New Zealand's third Omicron wave may result in hundreds more deaths from the virus before the year is out, a top epidemiologist warns.

About 2000 Kiwis have died from the virus since Omicron arrived in the country last summer – a figure more than six times last year's road toll – and modellers tracking daily case numbers say it now appears likely another surge has begun.

Given uncertainty surrounding driving factors like waning immunity, relaxed health measures and new subvariants, it wasn't clear just how large this wave might grow over coming weeks.

But experts point out that any jump in infections inevitably means more hospitalisations and deaths, on top of an ongoing Covid-19 burden that our health system hasn't stopped shouldering.

Otago University epidemiologist Professor Michael Baker said that, over an eight-month period that's brought two case peaks and varying mortality trends, the daily average of deaths attributed to Covid-19 has been around 8.5.

"Simple extrapolation would suggest we might see another 700 deaths for the remainder of this year if that mortality rate continued," Baker said.

"What actually happens depends on multiple factors, particularly the impact of new sub-variants and waning immunity."

Last week, the Omicron subvariant BQ.1.1 was detected in New Zealand for the first time.

It's thought to have a growth advantage over its cousin BA.5, which drove a mid-winter wave that temporarily made Covid-19 our leading cause of death.

"If the average mortality rate seen with Omicron continues to the end of the year we could see around 2700 deaths in total, which would account for more than 7 per cent of total deaths for the year," he said.

"That would put Covid-19 at a similar level to stroke and lung cancer, but behind ischaemic heart disease, which is our leading cause of death.

"This estimate depends on the behaviour of the pandemic over the next three months, which is unpredictable, so we might finish the year with fewer or more deaths."

This year, New Zealand's excess deaths – measuring the difference between how many people died throughout the pandemic period from any cause, and how many would've been expected otherwise – was estimated at around 2000, which Baker noted was "remarkably similar" to our Covid-19 toll to date.

"Since February 2022, we've seen mortality rates about 10 per cent higher than the baseline level we would have expected based on historic trends," he said.

"Because New Zealand was so effective at controlling Covid-19 during 2020 and 2021, we also reduced circulation of influenza and other respiratory infections."

The net effect of that was negative excess deaths since the start of the pandemic in January 2020 up until now, making ours one of the only countries with fewer than expected deaths since the start of the pandemic.

Over recent months, however, Covid-19's spread through our population had brought our per capita daily death rate closer to other comparable countries.

While virus-related hospitalisations appeared to be currently levelling out at about 150 to 200, Baker said this figure would begin trending upward on the back of a rise in cases.

"We know that numbers climbed over 1000 in March, and 800 in in July, so it is sensible to plan for those kinds of numbers - but hopefully we won't see that happen again," he said.

"Fortunately, we have new tools such as highly effective oral antivirals to help keep people out of hospital."

Covid-19 modeller Professor Michael Plank said he'd "be hesitant" to give an estimate of the number of deaths this Covid-19 wave could cause, but said the immunity the population had built up over time from vaccination and infection could help blunt its impact.

"That's generally the pattern we've seen over time, with the death rate decreasing," he said.

"But that's not to say that there won't be further deaths, because there will be: and it's quite possible we'll see a significant number in this next wave."

Plank expected that, as had been shown throughout the year, deaths would be concentrated in older age groups.

A recent Government analysis of nearly 1800 deaths also highlighted troubling inequity among Māori and Pacific people, who, relative to the population under 60, had a risk of death 3.7 and 2.9 times higher respectively.

Encouragingly, it found vaccination made a difference: the analysis showed a 62 per cent reduction of risk of death among people who'd received two or more doses.

"The best way to protect yourself from Covid-19 infection and severe effects is to be up to date with vaccination and boosters," Baker said.

Antivirals – available to those more vulnerable to severe illness - were also effective at reducing illness severity, but had to be taken within five days of the onset of symptoms.

Alarmingly, a Pfizer-funded survey released on Friday found more than half of Kiwis eligible for the medication knew little about it.

For vulnerable people especially, it remained important to minimise risk of infection.

"That means wearing a respirator-style mask when mixing with other people indoors and trying to shift socialising to well ventilated environments."

Baker added that anyone was at risk of developing long Covid following infection, with high-quality studies indicating this syndrome could accompany at least 6 per cent of cases.

"Assuming 50 per cent of adults in New Zealand have had Covid-19 infection, then that could add up to at least 120,000 people with long Covid or three per cent of the adult population."

While prevalence of long Covid could be declining as some people recovered, another wave would add many more people to that group.

Another review into Covid settings under way: Hipkins

Meanwhile, acting Covid-19 Response Minister Chris Hipkins won't say whether New Zealand's Covid-19 settings will change again before the end of 2022 – or if the coming wave could see some measures brought back.

"We keep our Covid-19 settings under regular review which includes an assessment of things such as isolation requirements," Hipkins said.

"As a review is currently under way, if any settings were to change further announcements would be made at a later stage."

Measures needed to be "proportionate" and to carefully balance risk with the effectiveness of imposing extra restrictions.

"Future variants of Covid-19 were always likely to continue appearing and we are able to adapt our response if needed."

Hipkins said New Zealand now had "many layers" of protection in place, including high rates of vaccination and natural immunity and increased availability of anti-viral medicines.

Acting Covid-19 Response Minister Chris Hipkins. Photo / Mark Mitchell

"To provide additional protection we have kept some of our most effective measures in place including mask wearing in certain healthcare settings and continue to require cases to isolate for seven days."

Hipkins didn't directly respond to a Herald question over whether New Zealand would keep that mandated isolation period in place after Australia removed its own requirements.

Baker said he wanted to see the Government and all parties collaborate on a new, "science-informed strategy" to manage the pandemic and reduce spread of the virus.

"This measure could be supported by a simple alert level system for describing the level of risk, along with agreed proportionate controls," he said.

"A key part of this would be a strong reliance on mask use and improving indoor air quality to make these environments safer for all of us.

"The public need clear guidelines on how to run Covid-safe events, workplaces, and schools."

As well, Baker saw a need to reinvigorate efforts to promote vaccination and boosters, retain what public health measures we had in place, and invest in more infrastructure – namely an infection prevalence survey that scientists have long been calling for.

A Ministry of Health spokesperson said prevalence surveys were aimed to launch before the year's end.

"The timing will depend on how quickly consultation can be completed, the necessary digital tools can be built, funding arrangements can be finalised, and ethics approval can be granted."

Hipkins insisted New Zealand maintained a high level of preparedness for variants.

"Implementing many of the measures from the old traffic light system are likely to have a marginal effect on cases and hospitalisations."