Analysis: As Auckland prepares to move to Level 2 at the end of the weekend, the persistence of community cases that haven’t been linked to the current cluster is raising concern among experts, Marc Daalder reports

The big news from Wednesday’s daily Covid-19 update was enough of an afterthought that Ashley Bloomfield only divulged it in response to questioning: Five cases linked to a Mt Roskill church haven’t been connected to the Auckland cluster.

The Director-General of Health said he was confident a link would arise to what he framed as a “mini-cluster”, but in the absence of any epidemiological or genomic connection to the cluster of 107 cases that pushed Auckland into Level 3, experts are warning the move to Level 2 at the end of the weekend may have to be delayed.

“I’m worried about what it means for us moving out of Level 3 on Sunday here in Auckland. Because if we have a cluster where we haven’t got all the strings tied together, then I’m just worried what that might mean in terms of once we start moving around more come Monday – whether that’s going to mean that there’s transmission happening that would have hopefully been slowed or stopped at Level 3,” Siouxsie Wiles, a microbiologist and expert on infectious diseases at the University of Auckland, told Newsroom.

A second outbreak?

At issue is the Government’s claim that it has the current outbreak ring-fenced. The vast majority of the 115 community cases that have cropped up during the outbreak have been close contacts of existing cases, who were already put into isolation and proactively tested. That has given officials confidence that, alongside the massive surge in testing over the past 14 days, there are no missing chains of transmission or second outbreaks lurking in the community.

But the new cases threaten that confidence in two ways. First, they raise the possibility of a second outbreak, unassociated with the original cold store cluster.

The prime way of determining this is genomic sequencing, which is being performed on all unlinked community cases. The results of this testing identified the Rydges Hotel worker, whose virus genome linked him not to the community outbreak but to a returnee from the United States who tested positive for Covid-19 in late July.

Genome sequencing is still processing for the five church cases, for whom an epidemiological link to the cluster – ie, how the virus was transmitted to them – has not yet been identified. It is unclear whether officials have received the genome results for the two other cases yet to be officially linked to the cluster: the relative of a person who travelled to Hobbiton, who tested positive for Covid-19 despite being asymptomatic, and the man who turned up at North Shore Hospital on Friday evening with severe Covid-19 symptoms.

Each of these cases and scenarios poses different concerns and risks.

For starters, if any come back with a different virus strain than that of the cold store cluster, that would mean there is a second outbreak ongoing. Such a revelation would be enough to justify delaying the move to Level 2 in Auckland, Te Pūnaha Matatini director and Covid-19 modeller Shaun Hendy said.

“With very high testing rates we had last week, they suggested there wasn’t a large second cluster out there that wasn’t linked to this main one. But if there is one out there, there’s a chance it will grow. If we spot it, then we’re in the same situation that we were in two weeks ago,” he said.

“If the genomics doesn’t link them, that would definitely be alarming and I wouldn’t want to see us shift out of Level 3.”

Missing links

Going case by case, University of Otago public health professor Michael Baker said the Hobbiton case struck him as less concerning than the others. That person had returned to New Zealand in June and tested negative while in managed isolation, but officials have hinted that the positive test result may have indicated he had previously been infected but is no longer infectious.

The PCR tests used for detecting Covid-19 in New Zealand are very accurate, but have the ability to detect traces of the SARS-CoV-2 virus from long ago infections, long after the person is not contagious or even no longer ill.

“We have had a few of these examples of testing which has picked up people who were infected a long time ago and there seems to be no other explanation [for when they might have been infected]. Generally, if you think that’s what you’re dealing with, then you can probably take them out of the equation,” he said.

The remaining cases – the man in North Shore Hospital and the five church cases – could indicate that we’ve missed a few chains of transmission.

“The other examples would all be consistent with, basically, asymptomatic but silent transmission. You’d expect in investigating a cluster, you’re going to find a few examples like that where there is a missing link but the genomics says it’s part of the cluster. If it was even one generation [of transmission] who didn’t know they were ill, they wouldn’t be known to either of the other cases. They could just be not picked up at all,” Baker said.

Hendy said this was possible but not a major worry to him. The lack of an identified link also doesn’t mean there isn’t one out there – contact tracing can take time and the interactions that spread Covid-19, from sharing an elevator to riding on the same bus as a positive case, can be hard to identify.

“It is more concerning but it’s not as concerning as if we spotted a second [genomic] clade. As we’ve seen, some of the contacts that people have had have been on buses. Those kinds of interactions can be quite hard to connect people via,” he said.

“Yes, you want to be able to link everything, but the really alarming thing would be a clearly unlinked case.”

Moving down the levels

Wiles agreed that a case with a different virus genome would be a game changer, but the proliferation of this handful of unlinked cases over the past few days is also cause for concern. She compares it to firefighting, where the few daily cases are embers which could roar back to life under favourable Level 2 conditions.

“The question is, how many embers have we got? And if we say, okay, let’s move down the alert levels and let’s just rely on our contact tracing and on the interventions we’ve got, are they going to be enough to stop them from sparking a big enough fire that will require more than just a fire extinguisher?” she asked.

It’s less about who the church cases might have infected because Wiles is hopeful that contact tracers can draw a ring around the “mini-cluster”. The issue is really those missing links in the chain of transmission – and who else they might have infected beyond the index case for the churchgoers.

“The last thing we want is lots of those types of cases popping up, because that shows there are links in the chain that we don’t have yet and my concern is that the more we start to move around and contact each other, the more chance there is for those to spread,” she said.

“My worry is there’s such a keenness in everybody to get down the alert levels that I really hope we don’t do that without having got this outbreak fully under control. Because it’s a false economy, if we end up having to put restrictions in place again because we haven’t nailed it this time.”

In order to have confidence in moving down the levels, Wiles would like to see the existing cases linked to the cluster, or at least no new unlinked cases arising in the coming days. Hendy said, for him, establishing the epidemiological link wasn’t as important. What would lend him confidence, however, would be declining case numbers as the Sunday evening deadline nears.

“We want to see these numbers dropping this week. I’d like to see us having, by the end of the week and over the weekend, numbers we can count on one hand or even zeros,” he said.

“But if there’s a case that pops up tomorrow and it’s not genomically linked, that would definitely be alarming and I wouldn’t want to see us shift out of Level 3.”

“I think it really will depend on how the testing goes for the rest of the week,” Wiles agreed.

“I’m obviously firmly in the camp that I would much rather reduce the number of cases we had completely, because every case that we get is a chance that somebody is going to end up with either a severe infection and potentially death or long-term health consequences. I favour a short, sharp shock or doing what’s needed to get it well and truly under control, over the, ‘Let’s ease down and see if we can control it’, because it’s a big risk if we can’t.”

In other words, stamp out those embers completely or risk them reigniting the conflagration.

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

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