"What we are likely to see this coming winter is this A-Victoria virus, H3N2, visiting us again," said Dr Jennings, of the Canterbury District Health Board's laboratories.
"Potentially other centres in New Zealand could be affected as severely as Canterbury was last year, and perhaps as severely as we've seen in the Northern Hemisphere, in America."
A-strain H3N2 viruses are often associated with worse outbreaks of influenza than other strains and an increased death rate among older people and other at-risk groups. They have also shown a greater tendency for drift in their composition, leading to the need for frequent changes in vaccine formulation.
Dr Huang, of the Institute of Environmental Science and Research (ESR), said they were typically the most common strain in New Zealand, but that pattern had been disrupted.
"H3N2 was the predominant strain last year. Christchurch was the one to have a very sharp increase, especially in their hospital admissions, but other regions, like Auckland, also had quite high activity as well. Overall last year in New Zealand we were in the medium level of H3N2 activity.
"It hasn't been the predominant strain for quite a few years.
"For example 2008 was predominated by a B strain and then the A-H1N1 pandemic took off in New Zealand in 2009. Then 2010 was another pandemic year and 2011 was B-predominant. So last year was the first year since 2007 that was H3N2-predominant.
"The two years of pandemic-predominant seasons disturbed our usual H3N2-predominant pattern."
The effect was that the population - through lower rates of natural infection and insufficient immunisation - was left more vulnerable to it than in 2007.
In 2009, more than 1400 people with influenza were treated in hospital, compared with about 1000 the following year, a similar number last year, and 526 in 2011.
The 2012/13 United States flu season in several weeks reached the country's definition of an influenza epidemic: more than 7.2 per cent of deaths being caused by pneumonia and influenza. The peak was nearly 10 per cent.
Some cities declared public health emergencies. There were relatively high numbers of elderly people admitted to hospital with influenza.
But it's not clear whether New Zealand will follow the US pattern.
Dr Huang said H1N1 and B-strain flu viruses had dominated in Europe and that part of the world had not been affected as badly as the US. Predictions on how New Zealand would fare this winter depended on which strain became the most common.
"How to predict which strain of the three would become the majority of the isolations is difficult. They don't follow patterns; that is the problem."
Concerns have emerged in the US over the effectiveness of influenza vaccination, particularly among the elderly.
The US Centres for Disease Control and Prevention (CDC) estimated at the end of the flu season there that the vaccine was 56 per cent effective, when averaged across all ages.
"Effective" was defined as protecting against having to go to the doctor because of flu illness. The CDC concluded that this was "moderate effectiveness for most people".
"The one exception to this was the VE [vaccine effectiveness] among people 65 and older against flu A (H3N2) viruses, which was lower."
The estimate was 9 per cent - but the margins for error were so broad that this result was not statistically significant, so "should be interpreted with caution".
New Zealand health authorities acknowledge that the vaccine is less effective in the elderly than in younger adults, and also less effective in young children - but argue vaccination remains the best protection available. "It's not a perfect vaccine," said Dr Jennings.
He quotes estimates of effectiveness at preventing influenza infection of 70 to 90 per cent for healthy adults.
"What it does in the elderly, of course, even though the effectiveness of the vaccine may drop down to 50 per cent, it prevents more-serious illness even if you become infected with the virus, and lessens the risk of developing pneumonia and admission to hospital and dying from influenza.
"The other issue, particularly in the young, is the closeness of the fit between the virus that's circulating in the community and the contents of the vaccine.
"Younger children, under 2 years of age, are very dependent on having a vaccine that's exactly right and it becomes less effective if there is variation. So last year, for example, when we had the H3N2 Victoria virus circulating, that had drifted from the previous H3 virus so the vaccine match wasn't as good."
He said the main issue in the US was the predominance of the H3N2 strain "and traditionally in older people the response to that component of the vaccine is not quite as good as the response to the H1N1, even though it was a close match.
"They don't really understand whether it was this particular virus circulating or what - there's no good scientific explanation at this point."
He said elderly people's immune systems were declining, which accounted in part for the reduced effectiveness of influenza vaccine.
"There are other things that can be done - nursing homes ensuring that staff receive the vaccine, and parents ensuring family members in regular contact with the elderly get vaccinated, and health care workers getting vaccinated to help protect those in hospital who are at greater risk of serious outcomes if they get influenza in hospital."
And he urged that people who caught influenza and were at risk of complications be treated with the anti-flu drug Tamiflu, which lessened the severity of the illness.
Pharmac is extending the free vaccination programme to children under 5 with significant lung disease from next Monday, although the injections cannot be given to children under six months because influenza vaccines are not licensed for that age group.
The extension - expected to add $1.2 million to the Government's five-year bill of more than $20 million for the vaccine scheme - is based on a CDC-funded study in Auckland which last winter found that children under 4 were the age group with the highest rate of hospital admission with influenza.
More than 1 million vaccine doses were given last year, suggesting that about a quarter of the population received the jab. Pharmac hopes to increase that to 1.2 million doses this year.
It wants GPs to "ring-fence" stocks of the GlaxoSmithKline Fluarix vaccine for children under 9. This is because bioCSL's Fluvax was in 2010 associated with an increased rate of fever-related convulsions in children - convulsions which the Health Ministry said could be alarming, but which did not cause long-term harm.
Fluvax is not currently licensed to be used for children under 5 and is not recommended for children from 5 to 9. Children under 9 having their first flu vaccination are given two doses, unlike other people, who are given one.
The Immunisation Advisory Centre at Auckland University said bioCSL's investigation concluded that its flu virus splitting method retained more virus components than those of other manufacturers.
"The particular characteristics of the 2010 virus components elicited an excessive immune response in some young children, triggering increased fever and fever-related convulsions."
BioCSL spokeswoman Joanna Hayward-Slattery said: "It's assumed that the vaccine is more immunogenic as a result.
"You always have this trade-off between immune response and the body responding too well and ending up with a high fever and consequent febrile convulsions."
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