Quebec to start screening positive tests for variants
COVID-19 samples will be sequenced to determine presence of spike mutation
As early as next week, Quebec will start screening all positive COVID -19 samples in the province for the mutation that is common to the three more transmissible variants that have originated in England, South Africa and Brazil, the head of the provincial coronavirus tracking program said on Tuesday.
Dr. Michel Roger, of the Laboratoire de santé publique du Québec, outlined to the Montreal Gazette the government's surveillance program for the new variants.
But he conceded that his lab, like others around the world, are “always behind the virus, which is evolving.”
The variants of concern are B.1.1.7, which emerged in Britain in December; B.1.351, which appeared in South Africa in December; and P.1, which swept through the state of Manaus in Brazil in late 2020. Although all three variants differ in many respects, they share the N501Y spike mutation.
Quebec has developed a PCR test that will screen for that mutation, Roger explained.
Five labs already have the capacity to conduct such tests. It's the positive results of the regular COVID-19 tests that will be screened for the N501Y mutation. The additional screening will add 24 hours to the existing two-day process.
“If the mutation is present in the PCR test, it will tell us we have one of the variants,” Roger said. “We won't yet know which one, but we will alert Public Health to respond rapidly. Public Health will contact the person at home and tell them to stay isolated.”
Roger's comments came the same day authorities confirmed in Quebec that the number of confirmed variants has increased from eight to 11.
One of the three new variants, detected in Montreal, has its origins in California.
The other two were identified as B.1.351 and were found in the Abitibi-témiscamingue region.
Dr. Horacio Arruda, Quebec's chief public health officer, said authorities traced the variants in Abitibi-témiscamingue to two “well-controlled outbreaks,” one at a fast-food restaurant and the other at a party.
The California strain, known as Cal.20c, has been identified in 35 per cent to 50 per cent of recently diagnosed infections in Los Angeles.
In his public remarks about Quebec's coronavirus surveillance program, Arruda has tended to focus on the genomic sequencing of positive samples, and has not fully explained the screening of the N501Y mutation.
Genetic sequencing of each sample takes seven to 10 days, and can conclusively identify the variant. To date, Roger's lab has sequenced 8,000 samples, of which 11 were confirmed to be variants. About 2,000 of those samples were collected in the fall and the start of winter. The goal is to sequence another 65,000 samples this year, Roger said.
Those samples will be drawn from the following priority groups:
■ Those returning from abroad who have tested positive.
■Those who have tested positive following outbreaks, including in some schools.
■ People who develop a COVID -19 infection despite being vaccinated.
■ Positive test results that may show some type of anomaly.
■ A small percentage of positive results in different regions of Quebec to determine the emergence of a new variant in the province.
■ Specimens with the N501Y mutation.
The Mcgill Genome Centre and Génome Québec will take part in the mass sequencing. Quebec has provided $11.1 million in funding for the effort.
Roger acknowledged the 11 variants detected so far in Quebec are likely a vast underestimate. The B.1.1.7 variant is reported to be doubling every 10 days in the United States, and has now been detected in 70 countries.
“We have the impression that we're always behind this virus that is always evolving, always chasing after it since the beginning of the pandemic. Now it's the variants, before it was setting up all the tests.”
“If there is a third wave with the variants, it will be difficult,” he added. “That's certain. Will the government ask us to increase our capacity to 60,000 to 70,000 tests a day? That would be a big step to take. It would be tiring.”
Ontario is also ramping up its capacity to check for variants, employing a similar two-prong strategy of screening and sequencing.
Still, Quebec is behind other jurisdictions like Denmark, which started screening all samples for variants last month.
If there is a third wave with the variants, it will be difficult.