Shoppers at the Toronto Eaton Centre in Toronto, Dec. 22, 2021. Public-health officials are watching the steep rise in cases, particularly in Quebec and Ontario, and wondering just how high the numbers will go.STRINGER/Reuters
This week, the battle against Omicron got personal for Angela Rasmussen.
Dr. Rasmussen, a virologist who came to Canada earlier in the year to take up a position at the University of Saskatchewan’s Vaccine and Infectious Disease Organization, was looking forward to spending Christmas with family near Seattle.
Her husband had already departed, and she was planning to follow on Tuesday. But the growing chance of picking up an infection en route, potentially endangering family members, including a three-year-old niece who is not vaccinated, changed her mind.
“It sucks, but I think I made the right move,” Dr. Rasmussen said. Colleagues in Saskatoon have invited her to spend some time over the holiday, she said, “so it won’t just be me alone listing to Christmas music, crying.”
On top of personal considerations, Dr. Rasmussen said she does not want to be caught up in quarantine or travel delays outside Canada while an Omicron wave is imminent. She expects to be back in her lab at the start of the new year overseeing experiments that will test the ability of the variant to jump from humans to about 30 other animal hosts, including domestic pets, livestock and wildlife from beavers to bears.
Ontario, Quebec exploring ways to keep health care staff on the job even if exposed to COVID-19
Alberta, Montreal urge residents to rely on COVID-19 rapid tests amid surge in demand for lab tests
Surveillance by Environment and Climate Change Canada has shown that earlier versions of the coronavirus made it into white-tailed deer in the Eastern Townships of Quebec. Dr. Rasmussen said she hopes her work will identify avenues for new and increasingly diverse variants to emerge.
“It’s going to help us assess the future risk that any variant including Omicron could spill into some Canadian animal population, circulate undetected and then present a danger to people later on,” she said.
Dr. Angela Rasmussen, a virologist who came to Canada earlier in the year to take up a position at the University of Saskatchewan’s Vaccine and Infectious Disease Organization.David Stobbe/Courtesy of manufacturer
The experiments could also illuminate the origins of Omicron, which is the most genetically distinct COVID-19 variant of concern to date. Although it is considered to be part of the 20B clade, or lineage, of the virus, it is far removed from other members of that group. One proposed explanation is that the variant evolved in another animal before returning to humans. Another is that it endured a lengthy selection process for months inside one or more immunocompromised individuals. Or it could have spent most of the past year and half in a group of people who are outside the scope of global genomic surveillance of the virus.
Fiona Brinkman, a genomics researcher at Simon Fraser University in Burnaby, B.C., said she thinks the mutations in Omicron are more consistent with the idea that the virus underwent some adaptive evolution within another animal host.
“But truthfully, we don’t really know — and we’ll continue not to know until someone finds a closely related sample,” she said.
Whatever the answer, understanding the history of Omicron is more than an academic exercise. The new variant has so upended the course of the pandemic in the past month that it reinforces the need to track the evolution of the coronavirus to head off more of the same in 2022.
For the present, public-health officials are watching the steep rise in cases, particularly in Quebec and Ontario, and wondering just how high the numbers will go. Initial investigations have provided strong evidence that the variant wields two important adaptations to help it get an edge over human interventions.
Like the Delta variant that has been dominant since the summer, Omicron is highly transmissible – only much more so. Unlike Delta, it has also proved tenacious at evading vaccines. In combination, the two traits have led to projections that show the variant sweeping through Canadian populations rapidly if public-health measures are not tightened.
POSSIBLE COVID-19
EVOLUTIONARY TREE
Because Omicron shares many independently arisen mutations with other variants, experts are still uncertain about its placement on the evolutionary tree of the virus that causes COVID-19. But they do know it is not closely related to any other variant of concern.
Original COVID-19 strain
Clade 19A
Clade 19B
Clade 20A
Clade 20C
Clade 20B
Beta
Delta
Mu
Alpha
Lambda
Gamma
MURAT YÜKSELIR /
THE GLOBE AND MAIL,
SOURCE: COVARR-NET
Omicron
POSSIBLE COVID-19
EVOLUTIONARY TREE
Because Omicron shares many independently arisen mutations with other variants, experts are still uncertain about its placement on the evolutionary tree of the virus that causes COVID-19. But they do know it is not closely related to any other variant of concern.
Original COVID-19 strain
Clade 19A
Clade 19B
Clade 20A
Clade 20C
Clade 20B
Beta
Delta
Mu
Alpha
Lambda
Gamma
MURAT YÜKSELIR /
THE GLOBE AND MAIL,
SOURCE: COVARR-NET
Omicron
POSSIBLE COVID-19 EVOLUTIONARY TREE
Because Omicron shares many independently arisen mutations with other variants, experts are still uncertain about its placement on the evolutionary tree of the virus that causes COVID-19. But they do know it is not closely related to any other variant of concern.
