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Maj.-Gen. Dany Fortin participates in a news conference on the COVID-19 pandemic in Ottawa on Jan. 15, 2021.Justin Tang/The Canadian Press

Critical shipments of the Pfizer-BioNTech vaccine will be reduced by half for Canada just as the federal public-health agency warned Friday that the COVID-19 pandemic is on a “rapid growth trajectory.”

Pfizer needs to temporarily slow the delivery of its vaccines while it retools its Belgian manufacturing plant, in order to expand production in the long run. The news came as the Public Health Agency of Canada released updated pandemic modelling that showed a high incidence of the disease, driven by rapid growth in Quebec and Ontario.

Pfizer’s decision means Canada will get 50 per cent less Pfizer vaccine than expected between Jan. 25 and Feb. 21, but that loss will be offset in subsequent weeks, said Major-General Dany Fortin, who is leading Canada’s vaccine logistics. Canada was previously expecting to receive 208,650 doses in the last week of January and about 367,000 doses each week in February. Instead about 655,000 of those doses will be delivered later.

Based on publicly released delivery numbers, the drop will translate to approximately 327,000 people getting their two-shot vaccine later than expected.

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At a separate press conference Friday, Prime Minister Justin Trudeau said the setback was “out of our hands” and that’s why Canada has contracts with several vaccine developers.

“This does not impact our goal to have enough vaccines available by September for every Canadian who wants one,” Mr. Trudeau said. “Canada must still get ready for the ramp-up phase in Q2.”

Canada has secured enough vaccines to inoculate 3-million people by the end of March, 13-million people by the end of June, and the entire population by the end of September. If more vaccines are approved, the federal government has said that timeline could be sped up. Federal cabinet ministers were unable to explain why, if Pfizer was expanding its overall production capacity, Canada’s delivery timelines for the second and third quarter were not being accelerated.

Health Minister Patty Hajdu said the procurement department is in “constant negotiations with the vaccine manufacturers about earlier doses and more doses.”

The supply challenges underscored the message delivered by Canada’s top doctors Friday that the only way to slow a surging second wave is to limit physical contacts and travel. Updated federal modelling, released Friday, confirmed a worsening pandemic with the potential for 2,000 more deaths by Jan. 24 and up to 107,000 new cases in the same timeframe.

“Early signs of levelling off for most of December have been replaced by a sharp rise in cases in late December, following the holidays,” Chief Public Health Officer Theresa Tam said.

The modelling shows if people maintain the same level of contacts, Canada is on track to see 10,000 daily new cases by the end of January. If contacts increase, the modelling shows Canada could see 20,000 daily new cases in the same timeframe, but if contacts are reduced then case growth could shrink to 5,000 daily new cases by the end of the month.

“The vaccine, in the short term, is not going to make any difference to the transmission and that projection,” Dr. Tam said. She said that after the public-health agency’s November modelling showed the potential for 10,000 daily new cases by the end of December, the case growth levelled off but that reversed after Christmas.

The latest modelling was completed before Ontario’s stay-at-home order came into effect but after Quebec implemented a curfew. In all provinces west of the four Atlantic bubbles, the longer range forecast showed that “a stronger response is needed now.”

While the delay in the already limited supply of the vaccine won’t affect the overall trend of the pandemic, mathematical epidemiologist Jane Heffernan said it will still have an impact. The key in vaccination programs is to deliver them as quickly as possible and before the peak in cases in order to maximize the number of infections that are averted. She said her modelling shows Canada’s second wave will peak in late February or early March.

Still, Dr. Heffernan, who is an associate professor at York University and director of the Centre for Disease Modelling, said the delay in vaccines can be offset by reprioritizing who gets the vaccine in order to maximize the impact the vaccines have.

“It’s possible, even with less doses, to still get a good effect out of them,” said Dr. Heffernan.

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Ontario said it doesn’t yet know if the delay in Pfizer vaccines will push back its Feb. 15 goal of getting all long-term care residents their first shot. In Alberta, the government said the delay isn’t expected to affect the vaccination plan for long-term care residents but could complicate the delivery of second doses and slow the rollout for other high priority groups such as the elderly, Indigenous communities and health care workers.

“It will mean more people are on stand-by,” Alberta Health Minister Tyler Shandro said. Premier Jason Kenney has been critical of the federal government’s handling of the vaccine supply, pointing to places such as Britain and Israel, which have had a faster rollout.

B.C. Health Minister Adrian Dix said the delay will be significant just as the province was hoping to ramp up its vaccination program. He said no decision has been made, but the province will have to evaluate whether the 21-day time period between the first dose, and the second booster shot, will remain the same.

Provinces and territories will receive updated shipment numbers in the coming days, Maj.-Gen. Fortin said. He warned that given the unprecedented global demand, allocations will continue to fluctuate.

Pfizer’s spokesperson said the drug manufacturer is making the changes to ensure it can double its production goal to 2 billion doses of the vaccine in 2021. The changes “will provide a significant increase in doses available for patients in late February and March,” Christina Antoniou said in an e-mailed statement.

Even though Health Canada has approved Pfizer’s European and United States manufacturing sites, Ms. Antoniou said the company decided that Canada’s allocation would come from Belgium. Her statement did not address whether the decision was related to President Donald Trump’s December executive order that gave Americans priority access to vaccines developed south of the border. At the time, the Canadian government said the order would have no impact on Canada’s vaccine contracts.

“Decisions about which manufacturing sites will supply which markets are made by Pfizer at a global level and are subject to change through planning efforts,” Ms. Antoniou said.

Maj.-Gen. Fortin said all countries receiving shipments from the Pfizer facility in Belgium are being equally acted by the delay.

With reports from Kristy Kirkup, Justine Hunter and James Keller

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