Two U.S. children were infected with flu viruses that originated in pigs in the past two months, and an analysis of both viruses showed they had picked up genetic material from the 2009 pandemic influenza A H1N1 virus, government researchers said on Friday.

They issued a warning to health workers to watch out for suspect viruses because those that cross between species can be especially virulent.

In both children, one from Indiana and one from Pennsylvania, an analysis of the viruses showed they contained a gene of the 2009 pandemic flu virus, according to a report released by the U.S. Centers for Disease Control and Prevention.

Flu viruses that jump from one species to another are a concern because they can swap genes and form an entirely new virus, making them harder to protect against.

“Pandemic viruses get started when they reassort and they emerge as a new virus. That is why we have to keep close watch on new influenza viruses as they emerge,” CDC spokesman Tom Skinner said.

“They are constantly changing, and that is why we have to have really good surveillance systems in place to detect them when they do emerge,” he said.

So far, this new virus does not appear to be able to easily pass from human to human, but Skinner said the CDC is still investigating.

Since 2005, there have been about 22 cases of human infection from swine-origin influenza viruses similar to the cases now being reported, Skinner said. All 22 people have recovered.

In one of the two new cases, a young boy from Indiana who had gotten a flu vaccine last September developed fever, cough, shortness of breath, diarrhea and a sore throat in late July. He was taken to the emergency department and a swab of his throat indicated that he had been infected by an influenza A virus.

The boy was sent home untreated but returned to the hospital the next day to be admitted and treated for multiple chronic health conditions, which had gotten worse because of his infection.

The boy recovered and was sent home, but further testing by state officials suggested his virus had originated in pigs, and his sample was sent to the CDC for confirmation.

According to the CDC report, the child had no prior direct contact with pigs, but a child-care worker who looked after the boy did report having contact with pigs before the child’s symptoms appeared.

In the second case, a Pennsylvania girl under age 5 who had received a flu shot the prior year developed a suspected infection with swine-origin influenza A (H3N2) in August.

Later testing by state officials and the CDC confirmed that she, too, had developed a form of flu that originated in pigs, likely from direct contact at an agricultural fair.

The girl was not treated and has completely recovered.

So far, the CDC has not seen any additional cases of people developing a pig form of influenza, but Skinner said the CDC is publishing the report to remind doctors and health workers to be watchful for suspicious cases of flu.

The H1N1 pandemic flu strain was discovered in Mexico and the United States in March 2009 and spread rapidly across the world. The World Health Organization estimates about 18,450 people died from the virus up to August 2010, including many pregnant women and young people.

Seasonal flu vaccines being offered across the world protect against the H1N1 strain. Flu vaccines are made by several drugmakers including Glaxosmithkline, Sanofi and Novartis.

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By Julie Steenhuysen

CHICAGO