The Omicron situation

What the experts are saying, and what I think

When it comes to the Covid pandemic, it’s important to react quickly. Last time a major new variant emerged, we watched millions of Indian people die while we sat there and waited for U.S.-specific data before taking any kind of serious action. This was the result:

Fortunately, it appears that the world is reacting to the new Omicron variant with much more urgency than it reacted to Delta. But it can be difficult to cut through the noise. Back when Covid first started, I used to tweet out a series of “coronavirus tweets from the experts” every day, to help people keep up with what the most knowledgeable voices were saying. So I thought I’d reprise that here, and point to a few articles and Twitter threads that have helped me better understand this new threat.

First, of course, check out my video interview with Eric Topol. But in addition, here are some other points I’ve gleaned from the past three days of reading.

Point 1: Yes, Omicron is extremely worrying.

So why is Omicron worth freaking out about? Two reasons. First, it’s spreading fast, and taking over very quickly from the Delta variant. And second, unlike Delta and other variants, Omicron has evolved a whole suite of mutations that are thought to facilitate evasion of known antibodies, along with some mutations that may make it more transmissible. Read this thread by Christina Pagel to see why scientists and public health officials first became alarmed:

Prof. Christina Pagel @chrischirp

Because of this increase, COVID sequencing has been concentrated on samples from Guateng. Almost all recent samples from there (77) have been this new variant (blue dots) - taking over from a background of Delta (red) and C.1.2 (also a concerning variant, yellow). 4/16

Here is a Nature article explaining what we know about the new variant.

Trevor Bedford, a mathematical epidemiologist who is generally regarded as one of the most trusted voices on the subject of Covid mutations, has a thread explaining why the mutation pattern seen in Omicron is so alarming. Here, reposted from above, is a key graph showing just how big a genetic jump Omicron is compared to other variants:

The upshot:

Trevor Bedford @trvrb

Growth rate (in absolute terms and relative to Delta) will be become clearer in the following days, but at the moment, I believe we're looking at a variant that potentially has significant immune evasion and that appears to be spreading rapidly. 15/16

The WHO, meanwhile, believes that Omicron has a higher reinfection risk than other variants.

And here is a more technical thread about Omicron’s escape potential, from the Bloom Lab:

Bloom Lab @jbloom_lab

Here's how mutations in #SARSCoV2 Nu variant (B.1.1.529) will affect polyclonal and monoclonal antibodies targeting RBD. These assessments based on deep-mutational scanning experiments; underlying data can be explored interactively at jbloomlab.github.io/SARS2_RBD_Ab_e… (1/n)

jbloomlab.github.ioOverviewInteractive visualizations of Bloom lab deep mutational scanning measurements of RBD mutations that escape antibody binding.

(Note: At this point, the Omicron variant was still being called the Nu variant. That name was changed, for obvious reasons.)

A rumor is going around that Omicron is less deadly than other variants, but so far this is unsubstantiated. It’s based on an out-of-context quote from a South African doctor who found only mild cases among a group of young, healthy people. Once again, wishful thinking springs eternal, but don’t fall for it.

That said, the more dramatic graphs you’ve seen about Omicron spreading like wildfire may overstate the speed of its spread:

Scott Gottlieb, MD @ScottGottliebMD

Comprehensive article on Omicron's emergence. "Based on a comparison of different Omicron genomes, Andersen estimates that the virus emerged sometime around late September or early October, which suggests it might be spreading more slowly than it appears."

science.org‘Patience is crucial’: Why we won’t know for weeks how dangerous Omicron isLab tests and patterns of spread will show whether the new SARS-CoV-2 variant’s many mutations are a serious threat

Nevertheless, we don’t want to make the mistake we made with Delta. We’ll only know for sure how dangerous this variant is until after it does its damage. So we can’t wait to be sure; we must act now.

Point 2: No, this doesn’t mean we’re headed back to March 2020.

Before we talk about what actions we can take, here’s one more point that’s worth mentioning: Even if Omicron is an escape variant, that does not mean we’re “back to square one” with regards to this pandemic. It’s all a matter of degree. As Katherine J. Wu explains, our bodies develop a very diverse array of defenses against new viruses, and even a variant which evades some of those defenses won’t simply breeze past all of them. And as this paper in Nature shows, it takes many many mutations to fully escape antibodies to existing variants, and there’s also T-cell immunity to contend with. So the vaccination we’ve already done was not wasted, and the immunity we’ve built up is not useless. Booster shots of the existing vaccine will be useful, and we should all get them.

BUT, as that very same Nature paper shows, there’s a good chance that Omicron will be able to bypass existing immunity to a much greater extent than other variants. Michael Worobey has a good thread on this. Basically, the authors made a synthetic spike protein with a bunch of mutations they thought would allow it to escape existing known antibodies — many of which are now found in the Omicron variant — and they found that it was indeed very good at escaping antibodies. (It’s worth noting that at least one of that papers’ authors is quite pessimistic about Omicron.)

So while it’s still important to get a booster shot, we may need more if we’re going to beat Omicron.

Point 3: Travel bans on African countries are not going to stop Omicron.

OK so how do we stop this scary new variant? It’s important to realize that travel bans on African countries have no chance whatsoever at stopping Omicron from reaching our shores. This should be obvious from the fact that country-specific travel bans never stopped any other Covid variant. But it bears repeating. Omicron is already out there, and soon will be everywhere.

Trevor Branch @TrevorABranch

countries banned because of the omicron variant vs. countries with confirmed omicron cases

Florian Krammer has a thread suggesting that although Omicron was first detected in Southern Africa just a few days ago, it has probably been circulating internationally for a while.

