Spit Take

How researchers, robots, and a team of hundreds brought IU’s rapid COVID-19 testing to life.

Liz Kaye, for IU Studios.

“I think everybody kind of gulped a little bit when we got the charge to begin to work on this,” Jeff Zaleski admits. “You realized right away the magnitude — knowing how many students are on campus, knowing the gravity of the situation, the severity of the hospitalizations, and what hospital volume we actually have here in Bloomington. We realized quickly how important and significant it could be to do this well.”

The task? Set up a COVID-19 testing lab on the IU Bloomington campus — and get it done as quickly as possible.

Zaleski is interim vice provost for research and associate vice provost for sciences, in addition to serving as a provost professor in the College of Arts and Sciences’ Department of Chemistry. “There was pressure, as the calendar was moving toward the spring semester, to get [IU’s testing] volume up to something like 50,000 samples a week,” Zaleski notes.

IU implemented random COVID-19 testing in August 2020, but officials were relying on an outside lab to turn around approximately 15,000 tests each week.

“Those tests cost 10 times more than when we do it in-house, and it typically took two or three days to get the results back,” says the College’s Executive Dean Rick Van Kooten. “If somebody is tested and they’re positive and they’re walking around not knowing they’re positive for two or three more days, that really exacerbates the spread.”

In fact, those extra days could be deadly. Zaleski began assembling the team.

Lab work

“Craig Pikaard was one of the first ones to look into the actual type of test from the [scientific] literature,” Zaleski says. “He was convinced that we could pull this off from a biochemistry point of view.”

Pikaard is a distinguished professor and the Carlos O. Miller Professor of Plant Growth and Development in the College’s Departments of Biology and Molecular and Cellular Biochemistry. He’s also an investigator with the Howard Hughes Medical Institute. In lieu of the brain-tickling nasopharyngeal swab test, Pikaard’s team devised the implementation of a newer, saliva-based method of testing. The U.S. reported its first COVID-19 death in February 2020 and, one month later, the World Health Organization officially declared COVID-19 a pandemic. In April, the U.S. Food and Drug Administration authorized the use of saliva-based COVID-19 testing on an emergency basis.

Craig Pikaard, who serves as a distinguished professor and the Carlos O. Miller Professor of Plant Growth and Development in the College’s Departments of Biology and Molecular and Cellular Biochemistry.

“My lab members and I did not invent the saliva test,” Pikaard explains. “We adapted it, with only a few technical improvements … from a nice method published by a group at the University of Illinois.”

University of Illinois researchers permitted the IU team to visit and check out their lab.

“They were set up to do testing well before we were, so they shared all of their lab protocols,” says Distinguished Professor of Biology Matthew Hahn, who also directs the College’s Center for Genomics and Bioinformatics. “There’s a lot that goes into it — like barcode systems and collections systems — and we didn’t do everything they did.”

Pikaard, Hahn, and others considered how they could adapt — and scale — the testing protocols. Meanwhile, they’d also need to build and outfit a suitable lab.

Location, location, location

The best candidate was IU’s Center for Genomics and Bioinformatics, which routinely performed genetic analysis and sequencing of material from mice, fungi, and other lower-level organisms.

“That was all available,” Van Kooten says, “but it wasn’t approved for testing human DNA.”

Being able to run human samples would require a time- and labor-intensive Clinical Laboratory Improvement Amendments (CLIA) certification. But first? They would need to build a lab.

“We came from a standing start,” Zaleski recalls. “We had to ask a researcher to leave their lab and renovate the lab as quickly as possible.”

The lab they’d commandeered previously had been used for ancient DNA analysis.

“You basically are getting DNA that’s degraded from old bones,” Hahn says. “It’s very prone to contamination. So, they take all of these precautions and spray bleach on everything.”

Matthew Hahn, who serves as a distinguished professor in the Department of Biology and directs the College's Center for Genomics and Bioinformatics.

Hahn and the rest of the team realized quickly that they’d need to create a new facility from scratch. “We had to rip the entire lab out down to the walls,” he adds.

