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!”
Finding safe, efficient collection sites
Barzin became an expert at setting up COVID-19 testing sites last summer, while working alongside David Wohl, professor in the School of Medicine’s Division of Infectious Diseases. The pair were part of a team that set up around 10 test sites, including drive-up centers, across North Carolina.
In October, Barzin took the lead on adapting what he and Wohl learned about drive-up testing for the spring semester’s Carolina Together Testing Program. Instead of parking lots, they needed indoor spaces. Apart from the most obvious reason to move indoors — it’s cold in winter — Barzin learned from experience that the wind and rain can wreak havoc on temporary outdoor spaces, tousling tents and scattering supplies and paperwork. It’s hard for technicians to contend with the elements when they’re using both hands for holding swabs and vials. Drop a sample, and it’s ruined. And those are professionals. The Carolina Together Testing Program would rely on self-collection by students and others.
In his search for sites, Barzin put pen to paper and developed a checklist.
Topping the list? The sites needed to be large enough so that people taking the tests could stay physically distanced during the few minutes they are inside. The sites also needed to be accessible to all people, near bus lines and parking and close to where students live.
With the help of others, including Abbas Piran, director of the facilities technology group in Facilities Services, Barzin found spacious and adaptable sites at three locations: the Frank Porter Graham Student Union, UNC Rams Head Recreation Center and CURRENT ArtSpace + Studio at Carolina Square. Three locations may overshoot the team’s estimation of the daily number of people coming through, Barzin said, but he had his reasons for choosing three locations.
“In a medical setting, you want to do things that are replicable and controlled,” Barzin said. “You can get into an environment where you have more and more and more, but at some point you may lose efficiency and lose consistent ability to do quality controls. The more space you get, the more people you have to train and have at the site. So, there’s variability and consistency in making sure it’s done the right way all the time.”
Whether participants are driving up or walking up, Barzin learned from the Chick-fil-A consultant, the goal is to serve people in stages leading up to the payoff. At Chick-fil-A, customers order, pay and receive a sack of sandwiches. At Carolina’s testing sites, students and employees register with HallPass, receive a test kit and self-administer the nasal swab. The payoff is different, Barzin said, but the flow is similar.
They designed each site to require a couple of fulltime staff and a handful of workers from the Carolina COVID-19 Student Service Corps, a group of more than 400 undergraduate and graduate volunteers supported by the Office of Interprofessional Education and Practice.
Workers direct students to tables displaying test tube holders and bins in which to place their sealed specimens. Each center’s maximum capacity corresponds with the number of tables, anywhere from 15 to 18.
The team designed the sites to move people through safely and quickly. Hand sanitizer is available. Testing stations are 6 feet apart. Industrial-size particulate air filtration units circulate the interior air 24 hours a day. Plus, workers wipe down the testing stations on a regular schedule.
“We wanted to make sure that we were doing anything above and beyond that we possibly could,” Barzin said. “We want everyone to feel comfortable and safe and know that we respect them.”
Managing all that data
Early last November, Hussman School of Journalism and Media Associate Professor Steven King was returning from a fall baseball game with his children, when he got a call from Rick Wernoski. The senior vice provost for business operations told King about the beginnings of a plan to build a University COVID-19 testing program for spring. The program needed a secure, user-friendly, digital data management system to connect all the dots.
“He asked if it was remotely possible to build the system in such a short amount of time,” King said. “I told him, ‘I guess it is possible, but I sure don’t want to do it!’”
An hour later, King was on the phone with Mike Barker from ITS hashing out how their teams might work together on what would eventually be dubbed HallPass. Despite his trepidation, King was all in. Barker’s team would take care of the core infrastructure systems, integrations and data flows. King and his team in the Reese Innovation Lab would design the user experience, user interface and the application’s interface with mobile devices’ hardware.
They had two months to pull off what Barker believes would usually take a typical information technology project team at least a year to build.
“When there’s a need, we come together and find solutions. We don’t think about how we can’t do something. We figure out how we can do it. Any time University units come together, you can make magic happen.”
— Cheryl Stout, Transportation and Parking manager
Think of HallPass as the nervous system of the Carolina Together Testing Program. Without HallPass, there would be no way for students, faculty and staff to self-administer their weekly COVID-19 tests, set up testing appointments or receive text notifications with their results.
Above all, HallPass had to be secure. Barker knew that user privacy was essential for widespread adoption. He wanted to establish HallPass as a point of certainty in a tumultuous time.
“Part of what HallPass and the Carolina Together Testing Program are doing is giving some peace of mind in these fraught times. That peace of mind would be undermined if we did not attend to privacy issues, with singular focus and comprehensive due diligence, as a bedrock principle,” Barker says. “We do not compromise nor cut corners when it comes to protecting peoples’ personal information. Period.”
For that reason, the team chose to create a web-based application rather than a mobile application. Since the web-based application isn’t downloaded to any device, HallPass doesn’t contain any geo-tagging or tracking features, only the address listed under contact information, said Ethan Kromhout, director of applications infrastructure in ITS and one of the HallPass developers. Not only are web-based applications quicker and easier to build than mobile applications, they also automatically download any software updates, so users will never have to update HallPass.
Any medical data associated with a user is also protected by rigorously segmenting sub-systems and partitioning data.
“HallPass contains no health information at all. The most sensitive information stored on it is student schedules, addresses, phone numbers and names,” said Matthew Mauzy, emergency response technology manager in the Office of the Chief Information Officer. “The test results are contained in what’s called a lab information system that all operates on a completely separate set of networks that are partitioned from anything that is related to HallPass to keep medical information private and secure.”
