In the midst of viral outbreaks like Zika or Ebola, having the right information at the right time can be crucial. One of the best ways to track an outbreak is by charting the genome of the virus as it spreads, but scientists don’t have an easy tool that allows them to do this.
Dr. Trevor Bedford might have the solution to that problem.
Bedford is an evolutionary biologist at the Fred Hutchinson Cancer Research Center in Seattle, and along with Swiss scientist Dr. Richard Neher, he is the co-creator of Nextstrain: an open source platform that tracks the evolution of viral outbreaks.
Using code from the project’s GitHub page, scientists can turn data on a virus’s genetic material into a map of its evolution. The prototype of the tool has already built maps from data on Zika and Ebola DNA.
Today the project was awarded the first ever Open Science Prize, and along with it $230,000 in funding to build out the Nextstrain platform and make it easy to use for any viral outbreak.
The competition and the funding is an initiative of the National Institutes of Health, in collaboration with the UK-based Wellcome Trust and Maryland’s Howard Hughes Medical Institute (HHMI). The goal is to recognize and invest in global health projects that use open digital content, an approach that could have huge implications for a field that requires almost instant collaboration among scientists spread across the world.
Normally data on epidemics is collected for study and only released weeks or months later when those studies are published by journals. Bedford and Neher are hoping that Nextstrain can bypass that system and help researchers work together to share data in real time.
In a Fred Hutch news release announcing the award, Bedford said the open nature of the project will help scientists turn individual data points on the DNA of a virus into a roadmap on how it is mutating and spreading.
“Everyone is doing sequencing, but most people aren’t able to analyze their sequences as well or as quickly as they might want to,” Bedford said the release. “We’re trying to fill in this gap so that the World Health Organization or the U.S. Centers for Disease Control and Prevention — or whoever — can have better analysis tools to do what they do. We’re hoping that will get our software in the hands of a lot of people.”
But as advantageous as open source projects can be, the competitive nature of academic research means scientists are often hesitant to share data with each other, particularly because of the importance placed on publishing original work.
“The idea is that this Nextstrain platform would provide some neutral ground with which to share data,” Bedford said. “We’re not trying to make a flashy paper. We just want [the data] to be on the website so people can look at the latest thing and do analyses that aren’t stymied by publication practices. This kind of simple sequence sharing during outbreaks is something that if you could just push the [scientific] community a little bit, you could have some real-world impact in helping respond to epidemics.”
The release also notes that, while many scientists have shared their data on the Ebola epidemic, many fewer have shared data on the more recent Zika outbreak. Bedford said he hopes Nextstrain can serve as a tool to make that collaboration quicker, easier and more widely adopted.