UNM researchers use advanced computing to study COVID-19
A wide range of University of New Mexico researchers from across main and north campuses are utilizing UNM Center for Advanced Research Computing resources to study COVID-19. Researchers from several departments at UNM, including Anthropology, Biology, Computer Science, Pediatrics, Internal Medicine, and various Health Sciences research centers are studying different aspects of the coronavirus pandemic.
Since the US discovered its first case of COVID-19 on January 20th, 2020, scientists across the country have worked feverishly to understand this new and rapidly spreading disease. A collaborative team of researchers including Assistant Professor at the UNM Center for Global Health Daryl Domman, Assistant Professor at the UNM Department of Pediatrics Darrell Dinwiddie, Professor at the UNM Division of Translational Informatics Tudor Oprea, and biologists at the Los Alamos National Laboratory have been using advanced computing techniques to study the genetic variations of SARS-CoV-2, the virus that causes COVID-19. By sequencing the genome of SARS-CoV-2 samples taken from positive cases in New Mexico and Wyoming, the team has been able to track mutations in the virus. Oprea explains, “We’re trying to understand what the trends are with respect to the virus—whether it’s the same virus that came from Wuhan, or, does it mutate? How many flavors of the virus are out there? Do they cause different symptoms?”
Tracking the locations of precise coronavirus strains allows researchers like Domman to understand exactly how the novel coronavirus is spreading. “What we’re hoping to do with this information is really understand the spread of the virus within our community,” Domman reports. He explains, “Traditional epidemiology is about case count data—looking at contact tracing and who might have been exposed. This data is extremely useful but it’s inherently limited in answering questions about how the virus is spreading.”
Looking at which genetic variations of SARS-CoV-2 appear in specific locations can provide additional information beyond counting the number of positive cases in a region. Domman believes that sequencing samples of the novel coronavirus will allow scientists to identify local transmission chains, estimate how long the virus has existed within a community, and estimate how many cases are currently active within a region. Already, this project has revealed important insights into the local spread of coronavirus, including that the vast majority of early COVID-19 cases in New Mexico and Wyoming can be attributed to European travel.
Meanwhile, the New Mexico Decedent Image Database (NMDID), since its website launch in January of this year, has already been a source of valuable information for COVID-19 research. The NMDID is a free resource that gives researchers access to over 15,000 decedent full-body CT scans and a wealth of information about the deceased. CARC houses and maintains the database in collaboration with UNM Associate Professor of Anthropology and creator of NMDID Heather Edgar. Researchers at Johns Hopkins University have been using NMDID to better understand how COVID-19 affects its victims. Edgar reports, “They’re using about 34 or so CTs of decedents who died of pneumonia and comparing [them] to people who have COVID-19—basically looking to see how similar or different the new disease is to the things we’re used to looking at.”
Across campus at the UNM Moses Biological Computation Lab, Professor of Computer Science and Biology Melanie Moses and Research Assistant Vanessa Surjadidjaja are using CARC resources to understand how the human lung responds to a viral pathogen like SARS-CoV-2. “Currently, there is much to learn about how our immune systems are responding to the novel coronavirus. Our research aims to understand how the immune system, specifically T cells, find cells infected with SARS-CoV-2 dispersed in the lung,” Surjadidjaja explains. Their study uses laboratory data and computer simulations to visualize interactions between immune cells and viruses within the complex structures inside the lung. Their goal is to predict how viral load changes over the course of an infection, an important component of disease severity and transmissibility between people.
All of these studies are ongoing and will continue to develop quickly as scientists do their best to make a positive impact during this tumultuous time. Oprea captures the current mood of many research teams when he says, “Everyone works with a sense of urgency. We are well aware that until a vaccine is found, the world will be in stand-by mode. We’re just trying to do our part.” Domman stresses the importance of providing local authorities with the information they need to make prudent policy choices, commenting, “In the more immediate, it’s about providing that actionable data to the folks who will do some good with it.”
Photo: MinION, a portable, stapler-sized DNA and RNA sequencing device, is used in COVID-19 research at UNM. Courtesy of Daryl Domman.
In the news:
Genomic detectives (HSC Newsroom)
Where did the COVID-19 cases in New Mexico come from? (KOAT)
UNM scientists study coronavirus variations for clues about what comes next (KRWG)
UNM scientists track early appearances of coronavirus in NM to Europe, Australia (ABQ Journal)