Testing for COVID-19 variants inconsistent across the country

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Canada’s capacity to screen for more contagious variants of the coronavirus varies significantly across the country, as more evidence emerges that mutations first detected in Britain and South Africa are spreading in the community.

Health officials in Toronto confirmed Monday they detected the British variant of the novel coronavirus in two people at a meat-processing plant that is in the midst of a COVID-19 outbreak. Ontario also reported its first case of the South African variant, and officials have been unable to link it to international travel.

Testing for the variants differs considerably from province to province. For example, Alberta is testing more than four times the number of samples, per capita, as Ontario. Screening for variants allows public-health officials to gauge the degree to which mutations are circulating in the community, which will influence decisions around restrictions.

However, while screening for variants is spotty across the country, experts say well-designed surveillance programs can make up for a lack of capacity.

“You don’t need to be screening everything to know what strains are out there,” said Graham Tipples, medical-scientific director of public health at Alberta Precision Laboratories. “More does not necessarily mean better.”

Alberta is screening 300 COVID-19-positive samples for variants a day. This is more than double its capacity from two weeks ago. Screening results are back within two or three days.

The province has identified 51 cases involving the two variants, including six cases in three unrelated households that are not linked to travel, according to Deena Hinshaw, Alberta’s Chief Medical Officer of Health.

“Particularly as we see some early concerning indications that we may have some spread of variant cases in the community, we do need to maintain caution and proceed slowly,” Dr. Hinshaw said.

Ontario tallied nearly 2,000 new cases of COVID-19 on Jan. 31, but it can only screen a fraction of those for variants. Public Health Ontario last week projected it would screen an average of 214 samples a day by the end January.

An adult male in the Peel Region, west of Toronto, became the first person in the province to test positive for the South African variant. He has not travelled or been in contact with someone who has, although contact tracers found the man was in close contact with someone who works in health care.

“Without a link to any sort of travel, this does mean that the variant is circulating in the community, which certainly should give us pause especially as we look at revisiting the current closure measures next week,” said Dr. Lawrence Loh, Peel Region’s Medical Officer of Health.

The health care worker tested positive for COVID-19, but Peel has not yet received confirmation whether that person has the same variant, Dr. Loh said.

Meanwhile, Toronto identified its first workplace outbreak involving the British variant of COVID-19, saying it had been found in two employees of a meat-processing facility. There is also evidence of the variant’s transmission to three household members of one of the employees.

The people with the variant are not known to have travelled recently or been in contact with anyone who has, according to the city’s health department. These two were the only people at the facility to be screened for this variant.

The two cases of the variant were among 78 COVID-19 infections identified at Belmont Meat Products Ltd., according to the city’s Medical Officer of Health, Eileen de Villa. Toronto, which says this facility has no employees who interact directly with the public, began investigating a possible outbreak last Tuesday. The company shut down operations on Thursday and could not be reached for comment Monday.

Alberta and Ontario divert samples from international travellers; people who experience severe outcomes, such as landing in the ICU despite being young and otherwise healthy; people who have been vaccinated; individuals who are reinfected; and those tied to outbreaks. Alberta also screens samples from children in an effort to prevent variants from taking hold in classrooms. Some COVID-19-positive samples are also selected at random, as investigators try to detect community spread.

“It does depend not just on quantity, but also the quality,” said John Conly, an infectious diseases specialist at the University of Calgary.

British Columbia has primarily relied on genome sequencing to detect the variants, which is time consuming and means delays in getting results. The province is also using similar technology that is used in standard COVID-19 tests to screen for variants; it’s not clear how many of those tests the province can run, although it says it is increasing its capacity. The province currently has capacity to sequence 500 to 600 samples a day, the province’s Provincial Health Officer Dr. Bonnie Henry said, and is aiming to increase to as many as 1,000 tests a day.

The province has detected 18 cases of the variants, including three “unlinked community cases,” Dr. Henry said.

In Quebec, labs are screening 5 per cent of COVID-19-positive test samples for variants, which at current infection rates translates to about 70 samples a day. The province intends to spend $11.5-million to increase screening to 10 per cent of positive samples in coming days.

Quebec averaged 1,288 new cases a day last week. It has detected a handful of cases of the British variant, although none believed to be linked to community spread.

With reports from James Keller, Justine Hunter, Andrea Woo and Les Perreaux

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