Mini-Throughput: Omicron Edition

Art by Giovanni Guida, CC BY-SA 3.0 , via Wikimedia Commons

For the last week, the news has been filled with reports of the ominous Omicron variant emerging from South Africa. We’ve heard a vast array of conflicting claims. We’ve heard that it evades the vaccines, that it’s massively infectious but that it causes mild disease. Are these claims true? Should be worried?

Well, the TL;DR version is: we don’t know yet and anyone making definitive claims should be viewed with suspicion. Science is moving at the speed of light to try to figure out what the deal is with Omicron. But even at warp speed, it will take weeks before we know anything definitive. Until then, we should be prudent: don’t panic but be prepared if Omicron does turn out to be a particularly bad variant.

The long answer is … well, walk with me a bit.

I’ve written about variants before:

The way to understand mutation is to think of it as a game of telephone. A virus’s properties are encoded by the strain of DNA or RNA inside it — a string of compounds that is the virus’s blueprint. We abbreviate these sequences with the letters A, C, G and T. So, DNA is basically a long message that reads ACGTAAACTGTATCGGATC only zillions of letters long. When the virus is replicated, that genetic messages is copied into the next virus. For our telephone analogy, that is one person whispering what they heard into the ear of another. And just like every time one person whispers their message into another’s ear, there’s a chance the message may be garbled, there is always a chance that replicating a virus will garble the message. One or more of those letters may change. Instead of hearing ACGTAAACTGTATCGGATC, the next virus hears ACGTATACTGTATCGGATC. That change of A to T is what we call a mutation.

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Most of the changes in the viral message don’t matter. They don’t affect the behavior of the virus very much. They are useful for tracking the virus by looking at the spread of different “families”, but won’t affect the ultimate outcome. But the viral world is evolution on steroids. Viruses replicate so fast and in such massive numbers that bad mutations will die out almost immediately while advantageous ones spread quickly.

Omicron is not the first variant that we’ve had, nor is the first “variant of concern” — that is, a variant that has changes that make it either evade previous immunity or more infectious. The CDC has a list of variants, including some that were formerly variants of concern but turned out to be unable to compete against other variants.

The most famous of these variants of concern is now the dominant lineage world-wide: delta. Delta started with a handful of cases but rapidly came to dominate because changes to the spike protein — that bit of the virus that latches onto human cells and that antibodies target — made it twice as infectious as the original strain of COVID-19. Since viruses spread exponentially, this mean that, in a month, it could multiply 16 times faster. This is why we got a second wave this summer and why it spiked so fast and then faded relatively quickly.

The Omicron variant has two points of concern. First, the spike protein has many more mutations. So previous immunity may be less effective. And, based on at least the first outbreak, it also appears to be highly infectious.

Now a quick word about viruses that evade immunity. The anti-vax world has been saying the vaccines make viruses evolve to evade them. This was always hot nonsense — viruses are barely animate and don’t decide to do anything. But it’s double nonsense because viruses do not interact directly with vaccines. So, they can’t adapt to them. Viruses mutate all the time and yet our viral vaccines — smallpox, rubella, chickenpox, measles, etc. — continue to work. Even when the flu mutates in a direction we don’t expect and we give out the wrong flu vaccine, it still confers resistance.

If Omicron evades vaccine immunity, it will evade “natural” immunity too. Because both kinds of immunity use the same mechanisms to recognize and neutralize the virus. Now the body has multiple lines of defense, so most experts think it’s unlikely that Omicron will achieve complete immune escape. But it bears keeping an eye on.

Now there are also early indications that Omicron may be producing a milder course of the disease. But it’s not clear what to make of this. Those exposed may have had previous infections or been vaccinated.¹ They may be preferentially younger. Or it may be too early to tell: COVID-19 takes a couple of weeks to kill.

The hypothetical combination of greater infectiousness and lower mortality has revived one of the worse COVID skeptic tropes. Since this pandemic began, they have been claiming that viruses naturally evolve to be more infectious and less lethal so that they can spread more easily. I addressed that in my post on the Delta variant:

History is replete with viruses that never mutated into less lethal versions. It’s replete with ones that mutated into more lethal versions. Smallpox was absolutely devastating throughout its millennia-long reign of terror, sometimes killing as many as 30% of its victims. Most years the flu is fairly dangerous, but occasionally it comes back with a particularly vicious strain. If you expand to bacteria — which are even more prone to gene-splicing — the Plague kept coming back for centuries, including a version in the Black Death that was known to wipe out entire villages. During the 16th century, Mexico was essentially depopulated of its 20 million natives by Cocoliztli, a disease which we have still not positively identified. Whatever it was, it mutated into a much more lethal version, with later waves having fatality rates of 90% or more.

This is because viruses do not really care whether you live or die. All they care about is that you can spread the disease. As long as the virus doesn’t kill you before you spread it, it’s fine. In the early days, HIV was nearly 100% lethal. But because it took years to kill, it spread just fine. In fact, here we are, 30 years later, and the disease is still the leading cause of death in young women globally. Ebola and other hemorrhagic fevers have very high lethality rates but can also spread very rapidly (Cocolitztli might have been one).

I would add to this that viruses aren’t Pokémon. They don’t evolve to a final form and then just stay there. They keep changing. Even if Omicron is less deadly, that’s no guarantee that it will stay that way. And the more people it infects, the more likely it is to mutate again. Hell, you could argue that COVID is already the more-infectious, less-lethal virus. Earlier SARS viruses were far deadlier but killed their hosts too fast. The entire reason we had a global breakout was because COVID-19, compared to its earlier versions, was less lethal.

In short, I hope that Omicron is a milder version of COVID-19. But we don’t know yet. We don’t know what it will do once it moves out into a larger population and there is no reason to think more variants won’t emerge. So even if the earlier reports of a milder disease are sustained, that is no reason to let our guard down. We don’t need hypotheticals to know what COVID-19 can do with the right combination of mutations. We have tens of millions of dead to prove it.

Now all that having been said, is it time to panic? No. Caution is warranted. But panic is not. I said at the beginning of the pandemic that this was going to be a war. It was likely that it would last years, that there would be sacrifices and that the virus would have a trick or two up its sleeves. But if it is a war and Omicron is the new weapon, we too are in a better position. We have highly effective vaccines. We have anti-viral medicines (although monoclonal antibodies are a lot less likely to work against Omicron since they too target the spike protein). The pharma companies believe they can get an Omicron-spike booster ready within a few months. We have highly effective rapid tests, billions of masks and two years of experience.

So, what can everyone do while we wait for the science to move? First, if you haven’t been vaccinated, get vaccinated. At the very least, it will ramp up your resistance. If it’s six months or more since a prior infection or your last vaccine, get a booster. Boosters are nothing suspicious: many vaccines require multiple doses before they reach maximum efficacy. Finally, wear masks when appropriate and be prepared if social distancing measures come back.

There’s been a lot of noise over the last few months over the anti-COVID measures we’ve been using. We’ve had the luxury of indulging in this because most people are vaccinated. But the emergence of Omicron is a good opportunity to take a step back, take a deep breath and roll up our sleeves.

Maybe Omicron turns out to be a big load of nothing. Maybe it sets fire to the world all over again. We’ll know within a few weeks. But we’re still in a better position than we were two years ago. The fight goes on.

1. Contrary to claims of COVID-19 skeptics, South Africa has been very hard by the virus. On paper, they have few deaths because they lack the facilities for mass testing. But excess death data indicates they have lost far more per capita than European countries or the US.