With results from COVID-19 tests routinely taking one week or longer to complete, some labs are trying a new approach called sample pooling.
The idea is labs can save coveted supplies if they test samples from multiple patients at once. If the test finds no signs a pooled sample contains the coronavirus that causes COVID-19, the group of people tested are considered negative. A positive result requires each sample to be tested individually.
It’s another example of how labs are adapting to unprecedented circumstances that have stressed supplies, workforces and capacity to deliver meaningful and timely test results. But the testing method won’t deliver results more quickly, which remains a hurdle for labs struggling to keep pace in hotspot communities.
Public or academic health labs in California, Washington and Nebraska have used or gained approval for the testing method. And last weekend, Quest Diagnostics became the first commercial laboratory to get Food and Drug Administration authorization to conduct sample pooling. It’s part of the lab company’s effort to hike capacity to 150,000 tests each day by the end of July.
Dr. Anthony Fauci, the nation’s leading infectious-disease expert, described pooling as “a really good tool” during a Senate hearing last month. Dr. Deborah Birx, coordinator for the White House Coronavirus Task Force, told the health news site STAT last month pooling would hike capacity “from a half a million tests a day to potentially 5 million individuals tested per day.”
Dr. Emily Volk, a pathologist and president-elect of the College of American Pathologists, said pooling makes efficient use of limited reagents labs need to run tests. Public health, hospital and commercial labs are contemplating pooling because these chemicals are in short supply globally, straining labs capacity to deliver timely tests to diagnose and limit the virus’s spread.
“Testing is the tool we use to make our enemy visible during this pandemic,” said Volk, senior vice president of clinical services at University Health System in San Antonio. “If we had unlimited supplies of reagents, I think it would be wonderful if everybody could be tested every day … We’re nowhere near that ideal right now.”
Peter Iwen, director of Nebraska Public Health Laboratory, began pooling in March because his lab faced a shortage of reagents. He received authorization from the governor after the state declared a state of emergency.
He said his lab pooled 6,000 to 7,000 samples for more than one month until outbreaks at meatpacking plants sent the state’s positive rate too high to make such group testing feasible. It has remained too high to return to pooling, but he would like to resume when the infection rate lowers.
“It got us over the hump,” Iwen said. “We were able to save on reagents. We were able to keep the lab operating. And we felt like we were putting out good results.”
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‘Trade-offs with every diagnostic test’
Pooling is the latest tool in the nation’s improvisational testing strategy, which has shifted responsibility to state and private industry to test and slow the spread of coronavirus.
Pooling is used to process molecular-based tests that require a nasal swab sample from an individual. The sample is placed in a liquid tube called transport media and sent to a lab. When the lab pools samples, it mixes the liquid samples from several tubes while separating a portion of the original sample. If the pooled sample tests positive, lab workers then test the individual samples to determine which patients have the virus.
Pooling is not for point-of-care tests that can deliver quick results at doctor’s office or other clinical settings. Nor is it used for rapid “antigen” tests, which some promote as a lower-cost answer to screen more people quickly, albeit with less sensitive, or accurate, results.
“There’s a lot of controversy in the field right now. What’s more important, get highly sensitive tests or get more tests out?” said Dr. Yvonne Maldonado, director of infection control at Stanford Children’s Hospital.
Maldonado said it’s important to adapt to circumstances. If a sick patient shows up to a clinic or hospital, doctors might collect a specimen for a molecular test and a lab would process the individual sample as a test. But pooling samples might be appropriate when screening larger populations – such as university student returning to campus.
“(There) are trade-offs you have with every diagnostic test, really,” Maldonado said. “If you’re screening large populations to go back to school, I think the broader, pool-based tests could work.”
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Time, manpower and supplies
Pooled testing only works in limited scenarios, Volk said. If the method is used incorrectly, or labs must adapt their workflows, it can slow testing and waste valuable supplies.
Experts says the method is best used to screen patients who show no symptoms, and is mainly reserved for communities where fewer people are infected and rates of positive tests are low.
Kelly Wroblewski, the Association of Public Health Laboratories’ director of infectious disease, said group testing works best when disease “prevalence” does not exceed 5% to 7% of a community. When that rate reaches double digits, labs will get too many positive tests.
“That’s where it stops being a resource save and it becomes a resource drain,” Wroblewski said. “It takes more time. It takes more manpower and it takes more supplies.”
In Arizona, for example, the positive rates from molecular tests were 14.6% on Thursday, too high for the region’s dominant lab, Sonora Quest, to use pooling, said a spokeswoman.
The lab at the University of Washington, however, began pooling samples several weeks ago under the state’s emergency use authorization because COVID-19 infection rates there are low. Dr. Geoffrey Baird, interim chair of the university’s Department of Laboratory Medicine, said the UW lab pools four samples at a time, but is careful when choosing which ones.
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Labs also must make sure they have the right instruments to run the pool tests. Large commercial labs have “sample-to-answer” platforms that allow workers to input samples in machines that yield computerize results within four hours. The instruments are in high demand and also are experiencing shortages of reagents needed to run tests, Baird said.
UW has developed its own test to match the lab’s supplies. The test requires a slower, more hands-on approach, with lab workers interacting with robots that help process liquid samples. Halfway through the process, workers must take tubes out of one instrument and into another to complete the test.
The UW lab has purchased more robotic power and is hiring more licensed technologists to work in the lab.
“What we’ve done is we’re sort of shifted a problem of supply chain to a problem of workforce,” Baird said. “It’s still a problem it’s just somewhat more tractable.”
Quest Diagnostics will begin pooling at labs in Chantilly, Virginia and Marlborough, Massachusetts, and plans to add more throughout the United States. But company spokeswoman Kimberly Gorode offered words of caution.
“Pooling will help expand testing capacity but it is not a magic bullet, and testing times will continue to be strained as long as soaring COVID-19 test demand outpaces capacity,” she said.
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