A new COVID-19 variant has been identified with some very concerning features. Dubbed Omicron, it’s rapidly spreading in the southern region of Africa and an increasing number of countries around the world, and the news has rocked government policy and financial markets over the last two days.
Despite the drama, however, we don’t yet know very much about just how bad Omicron is, and the range of possibilities remains very wide.
So I’m going to break down this rapidly evolving situation, telling you what we know, what we don’t know, when we’ll know more, what to watch for, and what you can do about it.
- Omicron has a heavily mutated genome that’s worrying scientists
- It’s still early, and we’re not yet clear how bad Omicron is; whether it has increased transmissibility, virulence, or immune escape, and how much
- We will know a lot more about this in just two weeks
- Omicron does not appear to evade PCR or antigen tests — good news, we can track it!
- Omicron is not yet common in the USA and likely will not be for at least several weeks, even in the bad scenario. But it’s quite possible this can turn into a big deal.
- The big fear is that Omicron overcomes existing immunity (because of the high mutations) and becomes an ‘escape variant,’ which overwhelms our already-at-the-limit systems like hospitals.
- Vaccine companies are already rushing to update the vaccines, but it will likely take around 100 days to arrive (eg. March 1st). That’s enough time for Omicron to spread and cause damage, if it turns out to be as bad as early data signals it could be.
How to think about Omicron or any new variant: eyes on the data
The progress of the pandemic over the last year has been heavily influenced by the evolution of SARS-CoV-2. In our “think piece” on how to think about variants, in January 2021, we identified three properties a variant might have that could be important: greater transmissibility, greater virulence, and immune escape.
The major variants seen since then, which we now call Alpha, Beta, Gamma, and Delta, fall into all three categories. Alpha and especially Delta are more transmissible and virulent than the wild type, but don’t evade the immune system very much. By contrast, Beta efficiently evades immunity to the AstraZeneca vaccine, but not other vaccines or natural immunity, and Gamma evades natural immunity to the wild type SARS-CoV-2 virus, but not to vaccines.
My evaluation of Omicron will come within this same general framework: using data gathered from many sources to determine which of these properties Omicron has, and how bad.
What we know about Omicron: it’s heavily mutated and spreading rapidly
It’s only been a few days since Omicron first came to the world’s attention, and what we know is pretty limited. It comes from two main sources: genome sequencing and contact tracing.
Omicron’s genome has been sequenced, revealing a lot of important information. It’s heavily mutated, including over 30 mutations in the spike protein, which include both known mutations from major SARS-CoV-2 variants, and novel ones of unknown function.
Omicron is not a descendant of Delta, but appears to date back to some of the same lineages that gave rise to Beta, which also appears to have arisen in South Africa.
Viral geneticists have speculated that this kind of mutation pattern, with many mutations appearing all at once, could be the result of a chronic infection in an immunocompromised individual — those people are unique breeding grounds for mutations. The Beta and Delta variants also exhibit this kind of mutation pattern. With its large population of AIDS patients, South Africa may be particularly prone to create this kind of mutation.
The genome of Omicron does not appear to signal any incompatibility with existing tests. Both PCR and antigen tests should register cases of Omicron as well as they register cases of other variants.
So, good news: Omicron did not mutate an invisibility cloak.
Omicron is spreading rapidly in South Africa, where increasing numbers of cases of Omicron have been sequenced in recent days. This has been occurring at the same time as a rapid increase in COVID-19 cases in South Africa, but because of the low coverage of genome sequencing of COVID-19 cases in South Africa, it’s been hard to tell how related these things are.
The case data in South Africa over the last week have been extremely chaotic, with one day showing nearly 20,000 cases in one day, so the magnitude of the upward trend isn’t that clear. In addition, the case loads there were small to begin with, which means that individual super-spreading clusters can have an outsized impact on national aggregates. Although it looks like Omicron is outspreading other strains, mostly Delta, in South Africa, how much faster is unclear.
