When Eric Delwart's lab set out to test for traces of contamination in eight vaccines, he figured the results would reassure people who are leery of the lifesaving serums.

Instead, one result, made public in March, triggered the latest worldwide vaccine brouhaha.

Using powerful new DNA technology, Delwart's San Francisco team detected fragments of a pig virus in GlaxoSmithKline's Rotarix, which protects babies from a diarrhea-causing infection. The pig virus is common in pork products and is not known to cause disease in animals or humans. Still, the finding set off investigations, market upsets - and a new predicament for the U.S. Food and Drug Administration.

The FDA is now being urged to require all vaccine-makers to check for and eliminate barely detectable biological tagalongs, harmless or not.

"We expected to reassure; we ended up not reassuring," Delwart, a virologist with the Blood Systems Research Institute, said this week. "We ended up creating quite a bit of a storm."

For a while, that storm left American pediatricians and parents blowing in the wind. In late March, the FDA recommended doctors stop using Rotarix pending a review. But the agency didn't say to stop using a competing vaccine, Merck & Co.'s RotaTeq, when Merck announced last week that its own retesting found fragments of two types of pig viruses. RotaTeq had traces of the same virus found in Rotarix, plus another one that causes a wasting disease in pigs (but not humans).

On Friday, the FDA said go ahead and use both brands, which infants get by mouth. The agency concluded - as had its advisory panel - that the benefits of vaccinating against a diarrheal disease that annually kills half a million children worldwide far outweighed any theoretical risk.

"I've had questions from parents," said South Philadelphia pediatrician Theodore Tapper. "They ask, 'What's going on?' And, 'Was my child given the vaccine that's not supposed to be used now?' "

Tapper said his practice had always used RotaTeq, the first to come on the market. But in his opinion, the flap is "much ado about nothing."

Unlike the FDA, the World Health Organization and the European Medicines Agency did not advise any suspension in Rotarix use. Both Merck, which makes RotaTeq at its West Point, Pa. facility, and Glaxo, which has research centers in the region, have said they stand behind the safety of their products.

After RotaTeq was introduced in this country in 2006, the rate of young children hospitalized for acute stomach flu fell by nearly 50 percent in 2008, a federal study said Friday.

Physician Paul Offit, a vaccine expert at Children's Hospital of Philadelphia who helped invent RotaTeq, believes fear of unexplained illness - notably, autism - has clouded common sense.

"You could apply this new technology to things gummed by a 6-month-old - a Cheeto, a piece of apple - and find much worse" microbes than the pig virus, Offit said. "How does it help to find things that are not known to be harmful? It's like taking thimerosal out of vaccines. Has that made vaccines safer? No."

Vaccine critics lobbied for removal of the preservative thimerosal, believing it would cut autism rates; it has not. Those critics are now calling on the FDA and Congress to require vaccine-makers to prove that their products are free of the kind of innocuous contamination found in Rotarix and Rotateq.

This "is an important wake-up call for industry and government," said Barbara Loe Fisher, president of the National Vaccine Information Center.

To the layperson, the idea that a pig germ could get into a vaccine is, at best, disgusting.

But the fact is, cells and chemicals from animals and humans are essential for creating "live" vaccines, including Rotarix and RotaTeq. Such vaccines are made from living viruses that have been genetically disabled so they no longer cause disease, but still generate an immune response.

The leading guess for the source of the pig-virus contaminant is trypsin, a porcine enzyme used in vaccine production, the FDA said.

Historically, live vaccines have had some problems. But modern quality-assurance measures are so stringent that Delwart's team expected to find nothing unusual in live vaccines for yellow fever, polio, rubella, measles, mumps, herpes, and the diarrheal disease. Mostly, they were interested in the technological exercise.

"I definitely was surprised" to find the pig-virus particle in Rotarix, said Joseph G. Victoria, lead author of the study, published last month. "My first thought was that it was contamination introduced by our lab."

Although the researchers found just part of a pig virus in the Rotarix sample, it suggests the whole virus is present in the vaccine.

Such high-tech testing isn't cheap; the vaccine experiment cost about $10,000, Victoria said. Even so, he believes it would be a cost-effective way to make vaccine manufacturing even safer.

Delwart, meanwhile, stressed that vaccines were already safe: "You can't overreact. We are constantly ingesting viruses. If you want to avoid viruses, stop eating meat."

The FDA's position on testing remains to be seen. But Tufts University virologist John Coffin, a member of the advisory panel that met last week, thinks there is no turning back.

"There's no question that as more testing methodologies become available, they'll need to be applied," he said. "Whether the contamination is harmful or not, it's certainly better not to have it."