Otago University epidemiologist Professor Michael Baker has played an influential role in New Zealand's lauded response to the Covid-19 pandemic. Photo / Supplied
The Covid-19 crisis has brought out the best of New Zealand. It's also shown Kiwis the value of science, writes Jamie Morton.
Dr Amanda Kvalsvig has worked with Michael Baker long enough to know that when he's worried, we all should be.
"He's very, very astute and his long experience in public health has given him a sixth sense for how things are going to go," she said of her fellow Otago University epidemiologist.
So it was that when she returned from a Marlborough Sounds summer holiday - cut off from the world by a dead laptop – her reunion with her typically calm and softly-spoken workmate wasn't a cheery one.
"Michael had barely said hello before he started talking a mile a minute about a new virus outbreak in Wuhan, and how serious it looked."
Baker - now one of New Zealand's most recognisable scientists - had been reading over strange cases of pneumonia since Christmas.
From the wet markets of Wuhan emerged a new a type of coronavirus, and it was now jumping between humans.
Baker's colleagues on top international panels - having pieced together the true scale of infection within Hubei - all agreed the world had a pandemic on its hands.
Watching too, was Professor Juliet Gerrard.
Only days into the New Year, the Prime Minister's chief science adviser was busy discussing the outbreak with her counterparts overseas.
"There was immediate concern - which escalated rapidly when it became clear that health workers were becoming infected," she said.
Her respected off-sider Dr Ian Town, the Ministry Of Health's resident science adviser, was across the situation before he stepped back into the office in mid-January.
While there were only a few hundred infections to count, the virus later named SARS-CoV-2 had already spread to Taiwan, Hong Kong and the US.
On the same day Hubei's 58 million residents were locked down, New Zealand took its first step: forming an incident response team.
Within a fortnight, director general of health Dr Ashley Bloomfield was urging the expansion of by-then imposed travel ban on Hubei to cover all passengers coming from mainland China.
The global crisis was escalating at a surreal pace.
Not long after the first death outside Asia, the toll of the first Sars outbreak was eclipsed, and the number of cases away from China exceeded those within it.
When New Zealand became the 48th country to report Covid-19, on February 28, Town was looking down the track.
"By the time we were contemplating community transmission, the race was on to gather evidence about the virus, analyse it and consider the appropriate public health responses," he said.
Over March, he worked alongside director of public health Dr Caroline McElnay on what culminated in a four-tier alert level system.
The March 20 memo introducing it to Cabinet ministers made for especially grim reading.
Community transmission was likely already happening undetected, and New Zealand had reached a "tipping point".
"If community transmission becomes widespread," it stated, "we will have lost the opportunity gained by closing the border."
Gerrard recalled those chaotic weeks and the rush to get out the latest science - aware that it would quickly change again.
"There wasn't time to provide formal independent briefings, but there were many conversations between health officials, science advisers and decision-makers all the way through."
Baker wept with joy and relief when Prime Minister Jacinda Ardern followed the memo's advice to "go hard, go early" and announced a nationwide lockdown.
It was the sort of aggressive action he'd been lobbying for through his seat on the top-level Pandemic Influenza Technical Advisory Group, through the media, and through calls directly to decision-makers.
Sometimes, he'd been met with blank stares, or told the move was an over-reaction.
"That feeling of being a lone voice, out on a limb, that I had it all wrong, was very uncomfortable."
Town, who opted to spend lockdown in Wellington, away from his Christchurch home, said the decision proved the right one.
"In March, case numbers were rising exponentially so even waiting a few more days might have placed the strategy at risk," he said.
"In the event, once in level 4, the levels of community transmission dropped within 10 days - indicating that elimination might be achievable."
Gerrard agreed New Zealand acted just in time.
"The most important things to achieve elimination were the speed of the response - and the clear communication of what we were doing and why, to make sure that New Zealand understood what was being asked."
Kvalsvig felt Baker's critical role, and also that of fellow Otago public health expert Professor Nick Wilson, couldn't be overlooked.
"I've known Michael for a long time now - and I've seen him proven right time and time again."
An overwhelmed health system. Tens of thousands of people dying.
It wasn't the usual careful, positive talk that Kiwis hear from their Prime Minister.
