It also advised that the red setting would not be restrictive enough in some scenarios to contain the virus.
Meanwhile the independent advisory group chaired by epidemiologist Sir David Skegg told the Government that the new system would widen existing health inequities, particularly for Maori and Pasifika.
That was because they were less vaccinated, more likely to live in crowded houses, and had higher rates of comorbidities and more barriers to accessing healthcare.
Skegg's group said it was unclear why some measures were being proposed at different levels and not others.
"Some aspects surprise us: for example, why is symptomatic testing in the community included at the Amber and Red levels, but not at the Green level?"
The National Iwi Chair's Forum told the Government that 95 per cent of eligible Maori should be vaccinated before moving into the new system, the restrictions in the red setting needed to be stronger, and local communities should have the power to impose restrictions.
Eventually the Government decided to ditch its 90 per cent prerequisite for a 90 per cent target for each DHB region and moved the whole country into the new framework on December 3.
Earlier this week Covid-19 Response Minister Chris Hipkins revealed that concerns about pockets of low vaccination rates and active cases stopped the South Island, Wellington, and two regions from entering the traffic light system at green.
Director-general of health Ashley Bloomfield was also advised by his deputy Maree Roberts that Northland could start in orange, based on the area's case load and health system readiness, but the assessment committee eventually took a more cautious approach and recommended red for Northland and Auckland.
The Herald this week revealed public health officials at one stage wanted some regions to start the new response model at the least restrictive green setting.
The South Island, Wellington DHB areas, Hawkes Bay and MidCentral (between greater Wellington and Whanganui) were previously considered.
But some health officials also had concerns about areas with low vaccination rates and active Covid-19 cases, and so the green light was deemed too risky.
Cabinet decided to put Auckland, Northland, and several districts from Whanganui northeast to Gisborne in red, and everywhere else in orange.
Minsiters were more cautious than health officials in part because of fears of people taking the virus out of Auckland to popular holiday areas, a November 29 Cabinet paper noted.
The Covid decade?
We can expect Covid-19 to keep flaring up or presenting challenges for perhaps a decade.
That's what an independent advisory group including business leaders Sir Brian Roche and Rob Fyfe suggested in its "forward work programme", released in the document dump today.
New Zealand needed a deployable system to prevent and respond to Covid-19 over one, five, and even ten-year horizons, the advisory group said in August.
"New Zealand will be managing and dealing with Covid-19 for the foreseeable future," the Independent Continuous Review, Improvement and Advice Group said.
The system would have to shift from a crisis management response, and become part of a broader preparedness and response system sustainably managing Covid-19 while the wider health system delivered other functions as normal, the group said.
Strong case for saliva testing, document shows
A briefing on April 14 to Hipkins on surveillance tests and tools called for alternative testing platforms and more consistent tests at the border.
The briefing from the DPMC (Department of the Prime Minister and Cabinet) said there was a strong case for adopting saliva testing as the main testing method.
"It would likely be of benefit to have experts on hand to provide advice in this fast-moving field," the briefing added.
The same April document said testing wastewater and air samples were probably less worthwhile than previously thought.
"There is a need for a rigorous process, given that New Zealand has now started Covid-19 vaccination rollout," the DPMC April briefing added.
"Surveillance and testing strategies will need to tie in closely with an agreed overarching goal for the response and how the situation will evolve, before and after maximum vaccination coverage is reached and border policies change."
A Ministry of Health memo on October 14 discussed the possibility of "at least most" students being able to return to schools in level 3 areas in the week of October 25.
Ultimately only secondary school students in Years 11-13 returned on October 26, with the years one through 10 not returning until from November 17.
"Education is critical for young people's health and wellbeing and term 4 is particularly important for senior students sitting NCEA exams," the memo said.
"The impacts of education restrictions in Auckland are growing and consideration needs to be given to addressing these impacts."
Education in the classroom was "relatively low-risk", but interactions outside the classroom and in the community beyond school needed to be minimised.
