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As COVID-19 Gripped the World, NCSA Stepped Up to Make SHIELD a Success

A close up photo of a saliva test tube held by a Black U of I student.

Saliva test closeup. Credit: UI Public Affairs, Fred Zwicky.

In the fall of 2020, COVID-19 raged across the nation, no vaccines were yet available, and many college campuses sent their students home and resorted to online-only learning to keep the disease from spreading.

But at the University of Illinois and in the Champaign-Urbana community where the university comprises about 25% of the population, the story was different. The university, with a student population of more than 50,000, opened as planned in the fall and reported zero hospitalizations or deaths that semester. In the surrounding community, COVID-19 positivity rates generally stayed below 0.5%, with minimal transmission from the campus to the surrounding community.

“If you look at a map of COVID cases from those days, Champaign-Urbana was a little bubble where testing rates were much higher and transmission was minimized,” said Chris Pond, head of the scientific databases group at the National Center for Supercomputing Applications at the University of Illinois at Urbana-Champaign. “Our community was doing more tests than the rest of the country. It was a big accomplishment for a cause. The potential impacts motivated us.”

A mockup of the now retired Safer Illinois app on a smartphone screen.
The now retired Safer Illinois app provided a wealth of COVID-19 testing-related information across the University of Illinois campus in 2020.

Pond played a key role in the development and deployment of SHIELD, a three-pronged “target, test, tell” system that incorporated COVID-19 testing with data reporting, modeling and a smartphone app to enable exposure notifications and isolate anyone who tested positive. University researchers made a key breakthrough in summer 2020 when they developed a rapid, saliva-based COVID-19 test that made fast and frequent large-scale testing possible. The test required only a small amount of saliva and returned results within 24 hours.

However, the test was only a first step. Once the university had a testing system it needed a way to communicate results with students and staff. In addition, the system for managing tests – called a laboratory information system or LIMS – was adequate for the campus, but couldn’t easily scale up for testing in the community, the state or across the country. SHIELD became more than a campus COVID-19 testing strategy because NCSA was able to deliver technologies, software, hardware and modeling expertise to create a system that could track test data through the lab, deliver test results and notifications of exposure quickly, and produce models that could identify vulnerable populations and hotspot locations.

“The campus came to us on a number of fronts,” said Kenton McHenry, associate director of software at NCSA. McHenry’s group was already working on Rokwire, an open-source platform for creating mobile apps that was developed for use in the university’s Smart, Healthy Communities Initiative when campus leaders asked NCSA Director Bill Gropp to focus the center’s expertise on standing up a mobile app to manage COVID-19 test results and perform exposure notifications. As experts in the Grainger College of Engineering set out to build mobile testing labs to expand the testing system, campus officials turned to NCSA to develop a LIMS to manage the data pipeline from testing in the mobile labs through delivery of results to individuals. NCSA staff also worked on modeling to better understand community risk factors and pinpoint potential hotspots, and agreed to host data on Nightingale, the center’s HIPAA-compliant server.

Small Teams, Fast Work

To move quickly and cost-effectively, NCSA quickly assembled several small teams to work on different aspects of the larger SHIELD effort. 

“It was a big request, and we had a lot of people working on more than one thing at once,” said McHenry. “Rokwire was leveraged for exposure notifications and to provide test results. It just evolved from there to doing modeling to find vulnerable spots and populations, a LIMS system, and a place to store data that was HIPAA compliant.”

While commercial LIMS could have performed lab management functions for SHIELD labs, those systems can be extremely expensive and making them operational can take months, according to Pond. His group created the LIMS for managing the mobile labs, called mobileSHIELD, and McHenry’s team focused on adapting Rokwire so it could communicate with the LIMS and report information back to students and community members. Programmers and scientists in NCSA’s genomics group contributed to the project by creating models using data from surveys of students, faculty, and staff as well as test results.

The LIMS work enabled the university to spin up several versions of SHIELD beyond the UIUC campus testing. The first, called SHIELD CU, was a version for testing the Champaign-Urbana community, the second, called SHIELD Illinois, expanded the testing program across the state and the third, called SHIELD T3, was a commercial endeavor supported by the university that took the test nationwide through mobile labs.

“The workflow for the mobile lab was being worked out as we developed the software,” recalled Chris Stephens, lead database administrator who worked with Pond and Senior Research Programmer Steven Peckins to build the LIMS. “The timeframe was so tight that we had to make progress on the LIMS before the lab design was finalized. Honestly, it was the most stressful, most rewarding, most time-consuming project I’ve ever been on.”

