News

COVID-19 testing could expand with 'specimen pooling'

Group testing would save resources, speed turnaround time for results

A Stanford Medicine technician in Dr. Benjamin Pinsky's lab sorts through patient samples for the COVID-19 infection. Courtesy Steve Fisch/Stanford Medicine.

As COVID-19 infections continue to spread, demand for diagnostic tests has risen to a level that has pushed back California's mass-testing expansion plan due to a strain on resources. Now, "specimen pooling" could be a game changer, making hundreds of thousands of tests accessible to the public.

Dr. Sonia Angell, the state's public health officer, rolled back testing guidelines on July 14 to essential workers, those with symptoms of the virus and people who were in close contact with an infected person or who were in high-risk settings such as public transportation and mass gatherings due to a shortage of testing components and testing-result delays at laboratories.

The rollback puts a damper on the widescale testing and retesting that health experts say is crucial to control the outbreak and to protect the economy. Nobel Prize-winning economist Paul Romer, formerly chief economist of the World Bank, said in his proposal "Roadmap to Responsibly Reopen America" that to save the economy and lives, everyone in the United States should be tested every two weeks. Patients with positive results should self-isolate while the economy reopens.

If that's the case, then the U.S. has a long way to go. Currently, only 7% percent of the population is being tested every day, David Donoho, Stanford University professor of statistics, said in a recent SIAM News article that noted Romer's hypothesis. Donoho and his Stanford colleagues, Mahsa Lotfi and Batu Ozturkler, have researched worldwide emergent mathematical and statistical ideas regarding COVID-19 specimen pooling published July 13 in the publication by the Society for Industrial and Applied Mathematics.

"For context, only about 4% of U.S. residents were tested for COVID-19 from March through May," he noted.

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Specimen pooling, also known as group testing, can vastly increase the number of tests, save scarce resources, reduce costs and speed up results, he and his co-authors said. The method received a boost last weekend after the U.S. Food and Drug Administration authorized one laboratory, Quest Diagnostics, to conduct small-scale test batching through an emergency authorization, the company announced on Saturday, July 18.

Stanford Medicine is also in line for possible emergency-use authorization from the FDA for its specimen pooling, which could markedly increase its daily testing output.

"If we are doing 2,000 tests per day and convert to pooling we can do 20,000 per day," said Dr. James Zehnder, director of clinical pathology at Stanford Medicine.

In specimen pooling, nasal-swab samples taken for the polymerase chain reaction (PCR) diagnostic test, which identifies active virus infections, are still collected in individual vials through swabs used in a patient's upper respiratory system. The specimens are then combined into small batches. A batch that tests negative means all of those patients do not have the virus; if a batch has a positive result, then all of the patients in that pool are retested individually to find out who has an infection, Zehnder said.

"I'm a little concerned there's not a dialogue about reopening schools" using specimen pooling to track infections, he said.

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With disease-prevalence rates still low, that could amount to thousands of test kits being freed up. If the FDA approves Stanford's specimen pooling, the university's medical school lab could process up to 10 samples on a test, he said. Stanford could also save an estimated 25% in test and processing costs, according to Zehnder.

Pooling specimens would also help reduce shortages. Various components of the test kits have been in short supply at different times since March: pipette tips, reagent and other chemicals for transporting the tests to labs, Zehnder said. Stanford has been fortunate because it has largely been able to get around the shortages through its innovations. It created its own in-house test, which has FDA emergency-use authorization, and 3D-printed its own nasal swabs, he said. Border towns and areas with fewer resources and many cases have been less fortunate, and specimen pooling could help preserve precious resources and reduce backlogs, he said.

Stanford Medicine is also in line for possible emergency-use authorization from the U.S. Food and Drug Administration for its specimen pooling. Courtesy Steve Fisch/Stanford Medicine.

Specimen pooling has been successfully used for more than 70 years. It is currently used at blood banks to screen donations for a variety of viruses.

Donoho said specimen pooling was used in the early days of the HIV/AIDS epidemic, when antibody tests for the virus were restricted to a limited number of kits.

"There are many, many examples. It's proven itself over a lot of years. Mass testing gives us a safe path out of lockdown, and just by using math, we can do that today," he said.