Public health advice was that school could resumed once "appropriate precautions" were in place, covering IPC procedures, use of masks, and avoiding large indoor gatherings such as assemblies.
"We will provide further advice this week on whether (at least most) schools across the Auckland metro region might open safely the week of 25 October," the memo said.
The DPMC argued strongly for less invasive testing methods and said some of the Ministry of Health studies seemed to be lacking in intellectual rigour.
"The demand for less invasive testing is likely to enhance participation, independent of whether people are vaccinated or not.
"This alone should be a driver to invest significant resources in exploring less invasive testing opportunities, rather than remaining in the status quo."
The briefing said it was important to be open-minded to evolving science and make sure the best available tests were used.
The DPMC also said the cost of more asymptomatic surveillance testing should not be an excuse for ruling it out, especially when one considered the economic impact of lockdown.
Wastewater testing was probably, well, a waste of time and money, the DPMC briefing added.
It also pooh-poohed the use of air-sample testing and the practicality of testing produce leaving New Zealand.
But it said serology testing - where a blood component is tested - could be a smart way to validate vaccine passports.
Health staff 'tipping point'
A public health assessment on November 17 noted the pressure that testing labs were under, with only 49 per cent of tests being turned around within 24 hours.
Reducing testing for lower risk essential workers coming and going from Auckland was recommended to ease the pressure on testing labs.
This is despite a case in Canterbury having travelled to Auckland to attend a tangi in the last week.
Surge capacity for contact tracing had also been activated.
"The public health service is increasingly becoming stretched and is potentially reaching a tipping point where staff will be lost," the Minister of Health was told, as staff supported 5010 to isolate at home including 2238 cases," the Health Minsitry document, dated November 18, said.
Work was underway to change the way case investigation and contact management was done to make it more sustainable, but "the easing of workload is yet to be realised".
Shifting Auckland to step 3 of level 3 - which never eventuated - was of "little value" before moving to the traffic light system.
A Ministry of Health memo on October 14 discussed the possibility of "at least most" students being able to return to schools in level 3 areas in the week of October 25.
Ultimately only secondary school students in Years 11-13 returned on October 26, with the years one through 10 not returning until from November 17.
"Education is critical for young people's health and wellbeing and term 4 is particularly important for senior students sitting NCEA exams," the memo said.
"The impacts of education restrictions in Auckland are growing and consideration needs to be given to addressing these impacts."
Education in the classroom was "relatively low-risk", but interactions outside the classroom and in the community beyond school needed to be minimised.
Public health advice was that school could resumed once "appropriate precautions" were in place, covering IPC procedures, use of masks, and avoiding large indoor gatherings such as assemblies.
"We will provide further advice this week on whether (at least most) schools across the Auckland metro region might open safely the week of 25 October," the memo said.
Taking Delta out of Auckland
Cabinet did not appear to consider whether travellers leaving Auckland should need to be both vaccinated and have a negative test.
A November 15 Cabinet paper stated that the options to consider were for travellers to be either vaccinated or tested, or to have no travel prerequisites at all - though a substantial section of the paper is redacted.
"The Ministry of Transport estimates that the number of people travelling out of Auckland Airport could be between 7000 to 10,000 each day in December, including transiting passengers, and 60,000 to 70,000 each day by road. These numbers make the current high level of compliance checking at the hard road boundary impractical and would lead to delays of over eight hours," the paper said.
"Modelling tells us that when vaccination rates are at 90 per cent, up to 50 per cent of cases could be in vaccinated people, and 20 to 25 per cent could be in the under 12 population. This means that by testing unvaccinated over 12s, only around 25 to 30 per cent of cases might be caught, even with very high compliance rates.
"Requiring a predeparture PCR test as well as vaccination would increase the protection, but the Ministry of Health officials advise that this would be unsustainable for more than a very limited time as demand for tests would overwhelm capacity."
The paper also notes that police and transport officials will be busy over the summer period.
