TIPTON, Iowa—It may be crowded and carpeted in manure, but the long white building beside State Route 38 is one of the most pathogen-free homes a pig could have.

The animals don’t know the feel of grass, mud or sunshine, and hardly the touch of man, in their six months of life. But they are also free of many of the infections that slow the growth and occasionally end the lives of their outdoor cousins.

“We’re producing the most efficient animal, one that is healthy every day,” said Devon Schott, the 34-year-old farmer who owns the building. To do that, he said, “biosecurity is of utmost importance.”

Despite the buttoned-up methods of farmers such as Schott, many experts think pig farming presents a serious and overlooked risk to public health. Proof of that assertion—indirect but indisputable, in the opinion of virologists—is the 2009 H1N1 pandemic influenza.

Little is known about the origin of the novel H1N1. But one thing is virtually certain: The bug now infecting the people of more than 190 countries began in a pig.

Detecting such cross-species transfers quickly—or, better yet, preventing them—is an urgent priority in a field that has spent most of its energy in recent years worrying about the emergence of flu from birds in Asia. A major concern now is what might happen if the pandemic H1N1 virus spreads widely in pigs, and then out again into the human population.

“We really need to know more about what is happening in the pig population in the United States,” said Robert Webster, a leading avian influenza virologist. Scientists at the University of Minnesota and the University of Iowa revealed they had identified the H1N1 strain in seven pigs at the Minnesota State Fair in late summer as part of a study of virus exchange between swine and people.

Some of those animals may have caught the bug from the hordes of visitors at the 12-day event. But not all: One infected animal was swabbed while being unloaded and almost certainly arrived with the virus, said Gregory Gray, a physician and epidemiologist at the University of Iowa who helped run the study.

What worries virologists is the mixing of human and swine flu strains— or, worse, human, swine and bird strains. That can lead to “reassortment,” in which strands of genetic material are exchanged to yield a new virus, often with behavior not seen in its parents. Those features can include higher contagiousness, rapid growth, the ability to infect the lungs and, most important, an unfamiliar appearance to the immune system.

Reassortment is rare, and it’s even rarer when the product is a strain that can spread like wildfire. That’s one reason influenza pandemics occur only a few times a century. (The last one was in 1968.)