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Feature - Swine flu and the grid: A researcher's view

Feature - Swine flu and the grid: A researcher's view

As the name suggests, "Swine Flu" may have its origins among pigs, and then may have made the jump across species to humans. Image courtesy Janne Brodin, stock.exchng

(Editor's note: Swine Flu - or H1N1 influenza A - has been in the headlines lately. The World Health Organization has officially classified the latest outbreak a "pandemic," in response to its world-wide geographic spread. To find out more about how the grid fits in with research to fight this virus, we asked Ana Lucia Da Costa of HealthGrid, who formerly worked at CNRS France, to give her viewpoint from the lab.)

The emergence of a new influenza epidemic such as this is an opportunity for the grid to contribute to international public health response. It has highlighted the importance of providing the right information to decision-makers as quickly as possible.

Grid technology is particularly well fitted to improving global response to emerging diseases, at different levels. The grid provides:

  • a collaborative environment for reliable and secure distributed data management - a key point to solving international threats.
  • the necessary computing resources on demand in case of emergency, allowing us to virtually screen large quantities of new potential drugs ("high-throughput drug discovery") and design new DNA chips for rapid diagnosis.
  • a means to dynamically process the constant flux of new information collected when an epidemic propagates around the world, thus offering online monitoring of a virus's evolution, propagation and mutation.

Based on its expertise from previous experience with WISDOM data challenges on the EGEE grid, the Laboratoire de Physique Corpusculaire (CNRS/France), in collaboration with the HealthGrid Association (France) and research laboratories in Korea and Vietnam, has started to explore several of these lines of research. (See previous iSGTW article on WISDOM.)

The drug Oseltamivir (above), also known as "Tamiflu," is commonly used to block influenza viruses from spreading among cells in the body. Image courtesy Wikipedia

Watching a virus evolve

Considering that there are already a large number of antiviral drugs, such as Tamiflu, that are active against Swine Flu, our priority was not on the search for new drugs but instead focused upon developing tools for monitoring virus evolution.

The idea is to dynamically analyze the molecular biological data available on public databases (such as the Influenza Virus Resource from the National Center for Biotechnology Information, the Influenza Virus Database from the Beijing Institute of Genomics, or EpiFlu from the Centers for Disease Control and Prevention), and use the computing, storage and automatic updating services offered by grid technology. Bioinformatics methods of sequence alignment will highlight mutations on the virus genome that could impact the transmission mechanism, pathogenicity (ability to cause disease) or drug sensibility.

In addition, analyses will characterize swine flu's evolutionary history on the genetic tree of life - key to understanding the geographic and molecular source of this outbreak. Work is in progress for database management and deployment of a workflow for these analyses on the grid using the WISDOM production environment.

As well, discussions are starting with bioinformatics research teams to "gridify" computing methods - which could be used to more rapidly produce the thumbnail-sized silicon wafers with microarrays (alias "DNA chips," or, more loosely, "laboratory on a chip") that identify the genetic thumbprints of new virus strains. Quick diagnosis of a new strain is extremely important to quantify the outbreak and to monitor its evolution.

Reducing the delay to produce a quick diagnosis may influence very significantly the quality of early data made available to health policy makers. The grid has not really had any impact on the monitoring of the present influenza A pandemics. Our goal is to be ready to have an impact for the next.

-Ana Lucia Da Costa, HealthGrid/France, for iSGTW

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