DataScience@NIH

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1 Virus Outbreak Tracking Meets Open Data: Exemplar of How Open Science Benefits Public Health
Elizabeth Kittrie / 02.28.17

Today, the National Institutes of Health (NIH), in collaboration with the Wellcome Trust and the Howard Hughes Medical Institute (HHMI), announced the winner of the Open Science Prize. The winning team developed the nextstrain.org prototype for Real-time Evolutionary Tracking for Pathogen Surveillance and Epidemiological Investigation

The winning prototype exemplifies the power of open science by demonstrating how tools that foster the real-time sharing of open data from across the globe can accelerate the tracking of disease outbreaks. 

Nextstrain.org Models Open Science

Viral pathogens such as Zika and Ebola are threats to global public health, causing millions of infections and tens of thousands of morbidities (such as birth defects) and mortalities. Genome sequences of viral pathogens can provide exceptionally valuable insight into the spread of such epidemics, but to be useful and actionable, samples have to be collected, analyzed, and the results openly disseminated in near real-time.

At present, however, such speed is not possible.

Most of the available genome sequence data for viral pathogens resides in disparate databases or in publications made publically accessible long after the epidemic has subsided.  As a result, it can take years to collect and synthesize the information.

To address these challenges, the winning team developed a prototype system to ingest viral genome sequence data from openly available sources, perform rapid phylogenetic analyses to understand the ancestral relationships among those pathogens, and display the resulting phylogenetic trees on an interactive public website. As a result anyone with an internet connection can query the database and examine the spread of disease by country, region, or type of strain. Something that had previously taken years has been reduced to minutes!

The team behind nextstrain.org is led by Trevor Bedford of the Fred Hutchinson Cancer Research Center in the United States and Richard Neher of Biozentrum at the University of Basel, Switzerland. They hope their platform will deliver a customizable snapshot of an epidemic’s history to researchers, public health officials, and members of the public. "We want to build a foundation for groups to share and analyze viral sequences,” said Bedford. “Recent outbreaks of Ebola and Zika have shown that viral genome sequences are only really useful in context and only by comparing across datasets can real epidemiological insights be made," added Neher.

Open Science Prize Encourages International Partnerships

The Open Science Prize was a pioneering effort led by the NIH, Wellcome Trust, and HHMI to foster innovative solutions in public health and biomedical research using open digital content. The Prize breaks the mold around research funding by encouraging international collaborations around shared health data. Traditional funding models typically stop at a country’s borders. As many of the Prize submissions showed, data derived from geographically diverse sources enrich the research process and, in turn, enhance the resulting solutions. The success of the Open Science Prize also points to a cleared path other federal agencies and their partners can follow for funding global research partnerships.

Over the last decade, prize competitions have become a powerful tool for crowdsourcing innovative solutions to complex biomedical research issues. For the Open Science Prize, we opened the submission process to teams from around the world, regardless of background or affiliation. Submissions came from 96 teams totaling 450 innovators, including university researchers, small businesses, and citizen scientists. At all stages of the contest we invited public input, with 3,700 votes from 76 countries guiding our selection of the three finalists.  The judges selected the winner based on potential impact, degree of innovation, and perceived utility of the prototyped tool.

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