Original COVID-19 strain
Clade 19A
Clade 19B
Clade 20A
Clade 20C
Clade 20B
Beta
Delta
Mu
Alpha
Lambda
Gamma
MURAT YÜKSELIR / THE GLOBE AND MAIL,
SOURCE: COVARR-NET
Omicron
What happens next depends partly on which of these two traits is more central to the variant’s success. The more it depends on transmissibility, the more serious cases will arise mainly in the unvaccinated or partly vaccinated. However, if immune escape is Omicron’s big play, then the share of vaccinated individuals heading to hospital with COVID-19 in the next few weeks will rise simply because they are a much larger group.
However, there are hopeful signs the Omicron wave can be moderated if a few other properties of the variant break humanity’s way. One is that a third dose of a COVID-19 vaccine seems to restore immunity to levels that are similar to what people have had with two doses against Delta. And data suggests those levels are regained within seven days.
Another key development is accumulating evidence that the variant produces less severe outcomes, as indicated by two recent studies from Britain. The caveat is that a virus that increases the number of infections more than it reduces the rate of hospital admissions is still bad news.
“Even if most cases are mild, a very large number of cases can still be a large problem, " said Jesse Shapiro, an infectious disease specialist at McGill University.
The expected peak in hospital cases could be blunted somewhat if Omicron also requires shorter stays. Corinne Hohl, an emergency-room physician and researcher at the University of British Columbia, is leading a pan-Canadian project that has already accumulated data on 160,000 hospital patients with COVID-19. She said that project members will be closely tracking any changes in how the disease presents as Omicron takes over. But doctors have learned a lot from previous waves, including which treatments do not work.
“We are no longer intubating as many patients, and able to manage more patients on less invasive modes of ventilation, which has resulted in fewer ICU admissions,” Dr. Hohl said.
SCENES FROM A TAKEOVER
Genomic sequences from Canada, Britain and South Africa show the growing dominance of the Omicron variant as a fraction of total cases. The prevalence of the variant in Canada is underrepresented due to a lag in data release.
Omicron
Alpha
Beta
Delta*
Others
Gamma
CANADA
100%
75
50
25
0
July
2020
Oct.
Jan.
2021
April
July
Oct.
BRITAIN
100%
75
50
25
0
July
2020
Oct.
Jan.
2021
April
July
Oct.
SOUTH AFRICA
100%
75
50
25
0
July
2020
Oct.
Jan.
2021
April
July
Oct.
*All delta lineages combined.
THE GLOBE AND MAIL, SOURCE: COVARIANTS.ORG
SCENES FROM A TAKEOVER
Genomic sequences from Canada, Britain and South Africa show the growing dominance of the Omicron variant as a fraction of total cases. The prevalence of the variant in Canada is underrepresented due to a lag in data release.
Omicron
Alpha
Beta
Delta*
Others
Gamma
CANADA
100%
75
50
25
0
July
2020
Oct.
Jan.
2021
April
July
Oct.
BRITAIN
100%
75
50
25
0
July
2020
Oct.
Jan.
2021
April
July
Oct.
SOUTH AFRICA
100%
75
50
25
0
July
2020
Oct.
Jan.
2021
April
July
Oct.
*All delta lineages combined.
THE GLOBE AND MAIL, SOURCE: COVARIANTS.ORG
SCENES FROM A TAKEOVER
Genomic sequences from Canada, Britain and South Africa show the growing dominance of the Omicron variant as a fraction of total cases. The prevalence of the variant in Canada is underrepresented due to a lag in data release.
Alpha
Beta
Gamma
Delta*
Omicron
Others
CANADA
100%
75
50
25
0
July
2020
Oct.
Jan.
2021
April
July
Oct.
BRITAIN
100%
75
50
25
0
July
2020
Oct.
Jan.
2021
April
July
Oct.
SOUTH AFRICA
100%
75
50
25
0
July
2020
Oct.
Jan.
2021
April
July
Oct.
*All delta lineages combined.
THE GLOBE AND MAIL, SOURCE: COVARIANTS.ORG
Meanwhile, epidemiologists are looking for clues to how the variant will play out in Canada. Nazeem Muhajarine, a professor of community health and epidemiology at the University of Saskatchewan, said he is intrigued that, so far, Omicron cases are not growing as rapidly there as in the east. While it is too early to draw conclusions about why, such hints suggest the variant will peak at different times and in different ways across the country.
Looking further into the future, the variant could hasten the transition of COVID-19 to an endemic virus, which is continuously present at a predicable level, like influenza. But this would not necessarily be a welcome outcome if the long-term infection rate stays relatively high, a possibility demonstrated in a modelling study released earlier this month by researchers at Simon Fraser University.
Caroline Colijn, a mathematician who led the study, said a more co-ordinated global-health effort to immunize people and reduce the chances of new variants taking off is still the most reliable path to a future that is less disrupted by waves of COVID-19. “But we’re not there yet.”
Our Morning Update and Evening Update newsletters are written by Globe editors, giving you a concise summary of the day’s most important headlines. Sign up today.
Ivan Semeniuk