How a Memphis medical lab mobilized to fight COVID-19

By , Special to the Daily Memphian Updated: October 07, 2020 4:00 AM CT | Published: October 07, 2020 4:00 AM CT
<strong>Toh Gang (left) and Lakshmi Nellore process samples at Poplar Healthcare Sept. 22, 2020</strong>. (Patrick Lantrip/Daily Memphian)

Toh Gang (left) and Lakshmi Nellore process samples at Poplar Healthcare Sept. 22, 2020. (Patrick Lantrip/Daily Memphian)

David Waters
Special to the Daily Memphian

David Waters

David Waters is Distinguished Journalist in Residence and assistant director of the Institute for Public Service Reporting at the University of Memphis.

This article was produced in partnership with the Institute for Public Service Reporting at the University of Memphis, a non-profit newsroom specializing in investigative and explanatory journalism.

On March 17, the day Memphis Mayor Jim Strickland declared a state of emergency in response to the coronavirus pandemic, Jim Sweeney called his lawyers.

“I needed to know my options,” said Sweeney, the CEO of Poplar Healthcare, a locally owned medical lab across the street from FedEx World Headquarters.

Sweeney’s lab already was feeling the impact of COVID-19. Clinics were closing. Hospitals were postponing elective surgical procedures. Gov. Bill Lee was about to ban them statewide.


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Almost overnight, demand for Poplar Healthcare’s specialized diagnostic testing services – primarily for cancer and STDs – dropped by a third.

The company needed to cut expenses to pay its bills and to preserve cash for new equipment and supplies.

“Investing in COVID-19 testing was a major decision and would require a major investment of time and money,” Sweeney said, “not only to save the company but also to help the community fight the virus. It was obvious by then that the federal government wasn’t up to it.”

Poplar Healthcare was.

Since mid-March, employees of this local medical lab have mobilized to fight the spread of the coronavirus pandemic.

When the CDC failed to produce a reliable coronavirus test, and big national labs struggled to fill void, Poplar Healthcare built its own test.

When local test results slowed to a crawl in early summer, overwhelmed by a surge in cases and nationwide supply shortages, the local lab found new ways to expand its capacity.

Now, the city is relying on the lab’s aggressive development of “pooled testing” to provide mass, affordable “assurance testing” that will help schools, businesses and government agencies reopen and stay open.

“Everything they’re doing is a potential game changer,” said Dr. Manoj Jain, a local infectious disease physician who has been advising the city on its COVID-19 response.

For the past two weeks, Jain, Sweeney and other lab officials have been meeting with the FDA, city officials, Shelby County Schools and the Memphis Chamber to ramp up assurance testing.

Poplar Healthcare is the first lab in the country to receive the FDA’s emergency use authorization for pooled testing of 20 samples at a time and clearance to pilot 20 swabs in one tube.

The lab is also working on ways to use special mouthwashes and “lollipops” to test for COVID-19 in saliva.

All are innovations that could dramatically increase the city’s testing capacity by thousands a day and reduce the cost of each test from $100 to $5.

“They built a testing program from scratch right when we needed it,” Strickland said. “And they were among the first labs in the country to get approval for pooling, which will be crucial in our efforts to reopen schools. We could not have done any of this without Poplar Healthcare.”

Preparing the lab

After Sweeney called his lawyers on Tuesday, March 17, he began cutting the payroll. He started by cutting his own salary by 100%.

“If you want your troops to take the hill, they have to know you will take it with them,” said Sweeney, 62, who spent five years as an officer and civil engineer in the Army Corps of Engineers. “Lead by example.”

That Friday, March 19, Sweeney met with his 375 employees and told them the bad news.

He was suspending sales commissions, bonuses and the company’s 401(k) match. He was reducing salaries by up to 50% and weekly hours from 40 to 30. He needed to furlough about four dozen employees and he was taking volunteers.

Then he told them the good news. The lab already had the right machines and some necessary supplies to run the polymerase chain reaction (PCR) tests, the standard diagnostic tests for COVID-19.

Everyone knew what that meant.

