WASHINGTON — The new H1N1 influenza virus that continues to spread through the U.S. has ancestry in a swine flu outbreak that first struck a North Carolina hog farm more than 10 years ago, according to scientists studying the strain's genetic makeup.
The current strain hasn't shown up in surveillance of U.S. pigs, and it can't be caught by eating pork.
The finding about its genetic background illustrates how viruses mutate over time and in some cases jump among species.
"Until you look at that, you can't understand the epidemiology of it," said Peter Cowen, the animal disease moderator for ProMed, an online emerging disease early-warning system. "It's key to understanding what our challenges may be in the future and how the virus is acting in the population."
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The current strain's eight genetic segments are all associated with swine flu, said Raul Rabadan, a Columbia University scientist studying the new H1N1 genetic sequence that was made public this week by the Centers for Disease Control and Prevention.
Two of the segments, Rabadan said, appear to come from Eurasia and are somewhat mysterious in origin. The other six can be traced to the North American pig outbreak, which turned out to include a combination of avian, swine and human flu.
"This virus was found in pigs here in the United States," Rabadan said in an interview. "They were getting sick in 1998. It became a swine virus."
It spread among pregnant sows in Newton Grove, N.C., causing them to abort their litters, and then to swine in Texas, Iowa and Minnesota — putting epidemiologists on alert about the new viral strain and the potential for a human outbreak.
That didn't happen, but public health officials became more aware of the farm-by-farm monitoring system and its importance to public health.
"We cannot protect human health unless we're working with what's going on in the environment and animal species," said Barrett Slenning, who leads the Animal Health Biosecurity Risk Management Population Health and Pathobiology Department at North Carolina State University.
Scientists don't yet know when or where the current H1N1 strain first developed. They know only that it was first identified after people in Mexico began falling ill with the fevers and aches associated with flu.
The current virus hasn't been found in swine, and the country's pork industry is scrambling to reassure consumers about the safety both of pork and the U.S. farm system.
Still, this week's findings about the new H1N1 virus' ancestry also has reignited concerns about the health impacts of factory farms, where thousands of hogs are housed closely together and shipped among sites as they grow.
The Humane Society of the United States highlighted factory farms in its analysis of the new H1N1 virus' history. The animal-rights organization People for the Ethical Treatment of Animals on Friday called on North Carolina Gov. Bev Perdue to close the state's factory farms. And a report last year funded by the Pew Charitable Trusts emphasized that viruses can spread quickly among pigs in the close quarters of such farms. North Carolina has about 10 million pigs being raised on such farms.
"Pigs are amazing mixing bowls for creating new viruses," said Bob Martin, senior officer at the Pew Environmental Group. Martin was executive director of the study.
"It's a matter of when, not if," Martin said of the creation of new viruses on factory hog farms. "The structure of the system is the problem."
Cowen, who also is an epidemiologist at North Carolina State University's College of Veterinary Medicine, said factory farms have shown their ability to contain disease in their animals.
However, he said the current H1N1 outbreak shows the need to improve surveillance of healthy swine as well as pigs that show signs of illness.
"The key to being prepared in terms of responding to this threat from influenza, wherever its coming from — humans, swine or birds — is to know as much as we can about the viruses that are circulating," Cowen said.
This week's discovery is, in part, just another piece of the scientific puzzle in trying to understand the new H1N1 flu's history.
Scientists working around the world this week began tracing the virus' origins days after the CDC published its eight-chromosome genetic sequence.
Steven Salzberg, a computational biologist at the University of Maryland, was among the scientists who found that the new H1N1 virus contains strains from past swine viruses, including the one that swept through pig farms in 1998.
Salzberg said he doesn't blame factory farms for the current outbreak, because swine flu is common among pigs. He wants to know more about the H1N1 virus' ancestry.
That would require that scientists have more genetic sequences of swine flu taken from sick pigs over the past decade. Salzberg hopes the CDC will ask animal labs to send their existing samples in for coding.
"We really need many more," Salzberg said. "This outbreak is going to induce us to do that."
He may not have to wait long. Nancy Cox, the director of the influenza division at the CDC, said talks have already begun with the U.S. Department of Agriculture to begin collecting genetic sequences of swine flu found on farms in the future.
"If the samples haven't been collected from pigs, you won't have data to fill in the gaps," she said. "Going forward, it's going to be very important to have."
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