Epidemics"Networking" turns up flu virus tied to 2009 pandemic

Scientists using new mathematical and computational techniques have identified six influenza A viruses that have particularly close genetic relationships to the H1N1 “swine” flu virus that swept through the United States beginning in the spring of 2009. That virus eventually killed almost 18,000 people worldwide.

Biological studies focused on these strains of influenza virus could shed light on how the 2009 pandemic strain of influenza emerged, aiding in efforts to forestall another pandemic, the researchers say.

Five of these viruses were isolated from pigs, and the sixth had infected a human who worked with hogs.

The researchers arrived at these strains by using powerful computers to analyze the relationships between the genomes of more than 5,000 strains of influenza A that have been isolated over several decades and recently sequenced. Rather than using the conventional approach of constructing phylogenetic trees that illustrate organisms’ hypothetical ancestors, these scientists set up a network that captured paths leading from previously observed viruses to contemporary viruses.

A Ohio State University release reports that biologists for years have used a tree to trace how viruses change over time by undergoing mutations, some of which allow them to resist attacks from immune systems or drugs, jump from host to host and keep surviving. But viruses also exchange genetic material with contemporaries, most commonly when two or more strains infect the same host. This process is called reassortment, and this computer-based networking model is a novel way to see how it all happened in influenza in over time.

“It’s not unlike a social network, except that it’s tracking an exchange of genetic material rather than gossip,” said Daniel Janies, associate professor of biomedical informatics at Ohio State University and a co-author of the study. “This network gives us an explicit historical and molecular map of how influenza A viruses evolved from several ancestors to modern-day viruses.”

Janies conducted the work with Ohio State co-authors Shahid Bokhari, a research professor of biomedical informatics, and Laura Pomeroy, a postdoctoral researcher in veterinary preventive medicine..

The research is published online in the journal IEEE Transactions on Computational Biology and Bioinformatics

The scientists obtained data on all fully sequenced influenza A viruses available in a National Institutes of Health database as of 15 October 2009. There were 5,016 viruses in all, with isolates dating as far back as 1931.

They then used supercomputers to create a database outlining the differences and similarities