“The pandemic is probably the most significant event in our lifetimes,” the company’s vice president of operations Dr. Jim Allay said. “9/11 was significant, but that didn’t affect many of us directly. This affects all of us, our families, our community every day. We were built to take this on.”

With no cure or vaccine available for COVID-19, diagnostic testing was crucial to containing the spread of the virus.

But after weeks of bureaucratic delays and scientific breakdowns, the CDC had failed to produce a reliable test kit.

On March 12, Dr. Anthony S. Fauci, director of the National Institute of Allergy and Infectious Diseases, told Congress the nation’s COVID-19 testing system was “a failure. Let’s admit it.”

On March 13, President Trump declared a national state of emergency. He announced that the government was partnering with private companies to “vastly increase and accelerate our capacity to test for the coronavirus.”

The FDA gave two national labs, LabCorp and Quest Diagnostics, emergency authorization to launch their own COVID-19 testing systems nationwide.

Meanwhile, Roche Diagnostics, the world’s largest biotech company, got emergency authorization to begin manufacturing and shipping tens of thousands of test kits to hospitals and select labs across America.

The list included Sonic Healthcare, which owns American Esoteric Laboratories. AEL has labs in Memphis and Knoxville. It’s the largest independent lab network in the Mid-South.

The testing list did not include locally owned Poplar Healthcare, but Sweeney knew one lab would not have enough capacity to handle a pandemic.

“We had to develop our own test,” Sweeney said. “I knew we had the intellectual brainpower here to do it. What I didn’t know was how soon we could develop a test that worked, or how we’d get the materials we needed, or how we’d survive long enough to get it done.”


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Building a test

The first and most common form of COVID-19 testing begins with a collection kit -- a sterile swab and tube.

A long, slender swab is used to collect a sample inside your nose from the back of your throat.

The swab is placed in a tube filled with chemicals that deactivate the virus while preserving its genetic signature.

The tube is sent to a lab where trained technicians use specialized chemicals and machines to look for that signature.

The search relies on a technique called RT-PCR, or reverse transcriptase polymerase chain reaction.

Basically, it’s a series of steps that allow technicians to isolate, amplify and detect traces of the virus.

In the extraction part of the process, chemical “extraction kits” are used to isolate and remove the viral RNA from other cells in the sample and the swab.

The single-stranded RNA is converted to double-stranded DNA, which is more stable and easier to copy. This is the RT part of the process.

Then the PCR part of the process begins.

Lab technicians use special heating and cooling machines, chemicals and enzymes to create a chain reaction.

The chain reaction turns the analysis machines into Xeroxes that make millions or even billions of copies of the viral DNA.

Molecules of fluorescent dye plug into each copy, turning every viral signature into a neon sign.

No light, no virus.

The entire process can take six to eight hours, but large analysis machines can run dozens of samples at once.

Poplar Healthcare has six such machines capable of analyzing 4,000 samples a day.

Back in March, they started with one.


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Finding supplies

On Thursday, March 19, Sweeney assembled his troops and told them they had days, not weeks, to develop a COVID-19 test that would pass muster with the FDA and CDC.

The CDC was allowing certified labs such as Poplar Healthcare to build and perform the highly sophisticated molecular diagnostic testing.

The FDA was providing instructions for doing so.

But the government would not be providing all of the necessary lab supplies that were suddenly and increasingly in short supply.

At the time, the U.S. had conducted only 5,000 tests nationwide, reporting about 650 cases of Covid-19 and 25 deaths.

A week later, U.S. labs had run nearly a 100,000 tests and confirmed 75,000 cases. Millions more tests would be needed in the coming months.

“We are deeply concerned that, as the number of tests increases dramatically over the coming weeks, clinical labs will be unable to deploy them without these critical components,” the American Society of Microbiology noted in mid-March.

Labs were particularly concerned about the shortage of “RNA extraction kits” – the chemicals that isolate the virus' genetic signature. It’s a critical step in coronavirus testing.

Qiagen and Roche, major suppliers of the kits, already were dealing with back orders. Poplar Healthcare needed the kits immediately.

