Special Report: A century ago, one in five people who died in New Zealand were killed by an infectious disease.

Infectious diseases, as a group, took more lives in 1922 than heart disease. Twice as many people were killed by communicable viruses or bacteria as died of all forms of cancer combined.

These days, heart disease and cancer make up nearly three in five deaths each year. Mass mortality from infectious disease is considered a relic of the past or an unfortunate struggle for developing countries.

But it wasn’t that long ago that New Zealand, too, grappled with that same threat. Endemic diseases caused severe long-term complications (polio paralysis) or significant numbers of deaths (smallpox and tuberculosis).

Covid-19 could push us some of the way back to that older era, when infectious diseases were common enough to worry about regularly and posed a serious threat to the health system. The virus that causes Covid-19 continues to evade our immunological defences, raising the spectre of a permanent, endemic, but far from harmless illness. 

There is no reason, experts say, why Covid-19 wouldn’t continue to kill five to 10 New Zealanders a day for years to come. And that’s outside of the context of major seasonal surges, which remain on the cards.

Government policy and public attitudes since the peak of the Omicron wave seem to have been undergirded by an assumption that Covid-19 is over. The pandemic has hit us, swept through us, killed a few hundred people, and moved on.

Nothing could be farther from the truth. 

The virus is likely to become endemic in New Zealand, as in the rest of the world. But that doesn’t mean it will be harmless.

A permanent presence from Covid-19 means we are now in a long-term war with the virus. Reinfections will become the norm – a never-ending battle against an ever-evolving foe.

The only determinants of how many people will be sickened, disabled or killed by the virus are its own evolutionary leaps and our actions to shape its environment.

Hundreds of excess deaths

For weeks, the number of daily Covid-19 cases, deaths and hospitalisations has remained relatively flat. It looks increasingly like we’ve found our baseline for the virus, outside of the context of surges.

“The effective reproduction number is hovering about one in New Zealand because things are flatlining, so the cumulative impact of everything we’re doing is reaching this new equilibrium,” University of Otago epidemiologist Michael Baker told Newsroom.

The health burden of that new normal is higher than many people might have expected. Dozens of deaths are reported each week by the Ministry of Health. A small number of these end up being unrelated to Covid-19, but 80 percent are either caused directly by the disease or list it as a contributing factor.

Based on that, it’s been nearly three months since we last had an average “true” Covid-19 death count below eight a day. The daily average since then has been closer to 11, after accounting for unrelated deaths. Over a year, that would lead to more than 4000 deaths – eight times worse than the seasonal flu.

Covid-19 is also showing up in all-cause mortality statistics. Between the start of March and mid-May, 831 more people have died than would have been expected to, based on mortality trends from 2020 and 2021. That shows we’re already erasing the gains from the first two pandemic years with a 10 percent bump in mortality. Even against the pre-pandemic baseline, we have seen 446 excess deaths in that time period. By any standard, the wave of death sweeping New Zealand is more than just unusual.

Cases and hospitalisations have also stayed elevated, with the number of patients in hospital fluctuating between 350 and 400 a day and the number of new daily admissions barely dropping below 100. Director-General of Health Ashley Bloomfield said on Tuesday that current Covid-19 prevalence is twice as high as the Government’s modelling anticipated.

Clearly, we will not eliminate Covid-19. It also won’t go away through infection- or vaccine-acquired herd immunity.

When Omicron took hold in the United Kingdom, about one in every 10 new cases was a reinfected person. Now, as new Omicron sub-variants spread around the country, reinfections make up 16 percent of all new cases. Reinfections are expected to become commonplace. Mass infection isn’t the route out of the pandemic.

“It’s going to get to a point where not having some protection is going to be very rare,” University of Otago evolutionary virologist Jemma Geoghegan said. “So the population is forever changing and the virus is finding new avenues to explore to combat that protection. Reinfections are going to become more common as immunity wanes.”

Getting Covid-19 once doesn’t mean you’re safe for good. The aim now is to get infected as few times as you can, because the effects of multiple exposures are still poorly understood. Despite this, experts overseas say the average person will catch Covid-19 every three years or so.

“Barring some intervention that really changes the landscape, we will all get SARS-CoV-2 multiple times in our life,” University of Michigan epidemiologist Aubree Gordon told The Atlantic in May.

There has been an implicit assumption in the public mind, as well as in Government policymaking and the declining media coverage of the ongoing pandemic, that Covid-19 is bound to become harmless or simply vanish. The blindness to the continuing illness and death, let alone any lack of looking forward, calls to mind former US President Donald Trump’s ridiculous assertion in February 2020: “It’s going to disappear. One day – it’s like a miracle – it will disappear.”

As Mediawatch reported recently, an all-hands email to Stuff – the country’s largest employer of journalists – said “our audience have actively moved on from Covid content and the company needs to stay ahead of that trend”. And it’s not just the media. The Government insists the pandemic isn’t over but isn’t acting like it, health experts say. It’s even planning to scrap the Covid-19 legislation which gives it the tools to fight the virus.