"Workforce pressures and constraints on Police and Waka Kotahi would
be exacerbated by any road boundary. For Police in particular, this will be the holiday period, and road police presence will be required on roads and to provide support at events.
"There is also a risk that enforcement officers may unconsciously take a discriminatory approach to spot checks."
The paper, from Jacinda Ardern and Chris Hipkins, noted that easing restrictions on the Auckland boundary will see the virus being taken out fo the city to different parts of the country.
"The degree of undetected infection is the key factor for the risk of interregional transmission (detected cases are expected to stay at home and not travel).
"Any loosening of the boundary with Auckland, coupled with high numbers of reported cases in Auckland, would mean that we must expect infected people to travel across New Zealand."
The most likely destinations for Aucklanders leaving the city included Northland, Waikato (particularly in the Thames Coromandel district) and Bay of Plenty.
"In communities with lower rates of vaccination, transmission can be expected to be quicker. This means that outbreaks would be larger at the point they are detected, and harder to contain once they are detected."
These risks would be mitigated by increasing vaccination coverage, especially among the vulnerable, and starting Auckland in Red.
The Government went against initial advice on vaccine passes, which was to limit them to only high-use settings largely to retain social license.
In a briefing on September 17 to Prime Minister Jacinda Ardern and Covid-19 Response Minister Chris Hipkins, officials provided three options for vaccine certificates.
They included A - wide application, B - just high-risk venues, and C -relying on the private sector.
Option A included workplaces, hospitality, public facing services and venues and events to refuse entry to individuals that have elected not to be vaccinated. Supermarkets, pharmacies, educational institutions and other basic human need providers could be exempt.
However officials said this was "likely to generate the most public concern" and greater issues on equity.
Option B, which officials suggested should be further looked into, would include indoor and outdoor events of a certain size, for example live music events in summer 2021/22. It would be more acceptable given it was limited to high-risk events.
Ultimately the Government opted for a mixture of the options through the new traffic light settings, with passes still being used at green but widespread use at orange and red.
Eerie variant warning just before Delta cases
Plans to overhaul MIQ and allow vaccinated people to self-isolate were underway before Auckland's Delta variant lockdown started in August.
A DPMC leader met with the independent experts, and a major topic was how New Zealanders would reconnect in months ahead.
"Participants conveyed the need for greater clarity surrounding the timeline on Reconnecting New Zealanders, and changes to the border and customs arrangements more generally," minutes from August 10 revealed.
Grier Cox, DPMC chief of staff, noted epidemiologist Sir David Skegg's prior remarks that specific dates should be avoided, due to the need to manage public expectations. From the partially-redacted document, it wasn't immediately clear what those dates were.
But meeting minutes suggest Cox took seriously concerns about the constantly changing public health environment and emerging virus strains.
Concerns about the virus strains turned out to be prescient. Just after celebrating 100 days with no community spread, four cases were reported on August 11. And the day after that, Auckland went into lockdown.
Sir Brian Roche presented messages from Delta scenario planning talks, conducted in the context of an all-of-Government workshop held on August 9.
The workshop aired concerns that transmissible new variants meant the pace and capacity of contact tracing would have to be taken seriously, as would intensive care unit readiness.
"It will also be critical that health system capacity...is assured, in support of continued readiness."
Dubai, Singapore considered for MIQ
Former Air NZ chief executive Rob Fyfe shared his views on the managed isolation system. He told his panel colleagues MIQ was having struggles keeping pace with returnee demand expectations.
The expert advisory group raised the idea of alternative pathways to MIQ, and even whether quarantine hotels at departure points such as Dubai and Singapore could be used instead.
Echoing earlier talks about the possibly decade-long impact of the pandemic, Roche said he'd met with Minister for Covid-19 response Chris Hipkins earlier.
Roche said he and Hipkins discussed the expectation that residual pandemic impacts would last five to ten years - but the document did not elaborate on these impacts.