Pond and his team began developing the LIMS in August 2020. By November, they were using it in a demonstration lab and by December, it was in use in a commercial lab in California and at the University of Wisconsin. The LIMS manages the lab process workflow from receipt of saliva samples to delivery of test results. Pond estimated the system handled about 5 million tests.

 “We used open-source tools and Amazon Web Services to develop our LIMS system,” said Pond. The key for the LIMS was to have something that was HIPAA compliant and reliable, and could integrate with healthcare systems to get test orders and communicate with the mobile app to report results.”

In a separate but related effort, the scientific databases group pulled data from campus testing and surveys into the secure environment of Nightingale so it could be used to create models and for future research. All data were voluntarily collected and are still available to researchers. NCSA staff members work with them as needed to help them access the data, said Pond.

The genomics group created novel algorithms to analyze the data and assess risks, allowing campus administrators to offer guidance on how to stay safe. 

“The models were to assess comparative risk based on behavior,” said Weihao Ge, a research scientist in the genomics group. “We created a bar chart to tell students what was safe and what wasn’t and that was given to all instructional faculty and available in all classes.”

The modeling confirmed much of what we now know about COVID-19 and how to prevent its spread. For example, social distancing and masking were shown to be effective. Going to bars or the gym increased risk, but in-person classes and testing while following campus safety measures were generally safe.  

A Collaborative Effort Pays Off

The effort of the NCSA teams was nothing short of herculean. Stephens estimated the LIMS team worked as many as 70 to 80 hours a week in late 2020 and early 2021, including through the holiday break. The team continuously tweaked and improved the LIMS, fixed problems that were often caused by technicians struggling to rapidly learn the new system, and added workflow checks and data validation at lab stations to ensure technologists used the system correctly.

“There were at least three times I pulled an all-nighter before a new release,” recalled Peckins. “The stakes were high. I didn’t want to be responsible for misreporting someone’s health data.”

Sandeep Puthanveetil Satheesan, the senior research programmer who led the NCSA team that contributed to the development of the Rokwire platform and its integration with the LIMS, said his main challenge was working in an environment with constantly changing parameters while dealing with the impacts of the pandemic on his own life.

I think I am most proud that I contributed to something that had a major and quick impact on people’s lives at the university, in the community and, in some cases, beyond. I am happy that I was able to rise to the occasion and join hands with the rest of the folks at NCSA and the university to do our part in mitigating COVID-19.

Sandeep Puthanveetil Satheesan, Senior Research Programmer, NCSA

The NCSA teams worked collaboratively across campus, navigating the pressures of tight deadlines and many unknowns.

“I’ve never been part of a project that was developed in flight and where the stakes were so high,” said Christina Fliege, technical program manager of the genomics group. “We were able to put an oar in the water and just go. It was such a valuable experience.”

The hard work paid off; in addition to keeping the university open when many campuses were forced to close and reporting zero COVID deaths or hospitalizations, the work led to a paper published in Nature Communications. That paper, with chemistry professor Martin D. Burke, Ph.D., as the lead author, reported that Champaign County observed a statistically significant lower number of COVID-19 cases than predicted and the county reduced COVID deaths more than fourfold compared to expectations from July through December 2020. Additionally, the NCSA LIMS development team won two awards at the 2021 International Conference on High-Performance Computing Networking, Storage and Analysis for best use of high-performance computing in the cloud.

SHIELD team leaders posed for a group photo on campus. From left to right: Timothy Fan, William Sullivan, Martin D. Burke, Nigel Goldenfeld, Rebecca L. Smith and Paul Hergenrother.
Some of the SHIELD team leaders, from left: Timothy Fan, William Sullivan, Martin D. Burke, Nigel Goldenfeld, Rebecca L. Smith and Paul Hergenrother. Credit: UI Public Affairs, Fred Zwicky

“When you find the right group of people, it’s amazing what a small group can accomplish,” said Pond. “NCSA has all these really talented people. When you pair them with researchers on campus it’s pretty amazing what we can achieve.”

Added McHenry, “Many of us are a new breed of software engineers, globally calling ourselves Research Software Engineers (RSEs), that live in the academic environment and are embedded into research efforts. We could make more money in industry, but instead, we have pursuits similar to our researcher colleagues: inherent curiosity, a strong desire for impact and recognition, and overall wanting to make a difference. 

“This project showed how important these kinds of people are to science and how valuable and versatile an organized university body of RSEs can be.”

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