3 important questions about the Omicron variant

In a matter of days, the Omicron variant has upturned global COVID policy.

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Most of the confirmed cases have come from South Africa, but that’s in large part because the country has a robust surveillance network for detecting new variants. Researchers surmise that the virus emerged elsewhere, and was only identified in South Africa because of the country’s excellent surveillance. Cases have also been detected in Israel, western Europe, Hong Kong, Australia, Canada, and China.

The variant has caught the attention of public health researchers across the world largely because of its unusual set of mutations. “It has a very high number of mutations with a concern for predicted immune evasion and transmissibility,” said Tulio de Oliveira, director of the Centre for Epidemic Response and Innovation in South Africa, at a November 25 press briefing.

While this might sound nerve-wracking, it’s important to keep the significance of the variant in perspective. In the US, while deaths associated with COVID have started to decline, cases are still rising because of the delta variant. The fear is that a new variant that’s able to reinfect recovered patients might overcome population-level immunity from previous waves of COVID, and again overwhelm hospital systems in under-vaccinated communities. 

Right now, it’s impossible to tell if that new variant is Omicron. We probably won’t know for a matter of weeks the extent to which Omicron can dodge our immune system’s defense (acquired either from vaccines, previous infection, or both). As it spreads globally, we’ll get a better handle on its transmissibility and potential to cause serious illness. But for the moment, here’s what we know.

Does it spread more quickly?

In the South African provinces where Omicron has been detected, case rates have risen rapidly. In about two weeks, Omicron has become the dominant variant in South Africa, displacing delta.

This new variant, B.1.1.529 seems to spread very quick! In less than 2 weeks now dominates all infections following a devastating Delta wave in South Africa (Blue new variant, now at 75% of last genomes and soon to reach 100%) pic.twitter.com/Z9mde45Qe0

— Tulio de Oliveira (@Tuliodna) November 25, 2021

But it’s not clear that that means Omicron is more transmissible than the Delta variant. It’s hard to directly compare Omicron to Delta, because South Africa had very few cases of Delta (or any other strain) to begin with. Omicron’s quick spread could just be a product of circumstance. There might have been unlucky superspreader events, or the virus may have found its way into crowded housing conditions where it took off. (South Africa’s health minister noted Friday that some outbreaks were connected to college campuses.)

Some mutations on the virus do create a first-glance reason to worry about the virus’ transmissibility, however. Omicron evolved separately from previous variants like delta. But it shares many mutations with other variants of concern, including those that appear to allow viral particles to enter cells more easily and dodge some first-line immune responses.

[Thread] What is the potential impact of the new B.1.1.529 #COVID19 variant? @rjlessells:
1. It's relatively simple to detect some B.1.1.529 cases, as it's possible to use PCR tests to do this in some cases
2. B.1.1.529 = has many mutations across different parts of the virus pic.twitter.com/ytktqLzJUi

— Mia Malan (@miamalan) November 25, 2021

Unfortunately, the only way to find out whether it’s more transmissible is to watch it spread in the real world, says Krista Queen, who leads COVID sequencing work at Louisiana State University Health Shreveport.

“A lot of the countries where Omicron has been found—South Africa, Australia, Canada, the UK—have great sequencing surveillance,” she says. Over the next few weeks, those countries will watch to see if the proportion of Omicron cases rises sharply, which would mean that it’s outcompeting delta. “It’ll be: Are we seeing a lot of local transmission? Is it more isolated, and then when we apply measures to control the virus, do we see it go down?”

Is it more deadly?

How Omicron will affect disease severity is much murkier. We still understand very little about how mutations in SARS-CoV-2 affect virulence, so Omicron’s genome doesn’t offer many clues.

Again, the only way to learn will be to see how the virus spreads with time. “It’s way, way, way too early,” says Queen. “Without the power of the number of cases, you see a lot more individual differences in people who are infected, and not the overall [picture] of is this virus more virulent.”

In the case of the delta variant, it took months to determine whether increased hospitalization rates in the UK were due to a more severe virus, or more widespread transmission. And that was in the middle of a huge surge in cases. Even now, the data are ambiguous.

Angelique Coetzee, chair of the South African Medical Association, told Reuters that in her experience, patients infected with Omicron experienced mild illness. And an early report from Israel’s health authorities says that the variant may be less virulent than previous lineages. But the Israeli statement is based on only 12 suspected cases so far.

Do vaccines work?

What is clear is that the variant shares many mutations with previous lineages that made them better at escaping the immune system. Some of those mutations allow variants to dodge first-line immunity. Others change the target site for antibodies.

Took a look at the spike mutations in B.1.1.529 this evening, and colour coded them (details below)…there is…not much green.


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Originally posted on: https://www.popsci.com/science/3-important-questions-about-the-omicron-variant/