Just over two years since Covid-19 arrived in New Zealand, the pandemic is far from over. After Delta, Omicron, the vaccine roll-out and the end of elimination, what can we expect for the rest of 2022? Otago University epidemiologist Professor Michael Baker sketched out three likely developments for science reporter Jamie Morton.
1. There'll be more Omicron waves – and a new variant
Omicron's recent rise to become the pandemic's public enemy number-one was something that astonished many scientists, given the deadlier Delta's global dominance and remarkable viral fitness.
It's quite likely that succession could be repeated by whatever major variant emerges next – but not before we're forced to ride perhaps several waves of ultra-contagious Omicron, Baker says.
"What the pandemic virus will do is still probably the single biggest thing we have to consider in planning ahead," he said.
"One of the largest lessons from the last two years has been how much this virus can change – and far more dramatically than a lot of us first expected."
Back in 2020, Baker recalled discussions with evolutionary virologists who believed Sars-CoV-2 to be a relatively stable virus, given it appeared to have been mutating at about half the rate of influenza.
"Soon after that, Alpha emerged in the UK. The next surprise was Delta, which, of course, was both more infectious and more severe," he said.
"But Omicron was an even bigger surprise, because it branched off a lineage from quite early in the pandemic virus evolution, yet the different mutations it had accumulated were quite significant in terms of its structure, and ultimately, its behaviour.
"Now, the expectation is that this virus will just keep on surprising us."
Baker expected the next major variant would arrive sometime in the coming year.
To replace a variant that's proven among the most infectious viruses ever identified – Omicron is between two and four times more transmissible than Delta - it would need to pack a fresh trait that offered it a clear edge.
"I'm not quite sure how you'd top it. Whether the next variant actually replaces Omicron is hard to know – but it will have some evolutionary niche that at least allows it to co-circulate."
That niche, he said, was highly likely to be an inherent ability to evade the immunity provided by vaccination and prior exposure to previous variants.
"Basically, it will mainly have to out-compete Omicron based on immune escape rather than being more infectious, because Omicron won't have left it much room to move in that regard."
Unfortunately, he added, we couldn't bet on another variant that caused less severe illness – something the UK Government's Scientific Advisory Group for Emergencies (SAGE) considered a "chance event" in the case of Omicron.
Rather, the group warned, what came after it was likely to have the same pathogenicity as previous variants.
One scenario was a virus that caused severe sickness and death in a much greater proportion of the population than had happened so far.
The next variant could come via antigenic shift - an abrupt, major change in the virus that could occur though different strains recombining, and deem it largely unrecognisable to our immune systems – or from a freshly-mutated virus "spilling back" into humanity from infected animals.
Ahead of that next turn, meanwhile, Baker anticipated a period of relative calm across the globe.
"For us in New Zealand, it will mean a lot more virus than we're used to, but for most countries, it will mean a lot less, because they've been devastated by it on an almost-continuous basis."
In the medium-term, he also saw a realistic prospect of New Zealand suffering waves of re-infection with Omicron, which was circulating in our communities as two markedly different sub-types: the original BA.1 and the ascendant BA.2.
"As our vaccine immunity wanes, or as the virus gets a push from other factors like winter, it may well continue to keep coming back and then settle down into a more predictable pattern."
This phase may take several years, he added, hitting the unvaccinated and otherwise vulnerable in much the same way influenza does each season.
We still need to understand the long-term effects of Covid-19 infection, Baker added.
"If long-Covid is as common, severe, and prolonged as some research suggests, that would greatly increase the need to control spread of the pandemic virus".
2. Our virus-fighting tech will get smarter
With the arrival of sophisticated mRNA vaccines came the potential to adapt this new plug-and-play platform against whatever form the virus might morph into.
While the Pfizer vaccine offered impressive protection against symptomatic infection with both the original and Delta strains of the virus, its effectiveness against harder-to-beat Omicron dropped to around 67 per cent, according to one recent US study.
Scientists have been scrambling to produce an Omicron-targeted booster, but early trials have found it to be no better than what we have already.
They also face the real possibility that, by the time they have one ready, Omicron's successor will have arrived on the scene.
Still, Baker expected vaccine-makers to take more giant strides against the virus in 2022 – be it through edging closer to the holy grail of a pan-coronavirus shot – or simply providing less-intrusive ways of boosting.
In the US, researchers at the Walter Reed National Military Medical Centre are pushing forward with a universal Covid-19 jab, using an iron-based protein called ferritin that could potentially recognise multiple spike proteins at once – and hopefully that of coming variants.
Development of this "super vaccine" has reached the first of three clinical-phase trials – but whether scientists ever managed to create something that would give strong and lasting immunity against the virus, in all its potential forms, remained to be seen, Baker said.
He was just as excited about the progress of new vaccine delivery systems: notably those that can be simply inhaled, rather than injected.
Last month, Canadian scientists reported they'd made promising steps toward vaccines delivered directly into the respiratory tract, with early trials indicating broad, long-lasting protection against the original strain and other variants.
Because inhaled vaccines target the upper airways and lungs where respiratory viruses first enter the body, they were seen as far more effective at inducing a protective immune response at these mucosal sites.
Baker pictured a near future where Kiwis receiving their annual flu shot also took a shot of Covid-19 vaccine - and potentially topped this up with inhaled boosters during the year.
"That might be quite appealing to people who are more vulnerable, and there's also the possibility of taking an inhaled vaccine when early symptoms come on – although it's questionable whether that would work."
He also expected to see plenty more movement in the antivirals space.
Pfizer's own antiviral pills, sold as Paxlovid, were recently shown to perform well against Omicron, while also 89 per cent effective at keeping infected people out of hospital.
