Pooled testing could become a critical tool for clinical laboratories to spot the SARS-CoV-2 coronavirus among asymptomatic and pre-symptomatic individuals
COVID-19 testing for individuals has expanded in the US, but the number of people actually tested remains a small proportion of the country’s total population and clinical laboratory testing supply shortages continue to hamper progress. A technique known as pooled testing may help. Federal experts hope it will substantially increase the number of individuals who are tested for the SARS-CoV-2 coronavirus before it makes a possible resurgence in the fall.
One-by-one, some of the nation’s largest clinical laboratory organizations are developing the capability to do pooled testing. For example, on July 18, the Food and Drug Administration (FDA) announced it had issued Quest Diagnostics (NYSE:DGX) an Emergency Use Authorization (EUA) for its SARS-CoV-2 rRT-PCR test, and that it is valid for up to four individual samples as a pooled test.
Quest’s rRT-PCR test was the first COVID-19 diagnostic test to be authorized for use with pooled samples, the FDA noted in a new release.
In the FDA’s statement announcing Quest’s EUA for its rRT-PCR test, Stephen M. Hahn, MD (above), FDA Commissioner, said, “This EUA for sample pooling is an important step forward in getting more COVID-19 tests to more Americans more quickly while preserving testing supplies.” He added, “Sample pooling becomes especially important as infection rates decline and we begin testing larger portions of the population.” (Photo copyright: CBS News.)
Following the announcement of Quest’s EUA, on July 24 the FDA announced LabCorp’s (NYSE:LH) EUA for its COVID-19 real-time reverse transcription polymerase chain reaction (rRT-PCR) test. The test, the EUA states, is intended for the “qualitative detection of nucleic acid from SARS-CoV-2 in upper and lower respiratory specimens” in individuals suspected of COVID-19, using “a matrix pooling strategy (i.e., group pooling strategy), containing up to five individual upper respiratory swab specimens (nasopharyngeal, mid-turbinate, anterior nares or oropharyngeal swabs) per pool and 25 specimens per matrix.”
Exponentially Increasing Testing
In pooled testing, instead of performing a coronavirus test on every specimen received by a clinical laboratory, samples from each individual specimen are taken and then combined with samples from other specimens. A single test is then performed on the entire collection of specimen samples.
If the results of the pooled samples are negative for coronavirus, it is safe to assume that all the specimens in the batch are negative for the virus. If the pooled sample comes back positive, then it will be necessary to go back to the original specimens in that pooled sample and test each specimen individually.
In an exclusive interview with Dark Daily’s sister print publication The Dark Report, Steven H. Hinrichs, MD, Chair of the Department of Pathology and Microbiology at the University of Nebraska Medical Center (UNMC), noted that one pitfall of pooled testing is that it works best in areas of low virus prevalence.
“For pooled testing, the ideal level of low prevalence would be an infection rate below 10%,” he said, adding, “For COVID-19 test manufacturers, pooled testing has the potential to reduce the number of standard tests labs run by roughly 40% to 60%, depending on the population being tested.
“Cutting the number of COVID-19 tests would be a disadvantage for test manufacturers, because pooled tests would identify large numbers of uninfected individuals who would not require standard testing with EUA tests.
“On the other hand, this policy would be a significant advantage for US labs because pooled testing would cut the number of standard tests,” he continued. “Clinical labs would save money on tests, reagents, and other supplies. It would also ease the burden on the lab’s technical staff,” Hinrichs concluded.
“In our study, we show that it’s reasonable to pool five samples, although we realized that some people may want to pool 10 samples at once,” noted Hinrichs. “But even if one sample is positive in a pool of five, then testing five samples at once saves 80% of our costs if all of those samples are negative. But, if one sample is positive, each of those five samples needs to be retested using the standard test,” Hinrichs explained.
During an American Society for Microbiology (ASM) virtual conference, Deborah Birx, MD, White House Coronavirus Response Coordinator, said, “Pooling would give us the capacity to go from a half a million tests per day to potentially five million individuals tested per day,” STAT reported.
