Tool for Tracking Viral Outbreaks Receives Open Science Prize

Due to the devastation they can cause, researchers worldwide continually put their efforts towards getting a leg-up on infectious disease outbreaks. Although many advancements have been made in this area, outbreaks continue to take the world by surprise, leaving healthcare practitioners scrambling to find ways to control infection and prevent further transmission. Luckily, some researchers have been making advancements in making outbreak response a little bit easier.

In fact, the first international Open Science prize was recently awarded to researchers at the Fred Hutchinson Cancer Research Center and the University of Basel for a software tool that is capable of tracking viral disease outbreaks, such as Zika and Ebola, in real-time.

The software tool, “nextstrain,” was developed by Trevor Bedford, PhD, an evolutionary biologist at Fred Hutch, and Richard Neher, a computational biologist from Biozentum Center for Molecular Life Studies in Basel Switzerland, to “analyze and track genetic mutations” throughout the Ebola and Zika outbreaks.

According to Dr. Bedford, anyone can use the platform to “download the source code from the public-access code-sharing site GitHub to run genetic sequencing data for the outbreak they are following through the pipeline.” They can then build a webpage that consists of a phylogenetic tree, which will illustrate the “genetic history of the outbreak,” a process that takes only a few minutes.

With the $230,000 prize money, Drs. Bedford and Neher aim to make their platform adaptable to tracking any virus, whereas right now, the tool is mainly used for Zika and Ebola. Dr. Bedford notes that making their platform adaptable to follow other viruses will take a great deal of work, which is why he is currently working with a web developer.

In the press release, Dr. Bedford further explained the goal of their efforts. He said, “Everyone is doing sequencing, but most people aren’t able to analyze their sequences as well or as quickly as they might want to. We’re trying to fill in this gap so that the World Health Organization or the 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.”

Another goal that the researchers have is to encourage other researchers in the field to be more open about sharing their data, a notion that is central to the “open science” movement. Supporters of the movement believe that the sharing of “preliminary information” can lead to speedy discoveries that can improve human health.

As the name suggests, the competition for the Open Science Prize worked to encourage the development of “ground-breaking tools and platforms” that would make sharing and finding research or datasets easier, as well as to stimulate “excitement, momentum, and further investment.” Nextstrain “is an exemplar of open science and will have a great impact on public health by tracking viral pathogens,” according to Robert Kiley, lead of Wellcome’s work on open research.

Right now, nextvirus is “more of a now-cast,” according to Dr. Bedford, “but we really want to be doing a real-time forecast of what’s going on with an epidemic.”

There are many reasons why real-time tracking of genetic mutations that occur throughout infectious disease outbreaks can be particularly useful. With real-time tracking scientists can better understand what makes certain viruses “so severe,” and then they can use their findings to strengthen public health efforts regarding outbreak response. The only issue is that in order to do this, researchers would have to openly share their “genetic sequencing data,” something they may not do due to the “competitive world” they work in where they may instead opt to publish their findings “in prestigious journals and stake claims to discoveries.”

Despite the fact that some researchers are hesitant to participate in data sharing, the 2013-2016 Ebola epidemic proved how effective a platform such as nextstrain could be. According to the press release, earlier in the outbreak, researchers “sequenced Ebola genomes from patients and immediately uploaded them to the public database GenBank,” which led to “a surge in collaboration” amongst a number of experts in different fields. The collaborative effort that resulted in the open sharing of data helped the researchers “answer critically important questions as the outbreak was unfolding.” In fact, the sharing provided researchers with a wealth of vital information that was used to inform public health and medical interventions, such as insight into possible transmission routes and where and how fast the genetic mutations were occurring.

Unfortunately, it seems that less researchers are sharing their data regarding Zika virus genome sequencing, showing that outbreak response to Zika virus differs from the response to the Ebola epidemic. Gytis Dudas, PhD, a postdoctoral fellow in Bedford’s laboratory who worked on a number of Ebola analyses in the past noted, “I’m not seeing the same thing with Zika.” This may be because Zika is harder to sequence than Ebola, which might be the reason researchers are not sharing their data; they may be saving their sequences for publications, Dr. Dudas suggests.

Dr. Bedford conceded that he understands that publishing is very important. However, he concluded, “The idea is that this nextstrain platform would provide some neutral ground with which to share data." He added, "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."