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Tracking the swine flu virus

Since its discovery on a swab from a San Diego County boy two and a half weeks ago, the H1N1 virus has come to rivet flu scientists and health officials around the world.

May 03, 2009|Jia-Rui Chong and Alan Zarembo

The feds were on the phone explaining that a 10-year-old boy had a strain of swine flu no one had ever seen before.

As Dr. Michele Ginsberg listened, her mind flashed back to the days before the AIDS virus had been identified, when people were showing up at emergency rooms in California with a mysterious pneumonia.

Ginsberg, community epidemiology chief for San Diego County, where the boy was from, picked through her reports of unusual deaths, looking for similar cases. Nothing jumped out that April 16. And the county veterinarian didn't have reports of sick pigs.

Ginsberg's office called the boy's mother to see if he had been in contact with pigs or other animals that could transmit flu to humans. If he hadn't, it was likely that the virus had spread between people -- the last thing an infectious disease expert wants to hear.

"No animal exposure," Ginsberg wrote in her notebook.

But the boy's brother had been sick with fever and cough about two weeks earlier.

"Big deal!" Ginsberg added to her notes.

The virus has now traveled to 21 states and 18 countries, infecting more than 700 worldwide and killing about 115, all deaths save one in Mexico. It has riveted flu scientists and public health officials around the world. It appears to be relatively mild, perhaps no more deadly than a typical seasonal flu. But if it infects enough people, even a tiny death rate could add up to more fatalities than would be seen in a normal season -- perhaps many more.

In its early days, though, the virus was just a curious swab in a vial. The boy who had provided it was already better.

No one might ever have learned more about it except that the boy happened to come from a military family, and his sample was among those the Naval Health Research Center in San Diego was collecting as part of a study on a new flu test.

It came back as influenza Type A. Beyond that, the results were confusing. The Navy sent it to two labs in Wisconsin for analysis, but they couldn't figure it out either.

The tests showed what it wasn't: the dreaded H5N1 bird flu or either of two well-known strains of seasonal flu. But that did not explain what it was.

A distant cousin

The sample arrived by FedEx at Michael W. Shaw's laboratory at the Centers for Disease Control and Prevention on April 15.

Inside the package were two vials. In each, a cotton swab floated on a liquid the consistency of an egg white. Shaw and his colleagues bathed the samples in a chemical solution to crack open the virus and expose its genes.

For four hours, a polymerase chain reaction, or PCR, machine copied the virus' genetic material over and over, slowly revealing its odd genome.

Once he identified it as a swine flu, Shaw printed out a chart that showed how it fit on the family tree of swine flus -- it was out on its own lonely branch, a distant cousin to any other known virus.

"It's been out there somewhere unnoticed, possibly in people, possibly in animals," he said.

Six of the virus' eight genes were from a strain that had circulated among U.S. pigs for more than a decade. But two others looked like those found in pigs from Asia and Europe.

The most likely scenario was that a single pig had been infected by both strains, which reassembled themselves into the new virus, said Richard Webby, an influenza expert at St. Jude Children's Research Hospital in Memphis, Tenn.

That pig infected other pigs. Then, at some point -- nobody knows when, where or how -- the virus jumped to humans.

It was the scenario that "we've been on the lookout for," Webby said. Any new virus is worrisome, because nobody is likely to have much immunity to it.

Even so, when the CDC identified the virus on April 16, scientists still saw it as more of a curiosity than a threat.

"I didn't see anything to be alarmed about right then," Shaw recalled.

That was about to change.

A death in Mexico

A parallel story was unfolding south the U.S. border, though nobody yet had connected the dots. In Mexico, a strange respiratory illness had been going around for at least a month. On April 13, it claimed its first life: that of 39-year-old Adela Gutierrez, a census worker in the city of Oaxaca.

When she had arrived at the hospital four days earlier, gasping for air, doctors suspected SARS, the virus that killed 774 people in Asia and Canada six years ago. She was quarantined after testing positive for a coronavirus, the virus group SARS belongs to. But a second test came back negative.

Tests were positive, though, for Type A influenza -- an unrecognizable strain.

"This case was what really alarmed us," said Mexican Health Secretary Jose Angel Cordova.

Mexican scientists were not equipped to identify the killer on their own. So on April 17, Dr. Celia Alpuche Aranda, head of Mexico's national microbiology lab, sent an e-mail to Dr. Frank Plummer in Winnipeg, Canada, describing the outbreak of respiratory illnesses in several Mexican cities.

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