Sweeney gave the assignment to Will Duffel, the company’s director of operations and the “Radar O’Reilly” of the outfit. Duffel is a Memphis native and UT-Martin business graduate. Sweeney found him waiting tables at nearby TPC Southwind.

“That’s another thing I learned in the military,” Sweeney said. “You’re looking for people with character and talent who can be trained to do what needs to be done.”

It took Duffel a few hours, but he found another kit supplier: Promega in California. “You just have to stay on the phone and cobble stuff together,” he said.

Early Friday morning, March 20, FedEx delivered boxes of extraction kits, and Sweeney’s scientists started putting the testing process together.

Later that afternoon, Sweeney met with Duffel, medical director Dr. Shawn Kinsey and half-a-dozen other members of his leadership team.

He took a small bottle of Jack Daniel’s out of his desk drawer and passed it around to celebrate.

“We made it through the day,” Sweeney told them. “We were able to do what we had to do to stabilize the company. We had what we needed to build a test. Now we just had to get it to work.”


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Detecting the virus

Public health officials in England developed the first diagnostic test (the RT-PCR test) for COVID-19 in early January.

The CDC used its own RT-PCR test to confirm the first known case in the U.S., an American who returned to Washington from Wuhan on Jan. 15.

But the CDC’s protocol was flawed, and, by the time the agency acknowledged that and allowed other labs to begin processing tests, the virus had spread undetected for more than a month.

The virus is a stealth fighter. It sneaks into your body through your nose, mouth or eyes.

It can sneak down into your lungs, infecting and destroying the tiny sacs that shuttle oxygen into your bloodstream.

It also can sneak into your bloodstream and find its way to your heart, kidneys and other organs.

It can remain undetected for days, reproducing billions of copies of itself that infiltrate other cells.

It can be exhaled, fired like microscopic missiles at other potential human targets, even before you know you have it. That’s why you wear a mask.

The first confirmed case of COVID-19 in Shelby County was reported Sunday March 8, the second a few days later. The two people had traveled together to Mardis Gras in New Orleans.

A lab director at Baptist Hospital had to drive the samples to a state lab in Nashville, the only lab in the area that could test for coronavirus.

“We don’t have community spread,” Alisa Haushalter, executive director of the Shelby County Health Department, said in a March 11 press conference.

We did, but given the lack of local testing, there was no way to know. “We don’t have enough tests,” Strickland said March 20.

“The CDC failed us,” Jain said. “Fortunately, our labs here – AEL, UT and Poplar – bailed us out, or we could have been another New York.”


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Preparing to launch

At 6 a.m. on Saturday, March 21, Jim Sweeney and his scientists started moving up the hill toward their objective.

They had what they needed to conduct large-scale molecular diagnostic testing for COVID-19.

They just had to figure out how to make it work.

“We weren’t shooting in the dark, but we didn’t know how long it would take to perfect our aim,” the lab’s chief science officer Dr. Anami Patel said.

Patel was trained in clinical molecular pathology at St. Jude, and he launched and led Methodist-LeBonheur’s Molecular Diagnostics Clinical Service for 14 years.

“I knew we had most of what we needed to build a COVID test and that Will could get what we didn’t have,” Patel said.

The lab already had the biggest and most expensive equipment – two large thermal cyclers, digital ovens capable of heating and cooling dozens of sample tubes at precise temperatures (as high as 161 degrees F) for specific periods of time.

“Getting that equipment requires the longest lead time,” Allay said. “It has to be ordered, shipped, installed. Techs have to be trained. That gave us a huge head start.”

The lab also had machines and supplies (including the now-famous pipette tips) that are used to automatically extract DNA from samples – a laborious process if done by hand.

The CDC had published the protocols for COVID-19 PCR testing – a list of ingredients and instructions for mixtures, temperatures and times.

Duffel and others had worked the phones and scoured the internet to find all the ingredients – the primers, probes, enzymes and other chemicals needed to prepare the samples for the thermal cyclers.

They’d also managed to secure viral samples to test – synthetic RNA from a company called Integrated DNA Technologies, and 10 real patient samples previously tested by AEL.

