Supramapping Upcoming Pathogenic Storms

Pathogens like the pandemic H1N1 flu virus can now be as easily tracked as the weather using Supramap, a new web application that maps genetic mutations onto a virtual globe such as Google Earth or NASA World Wind. Here’s a video of a supramap showing the spread of the H1N1 virus:

The green lines in the video represent transmission pathways most strongly supported by the genetic data. Yellow lines indicate less certainty. Other lines are colored differently depending on whether they indicate an incoming or outgoing virus from a specific location.

Supramap is a completely new method of generating and sharing knowledge about evolution and biogeography. A supramap gives researchers a quick and easy way to integrate genotypic and phenotypic data into a geospatial context. “We are taking into account more data but at the same time, we’re making simpler visualizations, allowing users to choose what they want to see,” explains Daniel Janies, associate professor of biomedical informatics at Ohio State and senior author of a study recently published in the journal Cladistics. This study resulted in a supramap of H5N1 avian influenza — the so-called “bird flu” — a type A influenza virus naturally found in certain species of waterfowl and shorebirds.

As described in this Ohio State University news release, Janies’ team took genetic data on all publicly available isolated strains of the H5N1 virus and created a comprehensive, dynamic online map that can be used by health professionals and researchers to predict and monitor the path of a particular pathogen, like predicting the path of a storm front. The research involved the use of supercomputers to construct millions of phylogenetic trees to trace evolutionary relationships that show how viral strains are related based on shared mutations. The H5N1 supramap shows that this potentially deadly virus has been creeping across Asia and into Europe and Africa for more than a decade, picking up mutations along the way.

A medical assistant holds up a H1N1 flu shot at the Health Ministry in Algiers December 29, 2009. Credit: Reuters/Louafi Larbi“The task of preparing for flu pandemics remains urgent, and the world must guard against complacency in the wake of the H1N1 outbreak, which appears less deadly than a potential bird flu pandemic,” states a recent Reuters press release. The occurrence of the highly pathogenic avian H5N1 in Southeast Asia has raised concerns regarding a possible global pandemic. The White House Policy Coordinating Committee for Pandemic Influenza Preparedness and the U.S. Departments of Agriculture and Interior have developed an early detection plan for avian influenza in the United States.

The H5N1 supramap should prove useful in maintaining the vigilance needed to mitigate the risk of a global avian flu pandemic. Dr. Janies claims that the supramap represents the best approximation of avian flu transmission based on the genetic data available — short of obtaining a complete genome of every flu virus that ever infected a bird or human. However, no one map will likely ever fully track the evolutionary relationships, genetic histories, and specific locations of all outgoing and incoming viral transmissions.

Supercomputers construct millions of phylogenetic trees to trace evolutionary relationships that show how viral strains are related based on shared mutations.

“We’ve created an environment where people can avail themselves of flu information specific to their region of the world or their area of interest,” says Dr. Janies. “We waded through all of the complexities so people in the public health realm who want to determine how a flu virus got from point A to point B can find that out, and we’ll have better public health outcomes as a result.”

Influenza is one thing, but man-made pathogenic viruses are on the horizon. Ray Kurzweil and Bill Joy have called for the equivalent of a Manhattan Project, “to develop specific defenses against new biological viral threats, natural or human made.” The use of the Supramap application provides the ability to monitor blips on the pathogenic radar… which will hopefully give us time to prepare for a comin’ storm.

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