May 4 (Bloomberg) -- Pigs are getting slaughtered to prevent the spread of a new strain of flu. Ducks and humans may be more to blame.

While the new H1N1 strain that threatens to spark a pandemic evolved in swine, its ancestors came from waterfowl, says Richard Webby, who has analyzed the virus’s genetic code.

Viruses that circulate in aquatic birds are the genetic ancestors of all pandemic-causing influenza, including the 1918 Spanish flu blamed for killing 50 million people, according to Webby, head of a World Health Organization Collaborating Center in Memphis, Tennessee, that studies the ecology of influenza. Pigs are a mixing vessel for human and bird flu viruses because they are susceptible to both avian and mammalian strains.

“There is some quite good evidence that avian viruses get into swine barns through the practice of using pond water to wash down the barns,” said Webby, 38, who is also a virologist at St. Jude Children’s Research Hospital in Memphis.

Webby was one of the first scientists to comb through a database containing the genetic fingerprints of thousands of flu viruses to find the closest relatives of the strain that infected a 10-year-old boy in California last month and spread to more than 985 people in 20 countries. His search, completed during the past week, failed to identify an exact match, suggesting the emergence of a new virus to which people would have little or no immunity.

European, U.S. Relatives

“That particular genetic combination of swine influenza virus segments has not been recognized before in the U.S. or elsewhere,” Anne Schuchat, director of immunization and respiratory diseases at the Centers for Disease Control and Prevention in Atlanta, told reporters on April 23, when the threat was beginning to emerge.

Knowing the origins of this new strain, how it jumped from animals to humans and became transmissible among people, may help disease-trackers predict its behavior.

By analyzing the sequence of hundreds of amino acids coded by each of the flu virus’s eight genes, Webby found the virus’s closest relatives are an H1N1 flu strain that has circulated widely among North American pigs since the late 1990s, and one from Europe that’s been in swine for at least three decades.

Both parent strains descend from the H1N1 Spanish flu and contain human and avian-like components, he said.

Mixing Bowl

“It’s a mutt,” said Webby, who moved to the U.S. from New Zealand a decade ago to work under the tutelage of veteran virus sleuth Robert Webster, 76. “The sequence suggests that this thing wasn’t born in the U.S. It’s just different enough to suggest to me that somewhere, maybe in the southern parts of the Americas, there has also been this lineage of virus that’s been kicking along as well.”

Pigs, like humans, shed flu viruses in their nasal secretions, Gabriele Landholt, a veterinary researcher at Colorado State University, and colleagues wrote in a 2003 study. Pigs can catch both human and avian influenza because the cells of their respiratory tract are susceptible to infection by viruses common in people and birds, according to Japanese researcher Toshihiro Ito.

Scientists have yet to pinpoint exactly how pigs and humans exchange their influenzas, says Jennifer McKimm-Breschkin, a virologist at the Commonwealth Science and Industrial Research Organization in Melbourne.

Sneezing Snouts

“Does the pig sneeze and the human catch it? I don’t think anyone has done controlled transmission studies on pigs to humans,” McKimm-Breschkin says.

Fears of a lethal pandemic lie in the nature of flu germs, which mutate constantly and can become virulent by exchanging genes with related viruses. While the H5N1 bird flu that spread across Asia the past six years, killing millions of fowl and several hundred people, never gained genes to spread easily among humans, the new H1N1 strain already has.

“This virus is a sneaky and promiscuous critter,” says William Aldis, an assistant professor of global health at Thammasat University in Bangkok, who helped Thailand’s response to bird flu in 2005 and 2006 as the World Health Organization’s representative to the country. “A few years back, it could have gotten away with it. But by real-time sequencing and re- sequencing, Webby and his colleagues can catch it in the act.”

Its emergence in Mexico this year has put the world closer to a flu pandemic than at any time since 1968.

For those who study swine, the discovery isn’t completely unexpected, said Webby.

Cough and Fever

The disease, which causes fever, lethargy, cough and loss of appetite in pigs, has been found in U.S. hogs since the 1930s. At least a third of commercial swine have had a bout of flu and as many as a quarter of pig farmers may have been infected, according to the CDC.

At least four flu viruses circulating in pigs have shown signs of pandemic potential during the past 40 years, according to the WHO, a Geneva-based United Nations agency. Until last month, none had spread worldwide.

“Swine influenza in the past has been relatively mild when it has come into the human population,” said Ian Barr, deputy director of the WHO Collaborating Center for Influenza in Melbourne. “This might be a more severe form of what’s been around previously.”

Swine flu infections in people are seldom detected. The CDC says it receives reports of about one human case every one-to- two years, though a dozen cases were recorded from December 2005 to February 2009. Since April 21, the CDC has counted more than 220 cases in the U.S.

“Were we surprised?” says Webby. “No. Caught off guard? Perhaps a little.”

To contact the reporter on this story: Jason Gale in Singapore at j.gale@bloomberg.net

Last Updated: May 3, 2009 22:02 EDT