Swine Flu Genes From Pigs Only, Not Humans or Birds

The deadly H1N1 influenza virus that’s fueling fears of a global pandemic is a hybrid of two common pig flu strains, scientists who have studied the disease told Wired.com Tuesday. Earlier reports called it a combination of pig, human and avian influenza strains.
The findings may resolve some uncertainty about the nature of the virus, but much is still unknown about its origins and effects.
“This is what we call a reassortment between two currently circulating pig flu viruses,” said Andrew Rambaut, a University of Edinborough viral geneticist. “Why it’s emerged in humans is anyone’s guess. It hasn’t been seen before in pigs as far as I know.”
Rambaut analyzed the gene sequences of viral samples taken from two infected California children. The samples were collected by the Centers for Disease Control and Prevention, and made available to researchers through an international database of flu genomes.
His conclusions were echoed by Eddie Holmes, a virus evolution specialist at the University of Pennsylvania, and Steven Salzberg, a University of Maryland bioinformaticist. Both have looked at the CDC-provided sequences. The CDC could not be reached for comment, but a document released to scientists and obtained by Wired.com affirms their analysis.
Researchers believe the samples from California represent the same viral strain as one that is believed to have killed as many as 150 of an estimated 1,600 hospitalized Mexicans, and caused hundreds more infections worldwide, including at least 64 in the United States. However, as samples from Mexico have not yet been sequenced, the similarity is not conclusive.
The two strains whose genes are found in the California samples belong to influenza families known generally as North American and Eurasian pig flu. The former was first described in the 1930s, and the latter in 1979. The Eurasian strain is generally found in Europe and Asia, rather than North America.
Neither of the strains have ever proven contagious in humans. One of the genes inherited from the Eurasian strain has reportedly never been seen in humans. It codes for the neuraminidase enzyme — the N1 in H1N1 — which controls the expansion of the virus from infected cells.
“The new neuraminidase gene that came in from Asian swine is one we’ve never before seen circulating in humans,” said Rambaut. “That’s one of the reasons it’s spreading rapidly. Very few people will have any immunity to this particular combination, which is what gives the concern that this will be a pandemic rather than just a normal seasonal flu outbreak. It remains to be seen how much and to what extent there is existing immunity.”In medical terms, the genetic origins of the virus may not matter. Whether it come solely from pigs rather than a mix of pigs, birds and humans doesn’t change its immunological novelty.
However, understanding the origins could eventually help scientists determine how the virus evolved and where it originally emerged.
The earliest cases occurred in the town of La Gloria in the Mexican state of Veracruz, not far from a large and notoriously unsanitary hog farm operated by Granjas Carroll, a subsidiary of giant American food company Smithfield Foods.
Vercruz residents and some journalists have alleged that the virus could have evolved in the farm’s pigs, then passed into humans through water or insects tainted by infected waste. Many researchers, including the authors of a report issued last year by the Pew Commission on Industrial Farm Animal Production, have warned that unsanitary conditions at industrial hog farms could prove a breeding ground for new forms of influenza.
The World Health Organization has sent inspectors to the Granjas Carroll farm. The results of the investigation have not been announced. Smithfield issued a press release on Saturday stating that “it has found no clinical signs or symptoms of the presence of swine influenza in the company’s swine herd or its employees at its joint ventures in Mexico.” The company declined further comment, though CEO Larry Pope told USA Today that “(The term) swine flu is a misnomer.”
Rambaut, Holmes and Salzberg declined to speculate on whether the new H1N1 virus evolved on a hog farm or specifically in the Granjas Carroll facility.
However, it seems likely that pigs were the original host.
“That’s a logical conclusion,” said Salzberger. “It was probably two different pigs, or one who got co-infected from others. The two strains mixed, and now you have a brand-new strain.”
“Presumably somewhere there was a pig infected with both forms. We don’t know where or when. It could have been circulating in this form for a while,” said Rambaut.
What comes next is anyone’s guess.
“Influenza virus mutates remarkably rapidly so there is no doubt that the virus will mutate and evolve in humans,” said Holmes. “Quite what this evolution will result in is difficult to tell.”