Federal health officials said Friday that they will set aside $1 billion to jump-start commercial development of a vaccine against the new H1N1 flu virus now spreading worldwide.

The funding will be used to produce bulk supplies of two key components of a vaccine and to test them in humans. The most critical of the two is the vaccine’s active ingredient, a protein from the new flu virus designed to trigger an immune response. The second is a booster, called an adjuvant, that might be added to the vaccine to ramp up its potency if it doesn’t appear to work in early human trials.

“The actions we are taking today will help us be prepared if a vaccine is needed,” Secretary of Health and Human Services Kathleen Sebelius said in a statement.

Vaccine manufacturer GlaxoSmithKline confirmed Friday that the government has put in orders for both the active ingredient and a booster. Officials from the U.S. Centers for Disease Control and Prevention say they hope to have the seed viruses they’ll need to create a new H1N1 vaccine by the end of May. The letters and numbers refer to proteins on the viruses’ surface.

The first candidate virus arrived at the agency Friday, says Anne Schuchat, of CDC. “We’re analyzing candidate (viruses) to see whether they can generate optimal immune responses, then we’ll send them out to manufacturers,” she says.

In another new development, a research team led by experts from The World Health Organization, Mexico, Cambridge University and the CDC on Friday unveiled the new virus’ first detailed family tree. The analysis indicates that the new H1N1 virus originated in birds and then began circulating in pigs, where it picked up a unique mix of genetic segments. Six of its eight genetic pieces are from swine flu viruses, with snippets from viruses found in humans and birds. Two genetic segments come from Eurasian bird flu viruses.

This evolution occurs because flu viruses routinely swap their genes, often in pigs infected with multiple viruses. Pigs are the “classic mixing vessels” for flu strains circulating among humans and birds, says Peter Hotez, president of the Sabin Vaccine Institute at George Washington University.

“It’s an important finding. It’s a wake-up call that we have to have aggressive, ongoing monitoring of flu in pigs,” Hotez says.

The study’s senior author, Nancy Cox, director of CDC’s influenza division, says the virus is a genetic cousin of the germ that caused the 1918 pandemic, but one that lacks the so-called virulence genes that enabled the 1918 virus to kill an estimated 20 million people.

Cox and her colleagues studied full or partial genomes from seven new H1N1 viruses from patients in Mexico and 44 from 13 states in the USA. Their report was released online by the journal Science.

“From our analysis we have confirmed that the virus likely originated from pigs,” Cox says. The analysis suggests that the swine components of the new H1N1 virus remained relatively unchanged in pigs and humans until 1998, when the pig version began to diverge from the human strain, probably through exposure to avian flu.

The new virus that emerged in Mexico in April was dramatically different from any H1N1 virus ever seen before, apparently because it had picked up genes from Eurasian bird flu viruses. “This particular gene constellation has never been described before,” Cox says. That means the current seasonal vaccine, though it carries an H1N1 component, won’t protect against the new H1N1, she says.

Fortunately, she says, the virus is still susceptible to the antiviral drug Tamiflu, though researchers fear that it may eventually pick up drug-resistance genes as it circulates in humans or animals. Researchers also worry that the virus may mingle with the deadly H5N1 virus now ravaging global bird populations, which could make it more virulent.

Even if that doesn’t occur, the epidemic still may become much worse. “It’s virus that could come back in the worst way in the fall,” Schuchat says.

By Friday, CDC had identified 6,552 probable and confirmed cases of the new H1N1 influenza in the USA. Nine patients have died, Schuchat says. Worldwide, WHO reported 11,168 flu cases and 86 deaths.

Health officials told lawmakers Wednesday it took only two weeks to identify the genetic characteristics of swine flu, and they are in good position to quickly produce a vaccine if the flu takes a turn for the worse.

At the same time, the officials cautioned members of a House Foreign Affairs subcommittee that there are still elements of what they called the novel 2009 H1N1 influenza virus that they don’t understand, and it was not time for complacency.

Dr. Dennis Carroll, special adviser on pandemic flu to the U.S. Agency for International Development, noted that the 1918-1919 flu pandemic also began in the spring and was initially mild, but a much more lethal version hit six months later and the virus eventually killed 50 million worldwide.

Dr. Anne Schuchat, acting deputy director for science and program at the Centers for Disease Control and Prevention, also urged caution, saying they expected to see more people get sick and more serious cases. One factor, she said, is that the Southern Hemisphere is now moving into its flu season.

But she also stressed that “at no time in our history have we been more prepared to face this challenge.”

She said the CDC moved rapidly to determine that the virus circulating in the U.S. and around the world contains genetic pieces from four different virus sources and that within two weeks it was able to understand its complete genetic characteristics.

“We have isolated and identified the virus and discussions are under way so that, should we need to manufacture a vaccine, we can work towards that goal very quickly,” she said.

Anthony Fauci, director of the National Institute for Allergy and Infectious Diseases, said the CDC is currently at the stage of processing vaccine seed virus. If the need arises, they can coordinate with manufacturers on clinical trials, verifying the safety, efficacy and right dosages of the vaccine, and then move to mass production.