University of Auckland vaccinologist Associate Professor Helen Petousis-Harris said an outbreak amid New Zealand's normal flu season would prove a "double whammy" for under-pressure hospitals and GP clinics.
"We're talking about the same number of healthcare professionals, and the same amount of equipment, and we may get a lot more people with severe respiratory conditions that need care."
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The ministry's director of public health, Dr Caroline McElnay acknowledged a flu season outbreak "would be a challenge" and needed to be considered in planning.
However, she expected 2019-nCoV would emerge here as single "pop-up cases" that would be quickly quarantined to avoid further spread, as had been so far managed in Australia.
GP clinics across the county have already reported running out of masks and other protective gear – despite the Government holding on to 18 million masks.
"Maybe people who don't normally get their flu jab might want to consider it this year, to reduce the number of cases overall," Petousis-Harris said.
Over recent times, New Zealand's flu season had been peaking around August, although last year it began months earlier and brought higher than usual rates seen in 2016 and 2018.
The Immunisation Advisory Centre said two vaccines funded for this year covered four strains – including H1N1 and H3N2-like viruses.
Scientists around the world are scrambling to develop a vaccine for 2019-nCoV itself – either from scratch or with a repurposed one – and more than 80 clinical trials are underway.
But McElnay said it might be up to 18 months before one was available.
Professor Mick Roberts, an infectious disease modeller at Massey University, said it also wasn't clear how easily and quickly 2019-nCoV could spread in New Zealand.
"How the virus develops biologically in the body won't be too different from what's been seen in China, but the contact rates will be different, because in China you are in contact with a lot more people."
Professor Nick Wilson, of University of Otago's Department of Public Health, said there could be a need for the Government to order extra flu vaccines, given the heightened threat.
While public health units, primary care and hospitals have been getting prepared over recent months – and testing facilities are now operating in several diagnostic laboratories – Wilson was also concerned about how a 2019-nCoV outbreak would impact the health system.
In the latest Global Health Security Index, New Zealand scored just 54 out of 100 – coming in 35th in rankings of 195 countries, far behind Australia, and the US, the UK, Canada and France.
The country scored zero for some indicators such as "data integration between human/animal/environmental health sectors" and "exercising response plans" – and remained one of the few high-income countries in the world not to have a field epidemiology training programme.
"It goes right back to planning – and this index shows that our pandemic preparations are not that well developed," Wilson said.
That was despite New Zealand having recently updated its national pandemic plan.
The plan was now set at the "keep it out" phase – clearing authorities to screen or quarantine travellers, and prepare the release of pre-pandemic vaccines or antivirals.
As long as New Zealand remained coronavirus-free, Wilson saw this as a larger concern than the threat of a compounded flu season.
"The longer we can delay it, the longer we'll have to gain more knowledge to create vaccines and develop better control measures," he said.
"So I think it would be reckless to say, don't worry about letting it in here."
Ahead of a public awareness campaign being launched tomorrow, health authorities have split suspected 2019-nCoV cases into two categories.
People coming from China – now a "category one" country – would need to self-quarantine for 14 days, while doctors were being urged to be extra vigilant about any patients with flu symptoms who had returned from a "category two" country: Hong Kong, Iran, Italy, South Korea and Thailand.
The Ministry of Health has meanwhile assured people that New Zealand is "well prepared" and had a system for early identification and case management up and running.
McElnay urged people to phone ahead to their GP practice if they were concerned they might have the virus.
"If you have recently returned from a country or region internationally with a recent increase in cases and have a fever, difficulty breathing or a cough it's important you ring Healthline's dedicated Covid-19 number first or ring your General Practice before making a visit and potentially putting others at risk."