A new strain of swine flu has shown up in two children in Pennsylvania and Indiana who had direct or indirect contact with pigs. The virus includes a gene from the 2009 pandemic strain that might let it spread more easily than pig viruses normally do.

So far, there’s no sign that the virus has spread beyond the two children, the Centers for Disease Control and Prevention reported Friday.

"We wanted to provide some information without being alarmist," because people have contact with pigs at fairs this time of year and doctors should watch for possible flu cases, said Lyn Finelli, the CDC’s flu surveillance chief. "We’re always concerned when we see transmission of animal viruses to humans."

People rarely get flu from pigs — only 21 cases have been documented in the last five years — and it’s too soon to know how infective this virus will be, she said.

The new strain is a hybrid of viruses that have infected pigs over the last decade and a gene from the H1N1 strain that caused the pandemic two years ago. It is the first combination virus to turn up in people since the pandemic, said Michael Shaw, a lab chief at the CDC. It’s classified as an H3N2 virus.

The first case was an Indiana boy under age 5 who was sickened in late July. He had no contact with pigs, but a caretaker did in the weeks before the boy fell ill. He was hospitalized and has recovered, and no other family members appear ill.

The second case was a Pennsylvania girl, also under age 5, who had contact with pigs at an agricultural fair last month. She, too, has recovered, and health officials are investigating reports of illness in other people who went to the fair. No additional cases have been confirmed so far.

The viruses in the two children were similar but not identical. Both were resistant to older flu medicines but not to Tamiflu or Relenza.

The gene from the 2009 pandemic is one of the things that makes this new strain worrisome, said Dr. John Treanor, a flu specialist at the University of Rochester School of Medicine.

"There is some evidence that that gene is particularly important for transmission from person to person," he said.

This year’s vaccine, which is the same as last year’s, likely would not protect against the new swine strain, Treanor and Finelli said. They are encouraged that so far it does not appear to have spread easily between people, and that local health officials detected and reported the novel strain so quickly.

"Maybe it will be no big deal but it’s important to keep track of this," Treanor said.