In Monday’s tense national cabinet meeting, held as nearly half the country went into lockdown due to the spread of the Delta strain of Covid-19, the country’s chief health officers urged Scott Morrison to dump its commitment to AstraZeneca.

The Saturday Paper has spoken to several people with direct knowledge of how the emergency meeting late on Monday unfolded. There was a sense of panic and frustration from the prime minister, who also grilled the Australian Health Protection Principal Committee (AHPPC), the advisory body for chief health and medical officers, about making vaccines mandatory for aged-care workers.

“They wanted AstraZeneca abandoned,” one source says, “but Morrison wouldn’t do it.”

Instead, the meeting heard that a national no-fault indemnity scheme was now ready to be deployed. It would cover GPs who administered the AZ vaccine, which has been linked to rare blood clots, to people in age groups for which it was not recommended.

The drug is approved for use in Australia by the Therapeutic Goods Administration, but its guidelines for delivery have been written and rewritten by the Australian Technical Advisory Group on Immunisation (ATAGI), which is co-chaired by two eminent professors, Allen Cheng and Chris Blyth.

At the time of the national cabinet meeting, ATAGI’s advice was clear: the AZ vaccine could be used in adults aged under 60 where Pfizer was not available and “the benefits are likely to outweigh the risks for that individual and the person has made an informed decision based on an understanding of the risks and benefits”.

Now, with a Commonwealth indemnity scheme in place – which Health Minister Greg Hunt says covers both the GP and the patient in the event of serious complications or death – the federal government had a solution for an emerging problem.

Entire batches of the AZ vaccine are due to expire within weeks and months.

“They were worried about the optics of doctors having to throw out lots of AZ stock the feds had bought,” one source tells The Saturday Paper.

“But at the meeting [of national cabinet] there was no discussion about encouraging people to go out and get the shot.”

This version has been corroborated by other sources at the briefing. By his own admission, Morrison used the meeting to badger the AHPPC and get agreement for mandatory vaccinations of aged-care workers despite failing to deliver the program as agreed.

“When it comes to the issues of mandatory vaccines, this is not something that any government should do lightly,” Morrison said during a combative press conference on Monday evening, following national cabinet.

“And, as a result, you know, we have been considering this matter for some time now, based on the best possible medical advice. And it was only at this point this evening, after some determined questioning of the AHPPC by the national cabinet, and myself in particular, that we have arrived at the position tonight that supports that decision.”

Even so, the requirement is for aged-care workers to have a mandatory first dose by September, some five months after the federal government pledged to have completed the rollout of phase 1a.

What state premiers were not expecting at that press conference was an explicit push from the prime minister for young people to get AZ.

“But the advice does not preclude persons under 60 from getting the AstraZeneca vaccine,” Morrison said. “And so if you wish to get the AstraZeneca vaccine, then we would encourage you to go and have that discussion with your GP.”

The remaining members of national cabinet saw this as an ambush and, rightly or wrongly, it triggered a near complete collapse in the nation’s strained political response to Covid-19. The consequences will likely be serious.

Less than three weeks ago it was entirely conceivable the nation could – and probably would – slip back in the grips of Covid-19. But it was still difficult to imagine.

The first hint something had gone wrong in New South Wales was an inconclusive Covid-19 saliva test taken by a 60-year-old limousine driver on Tuesday, June 15.

That afternoon, the “not negative” result sparked the interest of the state’s contact tracers, who spoke with the man at length, late into the evening, to piece together his movements.

Already, authorities had a problem. The driver worked transporting overseas flight crews, both commercial and freight, and was required to take daily saliva tests as part of the state’s control procedures. None before June 15 had registered any anomaly.

By the Wednesday, a second more reliable test confirmed the driver was positive for the SARS-CoV-2 infection. Later that day, his wife became the second case in what would become known as the Bondi cluster.

Within days, the Sydney outbreak would seed itself in Western Australia and then Victoria, while a separate, unrelated series of quarantine leaks in Queensland – first with a goldminer and then an unvaccinated casual receptionist outside a Covid-19 ward in Brisbane – cascaded into the Northern Territory before being carried into South Australia via another miner.

As June came to a close, four state and territory capitals were plunged into lockdown. Townsville, Magnetic Island and Palm Island in Queensland, and Alice Springs and its remote satellite communities in central Australia, were also sealed tight.

Contact tracing works like a high-stakes puzzle, with shifting, context-specific pieces. Following the identification of the airport limousine driver and his wife as positive cases, NSW Health teams worked with the couple to figure out where they had been in public, how long they had stayed and the kinds of surfaces they may have touched.

It quickly became clear, based on analysis of the virus strain, that the 60-year-old driver was infectious in the community for as many as five days before he came on their radar. The NSW chief health officer, Dr Kerry Chant, revealed the virus was the highly infectious Delta variant, near perfectly matched to one circulating in the United States.

This was the clue that the man had almost certainly picked up the pathogen from flight crew. It also presented contact tracers with a greater challenge: this strain moves fast, with less effort than the first iteration of Covid-19.

