Mutations concerning

South Africa also has a high background of immunity: Studies suggest 40 to 50 per cent of South Africans were exposed to SARS-COV-2 in earlier waves. One paper estimated that the number of infections was likely 7.8-fold higher than recorded cases. That immunity, combined with vaccination, could be providing protection against serious disease, which could help explain why Omicron infections so far appear milder.

What concerns scientists is that Omicron has a surprising number of mutations on the spike protein adorning the surface of SARSCOV-2, especially the part that the virus uses to glom onto the cells in our bodies and that authorized vaccines target. Three changes in particular each make the spike better able to bind to our cells. “We've seen some of these three mutations in different variants of concern,” Otto said, but none before Omicron have all three. “When my colleagues saw that they were like, `Uh, oh.' ”

Seven cases of Omicron had been confirmed in Canada as of Wednesday. Cases have been reported in the U.S., Belgium, the Netherlands, France, Germany, Portugal, Italy and the United Kingdom.

It's not clear where or when Omicron first separated off from other SARSCOV-2 variants, but it may date back to 2020. “It could be in a population that was so isolated that Omicron evolved there and it never got out until now,” said Otto, a professor in UBC'S department of zoology.

It may also have been living within one or two immunocompromised people unable to clear the virus. SARS-COV-2 can reproduce to high loads, or linger much longer, in people with immune systems weakened by malnutrition, unclean drinking water, untreated HIV and other conditions, Miller said. And the longer the virus hangs around in the body, the more opportunities to accumulate mutations.

“It's possible that Omicron has been hiding out for most of 2021 inside somebody,” Otto said. “That would suggest that all these changes in the spike that we're seeing actually weren't selected to help transmit from person to person,” she said. “They were selected to survive and propagate within that person's body.”

And if that's the case, it's possible Omicron selected to be less severe, “so that it didn't kill that individual, and that individual was able to move around and eventually infect somebody else,” Otto said.

“But we really have zero idea. At this point I give it about a 50-50 chance of being more or less severe. That's how unsure science is at the moment.”

While Omicron has a jumble of mutations in the spike protein, “there's still a lot of spike that's not changed, and our immune reactions should recognize other parts well if we've been vaccinated,” Otto said. “But it will spread like wildfire among the unvaccinated.”

While Moderna's chief told the Financial Times this week he's anticipating a “material drop” in vaccine efficacy, Otto is more optimistic. With a high vaccination rate, “we've got a base of immunity, and it's not like (Omicron) has changed at hundreds of sites in the spike. It's just changed at 30.” In the South African city of Tshwane, where Omicron was first detected, 87 per cent of hospital admissions are among the unvaccinated, The Guardian reported.

What Otto does find unnerving is that a fully vaccinated traveller who arrived in Hong Kong from Vancouver contracted the variant virus from another traveller from South Africa who was staying across the hall in the same airport quarantine hotel.

Though just one case, it could mean that Omicron is better able to transmit through smaller particles in the air, which would mean more longer-distance aerosol transmission, Otto said.

If it can spread much more easily through the air, “and you need even smaller particles to get infected because it's so good at getting inside our body, that is a game changer,” Otto said. “That's my nightmare.”