Delta finally invaded New Zealand in August - and for the last three months the fight has been on to control the outbreak. So how did it persist in the face of lockdown, and ultimately spread all over Auckland? Derek Cheng tracks how it all unfolded, and what it tells
Big Read: Tracking the Covid 19 Delta outbreak - How it arrived, simmered through lockdown, then spread beyond reach
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From there, it eluded the considerable efforts of public health teams and then exploded all over the city, including into Waikato and Northland. In recent days, cases have popped up all over the North Island as far south as Masterton.
Efforts to eliminate it continue as vaccination rates edge higher, except in Auckland where the virus has permeated the whole city for several weeks, and where resources are now targeted to where they're seen as most needed.
Delta is now expected to spread all over the country in coming months as New Zealand transitions into the traffic light framework.
But the key challenge remains - how to protect vulnerable communities where infections will exacerbate already existing inequities.
This will become more urgent if, as is now expected, the country will move into the new traffic light framework before each and every DHB region hits 90 per cent of eligible people fully vaccinated.
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Transtasman beginnings
The outbreak came from New South Wales, where Kiwis were allowed to return from despite the loud and clear "flyer beware" warning from Prime Minister Jacinda Ardern when opening the transtasman bubble.
Delta in Sydney and Melbourne was exploding to such an extent that both cities had gone into lockdown. Stranded Kiwis on mercy flights from Sydney didn't even need negative pre-departure tests, but had to spend 14 days in MIQ.
One returnee from Sydney flew to Auckland on August 7, tested positive for Covid-19 after infecting people in an adjoining room at the Crowne Plaza, and was then moved to the Jet Park quarantine facility on August 9.
The genome from this case matched those that were in Sydney at the time, and he is probably the index case, but this is not certain.
"In Australia, there were about 20 people with that genome that they knew of," says ESR bioinformatics lead Dr Joep de Ligt.
"It could be that there were maybe two people, but they carried the same genomes."
How it spread into the community in Auckland is not known.
There are actually several genomic matches between community cases and MIQ cases, but no epidemiological link has been made between any of them.
It wouldn't be the first instance of "cryptic, weird transmission events", as described by evolutionary virologist Dr Jemma Geoghegan.
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"We can narrow down a timeframe and a likely source, but those steps in between have not been able to be resolved," she says.
Several likely transmission events since the start of the pandemic fall into this category, including shared airspace on a flight or in an elevator, or from virus-carrying air particles that shifted between MIQ rooms while their doors were left open at the same time for 50 seconds.
There has been speculation about a member of the public catching Delta while walking through the public atrium in the Crowne Plaza. The public and private areas were separated by a perspex barrier and, while this didn't completely seal them from each other, a review found the chances of cross-infection "negligible" - less than 1 per cent.
As a precaution, though, the gap between the perspex barrier and the ceiling was sealed.
Once in the community, the virus wasted little time hunting the unvaccinated.
Ministry of Health data from August 10 show that fewer than a quarter of Auckland's eligible population (16 and up at the time) were fully vaccinated, while 39 per cent had received one dose.
Coverage among Pasifika, who made up 70 per cent of the cases in the first weeks, was much lower at about 20 per cent of eligible people double-dosed. For Māori, who would by October become the main ethnic group among daily cases, it was 16.5 per cent.
About 800 to 1000 cases already circulating undetected
The first case in the outbreak was detected on August 17, by which time the virus had likely been circulating for at least a week. The following day, the whole country woke to level 4 restrictions.
There were already about 800 to 1000 undetected cases by then, including dozens who were part of a Birkdale network, which centred around a household that was connected to a tradesman's business in Devonport.
There was also the super-spreader event at the Assembly of God church service in Māngere, attended by 500 mainly Pacific people, from where someone carrying the virus hopped on a plane to Wellington.
The genome of the cases that seeded the church subcluster had a mutation, which allowed ESR scientists to track it.
Level 4 almost slammed the door on this subcluster, Geoghegan says.
"They were completely dominating this outbreak at the very start because of the super-spreading event, but it was remarkable how quickly it became under control. And we were convinced that it was extinct."