They spent most of the day Saturday and Sunday running various versions of their PCR test, making adjustments to get ratios and levels just right. Each run would take several hours.

“All these scientists are sitting around brainstorming – maybe this mix will work or that ratio,” Sweeney said. “I’m trained as an engineer. It’s all black and white with me. It was fascinating to watch how science works.”

Once they knew their PCR test worked, they had to run it again a number of times to make sure they could duplicate results over and over thousands of times.

By Monday morning, March 23, Poplar Healthcare was ready to start processing COVID-19 tests.

They submitted their test for FDA approval and waited for local customers. That’s when Sweeney realized he had misjudged the local market.


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Filling a need

Later that day, when Mayor Strickland issued his “Safer at Home” order, the number of confirmed COVID-19 cases was nearly in triple digits and rising fast.

But by then, St. Jude Children’s Research Hospital was testing its own employees, patients and family members.

LabCorp and Quest Diagnostics, two national companies with labs in Memphis, already were putting together their own test kits.

And the city already was working with the University of Tennessee Health Science Center to set up a drive-thru testing site at Tiger Lane.

UTHSC was assembling the test kits and processing them at AEL. Baptist, Methodist and other hospitals were also sending their samples to AEL.

“When we first got the test up and running, we targeted the city and local hospitals,” Sweeney said. “They were not interested and felt they had enough capacity with UT and AEL.”

Sweeney called again on his military training.

“When you make a decision to go into battle, you need to know the way out,” he said.

Poplar Healthcare widened its focus and began processing tests from hospitals in Arkansas, Nashville and hot zones in the northeast.

Meanwhile, tests began to pile up in Memphis. AEL was getting more than 20,000 tests a day from all over the country. UTHSC’s plan to open its own testing lab was delayed.

Some local test results were taking up to two weeks to be processed.

The first week of April, Christ Community Services, which began its community testing program in late March, switched from AEL to local Poplar Healthcare.

Sweeney’s lab began using its third and even larger thermo cycler, doubling its capacity.

The second week in April, local Methodist hospitals asked Sweeney if his lab could handle all of their tests. Sweeney leased three new thermo cyclers and dedicated them entirely to Methodist.

Within a month, Sweeney’s lab techs were working 40 hours a week again. Within two months the company had fully restored all bonuses and commissions, and made up the losses in 401(k) matches. Salaries were fully restored by June and made whole by September.

On May 5, Sweeney and his board decided to return unused the $5.5 million forgivable loan they’d received from the Paycheck Protection Program, the federal government’s small business rescue program.

“We didn’t need the help,” Sweeney said. “We did it ourselves.”


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Pooling resources

Local COVID-19 cases slowed in May, and health officials recommended testing to all who thought they might have been exposed to the virus.

But infections increased again after the Memorial Day and Fourth of July holiday weekends.

Meanwhile, national supply shortages delayed shipments of testing materials to local labs.

A scheduled shipment of 40,000 pipette tips to Poplar Healthcare just didn’t show up.

“We were doing tests for all pre-op patients and asymptomatic testing for city and county employees and nursing homes,” Sweeney said. “When you started adding all of these new sick people, the system couldn’t absorb it all.”

Non-emergency surgeries were delayed. Health officials recommended that only people with clear symptoms get tested. Local labs worked together to share space and resources. Slowly, the backlog was eliminated.

“For two weeks, all the labs were overwhelmed,” Sweeney said. “I knew we had to get aggressive about pooling.”

Pooling combines portions of samples from a group of five or more people in a single tube for a test run.

A negative result clears all of them. If a combined tube test positive, remaining samples from each individual are tested again.

Pooling can save time, cost and testing ingredients if it is used properly to screen large groups of asymptomatic people.

Jain had been talking to Strickland, Sweeney and others about pooled testing since April.

The previous November, Jain had seen pooled testing work in India for another highly infectious disease: tuberculosis. He also knew the state of Nebraska used pool testing for COVID-19 when test supplies were running low in March.