Also unclear is how much the greater spread, if it is sustained, is driven by higher R0, which would affect unvaccinated populations particularly badly, and how much by immune escape, which would partially nullify the advantages of vaccinated areas and populations. Unlike most developed countries, South Africa is only about 25% vaccinated.
Cases of Omicron have been sequenced in eight countries in the southern region of Africa, and also in Hong Kong, Israel, and Belgium. More countries will certainly follow. The index cases in Hong Kong and Israel were traced to South Africa and Malawi, but the Belgian case had traveled to Egypt and Turkey, not any countries in the southern region, which suggests that Omicron may already be more widely dispersed than we currently know.
However, certain countries, like Israel, the UK, and the United States, do engage in widespread genomic surveillance of COVID-19 cases, and if Omicron had significant case numbers in any of those countries, we would find out swiftly. This puts an approximate ceiling on any estimates of Omicron prevalence and dispersion.
What we don’t know about Omicron: Transmissibility, Virulence, and Immune Escape
There’s a lot we don’t know:
- Whether it’s more transmissible than Delta (higher R0)
- Whether it’s more virulent than Delta
- Whether it causes significant immune escape, and if so, how bad and from which sources of immunity
The noisy data from South Africa, combined with credulous interpretations, have led to some hyperbolic claims, like the notion that Omicron:
- Has an R0 500% higher than the Wild Type and 3.5 times as high as Delta
- Went from 1% to 80% of South African COVID-19 cases in less than two weeks
- Has driven a tenfold increase in COVID-19 cases in South Africa in one week
There is no grounds to conclude these things yet, and if I had to speculate, I would guess none of them will turn out to be true.
A lot of claims about Omicron will be floating around in the coming days, weeks, and months, and it’s critical to keep our eyes on the data, and the distinction between data and speculation.
The reaction to Omicron: Panic, travel restrictions, and a market crash
The WHO reacted swiftly, holding an emergency meeting only days into the new outbreak — good job team. At this meeting, the designation Omicron was bestowed on what had been known as B1.1.529, and it was designated a Variant of Concern. Scientists have clearly been rattled by the highly mutated genome and rapid spread of Omicron.
Governments around the world have reacted swiftly — good job team — imposing travel bans on (mainly) the eight countries in southern Africa that have most of the known cases. The USA has imposed heavy restrictions on travel from these countries to begin Monday, and airlines are expected to cancel their flights. Israel has also taken the step of preparing for an internal emergency, with Prime Minister Bennet saying he may ban travel out of Israel to protect other countries, and alerting national security and public health officials they may soon be working around the clock.
Epidemiologists have described travel restrictions as largely fruitless at attaining a hermetic seal and preventing a major new strain from entering countries, but have said that in some cases they can delay the emergence of a major outbreak in a new country by weeks or even months, by reducing introgression to a smaller number of cases. In cases like this the major question is what countries do with the time bought by travel restrictions, and whether the disruptions and imposition on the public is worth it.
Financial markets have reacted with dismay, as global equities have sold off by several percent, led by travel stocks and energy commodities, which are down about 10%. Many analysts expect the selloff to continue, especially if the bad news continues.
When we’ll learn the answers to the big questions
Certain important questions will be answered quickly. The trend of COVID-19 case numbers in South Africa, the role of Omicron in that trend, and the extent to which it’s driven by ongoing high R rather than superspreader events, will likely emerge over the next two weeks. In addition, scientists at pharmaceutical companies and in academic labs have said that early in-vitro results on Omicron’s relationship with vaccines, convalescent immunity, and antibody drugs, should be available within two weeks.
Some other forms of evidence will be slower to arrive, like reliable quantitative estimates of spread and R in different places, and hospital-based cohort studies which will produce early estimates of virulence. They may begin to arrive within the next few weeks, but a clear picture could take months to emerge.
What will happen if Omicron is a major immune escape variant
A lot depends on how bad the immune escape is. Both Beta and Gamma are partial immune escape variants, Beta against the AZ vaccine and Gamma against convalescent immunity, and they caused real problems in Brazil and South Africa, but neither proved to be a huge deal globally. Omicron could follow this path.