“There’s no biological reason why the three main consequences of Covid-19 [hospitalisations, deaths and Long Covid] will settle at any particular point. There’s nothing that says that Covid will somehow drop below that threshold and become like the four coronaviruses that cause the common cold,” Baker said.

Endemic isn’t harmless

Instead of attenuating until it is no worse than the flu or – like a miracle – disappearing, Covid-19 is here to stay. It will join the roster of infectious diseases that we grapple with on a regular basis, like measles, RSV and influenza. But the threat it poses to the health system and its ability to kill and cause Long Covid put it somewhat closer to those older diseases we have since put behind us.

“There’s a fair chance it’s going to sit in this tricky space where it is more serious than the flu but it’s not the existential threat that it was in 2020,” University of Canterbury mathematician and Covid-19 modeller Michael Plank said.

For more than two years, people have looked forward to Covid-19 exiting a pandemic state and becoming endemic, as if that marks the end of our struggle with the virus. In truth, this is just the beginning.

“Calling a disease endemic doesn’t at all imply that there’s a steady state or a mild disease,” University of Otago epidemiologist Amanda Kvaslvig said. “Covid-19 is turning out to be far worse than flu in terms of its public health burden.”

Polio was endemic in New Zealand at one stage. Smallpox was endemic all around the world for centuries and still killed millions of people.

In advice to the Government in December, the Strategic Public Health Advisory Group led by Sir David Skegg warned against seeing endemicity as a sign of harmlessness.

“With respect to Covid-19, this term has often been incorrectly conflated with concepts of severity and manageability, implying that an endemic disease is, by nature, mild and easy to manage,” Skegg wrote.

“Malaria is an endemic disease in large parts of the world: it causes much severe illness and is estimated to have killed over 600,000 people (mostly children) in 2020. Measles is a viral disease also endemic in many countries, and it is a major cause of sickness and death in children.”

The Government’s other key independent advisory group, led by Sir Brian Roche, similarly said in March that the Omicron wave won’t be our last.

“It may be tempting to view the current wave of Omicron as the final hurdle to overcome before a return to a sense of normality. However, it is important that this view is not relied upon as we move beyond the fulcrum of the wave. We need to avoid optimism bias in the face of continued uncertainty – a balance is required.”

All that “endemic” really means, epidemiologists say, is that a given pathogen is operating in a predictable manner.

“Endemic largely means it has become relatively stable and predictable as a threat. That doesn’t mean it’s at a constant rate, it might be that it has a seasonal pattern. We would consider seasonal influenza to be an endemic threat,” Baker said.

Covid-19, Baker said, is “still an epidemic disease, still a pandemic disease, because it’s not predictable. That continuing evolution has to be the big unknown.”

While others disagree, University of Otago infectious diseases physician Philip Hill told Newsroom the point at which the virus is considered endemic is not particularly important.

“From one point of the view, the pandemic is over and we’ve now got a new pathogen in our midst that we have to interact with for a while. The question is, how much of its transition into being that chronically with us endemic pathogen do we say has to finish occurring before we accept that it’s just simply a pathogen that’s with us,” he said.

An ‘evolutionary arms race’

Either way, we know that Covid-19 won’t be going anywhere. The next question is what a future with Covid-19 holds for us. Is the current baseline of cases, hospitalisations and deaths where we’ll end up in the long term, outside of seasonal or variant-driven surges?

“It’s certainly plausible that you’d be looking at the 200 to 400 hospital beds range and the five to 10 deaths a day range, in the medium term,” Plank, the modeller, said. However, the severity of second and third and fourth infections remains unknown – if they’re less and less severe, then that health burden could reduce.

“Look, the deaths we’re having per day now, that’s uncomfortably high for most people, I think. At the same time, we have not finished improving vaccines and we have not finished improving therapeutics, so we have not reached an equilibrium yet,” Hill said.

In order to take a guess at what comes next, we need to understand that we are now in an evolutionary war with Covid-19. New variants and seasonality are on the side of the virus. For our part, we’re relying on human innovation to produce new treatments and vaccines and on the will of governments and societies to undertake public health measures to reduce transmission.

“Both the host and the virus are in this evolutionary arms race where they keep changing to try and beat each other,” Geoghegan, the virologist, said.

“As the virus changes, so does the host, and then the virus has to change again to combat the host’s protections. It’s a never-ending battle. I don’t think stopping the evolution is actually going to ever happen.”

How could the virus change next? That’s hard to guess, Geoghegan says. We know it will select for any inherent transmissibility boosts that make it easier for the virus to enter cells. It will also preference mutations that enable it to evade vaccine- and infection-induced immunity.

The only way a new variant takes the world by storm is if it can outcompete Omicron, which continues to optimise for immune evasion through its various sub-variants.

None of this has any bearing on whether the virus becomes more or less severe (or virulent, in technical terms).

“It’s a fallacy to think that viruses always attenuate to become less virulent. There’s lots of examples where that hasn’t happened, for example, HIV,” Geoghegan said.

