Tracking pathogens in real time

A press release at Scientific Computing: Supramap, a powerful new Web-based application that tracks pathogens in time and space as they evolve, is designed to help public health officials and national security experts predict and respond to outbreaks of infectious diseases. Operating on parallel programming on high-performance computing systems at Ohio State University and the Ohio Supercomputer Center, Supramap allows any user to input raw genetic sequences of a pathogen’s strains and build an evolutionary tree based on mutations.

The branches are projected onto the globe with pop-up windows to show how strains mutate over space and time and infect new hosts. “This tool has a lot of predictive power,” says Ward Wheeler, curator in the Division of Invertebrate Zoology at the American Museum of Natural History. “If the movement of a pathogen is related to bird flyways, for example, and those routes are shifting because of something like climate change, we can predict where the disease might logically emerge next.”

The program was officially announced on April 9, 2010, in a paper in Cladistics. In the research paper, Wheeler and colleagues test Supramap’s capability on recent strains of avian influenza (H5N1). The evolutionary tree, based on 239 sequences of the specific gene polymerase basic 2, shows that host shifts are highly correlated with a specific gene mutation that allows avian viruses to adapt to mammalian hosts.

“We package the tools in an easy-to-use Web-based application so that you don’t need a Ph.D. in evolutionary biology and computer science to understand the trajectory and transmission of a disease,” says Daniel A. Janies, first author of the paper and an associate professor at Ohio State University.

Supramap depicting the westward spread of avian influenza (H5N1). Red tree branches indicate a genotype of lysine (K) at amino acid position 627 in the PB2 protein, which confers increase replication in mammals. White tree branches indicate a genotype of glutamic acid (E), the wild type for H5N1. Mutations at each node can be viewed in pop-up windows. Image and caption from the Scientific Computing website