendors to stay supplied.
Ledeboer said that shortages in the agarose gel and plastic plates used to make culture plates have contributed to the shortage. He also said that following the dramatic drop in routine test volumes at the beginning of the pandemic, vendors responded by cutting back production of the materials needed for this testing.
"It has taken a while for all of that to come back up to normal levels again," he said.
Meningitis testing has also run into supply challenges, Ledeboer said, and for a while his lab couldn't get meningitis panels, "so we simply couldn't offer that test for about a four-day period of time," he said. Instead, his lab relied on culture or single-plex molecular testing done in house or sent out to a reference lab.
"Certainly there was a turnaround time delay in that particular case, which also had the potential to be patient-impacting, because that is a result you need pretty quickly," he said.
In the case of flu testing, shortages have led the lab to stop offering the assay altogether, Ledeboer said. His lab no longer offers a standalone flu test, and anyone want to test for flu will need to order a respiratory pathogen panel or a mini-panel that includes SARS-CoV-2.
In some cases, Ledeboer said the lab has borrowed from its COVID-19 testing supplies to make sure they were able to cover testing that was absolutely necessary. For example, it couldn't ignore transplant patients, so it took pipettes from the supply meant for COVID-19 testing.
He added that in recent weeks the culture media supply situation has improved, though STI and gastrointestinal testing panels remain hard to come by.
Tsongalis said that his lab had slowed turnaround times somewhat for certain kinds of assays to deal with supply shortages, including some tests for genetic diseases which are meant to confirm a diagnosis, but whose results aren't promptly required.
"We were able to delay some of our other viral load testing, though we didn't delay those too much," he said. "Anything like that where there aren't [patient] management decisions waiting to be made immediately."
Tsongalis said that his lab put in time at the beginning of the pandemic validating several different assays using supplies from different vendors in the hope that this would prevent them from running up against shortages.
"We didn't have as much of a problem as people in other places around the country did, but we still ran into having to switch gears from one assay to another because we couldn't get what we needed for certain things," he said.