Using specimen pooling, 100 people can be accurately checked for the virus using 10 test kits, Donoho said. Researchers are examining ways to push the frontier further using math and statistics, squeezing the largest number of test samples into the fewest number of tests possible, he said.

More advanced research is also looking at ways to pinpoint people in group testing who test positive so they won't have to be retested individually, he said. Each patient's specimen is divided into a number of subsamples and applied to tests against different sets of patients. The results can be laid out in a table to identify individuals who are likely testing positive.

"We create a kind of a Sudoku puzzle and solve it using math smarts," to find out which people among a group have the virus, he said.

Specimen pooling may have some limitations, including lower test sensitivity if infection prevalence in a population is high, Zehnder and Donoho said. COVID-19 also has a five- to 14-day incubation period, so someone might test negative if they are still at the very early stages of the disease.

Quest's FDA-authorized testing guidelines note that specimens with low amounts of the virus also may not be detected in sample pools due to the decreased sensitivity of pooled testing. Donoho considers that's less of a problem with SARS-CoV-2, the virus that causes COVID-19.

"The reason is that the RT-qPCR (real-time polymerase chain reaction) test can detect as little as 10 virus particles in a sample," he said.

'We create a kind of a Sudoku puzzle and solve it using math smarts.'

-David Donoho, professor of statistics, Stanford University

A dilution of virus particles on a pooled test due to having more than one person testing negative wouldn't have much effect on the test sensitivity because when sick, a person will shed millions of particles, he said.

"It's been proven by several teams that moderate levels of pooling are not a problem," he said.

Quest's study also found no statistically relevant test-sensitivity loss. None of its 3,091 specimens incorrectly tested negative from a population with a COVID-19 community prevalence rate of 1% to 10%, the company said.

Specimen pooling could also make another goal possible: testing people frequently and repeatedly. Continuous testing would help catch the virus in its early stages even after someone initially tests negative, Donoho said.

Stanford's Dr. Benjamin Pinsky, associate professor of pathology and infectious diseases at the School of Medicine, used pooled specimens earlier this year to track the early prevalence of the disease.

Other parts of the country are already conducting pooled specimen testing, such as the state of Nebraska and University of Nebraska system, he said. Cornell University in Ithaca, New York, which will fully reopen this fall, will also pool tests. The university is enforcing a strict regimen of frequent and repeated testing to catch cases, he noted.

"With (repeated) group testing, the benefit is you catch it so early that people are not very infectious," Pinsky said.

Frequent, pooled-specimen testing "makes good sense for universities in college towns," Pinsky said, and he hopes Stanford can use similar testing on its campus, he said.

Dr. Jay G. Wohlgemuth, senior vice president and chief medical officer at Quest Diagnostics, was cautiously optimistic in a July 18 company statement that specimen pooling will help improve testing result times, with a caveat. Just five days prior, July 13, Quest had issued a statement that soaring demand for COVID-19 tests is slowing turnaround times to report results. On July 20, the company said testing was still strained by the demand.

"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. Each of us can practice behaviors that will reduce COVID-19 infections in our communities, so our national healthcare system can better respond to this crisis," he said.

Find comprehensive coverage on the Midpeninsula's response to the new coronavirus by Palo Alto Online, the Mountain View Voice and the Almanac here.

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COVID-19 testing could expand with 'specimen pooling'

Group testing would save resources, speed turnaround time for results

by / Palo Alto Weekly

Uploaded: Tue, Jul 21, 2020, 6:27 pm

As COVID-19 infections continue to spread, demand for diagnostic tests has risen to a level that has pushed back California's mass-testing expansion plan due to a strain on resources. Now, "specimen pooling" could be a game changer, making hundreds of thousands of tests accessible to the public.

Dr. Sonia Angell, the state's public health officer, rolled back testing guidelines on July 14 to essential workers, those with symptoms of the virus and people who were in close contact with an infected person or who were in high-risk settings such as public transportation and mass gatherings due to a shortage of testing components and testing-result delays at laboratories.

The rollback puts a damper on the widescale testing and retesting that health experts say is crucial to control the outbreak and to protect the economy. Nobel Prize-winning economist Paul Romer, formerly chief economist of the World Bank, said in his proposal "Roadmap to Responsibly Reopen America" that to save the economy and lives, everyone in the United States should be tested every two weeks. Patients with positive results should self-isolate while the economy reopens.