Florian Krammer @florian_krammer

1) My gut feeling from hearing of Omicron cases in Botswana, ex-Malawi, ex-Egypt (2 now it seems) and in South Africa is, that the variant was flying under the radar in undersequenced countries for some time until Botswana and South Africa detected it and sounded the alarm.

So we should ditch the travel bans; at best they’re simply theater, and at worst they could give us a false sense of security. Even worse, banning travel from countries that find new variants simply punishes countries with good variant surveillance!

Stephanie Nolen @snolen

It's hard not to see this as South Africa being punished for the fact that it has world-class scientists, doing some of the best Covid surveillance in the world, and is transparent about what they find.

Stephanie Nolen @snolen

So I'm in my 3d hour on a tarmac at Schipol. While my flight from Jo'burg was somewhere over Chad, Europe went into variant panic; by the time we landed, we weren't allowed off the plane. They won't even let a catering truck bring us water.

Point 4: Variant-specific booster shots are already in the works.

So if travel bans won’t work, what will? The obvious approach to an escape variant is to use variant-specific boosters, sort of like we do for flu shots every year.

Florian Krammer @florian_krammer

6).....since it is likely that one 'variant-booster' would do the job. Our B-cells can be retrained to recognize both, the old version and the variant, and it doesn't take much to do that.

Here is a thread from Meg Tirrell about how vaccine manufacturers are already working on variant-specific boosters:

Meg Tirrell @megtirrell

What vaccine makers are saying about B.1.1.529: -Moderna notes it's shown it can get into clinic (human trials) within 60 days; question is regulatory process from there. Manufacturing new doses could take a few months. -BioNTech expects lab data within 2 weeks (1/2)

Moderna is also working on a multi-variant booster, sort of like what we use for flu shots.

So both vaccine manufacturers and the administration are on high alert. That means the ball on variant-specific boosters is now in the FDA’s court. It’s very important that they streamline the approval process. After that, it will be up to the CDC to recommend variant-specific boosters to the general public.

Meanwhile, as Topol noted in our interview, a pan-Covid “supervaccine” of the type currently being worked on by multiple labs would be even better than having to get Covid shots every 6 months or 1 year. It would allow us to put an end to this pandemic decisively, once and for all. So we need a new version of Operation Warp Speed to fund and coordinate the development one or more supervaccines.

My thoughts

OK, so those are the views of the experts. If you want more, you can follow my Twitter list of Covid experts. But I’d also like to give some of my own thoughts here.

Basically, the age when we could expect to stop the virus with non-pharmaceutical interventions — lockdowns, social distancing, masks, test-and-trace — is long, long over. Not only has popular appetite for this strategy waned to almost nothing, but new variants are so contagious that these strategies just aren’t sufficient to stamp out the virus. Every country except China is transitioning to a “live with Covid” strategy (and China is hurting itself by trying to maintain its “zero Covid” policy). So while you should still wear a mask, and while some cities may do some limited business closures, we should assume that distancing measures will not be our first line of defense against Omicron.

Vaccines will be our first line of defense. In the short term this means getting a booster shot of the existing vaccine, in order to restore antibody levels in time for the Omicron wave. Unfortunately, America has been doing an absolutely awful job of rolling out booster shots.

This isn’t because of antivaxers, who, while a pernicious force, are only about 20% of the population. Instead, it’s because America’s public health authorities dragged their feet on recommending that Americans get booster shots:

Eric Topol @EricTopol

The @CDCgov advisors today came out with a recommendation that adults age 18-49 "MAY" get a booster. It should be SHOULD. Here's why:

Eric Topol @EricTopol

Why should every adult get a 3rd shot (booster) when eligible (6 months after 1°💉)? 1. A randomized, placebo-controlled trial, the gold standard for assessing efficacy, showed restoration of efficacy to 95.6%, in >10,000 participants across all age groups https://t.co/zORXc5LuiK

As Topol noted in our interview, the biggest reason for this was that U.S. agencies like the CDC are extremely provincial, and basically ignored evidence from other countries. That’s very bad, and it fits with the general narrative of a crisis of competence at the CDC.

But another reason, which Topol acknowledges, is that some public health officials in the U.S. saw boosters as taking away vaccine doses from developing countries. With America now mostly vaccinated, these officials decided that recommending a third shot would harm global equity. The head of the WHO certainly made this argument, calling booster shots a “scandal”. There were op-eds in major papers and articles in reputable journals pushing the idea, and it was so widespread that I even saw articles about how to deal with guilt after getting a booster.

As I see it, this argument is ridiculous. The correct response to vaccine scarcity is not to imagine a zero-sum competition between the developed and developing worlds; it’s to simply make a lot more vaccine doses. As our successful ramp-up of vaccine manufacturing at the beginning of this year showed, we can very quickly expand our production a whole lot when we deem it a priority. But instead of making that our priority, we succumbed to the pernicious fantasy that the number of doses is fixed, and the result was that both Americans and people in the developing world died unnecessarily.

With Omicron, it’s likely that a similar mistake will cause a lot more deaths than it did with Delta. We face the terrifying prospect that an unholy alliance of antivaxers and misguided public health officials will stop us from getting boosters — including variant-specific boosters, when those come out.

We cannot let that happen. The Biden administration needs to overrule the public health establishment where necessary, and urge everyone to get boosters ASAP. And even more importantly, it needs to put a lot more resources into significantly ramping up vaccine manufacturing. As I’ve said since the start, this will be a long war. Omicron has reminded us that it’s far from over.

Update: Here’s a second post with one more week of info.

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