Delta Skelter: 'A formidable enemy' - inside the battle and what the Govt knew when

JUNE: A new enemy

A hundred days ago Delta didn't even have a name. Prior to it being dubbed by the World Health Organisation on May 31, it was known only as "Variant B.1.617.2".

It had first been discovered in India in late 2020, but found its legs in that country early the following year as the main driver of a brutal second wave that by May was killing more than 4000 people each day.

Dame Juliet Gerrard, the Prime Ministers' science adviser, dryly acknowledges Delta's first name was "not very catchy".

Gerrard's work early last year as a fast-moving virology aggregator had earned from her boss both a gong and a second term in her role, and she was still keeping abreast of developments.

"India was when it first caught my attention. Clearly, what was happening there was quite extreme and people inferred there was a new variation but it took a while for it to be fully characterised," she says.

Sir David Skegg, the Otago University epidemiologist tasked by the Government with mapping a path through the pandemic, also watched on with horror: "I saw the daily TV coverage of harrowing scenes in India – with countless bodies on funeral pyres. It became apparent that a new variant was involved."

"Variant update" briefing papers prepared regularly by Ministry of Health science advisers tracking the many mutants of the pandemic are colour-coded to aid regular readers. Over the past three months, many of the sections on Delta each week were printed red: Flagging new, and alarming, findings about its transmissibility and its breakneck spread around the globe.

Even with wildly suppressed international travel since the pandemic began, over the past three months, one country a day on average was reporting finding its first case of the variant. And once it found a home, it was proving extremely difficult to evict.

Genomic testing in Canada found in early April that only one in 50 of its cases were B.1.617.2. Eight weeks later more than four in five were Delta. It today accounts for 99 per cent of cases in both the UK and the US and has been detected in more than 142 countries.

A milestone study out of the UK in mid-June showed why: Delta was considerably more transmissible than its peers, with each case spreading on average to six others. This made it more than twice as infectious as the original strain that broke out of Wuhan in early 2020.

New Zealand had found its first case of Delta on March 9, detected and then trapped and starved of new hosts in managed isolation and quarantine, with a passenger who had flown out of India. It would be five months before it returned here with a vengeance, but our neighbours would not be spared for long.

Sir David Skegg watched on with horror as the virus swept through India. "It became apparent that a new variant was involved." Photo / Mark Mitchell

In April, Delta hitched a ride out of Fiji's MIQ system and within a month was replicating itself in more than 100 new people each day. And on June 16 in Sydney, a limo driver who worked ferrying international aircrew around the city tested positive for Delta. The case only had five days between being infected and being detected and isolated, but that was enough to seed a stubborn outbreak that would later shatter both inter-state and transtasman consensus on the pandemic.

With similar economies and political systems, and an elimination strategy that had largely been in lock-step with New Zealand, the bubble between the two countries had opened just months earlier in April. Wellington was now watching developments in New South Wales very closely indeed.

On June 23, after a tourist from Sydney tested positive for Delta on his return home, the Covid response experienced what Gerrard calls a "dress rehearsal".

If you were looking for a sign of official worry about Delta, this was it: The country's first alert level change without confirmation of community transmission. The mushrooming list of places of interest, and frantic efforts to find and test the more than 2000 people who had also been present, showed the extent to which the response was trying to outrun an opponent that was now faster than ever.

After a week of furious activity found no local cases, Gerrard says "we were lucky with our visitor to Wellington".

We could not stay lucky forever.

JULY: Panic stations

An appreciation of exactly how much Delta had changed the game was now beginning to dawn in Wellington. A Ministry of Health science update on July 2 was - unusually - triggered by not scientific papers but media reports from Sydney of multiple cases of transmission from only "fleeting contact".

Previously, contact-tracing and isolation efforts to manage Covid had largely been focused on those who had spent time in close proximity with an infected person.

This note said the risk of spread inside a household was still assessed as much greater - around 50 per cent - compared to only one per cent for casual contacts, but there was a catch to this calculus.

‌

"However, while an infected person may have only a few close contacts, they may have hundreds or even thousands of casual contacts, as has been seen in the recent case in Wellington."

Scientific publishing, usually a deliberate and slow-moving affair with layers of editing and peer review, had also evolved and dramatically sped up to try to match pace with Covid mutations. On July 10 - while drafting his third of three letters to the Government mapping out a way through the pandemic - Skegg was sent a preprint of a study assessing the spread of Delta earlier in the year in Guangdong.

The news out of China was, the professor says, "very concerning".

"This suggested not only that the Delta variant is far more infectious, but also that the time interval from when a person is exposed to the virus until they show a positive test is shorter than with earlier variants," Skegg recalled.