If that's the case, then the U.S. has a long way to go. Currently, only 7% percent of the population is being tested every day, David Donoho, Stanford University professor of statistics, said in a recent SIAM News article that noted Romer's hypothesis. Donoho and his Stanford colleagues, Mahsa Lotfi and Batu Ozturkler, have researched worldwide emergent mathematical and statistical ideas regarding COVID-19 specimen pooling published July 13 in the publication by the Society for Industrial and Applied Mathematics.

"For context, only about 4% of U.S. residents were tested for COVID-19 from March through May," he noted.

Specimen pooling, also known as group testing, can vastly increase the number of tests, save scarce resources, reduce costs and speed up results, he and his co-authors said. The method received a boost last weekend after the U.S. Food and Drug Administration authorized one laboratory, Quest Diagnostics, to conduct small-scale test batching through an emergency authorization, the company announced on Saturday, July 18.

Stanford Medicine is also in line for possible emergency-use authorization from the FDA for its specimen pooling, which could markedly increase its daily testing output.

"If we are doing 2,000 tests per day and convert to pooling we can do 20,000 per day," said Dr. James Zehnder, director of clinical pathology at Stanford Medicine.

In specimen pooling, nasal-swab samples taken for the polymerase chain reaction (PCR) diagnostic test, which identifies active virus infections, are still collected in individual vials through swabs used in a patient's upper respiratory system. The specimens are then combined into small batches. A batch that tests negative means all of those patients do not have the virus; if a batch has a positive result, then all of the patients in that pool are retested individually to find out who has an infection, Zehnder said.

"I'm a little concerned there's not a dialogue about reopening schools" using specimen pooling to track infections, he said.

With disease-prevalence rates still low, that could amount to thousands of test kits being freed up. If the FDA approves Stanford's specimen pooling, the university's medical school lab could process up to 10 samples on a test, he said. Stanford could also save an estimated 25% in test and processing costs, according to Zehnder.

Pooling specimens would also help reduce shortages. Various components of the test kits have been in short supply at different times since March: pipette tips, reagent and other chemicals for transporting the tests to labs, Zehnder said. Stanford has been fortunate because it has largely been able to get around the shortages through its innovations. It created its own in-house test, which has FDA emergency-use authorization, and 3D-printed its own nasal swabs, he said. Border towns and areas with fewer resources and many cases have been less fortunate, and specimen pooling could help preserve precious resources and reduce backlogs, he said.

Specimen pooling has been successfully used for more than 70 years. It is currently used at blood banks to screen donations for a variety of viruses.

Donoho said specimen pooling was used in the early days of the HIV/AIDS epidemic, when antibody tests for the virus were restricted to a limited number of kits.

"There are many, many examples. It's proven itself over a lot of years. Mass testing gives us a safe path out of lockdown, and just by using math, we can do that today," he said.

Using specimen pooling, 100 people can be accurately checked for the virus using 10 test kits, Donoho said. Researchers are examining ways to push the frontier further using math and statistics, squeezing the largest number of test samples into the fewest number of tests possible, he said.

More advanced research is also looking at ways to pinpoint people in group testing who test positive so they won't have to be retested individually, he said. Each patient's specimen is divided into a number of subsamples and applied to tests against different sets of patients. The results can be laid out in a table to identify individuals who are likely testing positive.

"We create a kind of a Sudoku puzzle and solve it using math smarts," to find out which people among a group have the virus, he said.

Specimen pooling may have some limitations, including lower test sensitivity if infection prevalence in a population is high, Zehnder and Donoho said. COVID-19 also has a five- to 14-day incubation period, so someone might test negative if they are still at the very early stages of the disease.

Quest's FDA-authorized testing guidelines note that specimens with low amounts of the virus also may not be detected in sample pools due to the decreased sensitivity of pooled testing. Donoho considers that's less of a problem with SARS-CoV-2, the virus that causes COVID-19.

"The reason is that the RT-qPCR (real-time polymerase chain reaction) test can detect as little as 10 virus particles in a sample," he said.

A dilution of virus particles on a pooled test due to having more than one person testing negative wouldn't have much effect on the test sensitivity because when sick, a person will shed millions of particles, he said.

"It's been proven by several teams that moderate levels of pooling are not a problem," he said.

