Australia’s vaccine rollout has suffered a major shock, with an advisory slapped on the AstraZeneca vaccine warning people under 50 it may cause extremely rare but potentially deadly blood clots.

On Thursday evening, the Australian government announced it had accepted expert advice that Pfizer should now be the preferred vaccine for under 50s, who will be warned AstraZeneca should only be taken if it is clear the benefits outweigh the risks.

The chief medical officer, Paul Kelly, stressed the incidence of blood clots was extremely rare, at four to six cases per million vaccine recipients, but the complication can cause a death rate of up to 25% when it occurs.

Australia’s vaccine rollout, which has just reached the 1m mark, has so far administered 400,000 AstraZeneca doses, with just one instance of the blood clot issue, which has shown up in Britain and the European Union, where the rollout is further advanced.

The advisory will place great strain on Australia’s vaccination timeline, as 50m doses of AstraZeneca to be produced at CSL’s facility in Melbourne are the centrepiece of Australia’s supply. Expert advice recognised the safety concern would increase vaccine hesitancy and delay the rollout.

The prime minister, Scott Morrison, told reporters in Canberra the Australian government had taken “necessary precautions” and acted on the “best medical advice” although the decision was one of the “setbacks and heartbreaks” in Australia’s Covid-19 journey, which was otherwise world-beating in its success.

Morrison was frank that it was “too early to say” what impact the development would have on the timetable of the rollout, which has already missed its target of 4m by April and the promise Australians would be fully vaccinated by October.

“Our purpose here tonight is to reassure Australians – to reassure them that we’ve been very clear about what the very low level of risk is here,” he said.

The Australian Technical Advisory Group on Immunisation (Atagi) has recommended Pfizer for under 50s in recognition of the fact the blood clot syndrome is more common in that age group, and for those over 50 the potential effects of Covid-19 are far worse.

Atagi’s full advice recognised the safety concern “likely impact on confidence in being vaccinated with AstraZeneca vaccine in all age groups”

“Until the government can increase supply of Covid-19 vaccines other than AstraZeneca, overall coverage under Australia’s Covid-19 vaccine program will likely be reduced,” it said.

“This will likely impact the time frame to which the Australian population is protected against COVID-19.”

Kelly said that people who had had their first dose of the AstraZeneca vaccine without any serious adverse events could safely be given their second dose.

Kelly warned that the rare syndrome was “spontaneous” and “can’t be predicted”, but GPs would be given updated advice to help warn patients about potential symptoms.

The Atagi advice is based on the current epidemiology and incidence of Covid-19 in Australia, where there is no community transmission and only cases in hotel quarantine. Kelly flagged that if a larger outbreak were to occur, the advice could change to reflect greater risk.

The health department secretary, Brendan Murphy, said people aged 50 and over were still “strongly encouraged” to take the AstraZeneca vaccine.

The Australian government will now revamp the vaccine rollout to skew more of the supply of Pfizer to under 50s in category 1B, such as those with underlying medical conditions. Murphy said this would be easier as aged care vaccinations finish and more Pfizer vaccines are freed up for that group.

Given only AstraZeneca and Pfizer have the necessary approvals and supply in Australia, the setback leaves the Australian rollout in a precarious position and looking to alternatives.

Murphy said that the approval process for a third candidate, Novavax, was well advanced and noted Australia had contracts for 51m doses of that vaccine.

The health minister, Greg Hunt, said the first deliveries of Novavax were expected in the third quarter (July to September) of 2021.

Despite disputes over the EU blocking Australia’s supply of AstraZeneca, Hunt expressed confidence that Australia will continue to get a good supply of Pfizer.

He said he had been “very heartened” by the continuity of supply from Pfizer and that Europe had no quarrel with export of all vaccines but rather a specific dispute with AstraZeneca.

Earlier on Thursday, Morrison urged people to “maintain a perspective” on the issues with the AstraZeneca vaccine, saying the advice in the UK was that “some 6,000 people’s lives [there] have already been saved by this very vaccine”.

Morrison compared the incidence of blood clotting from AstraZeneca to the combined oral contraceptive pill, which he said can have “adverse side-effects of venous thromboembolism, VTE, [in] seven to 10 per 10,000 [patients]”.

Campaigning in Tasmania ahead of the state election, the federal opposition leader, Anthony Albanese, took aim at the Morrison government’s performance during the rollout, which he said was “pretty appalling” with Australia falling “way, way short” of its initial targets.

The vaccine rollout and updated advisory will be discussed by state and territory leaders at national cabinet on Friday.

This content first appear on the guardian

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