Multiple visits to a Vaucluse eatery across five days from June 11, saw Belle Cafe  registered as a test and isolate site. A member of the driver’s household also attended an afternoon screening of Hitman’s Wife’s Bodyguard at Bondi Junction’s Event Cinemas on Sunday, June 13. Health officials declared the entire window between 1pm and 4pm at the cinema complex as concerning, but especially for anyone who had been to the 1.45pm screening of the action flick.

By June 17, 700 people had been instructed to get tested and isolate.

Cases began to flourish in Sydney’s eastern suburbs and then across the city. A Perth physiotherapist who visited Lyfe Cafe in Bondi returned home to Western Australia, taking the virus with her. Exposure sites blossomed across Sydney: west of Penrith, in the far north-west at Rouse Hill, past Camden in the far south-west of the city, and everywhere in between.

For five days in a row, the state recorded two new locally acquired cases during each 24-hour period. By June 22, the government had announced five cases in a single day. This figure doubled to 10 the following day.

Then, on Wednesday, June 23, authorities discovered a birthday party held in West Hoxton had become a super-spreading event. At the time, eight people tested positive and NSW Health contact tracers believed there were 30 attendees. These figures would shift over time and late this week authorities confirmed 27 people had caught the virus at the party, infecting another 12 people who were not at the party. The only people who did not contract the virus at the gathering were fully vaccinated and one who was partially vaccinated.

“Since the pandemic has started this is perhaps the scariest period that NSW is going through,” Premier Gladys Berejiklian said on Thursday, June 24, as the West Hoxton event filtered into the news.

“It is a very contagious variant but at the same time we are at this stage comfortable that the settings that are in place are the appropriate settings, but that is so long as everybody does the right thing. Please be extra cautious.”

While these transmissions had the focus of the nation, a healthy mineworker from Bendigo flew to Brisbane on June 17 and was required to quarantine in the Novotel Brisbane Airport hotel before catching a charter flight to the Newmont Corporation goldmine in the Northern Territory’s Tanami Desert.

This was a crucial error. The man was placed in a hotel room between two high-risk travellers and appears to have contracted the virus there before boarding the flight to the NT. His infection, however, was not caught until Saturday, June 26. NT Chief Minister Michael Gunner announced a 48-hour lockdown across the Top End the next day, and this was extended during the week. More than 900 miners, including those who had already left the mine for their homes in Darwin, Brisbane, Perth and Adelaide, were put into isolation.

On Wednesday, June 30, South Australian authorities announced five new cases of Covid-19 linked to the family of one of these miners. This man had flown back to Adelaide via Alice Springs, which also placed that regional centre into a lockdown.

The middle of the week just gone also marked the moment an uneasy co-operation between governments of all levels exploded in a messy, very public way.

Queensland’s chief health officer, Dr Jeannette Young, launched an extraordinary intervention regarding the AZ vaccine – triggered by Scott Morrison’s unexpected announcement.

“No, I am sorry if I hadn’t made that clear. I do not want under 40s to get AstraZeneca because they are at increased risk of getting the rare – it is rare – they are at increased risk of getting that rare clotting syndrome,” she said during a press conference on Wednesday.

“We’ve seen up to 49 deaths in the UK from that syndrome. I don’t want an 18-year-old in Queensland dying from a clotting illness who, if they got Covid, probably wouldn’t die. Now, wouldn’t it be terrible if our first 18-year-old in Queensland who dies related to this pandemic died because of a vaccine?”

Asked if her view was consistent with other state chief health officers, Dr Young said, “Yes.”

Using less incendiary language, Premier Berejiklian announced that the NSW government would not be offering the AZ vaccine to anyone under 60, unless it was a second dose for someone who had already had the first.

The rationale was clear: mass state vaccination hubs are not a place where people can receive informed medical advice, which is what the official recommendation dictates.

“If you’re under 60 and want the AstraZeneca, you should have a conversation with your GP,” Berejiklian said on Wednesday.

“And what the NSW government will continue to do is follow the health advice of the federal regulators.”

On Thursday morning, Chris Blyth, co-chair of ATAGI, reiterated the body’s advice: Pfizer remains the preferred vaccine for under 60s. When pressed on whether young people should be getting AZ, he said: “There are some pressing situations where that would be warranted, but they are quite small.”

The Saturday Paper reported last week that the Commonwealth plans to phase out AstraZeneca entirely by October, three months from now, as new supplies of Moderna reach Australia and Pfizer stock soars. Barring major changes, this will be the last hurrah for the AZ shot developed by Oxford University.

For those who have had their first shot of AZ, which provides some Covid-19 protection, the second will be administered after a 12-week gap.

By Thursday morning, some 2616 people under the age of 40 had already received their AstraZeneca shot “with informed consent” following Morrison’s Monday evening press conference.

One senior source associated with the vaccine rollout told The Saturday Paper Morrison’s bizarre intervention in that press conference was the “wrong process, right outcome”.

But the aftermath torpedoed what was left of a fragile coherence on vaccine policy, made all the more troubled by constraints on supply and hesitant older Australians. Once again, the rollout is stricken.

An end to the pandemic seems a long way off, pushed further out by a breakdown in politics.

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