Within two weeks, daily case numbers had seemingly peaked at 83 and, by early September, level 4 stamped out the Wellington chain. The regions outside Auckland, including Wellington, were moved to level 3 on September 1.
The church subcluster had some 330 cases by then but was now climbing at a much slower rate (it would top out at 386). Daily cases started to tip below 20, and the goal of zero cases looked like it was only a matter of time.
But health officials and Covid-19 modellers knew that it was going to be a challenge, particularly as cases were among larger, intergenerational households where communal living spaces were more common.
"The Pasifika positivity rate remains around 1 per cent," said a September 8 email from Rodney Jones, principal at Wigram Capital Advisors and a Covid adviser to the Government.
"This is far too high for an elimination strategy, and suggests that there remain undetected background cases. To get a handle on this, we need to start surveillance testing among the Pasifika community in South Auckland. This is critical."
Emily Harvey, a principal investigator at Te Pūnaha Matatini, replied that it was better to target those with symptoms as well as areas with unlinked cases and new locations of interest: But Jones said this wasn't enough because of the number of "asymptomatic carriers".
The next day, the ED at Middlemore Hospital treated a woman for a health issue unrelated to Covid. A health screening did not indicate any Covid symptoms.
Before she left and returned to where she was staying - the Mongrel Mob Pasifika gang pad in Takanini - she agreed to be tested, which came back positive.
A mobile testing station was set up and a gang member who also lived there soon tested positive.
Meanwhile Auckland remained at level 4, while regions outside Auckland were at level 2.
"People in Auckland were not moving about and the reproductive number was low, but the virus was sort of simmering in the background," says de Ligt.
"That's the part that found the inequity. These are populations that don't have the ability of not going to work, or keeping their kids at home, or all those other things that are easier for others that have financial security or extensive support networks.
"Everywhere around the globe we see that Covid at some point finds inequity, and then it explodes. We've seen something similar here in New Zealand."
Chasing elimination
A few days later, on September 12, Ardern signalled Auckland stepping to level 3 in a week's time, describing the number of active unlinked cases as only a small handful.
Bloomfield reiterated this in the next day's press conference: "It's really only a small number of cases that we are investigating very thoroughly just to make sure there is no ongoing community transmission. Another week in alert level 4 in Auckland gives us our best chance to really finish the job off here."
The Assembly of God subcluster was all but closed off and, while Māori were becoming increasingly prominent in the proportion of daily cases, those numbers remained low.
Ardern and Bloomfield asked people with or without symptoms to get tested in seven Auckland suburbs - rather than by ethnicity - where missing links to mystery cases might still be circulating under the radar.
Meanwhile particular genomes thought to have been caught in workplace transmissions also seemed to run out of steam.
"There was some intense focus on essential workplaces under level 4 to try to minimise the spread, and a couple of them were caught and nipped in the bud," de Ligt says.
"The ones we were aware of, we haven't seen them go on to seed any of these clusters. If there was a specific mutation that happened at one of those places, we've not seen them since."
It was around this time that a new genome appeared, one that was missing 10 nucleotides.
"When we compare each of the genomes, there's a gap in that one," says Geoghegan. "This is quite a common occurrence, but it enables us to group these cases together from a single deletion event that's happened."
De Ligt says the first such genomes started appearing in sequencing results in mid-September, but it's hard to say when and where it first started circulating.
"It wasn't one neighbourhood or one certain group of people. It has been associated with emergency housing and marginalised communities, but we don't necessarily have any reason to believe that that is where it originated.
"It most likely originated somewhere in that sort of background noise in the community, and then made its way into those vulnerable communities, rather than the other way around."
The outbreak, though, continued to appear on the wane, with the number of new daily cases falling to almost single digits.
Auckland moved to level 3 on September 22, which experts called a "calculated risk", and which would later lead to speculation over whether it was the wrong move.
By then, the Government already knew that the virus was among marginalised communities. Ardern has said the move didn't add any material risk, given that those groups were unlikely to change their behaviour depending on what alert level it was.
This is also understood to have been the advice of public health teams on the ground. Cases did eventually start trending up, but it's impossible to say whether the numbers would have been lower if level 4 had been maintained.
Ardern had said that good testing numbers would provide assurances around any undetected transmission, but what if the people who should be tested aren't coming forward?