‌

He briefed Prime Minister Jacinda Ardern, laying out the lessons being learned hard in Australia that Delta was a "game changer". Ardern cited the rapidly evolving advice when suspending the travel bubble with Australia on July 23: "The Delta variant has materially changed the risk profile," she said.

Several insiders spoken to this week say the end of the bubble - despite its establishment having been a public, commercial and political fixation for more than a year - landed with more a whimper than a bang. There is now deep scepticism in the Beehive over prospects of it reforming.

Skegg's advice to the Government evolved too. Noting his earlier observations of "abysmal" rates of QR code scanning - combined with the window to find new cases before they become infectious having now halved from four to two days - his third letter flagged enormous challenges to a system that was already trying to come to terms with a need to now identify even fleeting contacts.

"Outbreaks caused by the Delta variant will be more difficult to control by testing and contact tracing alone," Skegg wrote in his final letter of advice to ministers on July 27.

"Even with current settings, New Zealand is liable to experience an outbreak similar to New South Wales over the coming months - although presumably, we would go into lockdown more quickly."

‌

AUGUST: The MIQ canaries

The variant updates from the Ministry of Health were by now sounding imminent alarm. Not only were cases beginning to reappear at the border but, within a matter of weeks, the variant had become the only show in town and guaranteeing that any future leaks would only be of Delta.

Since mid-July, out of 100 positive cases captured in MIQ and analysed with genomic testing, a full 99 were found to be the Delta variant. The speed of this takeover raises Gerrard's eyebrows: "It's been astonishing. It's evolution in action. It's just a fitter version of the virus," she says.

‌

The risks from an unimpeded spread of Delta were stark. A simulated outbreak run for the New Zealand Herald by modeller Shaun Hendy shows that under level 1 restrictions, a single case of Delta, with New Zealand's vaccination rate of early August, was within a single month likely to cause enough hospitalisations to overwhelm New Zealand's intensive care unit capacity.

The simulation showed Delta would, without any alert level changes, crash the health system in just 31 days, a significant shortening compared to the 38 days taken by wild strains such as those stamped out in March and April of last year.

Adding tertiary health care was shown to be of limited value if spread could not be contained. The simulation showed even a doubling of New Zealand's intensive care unit capacity bought only two extra days grace before the health system would be on its knees.

A Covid-19 testing station in Otara, Auckland as the country plunged back into Level 4 lockdown. Photo / Dean Purcell

The message the Government was keen to push at this time was optimism. Skegg's advice on how the Covid response could evolve after the vaccination drive formed the spine of a Wellington event on August 12 hopefully titled "Reconnecting New Zealand".

The business community, who have long been demanding certainty in uncertain times and are understood to have been the key target for this event, only had ears for the possibility of re-opening.

Skegg himself that day was grimmer. His roadmap through the pandemic had clearly labelled hazards and, from the podium, he described Covid management as a war that was being lost.

"In a sense, this is going to be a drawn-out war — between the human race and a microbe. It may seem odd to describe a tiny virus as an enemy but it is a formidable one. And despite remarkable scientific progress, in developing highly effective and safe vaccines, the virus is still winning the war."

It was "improbable that it wouldn't come," Dame Juliet Gerrard said. Photo / Greg Bowker

Gerrard was also present that day and swapped notes with epidemiologists. "We were discussing how New Zealand was the only place in the world where Delta hadn't arrived, and it was becoming increasingly improbable that it wouldn't come," she says.

Investment banker Rodney Jones, credited by Finance Minister Grant Robertson for first alerting him to the dangers of Covid in early February 2020, recalls his incredulity at the backslapping that day from business leaders.

"I felt like the only wowser at a party," he says.

As the speeches ended and the applause rolled in, it turned out Delta was already here. The week before it had finally made the leap out of MIQ and was circulating, undetected.

Over the coming weekend, it spread further - to sporting fixtures and bars, casinos and church services - multiplying from one case to more than 200.

On August 17, Prime Minister Jacinda Ardern announced the country would go into level 4 lockdown after it was confirmed the Covid-19 Delta variant was in the community. Photo / Getty Images

Director-general of health Dr Ashley Bloomfield was alerted just after noon the following Tuesday, August 17, to New Zealand's first case of Delta in the community.

"No one was thrilled when the news broke," Gerrard says of the mood in the Beehive that day.

"But I didn't see anyone who was surprised. We had been braced."

Hours later, an emergency meeting of Cabinet plunged the entire country into level 4 lockdown.

The forecast storm had finally arrived.