Last week, the US said it would provide the pills at no cost to Americans who tested positive with the virus, and who were at risk of severe illness.
Baker saw potential for such an arrangement here.
"You can imagine a scenario in the not-too-distant future whereby someone with cold or flu symptoms uses a rapid antigen test (RAT), finds they're positive, then pops a handful of antivirals for a few days to protect themselves."
Pharmac has already pre-purchased 60,000 courses of Paxlovid and the other front-runner antiviral, molnupiravir, which has proven less effective against the virus in trials.
However, neither drug has been approved by MedSafe – and Omicron is likely to peak here long before they become available to Kiwis.
Baker said the pills wouldn't be cheap for the Government to fund: the Pfizer vaccine itself cost around $36 a shot.
"But we might get to the point where they're prescribed to vulnerable people who don't get a great immune response from the vaccine. It's much cheaper to have a treatment course of antivirals than risk going to hospital."
Other big gains would come from using existing technology in smarter ways.
"I'm particularly keen for New Zealand to develop a national mask strategy to make the most of this simple tool which protects against all Covid-19 variants, as well as other respiratory pathogens."
3. New Zealand will find a long-term strategy
New Zealand spent the first two years of the pandemic largely trying to keep the virus out: something that paid untold dividends for our health.
In an analysis last month, Baker and colleagues calculated that, had New Zealand suffered the mortality rates of other countries on a per capita basis, we might have lost 19,900 Kiwis (the US experience), 13,700 (UK), 9470 (Sweden), or 5530 (Denmark).
But with our barriers finally breached – our peaking Omicron wave has given New Zealand one of the highest R-values in the world – the Government needed a durable plan to manage the virus over the long term.
In early February, Prime Minister Jacinda Ardern laid out a five-step re-opening of the country, which international tourists and students will be able to visit from October.
The risk of travellers carrying the virus into the country would be mitigated by requiring them to be fully vaccinated and have a pre-travel Covid-19 test. Visitors would be given RAT tests at the airport to self-administer.
Baker supported this opening-up plan, but felt New Zealand needed to keep the ability to use the natural advantage of its isolated borders throughout the rest of the pandemic if needed to fend off future dangerous variants.
While MIQ would be effectively wound up, a core quarantine capacity would be maintained that could be scaled up as required, forming the basis of a future National Quarantine Service.
Baker saw this as a key step forward – and the Government would need to look at what accommodation it could draw on in the event it suddenly needed to surge quarantine capacity. He also considered there was a need to consider building specialised quarantine facilities.
As for other elements of what he broadly called our "public health infrastructure", he said New Zealand would remain stronger for having built up contact tracing, testing and whole genome sequencing and disease modelling capability.
"We now have new science infrastructure, and that's going to continue to be critical to identify and track emerging pathogens," he said.
"We've now got a brand-new national immunisation register, which is desperately needed, because the old one was falling over. I'm also pleased to see we're investing more money in modelling."
Like other experts, Baker had long despaired at the state of New Zealand's public health infrastructure, which was found to be run-down and lacking at the pandemic's outbreak.
But he saw much more room for improvement - or opportunity for what he called "legacy benefits" of the pandemic.
One priority, he said, should be further strengthening the country's front-line health services, including public health services and primary healthcare.
Another should be to review of the country's decision-making apparatus for major health crises like this one.
"We've never had a high-level science group, with experts representing all relevant disciplines, where key end users sitting at the other end of the table can ask what we do and don't know, and what strategies and interventions have the best evidence base," he said.
"It would be a good opportunity to use the best science and knowledge at every point – but also to discuss wider societal issues that need addressing."
Baker, who sits on the Ministry of Health's Covid-19 Technical Advisory Group (TAG), said we also needed a way of promoting cross-party political support for responses to emergencies, particularly if they are prolonged.
He cited the Epidemic Response Committee set up by Parliament in 2020 – in which MPs from all parliamentary parties could discuss the Government response and be briefed by leading experts like Professor Sir David Skegg.
One of his greatest disappointments had been the lack of a well-resourced research strategy during the pandemic.
"How can we refine our interventions and learn from the response if we are not constantly researching and evaluating everything we are doing?"
Finally, he expected to see further tweaks this year to our working playbook – the traffic light system, or Covid-19 Protection Framework as it's formally known.
Ardern has said the Government will look to lift more restrictions when the country is "well beyond the peak" of Omicron – and re-emphasised that vaccine passes for the whole of the country were only a temporary measure.
But she didn't go as far as setting an exact date for when those changes would happen – and signalled they'd remain important in some areas, "for some time".
Baker said that, while vaccine mandates wouldn't always be needed for the whole population, they could be retained in areas like healthcare, emergency services and the border workforce.
"It does make sense, because, if you're one of these essential services, you don't want to have your workforce vulnerable, and potentially all off work at once because they got sick at the same time," he said.
"There is also the occupational health and safety requirement to protect these workers with the best available measures such as vaccination.
"We need to have a mature discussion about what mandates make sense - and then roll them out in a sustainable way."
Ultimately, he felt that the traffic light system, the previous alert levels, and border controls could be re-worked to provide a more nuanced framework for managing the current pandemic and future threats of this type.
"Overall, I think it's reasonable to say that we now know the kinds of interventions we'll need to roll out quickly if we're confronted with something that turns out to be worse than Omicron," he said.
Baker noted that the current major health sector reforms provide opportunities to strengthen our public health infrastructure with creation of new organisations such as the Public Health Agency and Māori Health Authority.
"The big question – and certainly the most complex and interesting – is how we'll better design, co-ordinate and manage this pandemic response in the future," he said.
"That's what I expect to see answered this year."