Three laboratories, two located in Utah, announced a collaborative effort to investigate the molecular evolution of the Sars_CoV-2 virus by analyzing the genetics of COVID-19. How are they doing it? Using specimens from Utah’s positive COVID-19 tests.
“We're looking to really get a good idea of how the virus has gotten to Utah—how it's spreading in Utah, how it's evolving in Utah, and then even hopefully get to the point where we can start acting in real time to say, 'hey, look, we got a hotspot coming up here. How can we get in there and target that area and stop that from spreading?'” said Dr. Kelly Oakeson, a chief scientist for next generation sequencing and bioinformatics from Utah’s Public Health Laboratory.
His team is using their experience in tracing food pathogens, like recent e coli outbreaks in lettuce, to sequence the genetic makeup of the virus causing COVID-19. They are working with the state’s ARUP laboratories and Gingko Bioworks of Boston—a collaboration that’s essential because so many samples are needed.
“Utah is probably one of a handful of public health departments that have undertaken this,” said Oakeson. “The public health labs are well situated for it. Every public health lab in the nation has at least one next generation sequencer in the building that they've been using for CDC’s foodborne illness surveillance program, PulseNet.”
Not all labs have the personnel time and expertise to generate and analyze all the data, according to Oakeson. So, he and his team have also been helping other states, especially neighboring western states, to get that knowledge. Analyses are sent from public health labs, industry, and academia, to the CDC SPHERES consortium, an open source collaboration to share information and strengthen mitigation response to COVID-19.
“That's one of the reasons why everybody across the world is trying to make all this data as publicly accessible as possible, as it can have very big impacts on vaccine development and on therapeutic development as well,” Oakeson said. “So there are those direct impacts and there's also you know a future planning. If we can understand how this happened, understand how it spread, we could use that information to plan to prevent future pandemics.”
