Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Open Science to track virus outbreaks

10.05.2016

In recent years, we have witnessed multiple epidemics of viral diseases such as Ebola or Zika. Rapid targeted intervention is key to containment. Real-time data integration and analysis can help public health authorities to maximize efficacy of intervention strategies. Dr. Richard Neher from the Max Planck Institute for Developmental Biology, Germany and Dr. Trevor Bedford from the Fred Hutchinson Cancer Research Center, Seattle, USA, won Phase 1 of the Open Science Prize Challenge for their proposal to develop an online platform for real-time evolutionary and epidemiological analysis. The results will be visualized using interactive web applications that make actionable results accessible.

Viral pathogens are a global threat to public health. Influenza causes an estimated 250,000 to 500,000 deaths per year, and recent outbreak of Zika virus believed to be on track to cause tens of thousands of birth defects.


Evolutionary tree of 1654 Ebola virus genomes and a visualization of the geographic spread of the infection

R. Neher/T. Bedford

Public health officials can only develop effective intervention strategies if the epidemiology and evolution of the viral infections is well understood. Genome sequencing provides excellent insight into the evolutionary and epidemiological dynamics of such viruses. To allow better, more targeted interventions, sequencing data from different groups, scientists or hospitals need to be analyzed in a timely fashion to maximize their value for public health.

This can only be achieved by rapid data sharing. Dr. Neher and Dr. Bedford have thus developed a bioinformatics tool that reconstructs a genealogical tree of the viruses by the mutations they randomly accumulate. “The tool pools data between sampling locations and research groups.

A new sequence can be integrated into our output within 24 hours”, explains Neher. The software is already implemented for influenza (www.nextflu.org) and will now be extended to other viruses.

The platform will be publicly available on www.nextstrain.org and the source code released under a General Public License in order to provide software containers that can also be used by other scientists and rapidly adapted to different diseases.

The tool will infer geographical regions that are sources in driving virus circulation, which can help public health officials to target containment effort such as mosquito control. In addition, the tool will enable tracing of transmission chains, which is vital for disease eradication. Additionally, mutations in the virus genome will be analyzed to identify mutations that are suspected to change the virus transmissibility or pathogenicity.

The platform also aims at motivating research groups to share their data rapidly. “I think that outbreak response is an area in which open science and data sharing can make a huge difference. We aim to have a platform that promotes insights from data without treading on the original data producer’s publication priority”, says Bedford.

The Open Science Prize is a partnership between the Wellcome Trust, the US National Institutes of Health (NIH) and the Howard Hughes Medical Institute to unleash the power of open content and data to advance biomedical research and its application for health benefit.

This first round of the Prize consists of a two-phase competition. For the first phase, international teams competed for funding to take new ideas for products or services to the prototype stage, or to further develop an existing early-stage prototype.

Prizes of $80,000 each were awarded today to successful teams. In the second phase, the phase I prize recipient judged to have the prototype with the greatest potential to advance open science will receive a prize of $230,000.

More information:
http://www.nextstrain.org
https://www.openscienceprize.org/

The web tools for influenza and Ebola will be integrated on nextstrain.org soon:
http://ebola.nextstrain.org
http://www.nextflu.org

Nadja Winter | Max-Planck-Institut für Entwicklungsbiologie

More articles from Life Sciences:

nachricht Another piece of Ebola virus puzzle identified
17.01.2019 | Texas Biomedical Research Institute

nachricht New scale for electronegativity rewrites the chemistry textbook
17.01.2019 | Chalmers University of Technology

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Ultra ultrasound to transform new tech

World first experiments on sensor that may revolutionise everything from medical devices to unmanned vehicles

The new sensor - capable of detecting vibrations of living cells - may revolutionise everything from medical devices to unmanned vehicles.

Im Focus: Flying Optical Cats for Quantum Communication

Dead and alive at the same time? Researchers at the Max Planck Institute of Quantum Optics have implemented Erwin Schrödinger’s paradoxical gedanken experiment employing an entangled atom-light state.

In 1935 Erwin Schrödinger formulated a thought experiment designed to capture the paradoxical nature of quantum physics. The crucial element of this gedanken...

Im Focus: Nanocellulose for novel implants: Ears from the 3D-printer

Cellulose obtained from wood has amazing material properties. Empa researchers are now equipping the biodegradable material with additional functionalities to produce implants for cartilage diseases using 3D printing.

It all starts with an ear. Empa researcher Michael Hausmann removes the object shaped like a human ear from the 3D printer and explains:

Im Focus: Elucidating the Atomic Mechanism of Superlubricity

The phenomenon of so-called superlubricity is known, but so far the explanation at the atomic level has been missing: for example, how does extremely low friction occur in bearings? Researchers from the Fraunhofer Institutes IWM and IWS jointly deciphered a universal mechanism of superlubricity for certain diamond-like carbon layers in combination with organic lubricants. Based on this knowledge, it is now possible to formulate design rules for supra lubricating layer-lubricant combinations. The results are presented in an article in Nature Communications, volume 10.

One of the most important prerequisites for sustainable and environmentally friendly mobility is minimizing friction. Research and industry have been dedicated...

Im Focus: Mission completed – EU partners successfully test new technologies for space robots in Morocco

Just in time for Christmas, a Mars-analogue mission in Morocco, coordinated by the Robotics Innovation Center of the German Research Center for Artificial Intelligence (DFKI) as part of the SRC project FACILITATORS, has been successfully completed. SRC, the Strategic Research Cluster on Space Robotics Technologies, is a program of the European Union to support research and development in space technologies. From mid-November to mid-December 2018, a team of more than 30 scientists from 11 countries tested technologies for future exploration of Mars and Moon in the desert of the Maghreb state.

Close to the border with Algeria, the Erfoud region in Morocco – known to tourists for its impressive sand dunes – offered ideal conditions for the four-week...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

Our digital society in 2040

16.01.2019 | Event News

11th International Symposium: “Advanced Battery Power – Kraftwerk Batterie” Aachen, 3-4 April 2019

14.01.2019 | Event News

ICTM Conference 2019: Digitization emerges as an engineering trend for turbomachinery construction

12.12.2018 | Event News

 
Latest News

Brilliant glow of paint-on semiconductors comes from ornate quantum physics

17.01.2019 | Materials Sciences

Drones shown to make traffic crash site assessments safer, faster and more accurate

17.01.2019 | Information Technology

Ultra ultrasound to transform new tech

17.01.2019 | Physics and Astronomy

VideoLinks
Science & Research
Overview of more VideoLinks >>>