Jain challenged local labs to try pooling. Patel was eager to try it. “Dr. Patel is a brilliant guy,” Jain said. “He’ll keep working and working until he gets it right. I knew he would get this right.”

In May, with Strickland’s approval, Patel began pool testing samples from hundreds of city police officers, firefighters and other workers who volunteered to participate.

Patel’s lab tested the samples in batches of three, five, seven and 10. Seven seemed to work best. Poplar Healthcare became the third lab in the country to get the FDA’s emergency use approval for the process. 

Meanwhile, the city set up a special testing task force and set aside $2 million in CARES Act funding for pooled testing. The city was hoping to pool test as many as 30,000 people a day, starting in July.

“Large-scale testing will allow the safer reopening of our schools, businesses, and increased testing in underserved communities,” Strickland said in his emailed weekly briefing May 29.

But as July approached, COVID-19 cases began surging again and testing supplies dried up again. Pooled testing was put on hold.


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Plug and play

From the outside, Poplar Healthcare’s two-story suburban office building looks as generic and as serene as its name.

Inside, the massive and mostly wide open first-floor testing area looks more like the interior of a Costco.

“When I designed this building, I wanted to have a lot of open space,” Sweeney said. “We needed to be agile, to be able to shift, change, adapt and expand as needed. Plug and play.”

In the company’s B.C. era — Before COVID — the lab operated about 10 hours a day, Monday-Saturday.

Now it runs 24 hours a day, seven days a week.

Depending on how many samples arrive and when, shift schedules are adjusted or ignored.

<strong>Argerie Marin processes COVID-19 samples at Poplar Healthcare's laboratory Sept. 22, 2020</strong>. (Patrick Lantrip/Daily Memphian)

Argerie Marin processes COVID-19 samples at Poplar Healthcare's laboratory Sept. 22, 2020. (Patrick Lantrip/Daily Memphian)

“We work a lot of long days and late nights,” lab tech Argerie Marin said. “I don’t worry when my shift is over. I’m not going to leave something undone for others to do. And people need their test results.”

When the lab decided to run COVID-19 tests, Sweeney asked for volunteers.

“Argerie never hesitated, despite the unknown risks at the time,” Sweeney said.

“I was a little scared, but risk is part of it,” Marin said. “And I was more curious than anything. I wanted to learn and I like to help.”

Marin is among the cadre of recent college graduates enlisted to help with the rising demand for testing.

In May, Gov. Bill Lee signed an order allowing anyone with an undergraduate degree in biology or chemistry to work without a license in a medical lab under the supervision of a lab director.

That was perfect timing for Gabriel Brown, a chemistry major who had just graduated from the University of Memphis, and Jose Lopez, a biology major who had just graduated degree from Fisk University in Nashville.

Last week, both of them were processing COVID-19 tests by “pooling” them — combining 10 samples into one tube.

“Normally, each thermo cycler can run 94 samples at a time, and that takes about three hours,” Brown said. “With 10 to 1 pooling, we can run 940 tests at a time. That saves about 30 hours per batch.”

Sweeney has hired more than two dozen recent college grads to bolster his forces.

“Memphis should be proud,” he said. “This is really a hometown effort. These kids are remarkable.”

In early August, the FDA gave Poplar Healthcare emergency approval to use pools of up to 7. Last month, approval was given for pools up to 10.

Later that month, Sweeney’s lab began pool testing samples from 13 private and public charter schools. It’s also pooling samples for pre-op patients.

The lab is now developing and seeking approval for 20:1 pooling, which could reduce the cost of each test from about $100 to $5.

Strickland, Jain and others believe such “assurance testing” is a safe, effective and efficient way to keep schools, restaurants, and businesses open.

“My hope is that we soon can be testing 5,000 people a week to show the public the benefits of regular, asymptomatic testing,” said Tiffany Collins, who is leading the city’s testing efforts as deputy director of general services.

Sweeney’s lab is ready. The lab has the capacity to process up to 4,000 individual tests a day and up to 25,000 or more with pooling.

“We’re still working to help people get back to their daily lives,” the former Army captain said. “There are new battles every day, but an army does its best work with its back against the wall.”

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