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People arrive at a COVID-19 vaccination clinic in Montreal, on June 1, 2021.

Paul Chiasson/The Canadian Press

A more transmissible COVID-19 variant is prompting Ontario health authorities to urgently retool disease surveillance and the vaccine rollout amid calls to prioritize vulnerable regions with second doses to try to head off the emerging threat.

The recently renamed Delta variant is the same one associated with a devastating acceleration of the pandemic in India. It was first reported in Canada in late April and evidence is mounting that it is spreading more readily than earlier variants.

Peter Juni, the scientific director of Ontario’s COVID-19 Science Advisory Table and a professor of medicine and epidemiology at the University of Toronto, said the Delta variant now makes up about one-quarter of COVID-19 cases in Peel Region, west of Toronto.

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Dr. Juni said his personal view is that the provincial government needs to flood the region with vaccines and make everyone there, regardless of age, eligible for a second dose immediately. “We have to control the Delta hot spot in Peel and therefore protect the rest of the province,” he said.

Brampton, Ont., in Peel Region, has been one of the cities hardest hit by the pandemic in Canada.

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On Thursday, Brampton Mayor Patrick Brown also urged the Ontario government to send more vaccines and to open eligibility for second doses to younger residents, including essential workers.

“If we do this right away, if the government reacts in a nimble, agile manner and focuses the fire extinguishers – these vaccines – on the areas where we know it’s going to spread, I think we can get through this and avoid a fourth wave,” Mr. Brown said.

The rise of Delta

A model based on daily reported COVID-19

cases in Ontario during April and May predicts

the Delta variant gaining ground over previous

ly identified variants of concern as a percentage

of all cases. The variant could account for three

quarters of new cases in the province by

mid-July.

Total daily new cases not caused

by initial three variants of concern

Measured prevalence

of Delta variant

80%

60

Proportion of cases

caused by Delta variant

40

20

March 31

April 20

May 10

May 30

June 19

July 9

THE GLOBE AND MAIL

SOURCE: Troy Day/Queen’s University

The rise of Delta

A model based on daily reported COVID-19 cases in

Ontario during April and May predicts the Delta variant

gaining ground over previously identified variants of

concern as a percentage of all cases. The variant could

account for three quarters of new cases in the province

by mid-July.

Total daily new cases not caused

by initial three variants of concern

Measured prevalence

of Delta variant

80%

60

Proportion of cases

caused by Delta variant

40

20

March 31

April 20

May 10

May 30

June 19

July 9

THE GLOBE AND MAIL

SOURCE: Troy Day/Queen’s University

The rise of Delta

A model based on daily reported COVID-19 cases in Ontario during April and May predicts

the Delta variant gaining ground over previously identified variants of concern as a percent-

age of all cases. The variant could account for three quarters of new cases in the province

by mid-July.

Total daily new cases not caused

by initial three variants of concern

Measured prevalence

of Delta variant

80%

60

Proportion of cases

caused by Delta variant

40

20

March 31

April 20

May 10

May 30

June 19

July 9

THE GLOBE AND MAIL, SOURCE: Troy Day/Queen’s University

A risk assessment conducted in Britain, where the Delta variant is a few weeks further ahead relative to Canada, reported preliminary evidence that infections owing to the variant are more severe, leading to increased hospitalizations in some regions, though that trend has not yet been confirmed.

Equally worrying are indications that the variant is more resistant to vaccines, particularly in people who are not fully immunized. This has heightened the urgency around getting second doses to areas of high vulnerability. Canada sits somewhere between India and Britain in vaccinations, in that a large share of its population has received a first dose but very few have had a second. Among adults in Peel, for example, the ratio is 72 per cent to 4 per cent for one and two doses, respectively.

The region has a major manufacturing and distribution sector that employs tens of thousands of people in jobs that can’t be done from home. Outbreaks have plagued some Peel workplaces, with infections acquired on the job spreading to large households made up of multigenerational families and international students.

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“That really means we have four weeks to try to get to widespread two-dose coverage in our community,” said Lawrence Loh, Peel’s Medical Officer of Health.

Ontario Health Minister Christine Elliott said Thursday the province’s vaccine task force is looking to extend eligibility for second doses to all age groups “to make sure that anybody who wants to receive the second vaccine can get one as quickly as possible.”

Her office later clarified that while second doses may be sped up, the province will still prioritize groups based on age and risk first, beginning now with those 80 and older, followed by 70 and older, and then based on the dates when people got their first shot.

Targeted surveys conducted by the province show that, by early May, the Delta variant was established in Peel as well as in Toronto and Waterloo, and outcompeting the variant that has now been designated Alpha. Alpha originated in Britain and drove Canada’s third wave of the pandemic.

“We estimate Delta has about the same advantage over Alpha as Alpha had over the earlier type,” said Troy Day, a computational biologist at Queen’s University. That would mean Delta is more than twice as transmissible as the version of the coronavirus that was prevalent in Canada through the summer and fall of 2020.

Based on a model developed by Dr. Day, the Delta variant now likely accounts for 15 to 20 per cent of cases in the province over all and will hit 60 per cent by July 1. A similar pattern is expected across Canada, though the timing may be different for other provinces. Far more difficult to predict is the effect of the Delta takeover on total case counts, which have been dropping steadily for the past month as the vaccine rollout continues.

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David Earn, a mathematician specializing in infectious diseases at McMaster University, said forecasts he and his team are preparing for the advisory table show what could happen, depending on how careful people are about their social contacts as the province emerges from its latest lockdown.

If contacts rise by as little as 15 per cent, the number of daily new cases could plateau rather than continue to drop through the month of June. If contacts rise by 30 per cent, daily case numbers could rise again in July. Dr. Earn cautioned that the forecasts are preliminary and sensitive to a range of variables that influence individual behaviour, including weather.

The forecasts include estimates similar to a British-based study that found the Delta variant reduced the effectiveness of the AstraZeneca and Pfizer vaccines to just 33.5 per cent after one dose. Sarah Otto, a theoretical biologist at the University of British Columbia, said that number should be viewed with caution because the study may have captured some individuals for whom the first dose had not yet generated its highest possible immune response.

Nevertheless, she said, the result “is enough to say there are signs of an important difference” in how the Delta variant responds when infecting those who are only partly immunized.

That difference has put a premium on tracking where in Canada the Delta variant is most active. The challenge is that the variant lacks a mutation common to other variants of concern. This has enabled it to dodge screening tests that were developed to flag the earlier variants.

Vanessa Allen, chief of microbiology and laboratory science at Public Health Ontario, said it is possible to create a separate test that can screen for the Delta variant and her lab has done so. However, rather than commit resources to rolling out the test, Ontario has increased full genome sequencing of a random share of all COVID-19 cases in the province. The change in strategy will allow health officials to better track the movements of all variants, including those that have not yet been identified.

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Dr. Allen said that, as of this week, the random sample includes the genomes of half of all the COVID-19 cases for which there is enough viral material for a reliable result - roughly 2000 cases.

Editor’s note: An earlier version of this story stated that Dr. Allen said that, as of this week, half of the 2,500 samples that the province sequences will be made up of a random survey of all COVID-19 cases. In fact, the random sample includes the genomes of half of all COVID-19 cases for which there is enough viable material for a reliable result. That's roughly 2,000 cases.

With a report from Laura Stone in Toronto

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