Advantages of using pooled testing for the coronavirus include:
Expanding the number of individuals tested,
Stretching laboratory supplies, and
Reducing the costs associated with testing.
Health officials believe that individuals who have COVID-19 and are asymptomatic are largely responsible for the rising number of coronavirus cases in the US, STAT reported.
“It allows you to test more frequently in a population that may have a low prevalence of disease,” Benjamin Pinsky, MD, PhD, Associate Professor, Departments of Pathology and Medicine at Stanford University School of Medicine, told STAT. “That would allow you to test a lot of negatives, but also identify individuals who are then infected, before they develop symptoms.”
Pooled testing also could be advantageous for communities where COVID-19 is not prevalent, in neighborhoods that need to be tested during an outbreak, and for schools, universities, organizations, and businesses that want to remain safely open while periodically monitoring individuals for the virus, CNN reported.
“The goal is to increase the capacity of testing in a relatively straightforward fashion,” Pinsky told STAT. “The caveat is that by pooling the sample, you’re going to reduce the sensitivity of the test.”
According to Pinsky, “pooling only makes sense in places with low rates of COVID-19, where you expect the large majority of tests to be negative. Otherwise, too many of the pools would come back positive for it to work as a useful surveillance tool,” STAT reported.
As Clinical Lab Testing Increases, Pooled Testing for COVID-19 Could Be Critical
Pooled testing has been used in other countries, including China, to test larger amounts of people for COVID-19.
“If you look around the globe, the way people are doing a million tests or 10 million tests is they’re doing pooling,” Birx said during the ASM virtual conference, CNN reported.
In a press release, the American Clinical Laboratory Association (ACLA) stated that about 300,000 tests for COVID-19 were performed per day in labs across the US in late June. That number was up from approximately 100,000 tests being performed daily in early April.
“All across the country, clinical laboratories are increasing the number of labs processing tests, purchasing additional testing platforms, and expanding the number of suppliers to provide critical testing materials,” said Julie Khani, ACLA President in the press release. “However, the reality of this ongoing global pandemic is that testing supplies are limited. Every country across the globe is in need of essential testing supplies, like pipettes and reagents, and that demand is likely to increase in the coming months.”
Clinical laboratory managers will want to keep an eye on these developments. As the need for COVID-19 testing increases, pooled testing may provide an efficient, cost-effective way to spot the coronavirus, especially among those who are asymptomatic or pre-symptomatic and who display no symptoms.
Pooled testing could become a critical tool in the diagnosis of COVID-19 and potentially decrease the overall number of deaths.
In their letter, the Representatives wrote, “As you are aware, the recently enacted Paycheck Protection Program and Health Care Enhancement Act (PPPHCE Act) invests $25 billion in the [Public Health and Social Services Emergency Fund (PHSSEF)], including $11 billion for states, localities, territories, and tribes, to enhance all aspects of COVID-19 testing capacity. This funding is in addition to the funds already appropriated to the PHSSEF under the CARES Act.
“While laboratories are eligible, along with other providers, for these funds,” they continued, “there have been no federal funds specifically designated for the laboratories that have stepped up in this public health crisis and have made significant investments to expand access to COVID-19 testing despite 40-60 percent reductions in regular commercial volume due to the economic lockdowns.
“As laboratories work to maintain their investments in critical resources for testing platforms, reagents, swabs, and PPE, as well as hiring, training, and overtime pay for the laboratory workforce, we urge HHS to direct a portion of funding that has not already been allocated towards these efforts. These funds will ensure that labs can continue to rapidly scale up diagnostic and antibody testing, particularly for healthcare workers, first responders, and other Americans on the frontlines of this pandemic,” concluded the Representatives.
ACLA President Made Similar Plea for Direct Funding to Clinical Laboratories
“In order to deliver accurate, reliable results for patients at a national scale, we must allocate funding to support [clinical laboratories’] expanded efforts,” she said in a statement following an April 27 meeting at the White House.
