Fast-spreading U.K. variant will likely become dominant in the GTA before the end of the month, study warns

Thestar.com
Feb. 19, 2021
May Warren

A new local study suggests a concerning rise in the B.1.1.7 COVID variant in the GTA, and predicts it will likely become dominant in the region before the end of the month.

The study, published online last week, was co-authored by researchers at Public Health Ontario, Sunnybrook hospital and Dynacare Laboratories.

“This new strain is transmitting very rapidly and it’s able to out-compete other strains that are circulating in Ontario,” said lead author Kevin A. Brown, a scientist at Public Health Ontario and an assistant professor at the University of Toronto.

The authors analyzed COVID lab samples from Dynacare that came from the GTA, in particular Markham, Brampton, Maple and Etobicoke, from mid-December to Feb. 3. The COVID test used (called TaqPath), was able to pick up the absence of a certain gene on the spike protein of the virus that signals the B.1.1.7 mutation, which first emerged in the U.K.

The researchers found that the prevalence of the gene marker rose from two per cent on Dec. 16 to 15.2 per cent on Feb. 3, even though the province was under lockdown for most of that time. Out of 11,485 positive COVID-19 tests, 448 overall had the gene marker (about four per cent).

The team then sent 59 samples to the lab for a full genomic sequencing, and 53 turned out to be B.1.1.7, suggesting the gene marker is a good “proxy surrogate measure,” for that variant, Brown said.

The study has not yet been published in a peer-reviewed journal, considered the gold standard of scientific research, but has been submitted to the The Journal of the American Medical Association, Brown added.

“We know from other parts of the world, and now in Ontario as well, that this variant is more transmissible than other variants, so we’re confirming that,” he said.

Not only did B.1.1.7 appear to increase quickly, it did so at a time when overall case numbers began to drop, and the province was under strict lockdown measures.

“It was still able to transmit in that context,” Brown said. “We’re having two different epidemics that are occurring at the same time.”

The fast-spreading variant is responsible for a tragic outbreak at Roberta Place long-term-care home in Barrie, which killed 70 people. Cases have also been found at North York meat packing plant.

The study comes as Toronto’s medical officer of health, Dr. Eileen de Villa, warned of the rising threat of extra-contagious variants of concern, at a Wednesday press conference.

“I have never been as worried about the future as I am today,” said de Villa, who co-wrote a letter with her Peel counterpart, Dr. Lawrence Loh, asking the province to leave restrictions in place in both regions until at least March 9.

“The variants of concern mean we face a deceptively dangerous situation,” she told reporters. “Right now the case count numbers don’t look so bad, they don’t sound bad, but today’s variant count is the tip of an iceberg.”

Steini Brown, dean of the Dalla Lana School of Public Health at the University of Toronto, presented modelling last week on the virus that also warned of the rise of B.1.1.7 and said it was on its way to becoming become dominant in the province.

The province is now screening all positive COVID test samples for the signal that they are cases of a variant of concern. If samples are flagged, genomic sequencing must be done to determine which variant they are.

As of Wednesday there were 348 confirmed cases of B.1.1.7 province-wide, 10 cases of B.1.351, which originated in South Africa, and one case of P.1, first detected in Brazil.

Over 500 people at a Mississauga condo were tested over the weekend after five residents tested positive for B.1.351.

Toronto Public Health has added information on variants of concern to its COVID-19 dashboard, including 57 confirmed cases (56 B.1.1.7 strain and one P.1), and 341 cases that have screened positive for a mutation.

The agency has “focused efforts towards contact tracing COVID-19 cases associated with variants of concern,” said Dr. Vinita Dubey, associate medical officer of health, in an emailed statement.

“All Torontonians are asked with renewed urgency to keep contact as much as possible to those you live with, and to limit contact as much as possible with those you don't live with,” she added.

Dr. Larissa Matukas, head of the microbiology division and an infectious disease consultant at St. Michael’s Hospital, called Kevin A. Brown’s paper “incredibly important,” and said it shows how vital it is to have “early detection warning systems in place” for COVID mutations.

Brown and his coauthors noted limitations of the study include that a very low viral load could be a false positive, and that the samples were drawn from areas with very high COVID rates.

But Matukas said the false positives are such a small percentage they shouldn’t impact the overall trend the paper shows.

Jean-Paul Soucy, a PhD student in epidemiology at Dalla Lana School of Public Health, said surveillance of the new variants has been “haphazard and patchwork so far,” so it’s “really valuable to have these numbers.”

Brown is Soucy’s PhD supervisor but was not involved in the study.

“I think it’s concerning to see that, at least in this slice of the GTA, the same trajectory of these variants that we’ve seen in other places where they’ve become dominant, particularly in the U.K,” Soucy said.

“Once you kind of take the foot off the gas pedal and open up more, that just gives it fuel to spread even faster.”