In a recent interview with the Herald, Associate Health Minister Ayesha Verrall was blunt about the chances of elimination when Auckland was moved to level 3.
"The elimination tools we had against the original and other variants were not effective in the time that was sustainable for the lockdown."
She added: "We had substantial evidence that it wasn't working ... We had no chance of stamping it out, absolutely."
Zero cases slips out of reach
Māori health leaders in particular were nervous about what might happen. More than half of eligible Māori were still unvaccinated, and about 60 to 80 per cent of people homeless or living in vulnerable housing are Māori or Pasifika.
Two days later, there were only nine new cases, none outside Auckland, and two days after that - September 26 - the number of active unlinked cases dropped to five.
But the daily numbers are only indicative of what happened one to two weeks beforehand, and only paint a picture of known cases.
"When those alert level decisions were being made, people were convinced that there was not massive undetected spread," says de Ligt, "but the problem with undetected spread is that determining the size is almost impossible - because it's undetected.
"There's really large uncertainty with those decisions. Even the genomes, they were helpful, but if you're not seeing those cases, they are only providing part of the picture."
Looking back today with the benefit of hindsight, de Ligt says it's clear the genomes linked to the deletion event spread rapidly through some of those marginalised groups.
It wasn't the only subcluster that was still spreading, though. Genomes related to the index case also continued to appear, a sign that so-called cryptic transmissions had seen this lineage continue throughout level 4.
Daily case numbers fluctuated towards the end of the month and then started to trend upwards.
Covid-19 Response Minister Chris Hipkins continued to reassure the public that "we're still aiming to run this into the ground", but he later told the Herald that this was when the Government started to realise the goal of zero cases was slipping away.
By then, the virus had already spent weeks hunting the unvaccinated and the vulnerable. Māori and Pasifika made up the vast bulk of cases, as did young people. At least three gangs also had cases among their ranks or associates. Today, 178 cases in the outbreak have gang links.
Ministry of Health Pacific health director Gerardine Clifford-Lidstone gave some candid insight when she appeared before a parliamentary select committee on September 29.
"If we think about the current outbreak, how it seems to have seeded itself in a gang environment and the homeless, these are people that are less likely to be trusting of the health system," she said.
"Finding people within these communities that can promote the vaccine will be very important."
Less trustful also means less likely to get tested, vaccinated, or to talk to contact tracers.
Public health experts called for a proactive, targeted strategy, including door-knocking in suburbs of interest and in transitional housing facilities. This had to involve health teams - including those experienced with substance abuse - with the appropriate cultural and community mana.
How do you engage people who feel ignored or even mistreated by the state, who have experienced institutional racism, who are more worried about their next meal or a roof over their heads than whether they're breaking level 3 rules, or who aren't even on the health system's radar?
Politicians and health officials talked about leaving no stone unturned, but by the end of September, only nine out of 100 door-knocked houses had agreed to be tested. In the suburbs of interest, only 7 per cent of the population were tested.
It wasn't because of lack of effort.
"We have thrown everything at this in terms of containing every cluster, every household, and we've done a very good job, to be honest," said National Māori Pandemic group co-leader Dr Rawiri Jansen who, among other things, fronted a hui with Mongrel Mob members in Waikato to convince them to get vaccinated.
"But Delta is so transmissible and so difficult."
On October 4, with cases having spilled into Waikato - now at level 3 - and numbers continuing to grow in Auckland, Ardern announced that Aucklanders would be able to have outdoor picnics.
It was couched as a low-risk way to relieve lockdown fatigue for Aucklanders entering their eighth week in lockdown, but it again raised concerns about throwing young Māori to the Delta frontline.
The goal of zero cases in Auckland had been replaced by "the transition": keep numbers low enough so health services aren't overwhelmed, with vaccination the key to exiting lockdown.
On October 5, Auckland public health physician Nick Eichler said on Twitter: "For anyone upset or anxious about a move away from elimination, always remember that we couldn't get back to zero because Covid took hold in the communities that 'mainstream' society forgot. Our current situation is entirely due to poverty, housing and colonisation."
He added: "Same reasons our vaccine rollout is too inequitable to pull us out of lockdown."