In her letter, Khani wrote, “It is essential that HHS allocate $10 billion from the fund to support labs’ further expansion of testing capacity to fulfill the testing needs of all of the states and to protect the lives and livelihood of all Americans.
“Further,” she continued, “HHS should note that investing in the nation’s laboratories will not only enhance testing capacity in the short-term, but it also will allow the country to benefit from a robust testing infrastructure for the duration of the COVID-19 pandemic and beyond.”
President Trump signed H.R.266 into law on April 24. It includes $25 billion earmarked for research, development, validation, manufacturing, purchasing, administering, and expanding capacity for COVID-19 testing. According to the language of H.R.266, that includes, “tests for both active infection and prior exposure, including molecular, antigen, and serological tests, the manufacturing, procurement and distribution of tests, testing equipment and testing supplies, including personal protective equipment needed for administering tests, the development and validation of rapid, molecular point-of-care tests, and other tests, support for workforce, epidemiology, to scale up academic, commercial, public health, and hospital laboratories, to conduct surveillance and contact tracing, support development of COVID-19 testing plans, and other related activities related to COVID-19 testing.”
“As the demand for testing continues to grow, clinical laboratories need dedicated funding to plan for challenges that lie ahead. Strong federal coordination and leadership is essential, and we’re looking forward to working with HHS to ensure that laboratories have the resources necessary to continue to expand our role at the forefront of the nation’s response,” said Julie Khani (above), President of the American Clinical Laboratory Association (ACLA), in a press release following the June 8 letter sent to HHS by 30 members of Congress requesting funds from H.R.266 be sent directly to clinical laboratories. Khani will be speaking on federal policies now impacting clinical laboratories at the upcoming 25th annual Executive War College on Laboratory and Pathology Management in New Orleans on July 14-15. (Photo copyright: ACLA.)
Financial Struggles for Hospitals and Clinical Laboratories
This new round of stimulus funding comes at a time when many providers and clinical laboratories are struggling financially, despite the influx of COVID-19 patients.
“Across the country, laboratories have made significant investments to expand capacity, including purchasing new platforms, retraining staff, and managing the skyrocketing cost of supplies. To continue to make these investments and expand patient access to high-quality testing in every community, laboratories will need designated resources. Without sustainable funding, we cannot achieve sustainable testing,” said Khani in an ACLA statement.
As the COVID-19 coronavirus pandemic evolves, federal regulations, as well as emergency funding for COVID-19 testing that is provided by federal legislation, will evolve in unexpected ways. For that reason, clinical laboratory leaders will want to closely track announcements by such federal agencies as the Department of Health and Human Services, the Centers for Medicare and Medicaid Services, the Food and Drug Administration, the Centers for Disease Control and Prevention, and the Federal Emergency Management Administration as decisions are made about how to assign the $25 billion authorized in H.R.266 for “testing.”
Questions remain, however, over how much of the funding will actually reach hospital and health system clinical laboratories
For many cash-strapped clinical laboratories in America, the second round of stimulus funds cannot come soon enough. Thus, lab leaders are encouraged by news that Congress’ $484-billion Paycheck Protection Program and Healthcare Enhancement Act (H.R.266) includes almost $11 billion that will go to states for COVID-19 testing. But how much of that funding will reach the nation’s hospital and health system clinical laboratories?
The Department of Health and Human Services (HHS) announced the new influx of money to the states on May 18. In a news release outlining the initiative, the HHS said the Centers for Disease Control and Prevention (CDC) will deliver $10.25 billion to states, territories, and local jurisdictions to expand testing capacity and testing-related activities.
To qualify for the additional funding, governors or “designee of each State, locality, territory, tribe, or tribal organization receiving funds” must submit to HHS its plan for COVID-19 testing, including goals for the remainder of calendar year 2020, to include:
“Number of tests needed, month-by-month to include diagnostic, serological, and other tests, as appropriate;
“Month-by-month estimates of laboratory and testing capacity, including related to workforce, equipment and supplies, and available tests;
“Description of how the resources will be used for testing, including easing any COVID-19 community mitigation policies.”
