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Avian flu hunters at Cornell pore over bird samples in search for killer virus

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A cooler containing possible evidence of avian influenza is regularly sent by overnight express from New York City to the virology diagnostic laboratory at Cornell University's Animal Health Diagnostic Center. The cooler is packed with dry ice and loaded with up to 200 test tubes that have five samples each from birds in the city's 90 live bird markets.

More than 10 million chickens, ducks, turkeys and other poultry from numerous states in the eastern United States pass through these markets and come into close contact with humans. If any of the birds are infected with the deadly avian influenza virus, known as H5N1, the New York State Department of Agriculture and Markets wants to know immediately. That's why their agents scour the markets and take daily samples from birds' respiratory and intestinal tracts to ship to Cornell.

"Our job is to try to detect the footprint of the avian influenza virus in these samples from the live bird markets," says Edward Dubovi, director of the virology diagnostic lab and the virologist who recently made headlines when he isolated in greyhounds the equine influenza virus that has since been affecting dogs in 11 states.

Edward Dubovi
Alexis Wenski-Roberts/CVM
Edward Dubovi, director of the virology diagnostic laboratory at Cornell's Animal Health Diagnostic Center, recently isolated an equine flu virus affecting dogs. He is now leading an effort that tests for virulent avian flu viruses.

Using the federal protocol for biosafety level two, Cornell technicians wear protective garb and gloves and handle the arriving samples in biological safety cabinets. Under Dubovi's supervision, they first isolate any viruses or test for parts of viruses found in the samples. To further examine any virus fragments found, they conduct about 100 highly sensitive PCR (polymerase chain reaction) tests each week to amplify any small amounts of avian influenza RNA in the samples.

The researchers are on the lookout in particular for avian influenza viruses with so-called H5 or H7 proteins on their surface, since all of the highly pathogenic avian influenza outbreaks in poultry since 1997 have been due to these two types of viruses. Viruses with H5 proteins, however, have not circulated among humans in the last 100 years, if ever; that means that today's human population has not built up any immunity, making the pathogens exceptionally virulent.

Yet it is an H5 virus (H5N1 -- the N1 is another surface protein) that is now killing 100 percent of the birds it infects and half -- more than 60 to date -- of the Southeast Asians who have caught the virus from birds. But of the people who contracted this avian flu virus, scientists suspect that only one case, in Thailand, was the direct result of human contact. Both the carrier and the infected person died, and the virus went no further. All the other human infections have been contracted from chickens and so far haven't been contagious to other humans. The real danger to humans is if the virus mutates or changes in ways that allow it to replicate in humans and then transmit from human to human.

"If any of our tests come out positive for influenza virus, we then conduct another test to determine if any of the samples are the highly virulent avian influenza H5N1 or the less virulent H7N2 virus. If the samples are positive for either -- and we have yet to find any H5 strains in the 14 or 15 months since we've been testing -- then we send the samples directly to the National Veterinary Services Laboratory in Ames, Iowa, which then characterizes them," says Dubovi, noting that his lab sends up to a half dozen specimens weekly to be characterized.

The H7 viruses also can trigger illness, and occasionally death, in humans; even though it is a low pathogenic virus, it is a potential threat to becoming a major pandemic among humans.

"It is two major mutations away from becoming a virus that could kill a lot of chickens and become much more pathogenic to people," says Dubovi. The two random mutations would have to occur at the critical cleavage site in exactly the right way to threaten human health. It's much more likely, he believes, that a flu virus would get "reassorted" in a person who happens to be infected at the same time with the avian flu virus transmitted from a bird and a flu virus from a pig or human, or both.

"Then you have genes from all three of these viruses, and one of the dangers then is not a mutation but a whole range of reassortments of genes, and one could be a more perfect fit to replicate in humans. Then you've got a serious problem," he observes.

All poultry entering the live bird markets of New York City are supposed to come from virus-free farms. If any of the birds are infected, the highly contagious H5N1 virus not only could wipe out avian populations and potentially devastate the poultry industry, but it also would increase the chances that the virus would mutate in such a way that it could jump to and spread among humans.

Scientists hope that by ensuring that birds in the United States are not infected with the avian influenza virus, contact between the virus and humans is minimized and, therefore, so are the chances that the virus has the opportunity to jump to humans, mutate and then spread from human to human -- a scenario that sends a shiver down the spine of scientists around the world.

To try to prevent such a scenario, after government scientists characterize the H5 and H7 viruses that Dubovi sends them, they trace any threatening viruses back to their source to identify where the virus came from so they can then clean it out by destroying entire flocks of birds wherever the virus has been detected.

As more humans come into contact with birds in increasingly crowded environments, Dubovi says that the threat to human health increases. Yet, the Cornell virologist is skeptical that these events will occur the way that many scientists predict.

"Everyone speculates that H5N1 will be the next big issue, but I'd be surprised if it's the next big pandemic -- the next big break in flu probably won't be from what we expect, because viruses simply don't play by the rules."

The Animal Health Diagnostic Center, a division of the Department of Population Medicine and Diagnostic Science in the College of Veterinary Medicine at Cornell, partners with the New York State Department of Agriculture and Markets to improve the health of food and fiber-producing, companion, sporting, zoo and wildlife animals.

This is the second of five articles in the Chronicle Online series detailing Cornell researchers' roles in the global battle against avian flu.