"Networking" turns up flu virus tied to 2009 pandemic

in the genomes among all of these strains, coming up with about 100 million ways in which the genomes differed from each other. Finally, using the highly specialized Cray XMT supercomputer at the Pacific Northwest National Laboratory that was guided by their own algorithms, the Ohio State scientists churned out a network that efficiently tracked how all of these influenza A viruses are related to each other and which paths through the network led to pandemic H1N1 of 2009.

Discovering commonly traveled paths in the network helped the researchers identify what they called the “bottleneck” viruses – the six strains of flu most closely related to the pandemic H1N1 flu that emerged in 2009.

“These viruses just popped out at us,” Bokhari said. “We found that 3,600 out of almost 4,000 paths to pandemic H1N1 were passing through these six bottlenecks. That threw up a red flag and said there is something unusual about these six.

“These bottlenecks are the culprits just a few steps removed from the virus that caused the pandemic among humans. Biologists are encouraged to look at these viruses to determine what underlies the emergence of animal diseases in humans.”

The release notes that four of the bottleneck viruses were H1N2 strains isolated from pigs in China and Hong Kong between 2005 and 2007. Two H1N1 strains were isolated in Kansas, in a pig in 2007, and in Iowa, in a human who worked with swine in 2005.

All of these viruses reassorted with a Hong Kong-based H1N1 strain isolated in 2009 before the pandemic strain emerged.

Reassortment refers to an exchange of genetic material by two organisms. When viruses infect a host, they land on a cell surface and release their DNA into the cell. This effectively hijacks the cell’s internal replication machinery and forces the cell to make a new version of the virus rather than a copy of itself. If two or more viruses infect the same cell, then the DNA segments inside the cell are mixed, or reassorted, and the cell is tricked into creating an altogether new virus that contains genetic material from the original set of viruses.

“Reassortment is another way for viruses to evade our immune system,” Janies said. “They shuffle the deck, and there are few controls on it. This sloppy process is perhaps an advantage for the viruses. The genes regroup in a new virus to get to the next pig, or person, to survive.”

This network approach to studying the evolutionary history of organisms that exchange genes can be applied to other species as long as the genomic data are available, Bokhari noted. The researchers hope to use the model next to study how bacteria become resistant to antibiotics or become very pathogenic.