Dec. 4, 2020, the day Dr. Amir Barzin first witnessed the Amplitude, was a milestone for the UNC School of Medicine assistant professor.
Barzin, who has also served as incident commander for UNC Health’s Respiratory Diagnostic Center, had been working long hours for weeks with an army of others from around campus to help build from scratch a multifaceted coronavirus testing program on the Carolina campus.
He and his colleagues had found a reliable source for highly accurate nasal-swab tests with the added advantage of not requiring users to shove them deep into the upper reaches of the nasal cavity. They had secured three on-campus sites for sample collection and were developing a system for safely moving people in and out in mere minutes. Meanwhile, more than four dozen people from Information Technology Services and the Hussman School of Journalism and Media were working out the kinks on a web-based application called HallPass to securely and efficiently manage the data flow.
But even the most efficient sample gathering is meaningless without a quick turnaround of results. That’s where the Amplitude came in.
The Amplitude Solution, from ThermoFisher Scientific, is a suite of molecular diagnostic lab equipment that can analyze more than 7,000 COVID-19 specimens per day. With a robotic arm that looks like Steven Spielberg’s E.T. without eyes, the Amplitude is the centerpiece of Carolina’s campus lab, and on Dec. 4, Barzin gave it a test drive.
“The Amplitude is installed! I watched a wet-run,” he wrote in an email afterward. “I will tell you — it was one of the coolest things I have ever seen. I thought about how much time and effort was saved through automation. It was such a highlight for me!”
There have been many highlights — and quite a few struggles — over the past few months, as Barzin and many, many others worked to create the Carolina Together Testing Program. Here’s a look at how they pulled it off and why it matters.
The need for widespread surveillance testing on campus became clear to Carolina leadership early during the fall 2020 semester.
“I said all along that all of our decisions would be informed by data and by some of the pilot testing that we did throughout the fall semester,” said Chancellor Kevin M. Guskiewicz. The University began limited asymptomatic evaluation testing in August and ramped up the testing throughout the semester, experimenting with deep-nasal swabs, saliva-based sampling and front-of-the-nose swabs. By mid-October, Guskiewicz said, the data made it clear that comprehensive evaluation testing would be key to a successful spring semester — and that self-administered front-of-the-nose swabs offered the best mix of accuracy, ease of use and efficiency.
It was decided: The University would build its own asymptomatic evaluation testing program, including three main elements — test collection sites (aka testing centers), a processing lab and a data management system.
Having a highly accurate processing lab on campus was crucial, since third-party labs can take three, four and five days to return results. “Every hour that passes is another hour that someone could possibly infect someone else,” Barzin said. “It creates this game where you’re stringing it out, and the risk of spread goes up.”
The lab would need to be capable of polymerase chain reaction (PCR) analysis, since PCR is the gold standard for coronavirus testing. The lab must also meet the federal regulatory standards — including strict biosafety protocols — of the Clinical Laboratory Improvement Amendments, or CLIA, a process managed by the FDA, CDC and the Center for Medicaid Services.
And then there was the data management challenge. “For Carolina to become its own testing and reporting center required a monumental technology infrastructure of systems that interface, including HallPass, Connect Carolina, online identity management, lab information systems and reporting systems for the University and state,” said Michael Barker, Carolina’s vice chancellor for information technology and chief information officer, whose team dove in to help.
The Carolina Together Testing Program would need to be up and running by the week of Jan. 11.
That left nine weeks to get it done.
Building a PCR lab
Amy James Loftis was prepared for the challenge. As laboratory manager for Carolina’s Global Clinical Trials Unit, Loftis has helped build a handful of PCR testing labs around the world, most recently in rural Liberia. For that project, which is focused on Ebola testing in a place with intermittent power and no air conditioning, she and a colleague from the U.S. Department of Defense literally started with a blank sheet of paper, sketching out what they needed and where it would go, and built a Biosafety Level 3 lab from nothing.
“Setting up something that didn’t exist really teaches you how to think logistically about how you get things done, whether that’s working in a pandemic or through the Ebola crisis,” Loftis said. “It totally set me up to succeed in setting up a PCR lab at Carolina.”
Loftis is working with help from her Carolina mentor, Susan Fiscus, a former professor of microbiology and immunology who came out of retirement to help stand up the Carolina Together Testing Program. The team found 2,000 square feet of available lab space in the Genome Science Building. A Facilities Services crew swept in and got the space ready. Instead of starting with a blank piece of paper, Loftis now had three dimensions to work in. She marched over to the space with rolls of colored painter’s tape and began laying it out.
“I started taping off equipment, thinking through the flow: How would specimens come in? Where would we accession them? How would we get them through the PCR analysis?” she said. Here in Chapel Hill, not only did she have the luxury of power and AC, but she had access to architects.
The biggest challenge, she said, was the scale of the operation. With the University requiring most undergraduates to get twice-weekly asymptomatic tests, and making testing available once a week for faculty, staff and graduate students coming to campus, the numbers add up fast: an anticipated 7,000-10,000 tests per week, every week, throughout the semester.
Securing enough supplies was critical. “Everything from fridges to swabs to gloves to gowns to the tubes the swabs go in,” said Barzin, who helped Loftis with the lab and also took the lead on setting up the three testing centers. “All those pieces of the supply chain are really important. Even something as simple as the biohazard bags that all of it goes into. If you’re missing one or two of those pieces you can’t put it together efficiently.”
Loftis and Barzin worked for weeks ordering equipment and supplies. They were thrilled when a vendor guaranteed more than 250,000 sample tubes — and equally pleased to lock down a similar number of swabs and labels with barcodes.
“The hours are really, really long. One reason we’re working so hard is that we know we can do this. We know we can keep the community safe as possible for our students, faculty and staff. We’re doing it. And we can do it even better.”
— Amir Barzin, UNC School of Medicine assistant professor
“All these other things we ordered — incubators, cold storage units, you name it — started flying in,” said Loftis. Then, on Nov. 20, an 18-wheeler pulled up to Genome Sciences and offloaded 50 pallets full of crates containing the Amplitude, followed soon after by a team of ThermoFisher Scientific field service engineers who assembled it.
“One day, I looked around the lab, and it hit me,” Loftis said. “We are doing this!”