Furthermore, the former lab had been positively pressured, whereas the new lab would require negative pressurization. That meant reversing the airflow so that the lab’s interior air pressure would be lower than that of surrounding areas, thus preventing potential airborne contaminants from drifting out of the lab.

In addition to renovating the space, they also had to equip it.

“Then,” Zaleski notes, “we had to figure out how to make it as efficient as possible.”

As for the saliva samples themselves, a small technical team would need to be able to process some 4,000 tests daily. Pikaard suggested relying on liquid-handling robots.

“My plan also required that we collect the saliva in much smaller tubes than in the original [University of Illinois] method,” he says.

This would enable running batches of 384 tests at once. But the plans hit a temporary snag. “The availability of the robots was way down, because everybody else was trying to do this at the same time,” Van Kooten says.

Fortunately, Indianapolis-based pharmaceutical manufacturer Eli Lilly and Co. stepped in.

“Lilly loaned us one robot to get going, so that we could at least start working the bugs out,” Zaleski says. “We used that robot from November all the way out through January.”

The lab would need a full staff of humans in short order, too. The team hired David Merritt as COVID lab manager and Sumitha Nallu as laboratory supervisor, among others. Merritt and Nallu, in turn, hired numerous technicians and lab assistants to help with the effort. 

“[Dr. Nallu and Dr. Merritt] also shouldered most of the effort in getting the testing lab established as a CLIA-certified clinical laboratory,” Pikaard notes, “in partnership with Dr. Aaron Ermel at the IU School of Medicine.”

Shayli Ankenbruck (B.L.S. '20) works as a tester during the first day of spring semester 2021 on-arrival testing at Garrett Fieldhouse in Bloomington.

Data dump

With all of this work complete, the team was making major progress, but Hahn remembers, “There’s this whole other kind of infrastructure that had to be built. How do we get students in a building and spitting into tubes?”

Also, how would students be matched to their samples? And how would the samples — and test results — be tracked? Enter Lora Fox.

“I’ve kind of been the go-between,” the director of University Information Technology Services (UITS) Enterprise Business Systems explains. “Obviously, the labs have a big part in this, but we also have a whole team.”

Mid-pandemic, Fox traveled to IU’s regional campuses to switch them to the Bloomington-based lab. “Events went away during COVID, so [IU Events] had the bandwidth to be able to operationalize sample collecting,” she says. Staffers collected samples from COVID-19 mitigation sites, delivered them to IU Bloomington’s lab, and a web-based app helped manage the associated logistics.

“From a technology perspective, we needed to be able to tell students that they were selected to be tested,” Fox says. “We also needed to allow them to schedule appointments to come. And, once they arrived, we needed to be able to check them in and print that label that goes on the vial that then also creates that order for the lab.”

She continues, “Then when that goes to the lab, there’s a whole bunch more technology there that tracks that all the way through the different instruments. At the end, we get an output that’s been brought back into our system that communicates the results to the students. We also have to report those to the state.” 

Real results 

In all, the IU Bloomington lab processed more than 500,000 COVID-19 saliva tests — collected across all IU campuses — from the end of October through May. What’s more, results were provided within 24 hours at a fraction of the usual cost.

“It was about seven months total from the day we had our first meeting to the day when we got CLIA-certified,” Zaleski says. “This was a huge lift for a lot of people.”

He adds, “It really shows you how, when a pressing situation arises, people can drop what they’re doing, rise to the occasion, and do amazing things.”

Susan M. Brackney

Susan M. Brackney holds a B.A. in English from Indiana University. A professional writer since 1995, she has written for Boy Scouts, stoners, interventional radiologists, would-be beekeepers, depressives, the one percent, and many other walks of life. Her work has appeared in The New York Times, Discover, Organic Gardening, Hobby Farms, and Indianapolis Monthly Magazine, among others. Brackney is also a member of the American Society of Journalists and Authors and has published four nonfiction books, including Plan Bee: Everything You Ever Wanted to Know About the Hardest-Working Creatures on the Planet. Reach her at writer@susanbrackney.com.