To find some answers, 60 Minutes correspondent Scott Pelley went inside the federal government's $3 billion H1N1 vaccine project. This is the first time the public has seen where and how the vaccine is made.
It's true that for 99 percent of the people who get H1N1, it is just the flu - a few miserable days at home. But health officials warn that those who don't get vaccinated take a chance they'll end up like 15-year-old Luke Duvall, who we met in our.
In mid-October, Luke Duvall was in a fight for his life against H1N1. Pelley met him and his parents, Chad and Belinda, at Arkansas Children's Hospital in Little Rock.
Luke was breathing only with the help of a ventilator. He would be on the machine 17 days.
Nearly three weeks later, Luke was off the ventilator and in physical therapy. He is still being fed through a tube in his nose and he has a long way to go to get his strength back, but he has beaten H1N1.
"Well, the only way I can describe it to somebody who hadn't gone through it was its almost like somebody hit me with a cannonball in the chest," he said.
Luke's harrowing struggle wasn't lost on his neighbors. Before dawn Friday, people who had been praying for their local football star were lining up for vaccine. But supplies were scarce; Arkansas says it is short about a million doses.
We went to a mall in Manassas, Va., where after three hours they vaccinated 550 people, ran out of vaccine, and turned 350 away.
Last summer, the government said there would be 120 million doses of vaccine by fall; weeks later, it revised that to 40 million. Now, just over 17 million have shipped - 14 percent of the first estimate.
Experts agree the government decoded the virus to prepare a vaccine in record time, a real achievement. But then the project hit snags.
The vaccine took longer than expected to produce, and there were shortages of supplies, like the sprayer for the FluMist version.
The H1N1 vaccine is being produced in a sprawling, $250 million facility in Swiftwater, Pa. Like other vaccines, the H1N1 virus is grown in chicken eggs, in an updated version of a process that has been around since World War II.
"Viruses are unique in that they require a living host to propagate. And the egg provides essentially a small, self-contained, sterile factory for the production of the vaccine," Sam Lee, director of manufacturing technology at French drug company Sanofi Pasteur, explained.
The plant has to be as clean as a hospital operating room. Pelley and the "60 Minutes" team put on clean suits and hairnets and passed through airlocks to reach the production line.
Five companies are making vaccine, but this is the only one in America.
"I see all these needles going into the top of the egg. Is that the virus going into the egg itself?" Pelley asked, observing the production process.
"There's the needle that comes down," Lee said. "The virus is then introduced directly to the egg. The eggs exit the machine. And are loaded onto carts. These carts are then wheeled into incubators, where they're environmentally controlled for temperature and humidity."
The virus grows in the eggs; later it is killed and refined into vaccine. The process takes three months. Most of that is testing for safety and sterility. Sanofi Pasteur has a federal contract to make 75 million doses. They will go through millions of eggs.
Asked if the farms producing the eggs are near the vaccine plant, Lee told Pelley, "Because of security reasons, I'm not at liberty to share specific, exact locations."
"These are secret egg farms?" Pelley asked.
"We don't want to reveal the location for security reasons," Lee said.