Yet that was the alternative scenario Ardern painted in her March 23 lockdown announcement.
Over the weeks before, report after report had been flowing from modellers' computers to Beehive desks.
The rest of the country didn't get to see the grim numbers within them until the Government dumped the documents at the end of that month.
One warned an uncontrolled outbreak could infect two-thirds of the population; another predicted nearly 150,000 Kiwis might get sick enough to need hospital care.
One of the last projections that came in before that fateful Cabinet decision was a death toll of up to 14,400 - roughly the equivalent of Havelock North's population.
Wilson was one of the experts behind them.
"Fortunately, I had colleagues in Germany who I'd worked with back in 2009 on pandemic influenza modelling," he said.
"It meant we could get working on an updated version of it, called CovidSIM, which we used to inform the reports that we gave to the ministry."
Experts from the centre of research excellence Te Pūnaha Matatini meanwhile raced to build their own pandemic model.
It shouldn't have been such a scramble, given the Government had asked whether they could produce one in 2017 - but they'd never heard any further.
"Initially, I was a bit pissed off that, three years later, we hadn't really started the pandemic modelling as a country," said the centre's director, physicist Professor Shaun Hendy.
"Having said that, I'd gone through it in my head what we'd need to do, and we'd had a couple of summer students who'd helped work on the kind of data we might be able to use in the event of a pandemic outbreak.
"So we didn't have to start completely from scratch."
Hendy's tight team, based across universities and Crown research institutes, include some of the best brains in their field.
Among them: Associate Professor Alex James, Professor Mike Plank, Dr Rachelle Binny, Dr Audrey Lustig, Nic Steyn, and Hendy's fellow complex systems whiz at the University of Auckland, Dr Dion O'Neale.
They started with "SIR" models, an old standard for simulating outbreaks, and then developed smarter, more detailed stochastic models.
Their earliest modelling turned out numbers not much rosier than Otago's models.
It predicted up to 89 per cent of the population could become infected - within 400 days - if measures weren't put in place.
Media outlets calculated figures from that report to reach an upper-bound, worst-case scenario of 80,000 deaths - which inevitably made it into headlines.
"It was tricky and it was something we worried about, but, you know... I was definitely of the view that we put our work out there, and then just trust the public and media to deal with it intelligently."
Their modelling came to be relied upon heavily by ministry officials throughout the year - notably when Auckland was forced to lock down a second time.
It also underscored how important it was that New Zealand acted when it did.
For instance, the 29 cases reported on April 9 could have instead been 200 - with trajectory climbing only more steeply from there.
Delaying even another three weeks could have ultimately cost 200 lives, and 12,000 infections.
Plank said those crunch-weeks were gruelling.
"There were certainly a few sleepless nights, just worrying about your assumptions, and whether you've done the coding and simulations correctly."
Hendy spent much of lockdown perched at the kitchen table of his Grey Lynn home, scanning three screens with little time to breathe.
"We were all working furiously at the start, just getting ourselves to the point where we could advise the Government."
By the year's end, O'Neale and colleagues had managed to complete an ultra-sophisticated "network" model – something that ordinarily would have taken several years.
In future, it might change the way officials respond to new Covid-19 outbreaks, by predicting how quickly the virus can spread from city to city – or even suburb to suburb.
Baker's insistence for leaders to go harder and faster will be seared into the history of New Zealand's Covid-19 experience.
But he was far from the only leading scientist who pushed for action when it mattered most.
Dr Ayesha Verrall, now Associate Minister of Health, immediately saw New Zealand's ability to manage the pressures of the pandemic was sorely lacking in many areas.
An obvious weak spot was our feeble contact tracing capacity in the emergency's early stages.
On March 17, health authorities had identified 12 cases, out of 125 already in the country – and there was only capability to trace 10 active cases.
The next week, the Otago University epidemiologist and infectious diseases expert called for an urgent scale-up.
Verrall, who was working in a hospital at the time, also knew public health units didn't have enough staff to stay ahead of a major outbreak.
"As an expert, I think the first few months were pretty stressful, because I saw the gaps in our preparedness, and I worried that they wouldn't be filled in time."
