There were a few days that Michael Baker will always remember as the most intense of his working life. That was in March, only about a fortnight ago, but it feels like months, maybe even years. It was the time just before the lockdown.

Rewind a little bit. Baker is Professor of Public Health at the University of Otago in Wellington and one of New Zealand's leading epidemiologists. With his colleague Nick Wilson, he has co-authored papers with fun titles like Estimating the case fatality risk of COVID-19 using cases from outside China and Economic evaluation of border closure for a generic severe pandemic threat using New Zealand Treasury methods. In short, he has been thinking about this grim stuff on our behalf for years.

ROSS GIBLIN/STUFF Michael Baker is quietly optimistic about the direction we are taking over Covid-19.

As he explains by phone from his state of isolation in the hillside suburb of Brooklyn, there was a crucial moment when his thinking about Covid-19 changed.

"We had the plan everyone else has, the influenza pandemic plan," he says. By "we", he means New Zealand. "This is written on the basis that you cannot stop influenza. We were thinking you would roll out the standard mitigation measures to minimise the harm. That's all the stuff about flattening the peak and protecting the most vulnerable."

READ MORE:

* Coronavirus: Government confirms its goal is full eradication

* Coronavirus: Plausible worst-case scenarioshows 27,600 deaths, 146,000 hospitalised

* Coronavirus: Dire consequences if we don't lock down now, expert says

* Scientist has dropped everything to tell Kiwis about coronavirus

What changed? He and Wilson were persuaded by a World Health Organisation report on China that emerged at the end of February. It told them containment could work. Rather than mitigation or suppression, New Zealand could instead aim for elimination. That is the idea that grew into a strategy during March.

"You use the full force of your control measures to prevent the arrival of the virus and its establishment in New Zealand."

He wonders if this is widely understood yet in New Zealand. We have heard politicians talk this week about "eradication" – elimination is the proper term, Baker says – of Covid-19 in this country.

"I'm not sure everyone's aware of that, but it means we're taking our own unique path, amongst Western countries anyway. Many of my colleagues internationally are cheering us on, because they think it's absolutely the right thing to do, but it's going to be tough."

It's not flattening the curve but stopping the curve from even appearing. The worst-case scenario, in modelling by Wilson, Baker and others that was presented to the Government, would have seen more than 27,000 New Zealanders die from Covid-19.

Some countries that hoped to merely mitigate by using "herd immunity" strategies, such as the UK and Netherlands, U-turned once the public health cost and political horror of thousands of deaths became obvious. Sweden is staying the course for now, though. "History will say whether it was a viable model," Baker says, diplomatically.

But for a time Baker felt very alone as the loudest voice calling for lockdown. Then it all shifted. The prime minister delivered a press conference that sounded as grave as a wartime address. There were four alert levels. Within days, we hit the top level – lockdown.

"Obviously no-one in public health wants to suggest those fairly draconian measures but I did have a huge sigh of relief when that policy came in," Baker says. "It meant all those chains of transmission that might have been occurring around New Zealand were being effectively quarantined and could gradually extinguish themselves."

There were hugs, although that was probably against the social distancing rules, and tears of relief in Baker's department. He thinks the alert levels were "a brilliant bit of risk communication to the public and it brought people along".

Neither Baker nor Wilson works for the Ministry of Health but their disease modelling became crucial. Those weeks were a lesson in "how New Zealand as a village functions". All sorts of people were able to work with key parts of Government effectively.

"Normally you would write and publish something, which would then be considered by an expert committee. But none of those systems were fast enough any more."

Some new ways of working really paid off. The Government's science advisers were one and the Science Media Centre was another. Baker is on the advisory board of the latter. A small group of science commentators who meet regularly has expanded to about 40 people who share ideas and work with media.

"You go from a hierarchy to a networked way of operating. There's less paper. Even emails become too slow. You start doing everything by phone and text."

He remembers how his arm ached from all the phone time.

"There was a sense of unreality at many moments. New Zealand was on a knife edge. There was a period when it could have gone any way. I think it's gone the right way.

"Almost everyone seemed to be sitting on the fence. I do think that Nick and myself did wind up filling that void for a period. I do think we swayed opinion towards the alternative view, which has only been articulated in the last few days."

He is "quietly optimistic" about how it is now playing out, but he wants to see more community testing data before he and his team can know if community transmission is really being snuffed out. "Unfortunately this is a very infectious virus."

There was a moment in Baker's working life that was seminal. Just over 30 years ago he took a job in Parliament as a medical adviser to the government. This was the time of the Aids crisis. He helped create the needle exchange programme that was both world-leading and an enormous success.

"You look at the data and it was spectacular. That change in thinking meant we never had an epidemic of HIV in our injecting drug users.

"What I got out of that was that governments really can change the direction of an epidemic."

He jokes that such an early success also gave him "a slightly deluded view about how easy it is to get things done" in government.

One of his other public health initiatives was around reducing campylobacter contamination in chicken. He was shocked to learn that New Zealand had the highest reported rates of campylobacter in the world in 2006. Regulation meant that the rate of disease halved in about three months, saving about 60,000 or 70,000 cases of illness per year and tens of millions of dollars, he says.

That's how public health interventions work. It was only two months ago – again, it feels like ages – that Baker, Wilson and others wrote that the 2019 measles epidemic demonstrated the dangers of the "long-term erosion and fragmentation" of our national public health capacity.

"No high-income country like New Zealand should have a measles epidemic," he says. The Havelock North water contamination crisis also showed we need a new public health agency. And could Covid-19 now be a third example?

"Obviously this will be a very powerful demonstration of why those capacities are so important," he says. "We're not saying we told you so, but I don't know how many more examples we need.

"Short term-ism isn't going to get us through. We couldn't see this coming. If we can't manage this threat, there are other threats on the horizon which are far more destructive for all of us. Surely we need a whole new way of managing our society."

But he doesn't want to seem too doom and gloom, either. He hopes we can hold on to our new sense of collective problem-solving. He also notes that in the past, pandemic fears have led to health system changes. We might expect new legislation and new ways of looking at the world after 2020. That would be a bright side.