H1N1 Strain May Have Been Undetected in Pigs for Years

May 22, 2009— -- The swine flu virus may have been spreading undetected among pigs for years, according to researchers who have been studying its genetic sequences.

It's likely that other novel strains have also emerged but have not been noticed, according to a report online in Science from an international team of investigators.

The knowledge gap points out a "global need" for a closer watch on animal viruses, according to Nancy Cox, director of the U.S. Centers for Disease Control and Prevention's influenza division and one of the senior authors of the Science paper.

Exactly when and how the current novel strain developed, emerged from animal hosts, and began causing human disease remains unknown, Cox said in a telephone press conference.

But in the Science article they said the "relative lack of surveillance for swine influenza viruses" -- combined with molecular evidence of the ancestry of the genes in the current strain -- "suggests that this virus might have been circulating undetected among swine herds somewhere in the world."

The current novel strain is a so-called triple reassortant -- meaning it has genes from pig, bird, and human flu.

But while such reassortants have been circulating in pigs for several years, the precise combination of genes in the current strain had not previously been detected, Cox said. That could be because surveillance of pig flu viruses in the United States "is not very systematic" and elsewhere is even less so, she added.

Animal flu researchers around the world, she said, are now going back through their stored samples to see if they can find the "missing link" between known reassortant viruses and the current H1N1 strain.

"The paper underscores some existing concerns," said Dr. Marvin Bittner of Creighton University Medical Center in Omaha, Neb., who was not involved with the study.

Bittner said implications include the need to monitor pigs for new viruses, prevent the animals from acquiring viruses, and encourage measures to prevent transmission of viruses from pigs to humans.

Swine Flu Spread in Pigs Suggests Virus Is Flexible

But, he added, in some places, pigs wander freely, making such measures a challenge.

Many elements of the paper have already been discussed, "but the work has been done remarkably rapidly and comprehensively," said Dr. William Schaffner of Vanderbilt University School of Medicine in Nashville, Tenn., who was also independent of the research.

The study emphasizes flexibility of influenza viruses, he said.

"They swap and exchange genetic elements constantly -- and these genetic elements now can be traced over decades," Schaffner said. "This is an extraordinary achievement by the molecular virologists."

He added that the study "dramatically reminds us" that pigs can serve "mixing vessels" for flu elements from both bird and humans.

For the Science paper, the researchers analyzed the genetics of more than 70 samples taken from patients. They found:

All of the samples are genetically similar, suggesting they crossed to humans at either a single place and time or in several closely related places and times.

They do not react with antibodies to the current seasonal H1N1 flu.

They are lacking several properties known to be associated with the ability to spread among humans, suggesting some previously unknown factors may be allowing the virus to spread.

The designation H1N1 refers to two surface proteins -- hemagglutinin and neuraminidase -- that serve to identify different varieties of the flu. But even within a category such as H1N1, the proteins can vary substantially, causing marked differences in how they interact with antibodies -- and hence, how many people have natural immunity to the virus.

The novel strain was first identified late in April, in two unrelated pediatric cases in San Diego, as an un-subtyped H1N1 virus.

Within days, experts were aware that a rash of influenza-like illness in Mexico was being caused by the novel virus, which has since caused more than 11,000 confirmed cases in 42 countries, according to the World Health Organization.

At least 86 people have died from the illness, according to the World Health Organization.