UNC Charlotte creating data tools to help Department of Defense track pathogen migrations
In combating international threats to public health such as the Zika virus, data could be the most important weapon in the arsenal.
Several U.S. Department of Defense agencies, including the Defense Advanced Research Projects Agency, or DARPA, are working with the University of North Carolina at Charlotte on new data analysis tools created by the university that could help the agency accomplish anything from tracking contagious pathogens to helping anthropologists track population migrations.
UNC Charlotte researcher Daniel Janies, the Carol Grotnes Belk Distinguished Professor of Bioinformatics and Genomics, said his data analysis techniques differ from the dots on a map to which the public might be more accustomed.
“We’re taking DNA and RNA sequences out of the pathogens themselves, and by doing so, we’re analyzing that genetic information to connect all those dots,” he said. “We’ll be able to see how a pathogen is moving over space and time along those connections, and we’ll also be able to see what’s changing – those mutations that make the pathogen resist drugs or become more severe.”
What makes UNC Charlotte such an ideal partner for the project is that the university continues to be one of the nation’s leaders in collecting and analyzing “Big Data.” The UNC Research Opportunities Initiative, or ROI, has provided funding for UNC Charlotte’s Big Data project, and part of the funding has included Janies’ work.
The project reflects priorities in the UNC Board of Governors’ strategic plan, which includes research, technology commercialization, and community engagement. These goals support expanding foundational research and speeding the application of discoveries for greater use.
“Certainly, everything is data-driven,” Janies said. “We need to collect a lot of data, we need to aggregate data – there’s a lot of wrangling. On the computation side, when we create all those connections between the dots, that’s reasonably taxing on the computer, but we’ve gotten pretty good at making it run faster. Then we create visualization of the data to make the results more understandable.”
One of the biggest public health crises of recent years has been the growing threat of the Zika virus, which is most commonly spread by mosquitoes. It’s particularly risky for pregnant women, who could pass the virus on to their fetuses, substantially increasing the threat of birth defects.
“Zika started in Africa, then moved to southeast Asia, then island-hopped to across the Pacific and recently made its way to the Americas,” Janies said. “As it’s doing that, Zika changed to have much more severe disease outcomes. You don’t notice it until it hits a country with a big population, like Brazil. Zika has probably been in the Americas since 2014, but its severe epidemiology wasn’t noticed until 2015, and 2016 is when it really broke out, spreading from Brazil to the Caribbean to the northern part of South America, and now, to Florida and Texas.”
The big question for researchers, Janies said, is what is going to happen this summer – which mosquitoes carry it and where those mosquitoes travel in the United States.
“It’s a very interesting, ongoing, multi-layered story,” he said.
With the migration data available, researchers can look for ways to try to prevent the virus from spreading. Janies noted that the species of mosquito that carries Zika can travel throughout the southeast, including North Carolina, as well as to other parts of the country, including California. Janies said mosquito-control programs have been effective so far against the spread of the virus.
“Here, control has been pretty good,” he said. “It’s the places where there isn’t good infrastructure, like Latin America, where it becomes a big problem because many people don’t have screens, air conditioning, and so forth.”
While the data collection methodology can be applied to pathogens, it’s also being used for anthropological work. The American Museum of Natural History in New York is using similar tools to study human migration patterns across the world by analyzing speech, culture and genetics. DARPA’s role is to help UNC Charlotte and the museum work with other universities and companies involved in research to work together using the data collection tools.
Written by Phillip Ramati