Among the many programming challenges: writing an algorithm to classify users so they are prompted to get tested the correct number of times per week. King said his team’s best programmers, together with ITS staff on the Identity and Access Management and ConnectCarolina teams, had to work through complex logic to differentiate between off-campus an on-campus students or employees working on-campus versus remotely, and then calculate their exposure risk factor and direct them to be tested either weekly or twice weekly.
“Without exaggeration this is the most complex application with the highest stakes that I have ever seen built in such a short amount of time,” says King. “The teams have worked countless hours and sacrificed sleep and family to get us to a successful launch day.”
As that launch day approached, new logistical challenges arose. One example: moving test kits between the lab and the collection sites.
“We were bumping our heads against the wall,” Barzin said. “We said, ‘Let’s ask Transportation and Parking if they can help us.’
Transportation and Parking Manager Cheryl Stout remembers getting Barzin’s call. She convened her different managers — point-to-point, parking services, parking control, pay operations — and they got to work.
Eight hours later, Stout called Barzin back. Her team had mapped out everything and more: staff parking, visitor parking, sample transportation access. They secured a vehicle from Facilities Services and provided drivers for the pick-ups and drop-offs. They even penciled a dry run onto the calendar.
Barzin was elated.
“They were very appreciative,” Stout said, adding that she was happy to help. “I have one of the best teams on campus, and when there’s a need, we come together and find solutions. We don’t think about how we can’t do something. We figure out how we can do it. Any time University units come together, you can make magic happen.”
The weekend before the testing program’s soft launch, Chancellor Guskiewicz and Executive Vice Chancellor and Provost Bob Blouin toured the new PCR lab in the Genome Sciences Building and marveled at the Amplitude.
But Guskiewicz said it was the people who made the biggest impression on him — Barzin and Loftis, the lab techs and a handful of Carolina COVID-19 Student Services Corps members busily packaging the swabs and vials for the test kits in preparation for the Jan. 11 launch. “I felt very proud to see how committed the community is to joining arms to tackle this problem,” Guskiewicz said.
The day of truth arrives
On the morning of Jan. 11, the Carolina Together Testing Program got underway. Students and employees entered the Student Union, the first collection space to open, and were greeted by staff and volunteers, who directed them to more than a dozen well-spaced testing tables. A large white HEPA filter sat in the corner, scrubbing the air.
Each person through the door grabbed a test kit, scanned the barcode label into the HallPass web app and swabbed their own nose. That first day, more than 600 people got tested. The wait was never very long. By most accounts the process went quite smoothly.
Over at the Genome Sciences lab, things didn’t go so smoothly. The PCR testing itself worked perfectly, but a hiccup with the barcode labels disrupted the automation that had so enamored Barzin during that first wet-run.
Determined not to let a label issue derail the mission, the lab team — including Barzin, Loftis and lab manager Olivia Council, a post-doc research assistant from the School of Medicine’s department of microbiology and immunology — scanned the samples by hand. The going was slow. Barzin got home around 3:30 a.m. (and was back the next morning by 6:30). But the team processed all the samples by the next morning.
By day three, the barcode glitch was fixed, the automation was functioning, and the lab was churning out same-day and next-day test results.
As the week progressed, and more students returned to campus, long lines at the Student Union testing center became an issue, especially during the first weekend of testing. Barzin clocked the wait. He saw people standing in line for up to 35 minutes, which was unacceptable to him and his team. The goal, he said, is no more than five minutes, in and out.
King and Barzin met at the Student Union after hours and mapped out ways to improve the flow. They beefed up the reservation system and created two lines, one for those with reservations and another for walk-ups. “We’re trying to find the right cadence per day to put through each site,” Barzin said. “We’re working continuously to improve the process.”
Barzin has already begun to notice improvements. Even those getting tested are more efficient once they know the system. “Everyone is learning together,” he said. “My hope is over the next couple of weeks as we continue fine-tuning and as people get comfortable with the system, we all get into a rhythm, and the process moves along like clockwork.”
Like those the folks running the Chick-fil-A drive-through, Barzin and his collaborators are continuously seeking to improve the user experience. They’re listening to student feedback, providing updates and sending more staff and volunteers to work the lines. They’re working out software glitches. As of Tuesday, Jan. 19 — a couple days after the weekend’s long lines — they were already seeing improvements. In fact, they completed nearly 75% more tests on Jan. 19 than any prior day.
Despite the hiccups, the numbers from week one are impressive: nearly 7,000 students tested at the three testing centers and seven pop-up testing sites in residence halls across campus, all those lab results processed on campus and promptly reported and volunteer help from nearly 350 students and others who collectively logged over 2,000 hours. Barzin estimates he alone put in 120 hours last week.
“The hours are really, really long,” Barzin said. “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.
“I’m honored to be involved. I love this University. I don’t think I’d be where I am if I didn’t have an undergraduate degree from UNC-Chapel Hill. There’s no greater gift in my mind than giving back to our University community.”
Loftis agreed. “I’m overwhelmingly honored to have an opportunity to do this,” she said. “I’ve given service to Carolina for 20 years, but Carolina has given so much opportunity to me. My UNC family is my chosen family, and I would do anything to help them be healthy and safe. These students need to be able to thrive.”
For more on the Carolina Together Testing Program, read A testing how-to.