At UT’s Texas Advanced Computing Center (TACC), 448,448 processing cores of the world’s fifth-largest supercomputer, Frontera, transmit signals back and forth, twinkling like the command center of a spaceship. Across the world, hundreds of scientists log into the mainframe, creating simulations as grand as a replica of the city of Austin for tracking the coronavirus’ spread, and as microscopic as a model of the virus itself that can help vaccine scientists destroy it.
After campus shut down on March 13, many UT scientists, deemed essential, continued operating in their near-vacant labs on the Forty Acres, racing at warp speed to arm the city against the virus. Apart from using the ultra-powerful Frontera, UT researchers are making smaller-scale efforts—from designing medical equipment for respiratory therapists to translating a COVID-19 handbook to Spanish—across campus.
In mid-March, associate professor of molecular biosciences Jason McLellan published a research paper in Science mapping a beastly part of the virus’ external surface called the spike protein, which it uses to weaponize itself as it hunts for cells in the body.
Once McLellan’s structure of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein became available, Rommie Amaro, a biochemist at the University of California San Diego and a team of scientists began turning this viral “snapshot” into a 3-D image. Their goal, using a model involving 2 million atoms, is to find a weakness in the virus’ defenses, so that vaccine and drug developers can create products to target them.
“When the virus is inside of you, this spike protein is hunting for the right type of cell in your body to make a connection with to get inside the cell,” Amaro says. “If we can understand in a ton of detail what that interaction looks like, we have a better chance to design things that will stop the virus from working.”
While the nation’s top infectious disease expert Anthony Fauci estimated the COVID-19 vaccine development process could take a minimum of 12-18 months, UT scientists have been pushing the envelope in preclinical research and finding solutions in unexpected subjects—including a Belgian llama named Winter. In May, McLellan and a graduate student in his lab, Daniel Wrapp, published a paper in Cell that found an antibody specific to the llama (and other camelids, like alpacas) can neutralize SARS-CoV-2 and prevent it from infecting cells. If replicated in studies with rodent and human subjects, these antibodies potentially could be used to treat people infected with COVID-19.
Meanwhile, a team of researchers led by professor of integrative biology Lauren Meyers has developed an “SEIR” model that identifies susceptible, exposed, infected, and resistant areas of Austin. This simulation uses transmission patterns of the virus itself and behavioral patterns of how the population moves around the city.
Researchers, in collaboration with public health officials, can measure the impact of loosening social distancing guidelines by adjusting various parameters in this model and testing different scenarios, says TACC Director of Health Analytics Kelly Granier, who works with data visualization on many of Frontera’s models.
“There is a lot of pressure to get answers,” Granier says. “What keeps us up at night and gets us up very early in the morning is the fact that we live and breathe the death numbers every day. We are trying to keep those numbers from getting any bigger.”
While scientists at TACC track the spread of the virus virtually, a group of UT epidemiologists are using contact tracing to monitor its spread on the ground. The process, eerily similar to how the public health officials operate in the 2011 film Contagion, involves identifying exposed patients, calling them, and having them recall the people they interacted with, sometimes using text messages or even credit card statements.
Darlene Bhavnani, an epidemiologist at the Dell Medical School, leads more than 100 contact tracers, who each ring anywhere between 10-50 COVID-19 positive patients a day. Working in partnership with Austin Public Health, Bhavnani emphasizes the essential role contact tracing plays in tracking and preventing the virus’ spread.
“Our priority is to make sure all of a person’s contacts are safe,” Bhavnani says. “That’s the spirit of contact tracing.”
Despite efforts made to contain the virus, it has continued to ravage the country, overwhelming the nation’s hospitals and health care force. Images posted by physicians on social media in March and April showed deep grooves of facial bruising from having to wear unfitted or reused face masks. Without adequate protective equipment, providers risk contracting the virus.
That’s what motivated Texas Inventionworks director Scott Evans to design a durable, comfortable mask for Dell Medical School physicians. His product, created in collaboration with a software company that is undisclosed as of press time, maps the contours of a clinician’s face using an iPhone app, which is then made into a customized shell through 3-D printing. Then, the masks are sent to their team of engineers for a final fit test. The precision with which the machinery works is high stakes: One millimeter too large and SARS-CoV-2 particles could seep through the mask and infect the wearer.
“The normal product development process [includes] run-through testing with potential users and subjecting the masks to dropping, pulling, and high temperatures,” Evans says. “The challenge is accelerating that to where 12 to 18 months of activity is compressed into one.”
Mo Maniruzzaman, the principal investigator of the PharmE3D Lab, is also using the available materials in his lab to 3-D print face shields, nasal swabs for testing, and a more patient-focused drug delivery system that can target certain pathogens once they have entered the body. The testing kits have already been approved for clinical use and can be produced rapidly.
“If we could print all of those kits and devices needed for running COVID-19 testing, that would make a significant public health impact not only in Austin or the local community, but the whole state,” Maniruzzaman says.
Meanwhile, at a Texas Innovation Center lab on campus, a moment of inspiration sent an engineer to the scrapyard to collect windshield wiper parts for the Austin Bridge Breathing Unit (ABBU). The product, designed to replace manual resuscitation bags for patients in an ambulance or hospital, has smart features that can monitor and adjust a patient’s breathing across various settings, using windshield wiper motors from Toyota Camrys as its main power source, says Nitesh Katta, MS, PhD ’19, a postdoctoral researcher who is one of about a dozen engineers on the project.
“With ABBU, each attending physician will be able to monitor at least 10 patients at once,” Katta says. “If they had a manual bag, they could only take care of one patient at a time.”
The science behind these engineered products and computational models is intentionally a slow process, typically taking months or years to complete. But the virus’ rapid spread has instilled a sense of urgency in researchers around the world, who are working day and night to condense the process into a couple of short months.
“The virus didn’t take a day off,” Granier, of TACC, says. “In times like these, you can see the worst in humanity, but you can also see the best, and I have certainly been privy to seeing the best in humanity at UT.”
For more, watch “Longhorns in the COVID-19 Fight,” a video series produced by the Texas Exes and The University of Texas.
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