"With H3N2 ... we tend to see more severe outcomes in terms of hospital admissions, admissions to intensive care and death,'' Dr Jennings said.
Waitemata and Counties Manukau have the highest number of flu sufferers nationwide, but there has yet to be a rise in flu patients hospitalised in those districts.
Dr Jennings said this year's flu vaccine had the H3N2, H1N1 and influenza B virus in it.
"As far as we're aware at the present time, the H3N2 virus, that's affecting Canterbury at the moment, is similar to the antigens which are included in the current influenza vaccine.
"And similarly with the H1N1 and the B viruses largely in the North Island, as well as the H3N2, they're similar to the antigens in the influenza vaccine.''
However, influenza vaccines were not perfect, he said, and protected only about 90 per cent of healthy adults.
"That means among healthy [vaccinated] adults, at least 10 per cent will get infected with influenza.''
Dr Jennings recommended those who do get the flu to stay home, rather than going into work and infecting colleagues.
''[And] if they're concerned about their condition then phone their GP, don't rush into the practice, or to the emergency department, phone them and seek advice.''
The last time the country had a significant H3N2 outbreak was about 2006, he said.
Northern Hemisphere countries also had an outbreak of the virus during their latest winter, Dr Jennings said.
Tim Jelleyman, acting chief medical officer at Waitemata, said he expected the number of flu cases in the district to increase.
Canterbury medical officer Alistair Humphrey said a special ward had been set up at Christchurch Hospital to cater for up to 60 patients affected by the epidemic at any given moment. About seven patients had been admitted to intensive care, he said.
"It's certainly putting pressure on the whole health system. I work clinically as a GP in a 24-hour surgery ... My shifts have been absolutely full-on every time I'm there. It's putting pressure on GPs, on the emergency departments, on hospitals. Doctors and nurses are starting to get ill.''
The epidemic is expected to spread across the country in coming weeks, expedited by the return to school after the winter break.
Vaccination is free until July 31 for pregnant women, people aged 65 or older, and anyone with ongoing medical conditions.
National Influenza Specialist Group spokeswoman Brenda Saunders said almost 960,000 doses of the flu vaccination had been distributed so far this season - 28,000 fewer than the same time last year.
Public Health Surveillance's national report shows a steep increase in flu cases last week, almost double the number at the same time last year.
Humphrey said: "This year we are up [on flu cases] pretty much as high as we were during the swine flu epidemic. It's a serious illness. It's not something that should be ignored.''
What is H3N2
* H3N2 is an A-type virus.
* It descended from a virus that originated as a pandemic in Hong Kong in 1968.
* Canterbury Health virologist Dr Lance Jennings says H3N2 circulates through a population until the level of immunity has built up.
* Symptoms include hallucinations, crippling fevers and nausea.
* Once there is resilience in the population, H3N2 mutates so that it is more infective.
- APNZ / Herald on Sunday
