A new variant of the H5N1 avian flu virus has emerged in Southern China over the past year and has spread beyond China’s borders in what may be the third wave of H5N1 transmission since late 2003, an international team of researchers reported Monday.

The scientists believe existing poultry vaccines may not protect against this new variant, which they call Fujian-like, and further, that use of these vaccines may have actually given rise to this new subgroup of viruses.

The new variant could threaten gains made against H5N1 in places like Vietnam, experts say, and may require changes in vaccines used to tamp down levels of virus in poultry flocks in parts of Asia.

“The predominance of this virus over a large geographical region within a short period directly challenges current disease control measures,” the researchers say in the article, published Monday in the journal Proceedings of the National Academy of Sciences.

Officials of the UN’s Food and Agriculture Organization and the World Health Organization were to discuss the questions raised by the scientific article in a conference call Tuesday.

“It’s a very interesting paper and we want to look at it much more carefully,” said Dr. Juan Lubroth, head of infectious diseases for the FAO’s animal health service.

“We would need to see how widespread this Fujian-like virus is and . . . should we include this virus into the new vaccines that will be produced. That’s what we will be discussing tomorrow.”

The researchers, from Hong Kong University and St. Jude Children’s Research Hospital in Memphis, Tenn., discovered the new variant as part of an ongoing surveillance program looking for H5N1 infection in the live poultry markets of southern China.

From July 2005 to June 2006 they found 1,294 birds - mainly ducks and geese - infected with H5N1 among 53,220 birds tested. Though infected birds made up only 2.4 per cent of birds sampled, that is a significant increase from the rate of H5N1-positive birds found in markets from July 2004 to June 2005.

While China has a mandatory vaccination program for domestic poultry, officials of the FAO and WHO admit they aren’t certain if geese are being routinely vaccinated. Even if they are, it’s thought the vaccines are less effective in ducks and geese than they are in chickens - the species they were designed to protect.

The authors say the new variant appears to have emerged in Fujian province in 2005 and has since become the dominant virus type in southern China. It has spread to Hong Kong, Laos, Malaysia and Thailand, and has triggered human infections in China and Thailand.

The authors offer no opinion about whether it infects people more easily than earlier variants of the virus.

But they do hypothesize that the virus may have become dominant as a consequence of the mandatory vaccine program. The theory suggests that the poultry vaccines in use don’t protect against this subgroup of H5N1 viruses, allowing them to flourish while viruses the vaccines target fade from lack of opportunity to infect new birds.

Several scientists not involved in the research were unconvinced, saying that while that is a possible explanation for the emergence of the variant it could be an unrelated event.

“They could just have a new variant that’s emerged. And it’s very possible that it might just have nothing to do with (vaccination),” said Dr. David Halvorson, an avian influenza expert at the University of Minnesota.

Lubroth agreed.

“It may be the normal time clock for the virus to change,” he said, adding wider sampling of birds is needed to get a clearer picture of what is going on.

Still, though scientists said the paper doesn’t prove vaccine use spurred the emergence of the new variant, they also acknowledged it wouldn’t be surprising if this turned out to be the case.

It has been thought that the use of poultry vaccines - particularly if they aren’t well matched to the strains of virus circulating - could have this effect of allowing new variants to emerge and thrive.

That’s why human vaccines are changed year after year. But it’s not known whether the makers of agricultural vaccines the world over are as religious about updating their avian flu vaccines.

Michael Perdue, an avian influenza expert with the WHO’s global influenza program, said the findings highlight how entrenched the problem of H5N1 is in affected parts of the world.

“It’s going to be tough going to clear it out of the poultry,” Perdue, who was not involved in the study, said from Geneva.