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The Institute of Environmental Science and Research (ESR) has begun reporting each week on Group W Meningococcal disease (MenW), after the number of cases jumped from five in 2016 to 24 for this year.
GPs and emergency departments have been asked to be vigilant about possible symptoms.
Fatal cases have included Whangarei seven-year-old Alexis Albert, whose grieving mother has pleaded for a nationwide vaccination and awareness programme, and Kerikeri 16-year-old Dion Hodder, who died in Auckland City Hospital soon after becoming ill during a Motutapu Island youth camp.
Meningococcal disease is a bacterial infection that causes meningitis - an infection of the membranes that covers the brain - and septicaemia, or blood poisoning.
While meningococcal B (MenB) has long been the dominant strain in New Zealand, causing two thirds of cases of the disease, there were growing concerns over the rise of MenW.
The proportion of MenB cases dropped from 67 per cent in 2017 to 49 per cent over the year to date, while rates of MenW climbed from 11 per cent to 28 per cent.
ESR public health physician Dr Jill Sherwood said the increase in the past two years had been "significantly higher" than average annual notifications for 2012-2015, when just 2.5 cases were notified.
The strain was particularly worrying as it was harder to diagnose, was much more virulent, and was implicated in higher death rates – potentially up to 15 per cent of cases.
It also affected a broader age range, with more than 40 per cent of cases involving adults older than 40.
Concerningly, it was possible New Zealand might be following trends seen in other countries, such as Australia, where MenW became the dominant strain in 2016.
"Although the number of MenW cases in New Zealand is still relatively low, there is an increasing trend in notifications and a recent change in the sequence type similar to the UK, Australia and Canada."
If or when MenW did overtake MenB was hard to predict, as case numbers were few, Sherwood said.
ESR monitored meningococcal disease by looking for patterns based on basic demography such as age, sex, ethnicity, location, living arrangements and onset dates.
"For meningococcal disease we also review group and strain type and how many cases with the same strain and group who were not known to have had close contact with each other have occurred within specific populations within the past three months."
In the early 2000s, the government rolled out a nationwide vaccination programme following a menB outbreak, but it had since been taken off the vaccination schedule.
However, the Government was now considering publicly funding vaccinations against the new strains of meningococcal disease – including MenW.
Immunisation Advisory Centre director Associate Professor Nikki Turner said New Zealand had vaccines for some high-risk groups that could be bought, but they weren't on the national schedule.
"I am aware that our authorities have, and are continuing to, put thought into introducing these vaccines to New Zealand," Turner said.
"It is a little complex and many factors need to be weighed up."
Turner noted that vaccines, while effective, didn't give lifelong protection.
"Disease occurs mostly in infants, younger children and adolescents and the organism is usually mostly carried in the throats of adolescents but not exclusively," she said.
"Schedules that focus on these two ages are likely to be the most effective. We already have a lot of vaccines in the infant schedule, so adding in others can be done, but is not simple.
"Adolescents also are likely to need a dose and currently we have a vaccine schedule visit at intermediate school age, but not at high school, which may be a better age to get through the higher risk years of late adolescents before vaccine effectiveness wanes."
The other complex issue was the role of "herd immunity" – in which a largely immune population could help protect the few that weren't.
"If we did a campaign across all young people, we may be able to reduce the carriage of the organism in people's throats and therefore prevent more disease, prior to introducing a vaccine on the schedule."
New Zealand wasn't the only country struggling with how to best manage the disease, she said.
"I believe there is definitely a role for vaccines here, but sadly they will not be a magic bullet."
By the numbers
28 per cent: The proportion of Group W of all meningococcal disease cases this year – six of them fatal - up from 11 per cent last year.
49 per cent: The proportion of the dominant Group B of cases this year, down from 67 per cent last year.
15 per cent: The potential proportion of cases of MenW that are deadly.
40 per cent: At least four in 10 cases involve patients older than 40.