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Academic Labs Pivot To Fill Coronavirus Testing Gap03:24
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Michelle Cipicchio (right), process development manager on the Broad Institute's Genomics Platform R&D team, trains two lab technicians to extract viral RNA from patient samples. (Scott Sassone/Broad Institute)
Michelle Cipicchio (right), process development manager on the Broad Institute's Genomics Platform R&D team, trains two lab technicians to extract viral RNA from patient samples. (Scott Sassone/Broad Institute)

Massachusetts Governor Charlie Baker likes to point out that the state ranks fourth in the nation for coronavirus testing, per capita. That’s true. According to the most recent data from the COVID Tracking Project, Massachusetts has run more than 20,000 tests per million people, putting the state behind just New York, Louisiana and Rhode Island.

But only about 6% of those tests were conducted by the Massachusetts State Public Health Laboratory. And just ten — not ten percent, ten tests — were conducted by the federal Centers for Disease Control and Prevention.

More than 50,000 tests — about a third of the state total — have been conducted by hospital and academic labs. In an unprecedented pivot, these mostly small-scale labs have rapidly ramped up their capabilities, or totally reconfigured themselves, to fill the testing gap.

“Turning a research lab into a clinical diagnostic lab in a matter of basically a week is something that, before this kind of emergency situation, would just have been unthinkable,” says Aditya Mithal, an MD-PhD student at Boston University. “I don’t want to get political, but it’s a little shocking that in the wealthiest country in the world, this is what it’s come to.”

“Turning a research lab into a clinical diagnostic lab in a matter of basically a week is something that, before this kind of emergency situation, would just have been unthinkable."

Aditya Mithal, bu md-phd student

Mithal is a researcher at Boston University’s Center for Regenerative Medicine (CReM), which is heading up BU’s coronavirus testing efforts. The CReM has transformed itself from a basic research lab focusing on stem cell biology into a COVID-19 testing facility, run by a small army of volunteer students, postdocs and lab techs. Working with Boston Medical Center's pathology department, they now handle all the coronavirus testing for BMC in-house, with a less-than-24-hour turnaround.

Testing "war room" at BU's Center for Regenerative Medicine. (Todd Dowrey)
Testing "war room" at BU's Center for Regenerative Medicine. (Todd Dowrey)

George Murphy, a co-director of the CReM, says going from basic research to clinical testing was a steep learning curve.

“You can’t just start doing this testing,” Murphy says. “We have general biosafety rules, but we don't have the stringent record-keeping and all of the very, very specific rules and regulations that you have to follow to be a clinically certified lab.”

So, they got to work figuring it out. They repurposed lab equipment. They scrounged for test kits. And when the chemical solution used to transport the virus ran out, a team at BU made their own.

Richard Giadone, a newly-minted PhD in Murphy’s lab who is now pitching in with the testing effort, remembers the moment of truth: “You need to run a number of known positive and known negative patient samples from the state lab,” Giadone recalls. “And when we saw that we were able to detect positive and negative samples, everybody ran over to the machine at whatever, eleven o'clock at night, and we were all like, ‘Yeah!’ So that was a really exciting moment.”

Supplies donated to BU's coronavirus testing center. (Todd Dowrey)
Supplies donated to BU's coronavirus testing center. (Todd Dowrey)

Within a week the CReM got certification from the state, and emergency use authorization from the federal Food and Drug Administration (FDA).

The team at Boston University isn’t unique in its efforts. Similar scale-ups and transformations are happening at medical centers all over the state, at Tufts Medical Center, Massachusetts General Hospital, Beth Israel Deaconess Medical Center, UMASS Medical Center, and others. Some labs now have enough capacity to expand testing.

Nicholas Heger, the medical director of clinical laboratory operations at Tufts Medical Center, says that Tufts can now run about 800 tests a day, and has taken on the testing of some smaller medical centers in the state as well as some correctional facilities. Boston University’s testing lab is now expanding to community testing as well. And while commercial test provider Quest Diagnostics announced today that it no longer has a backlog and can deliver results with in 1-2 days, on average, that's still not as fast as most of the smaller, local labs.