In April, she was tasked to carry out an audit for the Ministry of Health, which picked up most of her recommendations.
"One of the most challenging decisions was how high contact tracing capacity should be, and in the end, I felt I couldn't live with myself if I specified anything less than 1000 [cases per day]."
That bottom line, since adopted, has been justified by further flare-ups; she noted Melbourne's second wave saw daily surges of up to 700 cases.
The holes in our system were just as apparent to Sir David Skegg - and he bluntly voiced them when it appeared the Government had the situation under control.
The Herald likened the country's pre-eminent epidemiologist to a "hurricane of fresh air" when he told Parliament's Epidemic Response Committee in late March that it was make-or-break time.
"If we don't eliminate it in the next few weeks," he said, "the shutdown will continue for many months, or we will have a series of shutdowns that will paralyse our society for a year or 18 months, and it will never be the same again".
Skegg rubbished suggestions alert levels should be relaxed, and chastised the Government over everything from tracing and testing to border measures and strategy.
Had our public health capacity not been so run down – a key criticism made in his 2019 book - New Zealand may have even avoided its rigorous lockdown, he said.
He remained an important scrutineer throughout the year, and reacted with shock when it was revealed in August that nearly two-thirds of border workers had never been tested.
As New Zealand's post-outbreak focus turned to preventive measures, another expert saw signs of complacency.
Dr Andrew Chen, a researcher at University of Auckland-based Koi Tū: The Centre for Informed Futures, has closely tracked daily QR code scans from the NZ Covid Tracer app.
As numbers plummeted from a peak of 2.5 million, amid the Auckland August outbreak, to fewer than a million, he used social media and news interviews to compel Kiwis not to let their guard down.
"Contact tracing tools like the app are preventative tools, so we need to be using them before an outbreak occurs," he said.
"And that rubs against the challenge of convincing people to do something when the threat is not present."
The pandemic has introduced Kiwis to a world of clever technology many might've otherwise never discovered.
The stand-out has arguably been genome sequencing.
Well before Covid-19, Dr Joep de Ligt and his ESR colleagues were using it to monitor health threats like anti-microbial resistance.
By using a virus sample to decode – or sequence - its entire genetic make-up, scientists could reveal its lineage and where it came from.
That couldn't be more important when untangling clusters, or linking community cases back to border breaches.
Sequences of the SARS-CoV-2 genome have also given vaccine makers an invaluable head-start on what specific parts of the virus' protein structure to target.
Just as with vaccines, the pace of the global genomics effort has been astonishing.
Chinese researchers produced the first complete sequence on January 10.
Only 15 days later, UK scientists released the first design for sequencing the virus, and sent the ESR team their materials to get their own systems up and running.
De Ligt's team made the call early on that they wanted to sequence every single case that turned up here.
"There was a lot of interest in the first couple of cases that we quickly sequenced - but that changed rapidly when the first wave hit for real, and lockdown happened."
Two pieces of equipment - a GridION sequencer and an Opentrons robot - allowed them to handle the larger volumes of samples that were soon streaming into their labs.
By May, ESR scientists were working with Massey University counterparts, Drs Olin Silander and Nikki Freed, on speeding up sequencing to near real-time.
Impressively, scientists ultimately managed to sequence the whole genomes of 649 separate cases from the first wave - representing about half of them - to reveal nearly 300 different introductions from different parts of the world.
They used that data to create visualisations and new research pipelines - but also to tout its potential to government officials and diagnostic labs.
"We were basically busy convincing everyone that what we were doing was not just another research project," de Ligt said, "but something that was going to impact decision-making and policy".
That couldn't have been illustrated more than when, last month, Health Minister Chris Hipkins confirmed a rogue case in Auckland had been genomically linked to a cluster already under control.
A small team of scientists had worked late into the night to match the genetic signature of the latest case to another existing one.
For Aucklanders, it meant there was no hidden outbreak, and that they wouldn't have to lock down for a third time.
In New Zealand, it now took around 10 hours to sequence a genome from a virus sample, compared with up to two days overseas.
The Auckland sample was matched only about seven hours after it was received.
De Ligt singled out his ESR colleagues Una Ren and Matt Storey for a year of hard work, which often saw them toiling over evenings and weekends.
