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Scientists Track Flu Progress in Detail

The discovery of swine flu in Mexico this spring has triggered an unprecedented effort to penetrate the virus's genetic secrets to figure out where it came from, where it's spreading and what it might do next.

An analysis of genetic sequences posted on the government's GenBank website shows that by Monday, researchers had posted detailed genetic information on nearly 1,400 viruses taken from patients in more than 30 countries, from China to Argentina.

"Never before have we been able to track the spread of a viral infection in such detail," says Vincent Racaniello, a microbiologist at Columbia University.

Flu viruses, like all other organisms, are designed to multiply and produce future generations. Flu stands out for its simplicity and its uncanny ability to change to assure its survival, Racaniello says. The source of that power is the double twist of genetic material, called DNA, that lies in its core and governs its behavior.

Flu's DNA is divided into a string of eight genes. These genes allow the virus to evade the immune system, penetrate human cells, make copies of itself and infect new cells and people. The virus changes through genetic errors that occur during its constant copying and by swapping genes or parts of genes with other flu viruses.

"It's an amazing machine," says Terrence Tumpey, a microbiologist at the Centers for Disease Control and Prevention. "It's so simple."

It can benefit from errors that occur when it copies itself, he says. "If the mistake provides an advantage to the virus, it will pass the mistake on. We've seen it happen with Tamiflu resistance. It came from someone who wasn't even getting the drug."

Having so many gene sequences allows scientists to calculate the virus's mutation rate and even when it leapt from pigs to humans, Racaniello says. "We can estimate that the virus was first introduced into the human population in January 2009 and circulated in humans without being detected for three months."

The CDC's Michael Shaw says the evidence suggests that the virus is made from a mix of genetic material from birds, pigs and humans. Six of the eight genes had been circulating in North American pigs for a decade. The two new genes came from Eurasian pigs. "This particular gene combination had not been seen anywhere, in any species, until its appearance in humans this spring," Shaw says.

Tumpey says that each week he looks for a single mutation that might make the virus spread more easily. The sequences also reveal when drug-resistant viruses have turned up and where. Doctors have identified seven cases, in patients from Denmark, Canada, Hong Kong and four from Japan.

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