Has the Delta variant disappeared in Canada?

Not only is Omicron the predominant COVID-19 variant circulating in Canada, but it also continues to dominate much of the conversation currently surrounding the pandemic. The latest update to draw attention involves the emergence of a new Omicron subvariant in Canada, with more than 100 cases already confirmed.

But with so much of the focus on Omicron, many may be left wondering whether other variants such as Delta continue to circulate in Canada at all.

The latest data from the Public Health Agency of Canada (PHAC) shows that while the Omicron variant now accounts for the majority of positive COVID-19 samples collected by the agency, a small percentage of Delta cases continue to be detected. During the week of Jan. 9, the most recent data on display, 92 per cent of 404 samples collected in Canada tested positive for Omicron. Meanwhile, 7.9 per cent of the samples tested positive for the Delta variant.

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“It's really being replaced by Omicron…but Delta is still out there,” Dr. Gerald Evans, chair of Queen's University's infectious diseases division in Kingston, Ont., told CTVNews.ca in a phone interview on Wednesday.

With Omicron proving to be highly transmissible and quick to replicate, it essentially superseded the variant that dominated before it, Evans said. Delta had done the same to Alpha when it first emerged as well, he said.

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“Delta is such a robust variant that it outcompeted Alpha, so we don't really see Alpha at all anymore,” he said. “It may just be that we need a little more time to see Omicron push Delta out.”

Similar to what’s being observed on a national scale, Omicron makes up the vast majority of samples processed through whole genome sequencing in Ontario. The province’s latest surveillance report on whole genome sequencing shows that during the week of Jan. 2, 97.8 per cent of cases sequenced were Omicron, while 2.2 per cent were Delta.

“It looks like [Delta] is still holding on in a small percentage of people,” Dr. Susy Hota, medical director for infection prevention and control at the Toronto-based University Health Network, said on Thursday in a phone interview with CTVNews.ca. “It hasn't been completely displaced.”

This trend of Delta remaining in circulation is true across most of the country as well, she said, not just in Ontario. In British Columbia, for the week of Jan. 9 to Jan. 15, 97 per cent of positive specimens sequenced by the B.C. Centre for Disease Control were Omicron, while three per cent were Delta. The most recent data logged by the province of Quebec on Jan. 8 shows that 94.6 per cent of screened COVID-19 cases were presumptive Omicron, while 5.4 per cent were presumptive Delta.

An important factor to consider in the reduced number of Delta cases being reported by provinces is the emergence of vaccines, said Hota. Two doses of COVID-19 vaccines have proven to be highly effective against the Delta variant, said Hota. But when it comes to Omicron, while several studies indicate that current vaccines are still effective, they point to the need for a third dose for optimal protection.

“The opportunity still remains for the Omicron BA.1 variant to be transmitted amongst people, whereas Delta is losing that opportunity because vaccines are more effective at preventing infections,” said Hota.

Both Evans and Hota said that the Delta variant is likely circulating in greater numbers among those who are unvaccinated, along with other vulnerable populations including those who are immunocompromised or older in age.

Despite the lower number of Delta cases being reported today compared to months ago, both Hota and Evans said it’s tough to tell whether the variant will disappear for good in the near future.

“With the continued low-level circulation of Delta in the community, Omicron may not be able to completely wipe Delta if it's got lots of people it can still infect,” said Evans.

Hota said she anticipates the Delta variant may linger in small amounts across Canada for quite some time.

“It all really depends on what happens with future variants coming along, what their characteristics are like and whether they end up displacing [existing variants],” she said.

NEW SUBVARIANT DETECTED IN CANADA

Canada’s Chief Public Health Officer Dr. Theresa Tam announced that more than 100 cases of the new Omicron subvariant, BA.2, have been discovered in Canada as of Friday. This is double the amount of infections from the subvariant that was reported earlier last week.

“We're one of the first countries to actually pick up on this variant, and we have at least over 100 identifications," said Tam during Friday’s federal COVID-19 update.

Dr. Jeff Wrana is a senior investigator at Lunenfeld-Tanenbaum Research Institute based in Toronto. He was involved in creating the platform to sequence and monitor all variants of concern that come through the joint microbiology lab between the University Health Network and Sinai Health Systems. Several BA.2 subvariant cases were first identified by the lab back in December through whole genome sequencing, he said.

“We detected the first BA.2 [cases] before New Years and since then, there's been kind of sporadic cases,” he told CTVNews.ca in a phone interview on Thursday. “But in the last couple of weeks, it's clearly expanding.”

According to PHAC, the BA.2 subvariant was first detected in Canada in November. Looking at the subvariant’s spread across the country so far, Wrana noted that the pace at which BA.2 cases are increasing is different than what was noted with the original version of Omicron in early December. 

“Omicron was basically like an explosion went off – it was just everywhere almost instantaneously,” he said. “This [subvariant] is kind of showing a little bit more of a leisurely expansion.

“But we're just starting to see the expansion now, so we don't really know what the shape of that curve is going to look like.”

BA.2 is a descendant of the Omicron variant and has already been detected in nearly 50 countries worldwide, according to global coronavirus data sharing platform GISAID. The United Kingdom recently designated it a “variant under investigation,” noting it could have an increased growth rate compared to the original Omicron lineage, BA.1. The Omicron variant has four sub-lineages: BA.1, BA.1.1, BA.2 and BA.3.

The BA.2 subvariant is considered "stealthier" than the original version of Omicron because some of its genetic traits make it harder to detect. According to the World Health Organization, the BA.2 subvariant differs from BA.1 in some of its mutations, including in the spike protein. Still, Evans said there isn’t a significant difference in the genomic structure of the BA.2 subvariant compared to that of BA.1.

“This is not a jump from Alpha to Delta, or Delta to Omicron,” said Evans. "It's basically Omicron with a few small changes in its genetic structure, nothing that would make it have to have a whole new Greek letter."

As viruses become endemic, they tend to exhibit this kind of behaviour, said Evans, referring to the small degree of mutational differences that are often adopted by viruses over time. While BA.1 is the most common subvariant of Omicron currently circulating around the world, Evans pointed to several countries that are seeing much more rapid growth of BA.2 compared to BA.1 such as India, Denmark, the U.K. and Germany.

According to Wrana, however, it is still too early to tell whether Canadians are likely to see another surge in infections as a result of the BA. 2 subvariant.

“We don't know yet if it's really going to be explosive or peter out,” he said. “There are other variants that came and went that we all got worried about, but they didn't really do anything.”

Evans said that very limited data suggests that the efficacy of current vaccines is similar to what it would be against BA.1. Additionally, based on reports so far, the new subvariant does not appear to be more severe than the original version of Omicron, said Hota, pointing to early data from Denmark.

“We do know that hospitalizations and deaths are lag indicators – they do happen later, so when you have a new change in variant, it can be a couple of weeks before you start to see that catch up,” she said. “But right now, there's no signal to suggest that it's resulting in a huge surge in hospitalizations or deaths.”

While Evans said the new subvariant should not be cause for concern at the moment, all experts said that more research is necessary to understand the true scope of BA.2.

“You shouldn't be worried at the moment about this BA.2, as opposed to the original Omicron BA.1,” said Evans. “People shouldn't be concerned about genetic changes unless those genetic changes actually mean something fundamentally different.”

“You basically can't predict how these variants will behave within the population,” said Wrana. “You can do lab-based experiments that show this, that or the other, but translating that into how the variant behaves in the population is not that easy.”

With files from Brooklyn Neustaeter and The Associated Press