August 17 2021
Auckland and Coromandel will go into level 4 lockdown for seven days – and the rest of the country for three days – from 11.59pm tonight.
When do we mark the death of New Zealand's elimination dream?
It might have been one year ago today – August 17, 2021 – when the country was plunged into a weeks-long lockdown, never to return to the virus-free world of level 1.
Or it might have been a fortnightbefore then, when a traveller jetted into the country from Sydney to Auckland's Crowne Plaza, infected with the feared Delta variant that had turbo-charged the global Covid-19 pandemic.
Whether this person was indeed the "primary case" that started it all is unclear: several other infected people who returned from Australia around the same time turned in samples with an identical genome.
Just how any of these cases proved the seed for community transmission – even after quarantine-free transtasman travel had just been scrapped – will likely always be a mystery.
What is known is that, by the time authorities discovered a fresh community case in Devonport and ordered a snap level 4 lockdown, the outbreak had probably already grown to between 800 to 1000 infections.
That included dozens of infections surrounding the Devonport "index case" - and many more from a super-spreader event at Māngere's Assembly of God church service - 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 in great detail.
Prime Minister Jacinda Ardern and director general of health Dr Ashley Bloomfield address media on the first day of New Zealand's Delta lockdown, on August 18, 2021. Photo / Mark Mitchell
Within two weeks, with daily case numbers seemingly peaking at just over 80 and a Wellington chain all but stamped out, scientists became hopeful the lockdown might be working.
The church subcluster itself had grown to around 330 cases but the rate was slowing – and when new daily cases fell below 20, a return to elimination appeared within reach.
Only, there was a picture of undetected transmission that we couldn't see – and it was already too late to have stopped Delta from taking root by spreading to larger, intergenerational households in Auckland.
When the city moved to level 3 on September 22, some experts were left uneasy at the possibility Delta was being let out of its cage.
Yet studies have since suggested it was unlikely the virus could have been snuffed out entirely here anyway.
One recent paper, drawing on data from more than 3800 genomes collected between mid-August and December 1, revealed a picture of a virus that spread far and wide, and clusters that resurfaced weeks after seemingly going "extinct".
Those cases being detected and reported didn't account for all of the pieces of the puzzle.
One of the study's authors, Otago University virologist Dr Jemma Geoghegan, said it was difficult to say how much of this silent spread owed to Delta's higher transmissibility – and how much was down to people flouting lockdown rules.
"I think both things hugely contributed."
In any case, our very strictest measures simply weren't enough to contain Delta.
"It was really going to be impossible to eliminate community transmission – but then, we were at a point where we were getting ready to move to a different strategy."
New Zealand effectively pivoted from elimination to suppression in early October, with a big focus on vaccinating the population.
In the study, scientists also pin-pointed a "deletion" of one of the proteins in the virus, which quickly became a common trait of the samples they were sequencing.
Before long, genomes with this trait appeared to dominate the samples they were sequencing, suggesting the virus had undergone a genetic shift once it arrived in New Zealand.
Interestingly, similar deletions in this same gene had been found numerous times in different regions and in outbreaks around the world – including in the New South Wales outbreak that preceded our own.
This genetic change seemed to impair the gene it involved, but, beyond that, its function – or whether it helped the virus spread faster through our neighbourhoods - was unclear.
Cars queue at a testing station in Otara, Auckland, soon after the first case in New Zealand's Delta community outbreak was announced last August. Photo / Dean Purcell
Up until that point, genomic surveillance was used as a precision tool to help officials carefully untangle chains of transmission, and provide genetic proof to cases they'd been unable to link epidemiologically.
This "track and trace" role quickly moved to one of population-level surveillance, with the proportion of cases sequenced falling from nearly 90 per cent to a third by the end of 2021 – and now to a small mix of border, hospital and community cases.
Delta has all but vanished in New Zealand: the last of more than 11,500 reported cases was sequenced back in early March.
But we couldn't be sure we'd seen the last of it.
"We don't know," University of Auckland computational biologist Dr David Welch said.
"There's probably a tiny bit of Delta out there somewhere."
Globally, the World Health Organisation (WHO) now considers it a previously circulating variant of concern, with clusters still occasionally reported in some countries where there's enough surveillance.
Geoghegan said sequencing every case under elimination served its purpose – just as elimination itself spared New Zealand the waves of death and severe sickness seen in other country's Delta outbreaks.
"And I think Delta helped us come to terms with the fact we weren't going to eliminate this virus – and that we were going to have to live with it, in some way."
On the afternoon of November 24, Covid-19 Response Minister Chris Hipkins told media that New Zealand had become one of the most vaccinated countries in the world, and out-lined a staged reopening of our borders for summer.
That same day, South Africa reported to the WHO a new Covid-19 variant, designated B.1.1.529.