In a nightmare scenario where Omicron proved completely resistant to immunity from convalescents, all vaccines, and monoclonal antibodies, we would be essentially back to square one, with control only attainable with public health measures like quarantines and lockdowns, until new vaccines and antibodies started arriving. But many experts seem to expect Omicron to follow a middle course, with greater immune escape than Beta and Gamma, but less than total evasion.
In addition, even if Omicron evades immunity to infect people, they may retain some protection from more serious outcomes — they get more sick than they would’ve from other strains, but not as sick as they’d get (eg. hospital) if they weren’t vaccinated.
To the extent that Omicron evades major vaccines, highly vaccinated countries and people will be made vulnerable again, and high levels of COVID-19 spread will be more likely to hit them. The world could be awash in cases of Omicron.
In addition, we’ll see a change in the speed of events, back to “fast.” Early in the pandemic, we remarked at the stunning rapidity of the spread of COVID-19, and reaction to that spread. With R at 2 in some places and .4 in others, tenfold and hundredfold changes in COVID-19 numbers could occur in weeks. As the pandemic turned into a trench war, with highly transmissible strains deadlocking with highly effective vaccines, and the public used to dialing precautions up and down, R started to become constrained in a narrow range, and major changes in trend started to take months. We’ve already seen events start to move faster thanks to Omicron, and this will likely continue if Omicron is a major escape variant.
We may see major differences in how Omicron evades different forms of immunity. Other escape strains have been like this; Beta evades the AZ vaccine almost totally, and Gamma evades convalescent immunity by over 50%, but neither of them does much to the Pfizer or Moderna vaccines. Right now, we have about 15 major vaccines worldwide, and about four major antibody drugs, plus natural immunity to several major variants in different populations. Depending on the pattern of evasion exhibited by Omicron, the path of events could look very different.
Although vaccines and antibodies may be evaded by Omicron, early analyses of the Omicron genome in relation to mechanisms of action suggests that small molecule drugs, like remdesivir and dexamethasone, and upcoming small molecule therapies like Pfizer’s Paxlovid and Merck’s molnupiravir, are likely to continue working against Omicron.
If Omicron does prove to be a major escape variant, affected vaccine and antibody manufacturers will generate new versions of their therapies as quickly as they can. As I’ve previously reported, mRNA vaccines will be quickest to transition to new versions. Pfizer and BioNTech have said they will be able to ship small quantities of an Omicron-optimized vaccine for early study in as little as six weeks, and produce them in volume in 100 days. Moderna may actually be able to ship an Omicron vaccine faster than Pfizer, because their Delta-and-Beta-based bivalent booster shot is already in the clinic, and may work against Omicron due to the mutations it has in common with Delta and Beta. However, adenovirus, protein, and attenuated virus-based vaccines, and antibody drugs, are likely to take longer to transition to new sequences and attain volume production.
What you can do about Omicron right now
The most important lesson of Omicron is general: the pandemic is not over. You still need to keep your preps up. This lesson applies even if Omicron turns out to be much less threatening than now seems likely.
The overall implication of Omicron as a major escape variant, if this scenario materializes, is that we may have to temporarily return to the kind of precautions we took before the vaccines hit the USA in force. You might have to stay home and cancel almost everything. N95 masks, instant COVID-19 tests, toilet paper and other items may sell out again, and it may start soon. If there’s anything you need to be prepared for this possibility, get it now.
It’s also a good idea to carefully think about upcoming large events and travel, and how you’d adjust your plans if the data on Omicron looked bad.
Luckily, we still have some time before Omicron could become common in the USA, likely several weeks to a couple of months. This is time you can use to prepare.
And, if Omicron does cause massive problems, it will likely end a lot more quickly than it did the first time. Vaccine manufacturers only have to transition their vaccines to new sequences, not start from scratch. An Omicron-specific booster would likely be only one shot. Distribution is already scaled up.
We’ll probably know in a few weeks whether Omicron is likely to cause serious problems in the USA. But you can prepare now, and the measures needed now are likely to be good ideas whether Omicron turns out to be bad or not.
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