Quest's study also found no statistically relevant test-sensitivity loss. None of its 3,091 specimens incorrectly tested negative from a population with a COVID-19 community prevalence rate of 1% to 10%, the company said.

Specimen pooling could also make another goal possible: testing people frequently and repeatedly. Continuous testing would help catch the virus in its early stages even after someone initially tests negative, Donoho said.

Stanford's Dr. Benjamin Pinsky, associate professor of pathology and infectious diseases at the School of Medicine, used pooled specimens earlier this year to track the early prevalence of the disease.

Other parts of the country are already conducting pooled specimen testing, such as the state of Nebraska and University of Nebraska system, he said. Cornell University in Ithaca, New York, which will fully reopen this fall, will also pool tests. The university is enforcing a strict regimen of frequent and repeated testing to catch cases, he noted.

"With (repeated) group testing, the benefit is you catch it so early that people are not very infectious," Pinsky said.

Frequent, pooled-specimen testing "makes good sense for universities in college towns," Pinsky said, and he hopes Stanford can use similar testing on its campus, he said.

Dr. Jay G. Wohlgemuth, senior vice president and chief medical officer at Quest Diagnostics, was cautiously optimistic in a July 18 company statement that specimen pooling will help improve testing result times, with a caveat. Just five days prior, July 13, Quest had issued a statement that soaring demand for COVID-19 tests is slowing turnaround times to report results. On July 20, the company said testing was still strained by the demand.

"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. Each of us can practice behaviors that will reduce COVID-19 infections in our communities, so our national healthcare system can better respond to this crisis," he said.

Find comprehensive coverage on the Midpeninsula's response to the new coronavirus by Palo Alto Online, the Mountain View Voice and the Almanac here.

Comments

20 minutes down under
Cuesta Park
on Jul 21, 2020 at 8:50 pm
20 minutes down under , Cuesta Park
on Jul 21, 2020 at 8:50 pm
2 people like this

What about the new report from Australia of a 20-minute test? Does it only work "down under"?


The Business Man
Old Mountain View
on Jul 22, 2020 at 9:53 am
The Business Man, Old Mountain View
on Jul 22, 2020 at 9:53 am
Like this comment

It has been 6 MONTHS since the COVID situation started.

The White House is saying it working on a PLAN to respond to this situation.

At the same time, it looks to try to shift blame for its failures to anybody and double speaks. Trump says he is responsible for responding but also says he is not responsible for the failure.

In so far as "test pooling" that is done when the scientists know they cannot provide enough resources to properly test all people. The REAL problem with this approach is that medical privacy laws are violated when mixing test samples. The others in the test group that test negative are assumed positive until proven otherwise.

My expertise with HIPPA tells me this is a violation of the HIPPA process. Mixing multiple samples from different people are not allowed. Thus this is just a desperate attempt to minimize the use of reagents because there isn't enough produced to achieve the timely testing we need.

Even if a test could complete in 20 minutes, it requires the reagents to be processed. The fact is that this country cannot produce them enough even with the implementation of the Defense Production Act. The facts are our testing delays of greater than 24 hours make contact tracing impossible.

Thus we are simply counting the sick and the dead and achieving nothing in return.

This problem is not going away until we start taking it seriously. But so far we have failed to do so.


To Business Man
Old Mountain View
on Jul 22, 2020 at 6:44 pm
To Business Man, Old Mountain View
on Jul 22, 2020 at 6:44 pm
Like this comment

I was tested in East PA last Friday using the POC method, which is meant to be give results on the spot, I was told 7 days.... been 6 days still waiting.


The Business Man
Old Mountain View
on Jul 22, 2020 at 7:29 pm
The Business Man, Old Mountain View
on Jul 22, 2020 at 7:29 pm
Like this comment

In response to To Business Man:

This means there is NO CONTACT TRACING going on in Santa Clara County.

YIKES.

The most important part of the process is contact tracing. Without it we are blind regarding spread. This is basic epidemiology.

I am also confused whether there is mislabeling deaths in the state of California, given that COVID tests are not done on all deaths. There is no scientific basis to determine we are getting an accurate count. Most likely many doctors are not reporting many deaths as COVID because the people were never tested for it.

I think we are not getting any accurate results at this time, but it is definitely an under counted problem.


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