Current thinking is that flu evolves each year in southern China and spreads around the globe. "It's the way they farm, out in the villages," says M. Louise Herlocher. "They keep the pigs in the house, and they raise the ducks right next to the pigs, so there's a lot of opportunity for close interaction of the three species. The theory is that influenza goes from the avians to the pigs, from the pigs to the humans."
In support of that theory, researchers at St. Jude Children's Research Hospital have isolated avian and swine flu genes in humans and avian flu genes in pigs, but they have not demonstrated the presence of swine or human flu genes in birds.
At the Pittsburgh Supercomputing Center, Herlocher is using the Zuker fold analysis program to determine the RNA folding of the smallest (890 bases) flu gene in the three species. It's known as the non-structural (NS) gene, and its function is not well understood. To accomplish this, Herlocher is using 70 genetic sequences -- avian, swine and human -- from a database at St. Jude.
"This may or may not tell us anything about host adaptation," Herlocher says, but the folding may highlight which areas of the NS gene's strand are the same in all three species, information that could in turn help pinpoint which parts of the RNA play an active role in disease-producing functions of the virus.
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