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Digital display boards at O.R. Tambo International Airport in Johannesburg show cancelled flights after several countries, including Canada, banned flights from South Africa following the discovery of a new Covid-19 variant Omicron.SUMAYA HISHAM/Reuters

Almost one year after the emergence of the first coronavirus variants rewrote the rules on dealing with the pandemic, scientists around the world are sounding the alarm about what looks to be yet another ominous development. A key question for Canada is whether strategies that scientists have developed over the past year to face such a moment will be sufficient for guiding the public health response.

On Friday, the World Health Organization declared the Omicron variant, previously known by its lineage designation, B.1.1.529, a variant of concern. It was reported this week in multiple locations in Africa, where it has been linked to a steep rise in the number of infections. According to the WHO, its first known appearance was in a specimen collected on Nov. 9. And while the full significance of the variant is still being assessed in laboratory and epidemiological studies, what is known so far has given experts plenty of reasons for concern.

Chief among them is the number of genetic mutations – 32 – that it exhibits on its spike protein. The spike is the coronavirus’ calling card, which it uses to enter host cells. Since all approved COVID-19 vaccines are designed to target the spike, the large number of changes in Omicron means it is less likely to be intercepted by antibodies raised through vaccination.

“We know for a fact that this variant will be more difficult to neutralize,” said Marc-André Langlois, a molecular virologist at the University of Ottawa who leads the Coronavirus Variants Rapid Response Network (CoVaRR-Net).

The network was launched earlier this year to co-ordinate Canadian expertise and to conduct research on the continuing evolution of the coronavirus that causes COVID-19.

Dr. Langlois said the network began mobilizing earlier this week as news of the variant began circulating among global health experts. On Friday, he and other academic researchers who are tracking variants of concern were locked in meetings with government officials anxious to gauge how Canada might be affected.

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While the variant has not yet been spotted in Canada, it could turn up in genomic surveillance conducted by provincial and regional public-health labs. The surveillance requires sequencing and analyzing the viral RNA extracted from positive cases of COVID-19 in order to obtain the precise lineage of the virus behind each infection.

Janet Wong, a spokesperson for Public Health Ontario, said any positive COVID-19 samples submitted to the province this month that are related to international travel will be screened for signs of Omicron. The new variant is detectable because it has a mutation that also occurs in the Alpha variant.

Starting Dec. 1, Ontario plans to resume routine screening for variants of concern – something it had recently discontinued because the Delta variant currently accounts for more than 99 per cent of all COVID-19 cases, Ms. Wong said.

A spokesperson for the British Columbia Centre for Disease Control said the centre would continue with its current strategy of sequencing all positive samples from returning travellers, cluster and outbreak cases, cases in hospital, vaccine breakthrough infections, long-term care cases and possible reinfections.

The worry among health officials is that Omicron will prove to be significantly more transmissible than Delta – a prospect that is indicated by initial data from Africa and elsewhere. Earlier this year, Delta’s higher rate of transmission enabled it to outcompete and all but wipe out other forms of the coronavirus in Canada. During the summer and early fall, it tore through the remaining unvaccinated population and likely contributed to a rise in breakthrough cases seen among the vaccinated.

Dr. Langlois said that while no laboratories in Canada have yet had access to samples of Omicron, its spike protein can be synthesized based on genetic data.

One of the tools the network established this year is a biobank of blood samples with antibodies from vaccinated Canadians, as well as people who contracted COVID-19. In the coming days, studies are planned that will investigate how well the antibodies perform against Omicron.

Antibodies are only part of the body’s full immune response to the virus. Even if the new variant proves better able to evade vaccines, it’s not yet clear if this will increase its ability to cause more severe disease.

However, the degree to which Omicron differs genetically from other variants of concern has led to a more serious and rapid response than to any other variant to date.

“It’s an astonishing number of mutations,” said Jeffrey Joy, a research scientist who specializes in evolutionary genomics at the University of British Columbia.

Dr. Joy said some of the changes in Omicron are already known from previous studies to worsen the impact of COVID-19. In addition to the mutations in the spike protein, the variant has differences in its nucleocapsid proteins that are known from previous variants to enhance the virus’s ability to enter and replicate in host cells.

On Friday, German vaccine maker BioNTech said that, if necessary, it could ship a new Omicron-specific version of the vaccine it developed in partnership with Pfizer in approximately 100 days. Meanwhile, U.S. vaccine maker Moderna said it will also create an Omicron vaccine candidate while, in parallel, continuing its work on two booster vaccine candidates designed to thwart a range of variants.

Zhou Xing, a vaccine researcher at McMaster University in Hamilton, Ont., said the latter strategy is likely to be more effective in the long run. He added that next-generation COVID-19 vaccines should aim at parts of the virus “that are much less prone to genetic mutations.”

Global authorities reacted with alarm on Friday to a new coronavirus variant detected in South Africa, with the EU and Britain among those tightening border controls as researchers sought to find out if the mutation was vaccine-resistant.


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