“As the nation cautiously begins the phased approach to reopening, this considerable investment in expanding both testing and contact tracing capacity for states, localities, territories, and tribal communities is essential,” said CDC Director Robert R. Redfield, MD, in the HHS statement. “Readily accessible testing is a critical component of a four-pronged public health strategy—including rigorous contact tracing, isolation of confirmed cases, and quarantine.” (Photo copyright: Center for Disease Control and Prevention.)
Funding Should Go Directly to Clinical Laboratories, Says ACLA
The American Clinical Laboratory Association (ACLA), argues the funding needs to go directly to clinical laboratories to help offset the “significant investments” labs have made to ramp up testing capacity during the pandemic.
“Direct federal funding for laboratories performing COVID-19 testing is critical to meet the continued demand for testing,” ACLA President Julie Khani, MPA, said in a statement. “Across the country, laboratories have made significant investments to expand capacity, including purchasing new platforms, retraining staff, and managing the skyrocketing cost of supplies. To continue to make these investments and expand patient access to high-quality testing in every community, laboratories will need designated resources. Without sustainable funding, we cannot achieve sustainable testing.”
Some States Are Increasing Testing, While Others Are Not
Since the first cases of COVID-19 were reported in January, the United States has slowly but significantly ramped up testing capacity. As reported in the Washington Post, states such as Georgia, Oklahoma, and Utah are encouraging residents to get tested even if they are not experiencing coronavirus symptoms. But other states have maintained more restrictive testing policies, even as their testing capacity has increased.
“A lot of states put in very, very restrictive testing policies … because they didn’t have any tests. And they’ve either not relaxed those or the word is not getting out,” Ashish Jha, MD, MPA, Director of the Harvard Global Health Institute, told the Washington Post. “We want to be at a point where everybody who has mild symptoms is tested. That is critical. That is still not happening in a lot of places.”
Meanwhile, Quest Diagnostics and LabCorp continue to expand their diagnostic and antibody testing capabilities.
On May 18, Quest announced it had performed approximately 2.15 million COVID-19 molecular diagnostic tests since March 9 and had a diagnostic capability of 70,000 test each day. The company said it expected to have the capacity to perform 100,000 tests a day in June.
LabCorp’s website lists its molecular test capacity at more than 75,000 tests per day as of May 22, with a capacity for conducting at least 200,000 antibody tests per day. Unlike molecular testing that detects the presence of the SARS-CoV-2 coronavirus, antibody tests detect proteins produced by the body in response to a COVID-19 infection.
As states reopen, and hospitals and healthcare systems resume elective surgeries and routine office visits, clinical laboratories and anatomic pathology groups should begin to see a return to normal specimen flow. Nonetheless, the federal government should continue to compensate laboratories performing COVID-19 testing for the added costs associated with meeting the ongoing and growing demand.
CMS Director speaks at ACLA meeting; acknowledges that labs are alerting the agency to problems with Protecting Access to Medicare Act (PAMA) private payer market reporting, but did not say whether a delay in implementing either reporting or lab test fee cuts would be possible
WASHINGTON, DC—Last week, it was symbolic that, as members of the American Clinical Laboratory Association (ACLA) assembled for their annual meeting, members of the House of Representatives were preparing to vote on the first of several bills intended to “repeal and replace” the Affordable Care Act.
The symbolism comes from the fact that the nation’s medical laboratories and the United States Congress find themselves at major crossroad. For medical laboratories, the issue is the substantial cuts to Medicare Part B clinical laboratory test fees that are scheduled to take effect on January 1, 2018. Predicted by the federal Centers for Medicare and Medicaid Services (CMS) to be a total cut of $400 million in 2018 alone, many expect these Medicare fee cuts to be the single most financially-disruptive event to hit the medical laboratory profession in 25 years.
There’s a similar make-or-break issue unfolding in Congress. Republicans in the House and Senate are caught up in battles to design and pass a series of bills intended to “repeal and replace” the ACA. At their respective crossroads, it remains unclear which path forward each group will follow. (more…)
