More study is needed to tell whether the new strain is more likely to kill patients and whether the current vaccine can protect against it completely, said Ian Barr of the World Health Organisation Collaborating Centre for Reference and Research on Influenza in Melbourne, Australia and colleagues.
"However, it may represent the start of more dramatic antigenic drift of the pandemic influenza A(H1N1) viruses that may require a vaccine update sooner than might have been expected," they wrote in the online publication Eurosurveillance.
It is possible it is both more deadly and also able to infect people who have been vaccinated, they said.
Flu viruses mutate constantly -- this is why people need a fresh flu vaccine every year. Since it broke out in March 2009 and spread globally, the H1N1 swine flu virus has been very stable with almost no mutation.
Scientists around the world keep an eye on all flu strains in case an especially dangerous new mutant emerges. While H1N1 turned out not to be especially deadly, it spread globally within weeks and killed more children and young adults than an average strain does.
WHO declared the pandemic over in August but H1N1 has now taken over as the main seasonal flu strain circulating almost everywhere but South Africa, where H3N2 and influenza B are more common. The current seasonal flu vaccine protects against H1N1, H3N2 and the B strain.
"The virus has changed little since it emerged in 2009, however, in this report we describe several genetically distinct changes in the pandemic H1N1 influenza virus," Barr's team wrote in the report, available at http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=19692.
"These variants were first detected in Singapore in early 2010 and have subsequently spread through Australia and New Zealand."
The changes are not significant yet, they said. But there have been some cases of people who were vaccinated also becoming infected, and also some deaths.
"Already this variant virus has been associated with several vaccine breakthroughs in teenagers and adults vaccinated in 2010 with monovalent pandemic influenza vaccine (protecting against only H1N1) as well as a number of fatal cases from whom the variant virus was isolated," they wrote.
But there is not enough information to tell whether there may have been other factors making the patients more vulnerable, they stressed.
"It remains to be seen whether this variant will continue to predominate for the rest of the influenza season in Oceania and in other parts of the southern hemisphere and then spread to the northern hemisphere or merely die out," they wrote.
WHO says 18,450 people worldwide are confirmed to have died from H1N1, including many pregnant women and young people. But WHO says it will take at least a year after the pandemic ends to determine the true death toll, which is likely to be much higher.
Seasonal flu kills an estimated 500,000 people a year, 90 percent of them frail elderly people, according to the WHO. The 1957 pandemic killed about 2 million people and the last pandemic, in 1968, killed 1 million.