He also praised collaborators Dr James Hadfield and Dr Jemma Geoghegan - both who co-incidentally arrived in the country when they were needed most.
Geoghegan, jointly based at ESR and Otago University, said her young family went into lockdown just 25 days after they moved from Sydney.
"Like all academics during that time I was juggling working from home, writing grants, teaching via Zoom, and entertaining a 14-month old who decided lockdown was the perfect time to start walking."
She put the success of the sequencing programme down to scientists here and overseas keeping their channels open, and sharing what's become a massive repository of data.
Associate Professor Siouxsie Wiles - the British-born microbiologist synonymous in New Zealand with pink hair and superbugs – wasn't sure what to make of the pandemic's early murmurings.
"In those first few days, I remember thinking, oh, this is interesting, but it may well be nothing, right? We've seen unknown things before, and they haven't turned into anything," she said.
"But when China began building new hospitals, it was like, wow. Okay, this is clearly serious."
Over a decade of blogging, podcasting, making kids' TV shows - all while leading the University of Auckland's Bioluminescent Superbugs Lab - she'd become the country's hardest-working science communicator.
In some ways, she said, all of that public outreach, and those countless media interviews, had been training for the big event that was Covid-19.
From January, she was fronting shows like RNZ's Afternoons to discuss the new virus, in what were the first of likely thousands of interactions with broadcasters and reporters across 2020.
"The phone was ringing permanently and I was reading everything I could get my hands on, from everywhere, just thinking about what needed to be communicated, and what people needed to understand," she recalled.
"It was absolutely manic. I was basically going to sleep at midnight, then I'd be up at 5am again, looking at what had happened overnight in other countries, and being ready to go again."
Wiles found her main megaphone in regular columns for The Spinoff, cleverly illustrated by comic artist Toby Morris.
Their work - traversing topics as varied as masks, bubbles, case lags and alternative handshakes - proved handy public resources to Ashley Bloomfield, and eventually even the World Health Organisation.
"For me, this year has kind of vindicated the importance of science communication, which has clearly been something I've been passionate about for a long time," she said.
"And yet, it's always been so under-valued and not seen as a good use of my time - like, I should be focused more on writing scientific papers, and things like that."
Her efforts have drawn praise and plaudits – the BBC called Wiles a "force of nature" in naming her among its 100 most inspiring and influential women of 2020 – but also nasty abuse.
Still, she hasn't shied from championing public health, even when it's meant having to counter contrarian academics arguing against policy overwhelmingly backed by their peers.
Wiles agreed much of New Zealand's lauded response owed to experts who hadn't just practised science, but fought for it by stepping into the media glare.
Baker, Wilson, Hendy, Verrall, Gerrard and Skegg have also proven enormously influential science communicators, as have dozens of others.
They've included Kate Hannah, who demystified the world's parallel epidemic in social media-driven misinformation, and clinical psychologist Dr Sarb Johal, who shared simple tips to help Kiwis cope with uncertainty.
Professor David Murdoch, a world-leading infectious diseases researcher who's helped guide vaccine efforts here and overseas, has been a regular voice in the media, as has Massey University's Professor David Hayman, a renowned expert in disease ecology.
The expertise of figures like Professor Graham Le Gros, Associate Professor Helen Petousis-Harris and Dr Nikki Turner will make them crucial figures when the first vaccines arrive next year.
Did an evidence-informed Government - and public – ultimately save New Zealand from the fate of other nations?
"I don't know… but I imagine our response will be studied in years to come, to find out what worked and what didn't," Wiles said.
"I was always hopeful the Government would make the hard decisions needed to get us on the right track – which they did – but I felt my role was to help people understand what was happening, and why those decisions were being made."
Indeed, Town said overseas counterparts have asked about many aspects of New Zealand's response, which was covered in a World Health Organisation round-table session this month.
"Interestingly, the more recent questions have been about communications and maintaining trust."
He remained "hugely proud" Kiwis placed their trust in science – something that was also built through Ardern and Bloomfield's 1pm addresses.
But while the evidence under-pinning it was critical, elimination could never have been achieved without the compassion shown by everyday Kiwis toward others.
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