A week later, ministers openly talked about Auckland having passed the tipping point, and to expect more and more cases.
By then, the majority of daily cases were Māori.
Genomes show it never stopped spreading
Today, the genome with the deleted nucleotides is the dominant genome not only in Auckland but in other centres where cases have popped up.
"That is the part of the phylogenetic tree that is now containing most of the cases," de Ligt says.
"It wasn't that it went to one neighbourhood first and then to a different neighbourhood. It just seemed to go everywhere."
Previous modelling from Te Pūnaha Matatini shows how interconnected Auckland suburbs are, and how quickly the virus can spread - even under lockdown conditions.
"The cases that were found in Northland are also genomically linked to that part of the tree, but because that is the most active cluster in Auckland, that is sort of almost a given," he says.
Waikato cases, also linked to the deletion event, appear to have come from a single introduction from Auckland. From there, the genome was taken to Palmerston North and Blenheim, and it has now popped up in the Tararua district.
The mutation associated with the Māngere church service also reappeared at the start of October, suggesting it had also been simmering away in the background.
"It just shows how the transmission of Delta can be rapidly happening in the background without being detected for a little bit of time when we were moving down alert levels," Geoghegan says.
"It hadn't been sampled in quite some time before some cases popped up. Parts of the tree that were not expanding anymore were actually just not being sampled."
De Ligt says it makes up a "very small part of the current outbreak".
"It could be linked to the people that seeded that church cluster, not necessarily the church cluster itself."
It also popped up in the Christchurch cases in October that were quickly contained without shifting alert levels.
Ardern and Bloomfield have repeatedly said that most of the transmission events have been indoor gatherings.
Ministry of Health bespoke analysis from August to October 11 found the secondary attack rate (the number of people catching the virus following an exposure event) was 0.6 per cent at workplaces.
Bespoke analysis by the Auckland Regional Public Health Service between October 1 and November 4 found no secondary cases linked to picnics, one linked to a barbecue, and three linked to a birthday party.
The risk of catching Delta was much higher at private gatherings, where the secondary attack rate was 10.4 per cent.
De Ligt adds that it's hard to say if any infections happened during the North Shore lockdown party, or the protests in Auckland or around the country. Health teams do not have a list of everyone who attended those events, nor would people necessarily be open with health officials about having taken part if they later tested positive.
Lessons learnt?
There are now too many cases for the ESR team to genomically sequence every one.
"It's still important if there's a rest home or a new incursion, like what we're seeing in Taranaki, where there is more of an interest in understanding how that came to be there and how it is related to the outbreak," de Ligt says.
ESR also still sequences every imported case in MIQ, and a representative sample of Auckland cases, including those from suburbs - Birkdale, Ranui, Manurewa, Māngere, Sunnyvale, Kelston - where undetected transmission is more highly suspected.
"In those regions where they're finding cases that they don't have a direct epidemiological link to, there is a massive outbreak happening, and, genomically, there's not a lot of difference between the people in that region," he says.
This week Ardern started to prepare the country to be moved into the traffic light framework before the previously stated target of 90 per cent for each and every DHB.
That means the move would happen while there are still hundreds of thousands of unvaccinated people who are more likely to catch the virus, especially among Māori and rural populations. There are also 750,000-odd children who are currently ineligible to get vaccinated.
The new framework would see restrictions on mixing and mingling among unvaccinated people, but this will be impossible to police in private homes. Localised lockdowns would also remain part of the toolkit.
Health experts continue to be nervous about how this will play out. The unvaccinated - where rates are highest among young Māori - will continue to be in harm's way.
The challenge remains what it was at the start of the pandemic: keeping people safe from unnecessary suffering and death in a way that doesn't exacerbate existing inequities.
"New Zealand is paying the price for allowing such a big gap to develop, over several decades, between the rich and poor in our society," says top epidemiologist Sir David Skegg. "Infectious diseases typically spread most rapidly among the poor and marginalised, including people in crowded housing."
At the end of October, the Herald asked Verrall whether the lessons of Auckland had been learnt.
"We are working with communities that traditionally we haven't engaged with as well as we should have," she replied.
"And I think that is one of the lessons we need to take away from the pandemic."
