* A new positive case has been revealed of a patient at Waitakere Hospital in Auckland, who had previously been in North Shore Hospital this week for an unrelated issue. Both hospitals are expected to reveal new precautions Friday morning. The new case takes to 22 the total in the community in this outbreak.
The link to MIQ is crucial for capping the possible extent of vast undetected upstream spread of the virus, but there will still be plenty of cases to find over the coming days, Marc Daalder writes
ANALYSIS: Health officials may well have breathed a sigh of relief when crucial genomic sequencing results came back from ESR showing a likely link between a case of Delta in MIQ in early August and the current community outbreak.
There are 30,000 chemical bases that make up the coronavirus. The virus genome from the returnee from Sydney who tested positive on August 9 is just one base apart from the sequence of the original community case. Given the virus tends to mutate once every two weeks, that 0.003 percent difference between the genomes shows they are likely to be closely linked.
While officials will continue to be vigilant for other potential sources of the outbreak, an MIQ breach is now the leading suspect. And from there, we can make a few other, evidence-based assumptions.
Upstream/Downstream
First, the virus hasn't been in the community as long as feared. When some of the cases reported they had cold and flu symptoms as early as August 5, that raised the spectre of two weeks of undetected transmission. Such a scenario could easily mean there were 100 cases in the community by the time the outbreak was first reported.
Now, August 7 – the date the Sydney returnee arrived in New Zealand - is the earliest possible start date for community transmission. The shorter the time between the start of the outbreak and its detection puts a hard cap on the possible extent of transmission, because it only leaves time for one or two generations. We know there's at least one grouping of 12 cases, all epidemiologically linked. There are also eight other cases that haven't yet been linked to the main cluster, meaning they could be offshoots of the missing link.
This is broadly good news. For the first 48 hours of the outbreak, the focus was on finding the origin and hoping we didn't have hundreds of undetected cases upstream of our original case.
The focus now has to shift to downstream transmission. In other words, we are now less interested in finding the source of each new case's infection than in finding out who they may have infected. It is by chasing all of these branches of transmission to their ends that we can ring-fence the outbreak.
Some attention will still go to upstream contact tracing, as it will help us find branches of transmission that spun off our missing link. But the downstream infections from this cluster of young people who have frequented crowded indoor spaces are now likely to make up the largest chunk of the outbreak.
University of Canterbury mathematics professor and Te Pūnaha Matatini disease modeller Michael Plank told Newsroom that the age and social patterns of many of the cases are only just being factored into the models.
"What's a bit tricky to factor in is what we now know about the spreading in this group. Lots of close contacts in some of those locations of interest. That's harder to quantify. That probably pushes us toward the upper end of whatever the model comes out with," he said.
Plank later told Newsroom the results of the latest model run, completed on Thursday evening. Based on an MIQ leak into the community between August 7 and 9, it's more likely that fewer than 50 people had been infected by the time the outbreak was discovered. But factoring in a number of cases which developed symptoms late last week brings the estimate back up to 100 - the same figure Shaun Hendy gave Newsroom on Wednesday evening.
"I think what this shows is that a range of outcomes is still possible at this stage. The good news is that if the border link holds up, it makes it a lot less likely there is a whole other parallel cluster around somewhere that we haven't found yet," Plank said.
He added that it's difficult to estimate with accuracy at this early stage of an outbreak, so the figures provided have large error bars around them.
Contact tracing and testing
This is part of what Cabinet will be considering when it meets at 1pm today to confirm the Level 4 status for Auckland and the Coromandel and to decide what happens with the rest of the country. The extent of the downstream transmission is probably yet to become apparent.
Another crucial thing they'll be looking at is results from contact tracing and tests of contacts. As of Thursday afternoon, only 362 specific contacts had been identified as part of the outbreak and it wasn't clear how many of them had been tested. That number is expected to spike to well over 1000 once contacts from some of the larger exposure events - like the Auckland Central church or Avondale College - are added in.
On the one hand, there's less pressure to rapidly contact trace now that we're all in Level 4. Unless someone is an essential worker, they aren't likely to infect anyone outside of their bubble. That's part of the reason Director-General of Health Ashley Bloomfield stressed that essential workers in particular should keep an eye on the locations of interest page on the Ministry of Health website.
On the other hand, as long as there are hundreds if not thousands of unidentified contacts out there, it's hard to justify lowering alert levels anywhere in the country. That's because contact tracing is our best tool for discovering downstream spread and for finding out whether the virus may have made it out of Auckland. As long as contacts are unidentified and untested, Cabinet can't get a good view of the Covid-19 situation.
Testing, therefore, is another indicator Cabinet will be looking at. The 600 tests taken in the Coromandel on Wednesday represent 2 percent of the region's population. The 16,000 tests in Auckland represent 1 percent.
These give good odds for finding new cases, particularly if they're kept up over multiple days. But most tests taken on Wednesday will only come back today, meaning Cabinet will only have results from the first round of mass testing in front of them when they meet.
That will provide a good indicator of potential spread, but not the full picture.
It's also unclear what the testing rates might be elsewhere in the country. For those in the South Island or lower North Island anxious to leave Level 4, the best thing to do is to get tested if you have symptoms. The higher the testing rates, the easier it is for Cabinet to justify moving down alert levels.
What next for New Zealand?
There's a catch, however. People who may have been infected over the weekend or early this week may still be incubating the virus. That means contacts who test negative over the next few days could end up becoming infectious next week.
"Certainly [Cabinet will] want to see high testing rates around the country. But the important thing to bear in mind is that people could have travelled to Auckland or to the Coromandel over the weekend or the early part of the week and then travelled home to different parts of New Zealand and they could still be in the incubation period for several more days to come," Plank said.
"It may be into more like the middle of next week before they might develop symptoms."
With that in mind, it's hard to imagine much change in the alert levels.
"I think the precautionary approach would be to leave the whole country at Alert Level 4 - or maybe you could think about Level 3 for parts of the country," Plank said.
Given the immense caution with which the Government has treated this outbreak so far - putting the entire country into Level 4 over the detection of a single case - it seems likely that Level 4 is here to stay for a little while longer.
It will still be several more days before a mixture of contact tracing, testing, wastewater surveillance and the simple passage of time turn up all of the hidden cases that might still be lurking out there.