“We’ve seen this through the pandemic how Delta was more virulent compared to Alpha, whereas Omicron is somewhat lesser than Delta. So we don’t actually know what variant, in terms of virulence, will hold. It could go either way.”

Omicron’s sub-variants appear to be arising from mass infection and random mutation. But there are other processes that could cook up nasty new immune-evading variants as well. One is a chronic infection in an immunocompromised person. This is thought to be how many of the variants of concern that we’re familiar with first arose.

For months, the virus will have fought with a patient’s weakened immune system. It won’t be strong enough to kill the person, but they won’t be strong enough to kick it out. For the virus, rapidly replicating and infecting cells inside a chronic, immunocompromised person, the weakened immune system provides the perfect training ground for effective evolution.

Another potential avenue, Geoghegan said, is recombination of different variants, perhaps in an animal host. This is how new strains of influenza arise – the 2009 swine flu pandemic, for example, came from a fusion of human and avian flu in a pig.

“The fact that there’s many, many mammals that are susceptible to SARS-CoV-2 means that that’s a real risk for the emergence of new variants as well.”

Upgrading our arsenal

To protect ourselves from the ongoing onslaught of Omicron and the threat of new variants, we desperately need an upgrade in our virus-fighting pharmaceuticals. Next generation vaccines, in particular, could be immensely useful. These would either be variant-proof shots or immunisations which give mucosal immunity to block infections in the first instance.

While several of these vaccines are in development, funding for research has dried up after the first wave of vaccines arrived on the scene. A divided United States Congress has failed to renew funding for both domestic pandemic control measures and new R&D, when American cash helped bring many of the initial vaccines to market.

Likewise, new treatments to reduce the severity of illness will become crucial if we want to lower our daily death toll. Paxlovid remains one of the only treatments that is both widely available and hasn’t been overtaken by viral evolution. But as previous treatments, like monoclonal antibodies, were rendered ineffective by Omicron, putting all our eggs in the Paxlovid basket seems ill-advised.

Despite the dour outlook on the innovation front, experts agree that this is our best bet if we want to reduce the impact of Covid-19 to something closer to the flu.

“I would say that’s the big game changer, having that advance in technology. If we don’t get that, we’re just stuck with the virus and where we would be on this equilibrium, which is going to be this endless… well, we’re seeing what that looks like now,” Baker said.

“If we can get a vaccine that can reduce transmission, that will be the big structural change in the response, but until that point we need these other background measures and focusing on protecting those most at risk,” Covid-19 Modelling Aotearoa lead researcher Emily Harvey said.

That puts the onus on the Government to respond to the higher-than-expected mortality. Not only will interim measures likely be needed going into winter, but ministers need a plan for the sustainable management of Covid-19 going forward. Merely hoping it goes away won’t be enough.

“The case is building for New Zealand to adopt a high suppression approach to Covid-19. Until we have a new generation of vaccines that can induce lasting immunity the best way to prevent a heavy population health burden and health system overwhelm is to adopt a Vaccines Plus approach and actively reduce community transmission,” Kvalsvig said.

Plank said we need both a temporary set of measures for new surges and a toolkit for ongoing transmission.

“I think, thinking about the sorts of measures and interventions that we might take against Covid, it’s helpful to try and think about measures that are temporary interventions that you might use if you’re in a wave, if you need to flatten the curve, if you need to reduce demand of healthcare systems in a busy period, that sort of thing. And then to have a sort of separate category of things that actually are long-term, sustainable measures that we can have in place that have broad benefits, maybe not just Covid but other things as well, that are actually good investments to sink some resource into.”

That latter category includes things like ventilation improvements in buildings – not sexy, but crucial to slowing spread. Covid Modelling Aotearoa’s project lead Dion O’Neale added that systemic changes to sick leave arrangements could also provide a long-term boost to the fight against the virus.

“If you want to go the policy route, there’s things like isolation and quarantine which are really effective at stopping spread,” he said. That only works if contacts and cases can afford to isolate until the virus clears their system, which could take well over the seven days currently recommended by the Ministry of Health.

The new Covid-19 Response Minister Ayesha Verrall declined to comment for this article. A spokesperson said she would be able to give more specifics about the Government’s plan for Covid-19 going forward when its variant plan is released later this month.

In the end, Kvalsvig returns to the comparisons of Covid-19 to other illnesses. Rather than the flu, however, she likes to look at it next to polio.

“Polio is highly infectious so when it’s endemic it can cause large outbreaks each year with significant spikes in case numbers. It does terrible damage to children’s health as an endemic disease and that’s why we don’t tolerate it,” she said.

“Covid-19, another highly transmissible infection with long-term consequences for health, may well end up in that same basket of diseases that are simply too infectious and too harmful to tolerate ongoing high levels of community transmission.”

And without any other interventions, high levels of community transmission are what we’re destined to get. The Covid-19 pandemic may be coming to an end, but our fight against the virus is just beginning.

Marc Daalder is a senior political reporter based in Wellington who covers climate change, health, energy and violent extremism. Twitter/Bluesky: @marcdaalder

Leave a comment