University of Vermont Microbiology Laboratory Identifies Inefficiencies When Performing Pooled Testing for COVID-19
The key to success with pooled testing, says the lab’s director, is having the right personnel and equipment, and an LIS that supports the added steps
Experts believe pooled testing for COVID-19 could reduce the number of standard tests for SARS-CoV-2 by conserving testing resources and cutting lab spending on tests and testing supplies. However, some clinical laboratories have found pooled testing causes inefficiencies due to the lab’s lack of staff, limitations of existing equipment, and biosafety hood space, as well as not having a laboratory information system (LIS) that can manage the large volume of specimens and retesting involved in pooled testing.
One such example is the microbiology lab at 562-bed University of Vermont Medical Center (UVMC) in Burlington, Vt. After evaluating the pooled-testing method, Christina M. Wojewoda, MD, pathologist, Director of Clinical Microbiology at UVMC and an Associate Professor at the Larner College of Medicine at University of Vermont, decided last summer not to do pooled testing, due to the manual steps that the process requires.
The manual steps include having clinical laboratory scientists work under protective hoods to limit the virus’ spread, and both hood space and med techs are in short supply at UVMC, she explained during an exclusive interview with The Dark Report, Dark Daily’s sister publication.
“Our evaluation then is the same as it is now,” she commented. “The barriers to pooling still hold true. Instead of pooling, we keep up with the volume of COVID-19 samples by balancing in-house SARS-CoV-2 testing and send-out testing.”
Low Viral Load a Problem in Pooled Testing for SARS-CoV-2
Another problem, Wojewoda added, is when one patient’s sample in a pool of specimens has a low viral load of SARS-CoV-2. Clinical labs in some states have found that when the prevalence of the novel coronavirus in the population is below 5%, then pooled testing could be an effective testing strategy. However, although Vermont has a relatively low presence of the COVID-19 virus in the population, Wojewoda remains concerned about the viral load in a pooled sample.
“For us, it is less of an issue with prevalence in the population than an issue with low viral load in one patient sample, and that can happen with any prevalence level,” she said. “If there is a low level of virus in one sample, and that sample is combined with samples from four other patients to create the pool, you could dilute the virus below the assay’s level of detection. That means you could miss low-level positive patients.
“When we first considered pooling, we worried about missing those patients, but since then we’ve learned more about the SARS-CoV-2 virus,” she continued. “Now, we now know that patients start producing high levels of virus quickly and that low virus levels often occur toward the end of their infection, after they’ve probably been tested or identified.
“That means we’re less concerned with low levels of virus now than we were initially, at least when pooling five specimens in one tube. But it’s still something to watch for,” she noted.
What About Too Much Virus?
The opposite of this problem also is a concern. If the incidence of infection is too high in a population, then pooled testing could produce too many positive results. The required retesting then makes the process inefficient.
Wojewoda has heard similar concerns from her colleagues at other medical laboratories. They said they were not doing pooled SARS-CoV-2 testing for some of the same reasons.
“When we looked into pooled testing, a number of complications made it impractical,” she said. “Instead, we have been testing each patient individually.”
Since the spring, UVMC’s microbiology lab has run 200 to 500 molecular COVID-19 tests per day on two Hologic Panther instruments and has run a laboratory-developed test (LDT) from the federal Centers for Disease Control and Prevention (CDC) on the ABI 7500 from Applied Biosystems of Waltham, Mass., a Thermo Fisher Scientific (NYSE:TMO) company.
When patient COVID-19 samples exceed 500 in a day, UVMC sends those specimens to the Broad Institute in Cambridge, Mass., for testing.
During the summer, the rate of COVID-19 infections in Vermont was at about 1%, Wojewoda noted. In the last week of December, the Vermont Department of Health reported the seven-day average percentage of positive tests was 2.2%.
Laboratory Information System Challenges When Doing Pooled Testing
In addition to her concerns about the level of detection, UVMC’s laboratory information system (LIS) was another worry. “Clinical laboratories are designed to test one sample and get one result, and that one result goes into one patient’s chart,” she explained. “But when the lab makes a pool of, say, five patients’ samples, those five results need to go into five patients’ charts.
Wojewoda estimates that manual data entry for each of those results takes a solid minute per sample. “That’s not a lot, but it adds up over time, and it’s not something we do normally.”
Normally, lab test results get filed automatically into the patient’s chart, and then those results are available to patients online, she noted.
“There may be multiple fixes for this problem of accurately and efficiently getting pooled test results into the LIS, then reported to each individual patient, but for us the current state of our computer system requires that we enter each result into each patient’s chart manually. We try not to do that as much as possible because of the potential for errors from manual entry,” she said.
When Automation Falls Short
In addition, Wojewoda said that pooled testing cannot be automated the way most standard clinical laboratory tests are run.
“With routine testing, we put a sample on the instrument and let the test run,” she explained. “When we get the result, it goes into the patient’s chart. But, for pooled testing, we have to collect five samples and then pause to manually put a little bit of each of those five samples into one tube. Then, we put that tube on the instrument.
“After we get the results, we manually report the negative results into each patient’s chart,” she continued. “But if they’re positive, then lab staff must find the five tubes and test each one individually. Therefore, we’re doubling the time it normally takes to produce and report a positive result for SARS-CoV-2.”
Any positive results in a pooled sample, she explained, are held up at the instrument so that the lab staff can pull those five samples from the pool and test each one individually. “Then those individual results go into each patient’s chart, because potentially only one of the five might be positive. We don’t want all five of those patients to be labeled as positive if only one is positive,” she added.
Shortage of Lab Techs and Hood Space Compound Inefficiencies of Pooled Testing
Another problem is the requirement to pipette each specimen, she noted. “All infectious samples require hood space and a lab technician to do the work under the hood. But both hood space and lab techs are in short supply.”
Wojewoda explained that some tests being run at the UVMC lab are not being tested from the primary tube.
“There’s often a step where we take some of the primary sample and put it into a tube or cartridge for the test. Then, we put multiple samples together, and we have to pipette each one into the tube without cross contaminating the other samples,” she explained.
“At the same time, we have to track the five patient samples so that we can find the original specimen for testing if we need to do so later. All those steps take more staff time.
“So, while pooled testing saves reagents, it also takes more staff time for pipetting and data entry and the need to record which samples are in which tubes,” she noted. “That might require a spreadsheet or other electronic means to track which samples come from which patients.
“An automated way to do the pipetting would be helpful and would increase staff safety,” she added. “I worry when we’re working with something as infectious as SARS-CoV-2, because the lab techs must dig swabs out of liquid media before discarding them, while being careful not to contaminate anything around them.”
Pooled testing for COVID-19 clearly has potential. But, as Wojewoda explained, it brings complications that can cause inefficiencies. Clinical laboratory managers will want to evaluate existing instrumentation, automation, staffing, and laboratory informatics capabilities to determine if and how their labs would experience similar inefficiencies before a final decision to begin a program of pooled testing for COVID-19.