“Initially when we started this, we thought there would be big commercial labs that would kind of swoop in, take over and we would be like, great,” says Murphy. “But now what we understand is that they're not going to swoop in and save the day… It's going to be these small academic or small commercial labs that are going to take the initiative to start running these tests. And they are going to bear the load.”

"It's going to be these small academic or small commercial labs that are going to take the initiative to start running these tests. And they are going to bear the load.”

George Murphy, CreM co-Director

One of the biggest load-bearers is the Broad Institute of Harvard and MIT, which has converted its DNA sequencing facility — one of the largest in the world — into a large-scale testing center. They are now the second-largest test provider in the state.

At the Broad Institute, the transformation from basic biomedical research to coronavirus testing facility began with a phone call from Deborah Hung, a faculty member of the Broad and an infectious disease physician at Brigham and Women’s Hospital.

“I was walking into a yoga class Monday night, March 9th. And I got a call from Deb,” recalls Stacey Gabriel, director of the genomics platform at the Broad. “The number of cases of COVID-19 in the state was growing, and she was worried about capacity. She was worried about large-scale testing.”

“And so she said, ‘Stacey, you have this clinical lab that has the appropriate licenses and the appropriate abilities to perform clinical testing. You also have an enormous operation with lots of automation and the ability to handle hundreds of thousands of samples," says Gabriel. "She said, ‘You should do this.’”

(Scott Sassone/Broad Institute)
(Scott Sassone/Broad Institute)

Much of the technology and processes the Broad uses for research are identical, or at least similar, to those used for diagnostic testing. And although they had never done the particular biological test needed to diagnose SARS-CoV-2, they quickly figured it out. In late March the Broad announced a capacity of 1,000 tests a day. Gabriel says they can now run 4,000 samples a day and may scale up further.

“It's very much in our sight to get to many tens of thousands of samples every day,” says Gabriel. “In the days of the Human Genome Project, we would handle and process a quarter million samples per day just as a routine activity. So we're ready to do it, and just growing that capacity now.”

“It's very much in our sight to get to many tens of thousands of samples every day.”

Stacey gabriel, the broad institute

Broad Director Eric Lander says that because of social distancing the Broad had already ramped down much of its biomedical research, so the coronavirus testing is not muscling out other investigations. He also notes that the Broad is able to run tests much more cheaply than commercial labs because they are providing the service at cost.

The Massachusetts National Guard is now testing all nursing homes in the state, as well as many assisted living facilities, and sending the tests to the Broad for processing. Another beneficiary: small health centers like the Lynn Community Health Center. Last month, the turnaround time for tests was 7-8 days.

“That just wasn’t satisfactory,” says Geoff Pechinsky, chief medical officer at the center. With expanded testing from hospitals and the Broad, the turnaround time is down to 24 hours, and he’ll be able to offer about 100 tests at a clinic this week. Two weeks from now, he says, “It’ll be great if we’re doing 300 tests a day.”

The Broad’s Eric Lander says that sort of widespread testing will be needed to get the pandemic under control.

“We need to be thinking about tenfold higher testing or more if we're going to open the Commonwealth,” Lander says. “We're going to need really intensive testing to be able to pick up people early in infection so that they're not spreading it to others.”

While Lander says that the Broad is "committed to play a role as long as it's needed," it’s unclear how long academic labs can — or should — shoulder such a large portion of coronavirus testing.

And while President Trump said yesterday that “testing is a local thing,” Governor Baker, for one, would like to see more help from the federal government.

“We are constantly talking to the players in the lab community about increasing capacity. But some of the work associated with increasing capacity is going to require the CDC and the FDA to do more,” Baker said at a press conference last Friday. “If there is going to be another federal endeavor that comes on the heels of the three stimulus bills, they absolutely, positively need to include in that significant resources for the CDC and the FDA to up their game, because they are a major player in establishing a far more significant testing capacity in the United States.”

[Correction: In the original version of this story, Nicholas Heger's name was misspelled as Nicholas Hager. We regret the error.]

This article was originally published on April 20, 2020.

This segment aired on April 20, 2020.

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