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The Centennial College Scarborough COVID-19 vaccine clinic in Toronto sits empty on Wednesday, April 14.Melissa Tait/The Globe and Mail

The Public Health Agency of Canada acknowledged Thursday the challenges provinces and territories are facing with the disruptions in COVID-19 vaccine shipments from Moderna, as it confirmed the next delivery will also be delayed.

Shipments from Pfizer-BioNTech and Moderna have increased significantly in volume since January but while vaccines from Pfizer arrive regularly each week, more than a month has elapsed since a shipment from Moderna arrived complete and on time. The inconsistencies have left some provinces scrambling to cancel or postpone appointments. Others have chosen to hold doses in reserve to avoid disruptions, but that can slow down the pace of administration.

“Several provinces have experienced the delays or have had to reschedule appointments and we’re working with them closely on managing that so the effect is not felt as much moving forward,” Maj.-Gen. Dany Fortin, who is leading the health agency’s vaccine logistics, said at a federal vaccine briefing on Thursday.

“Provinces are all intent on distributing or vaccinating as rapidly and as effectively as possible,” he added, noting that the delays ”negatively affect the campaign for sure.”

To date, 12.5 million doses of vaccine have been distributed to the provinces and territories and 8.8 million doses have been administered, officials said at the vaccine briefing. By the end of June, the federal government has said that number will reach 44 million shots. In order to effectively scale-up vaccination campaigns, Maj.-Gen. Fortin said the provinces and territories need predictability in deliveries.

Canada only has delivery schedules for the Pfizer and Moderna vaccines. The next shipment from AstraZeneca is expected in June and will contain one million doses. The first delivery from Johnson & Johnson will arrive by the end of the month, but the federal government has not yet said how many doses it will contain.

This week, Prime Minister Justin Trudeau played down the impact of the Moderna delays, calling them in the House of Commons the difference of a “day or two.” However, data reported by The Globe on Thursday showed the delays are closer to a week, something Maj.-Gen. Fortin confirmed.

He said the Moderna delay is usually between a week and 10 days, and the government is trying to narrow the delay and give provinces as much warning as possible about any disruptions, “so that they don’t find themselves in a situation where they have to constantly react to perceived delays.”

The shipment of 1.2 million shots from Moderna that was supposed to come next week is also delayed by one week. Maj.-Gen. Fortin said he hopes to have all of the shots distributed by the end of the month, but it’s possible that could spill into early May.

“We’re not working on hope, we’re working with a high degree of probability that those doses will be picked up in that time frame,” he said. Ontario said Thursday that it is only expecting its share of Moderna doses to arrive in the first week of May, but Maj.-Gen. Fortin said while that’s not impossible it’s more likely to arrive by the end of April.

On Wednesday, Procurement Minister Anita Anand rejected any suggestion that there was a supply issue, despite comments to the opposite not only from Conservative Premiers but also from health officials on the front lines.

For example, the clinics at the University Health Network in Toronto have the capacity to vaccinate 35,000 people a week, but only has about 2,000 Pfizer doses confirmed for each of the next two weeks.

Deliveries of a total of 1.5 million doses of the version of the AstraZeneca vaccine made in India, and sold under the name Covishield, were expected in April and May but those have been delayed and no new delivery date has been released.

“For the doses from India, there will be a delay in light of the current situation of exports not coming from India. So now we’re looking at the month of June. And we’re also in discussions with AstraZeneca about the possibility of something happening sooner,” Joëlle Paquette, director general at Public Services and Procurement Canada said Thursday.

With a report from Bill Curry.

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