The Omicron/Nu Covid-19 variant. Here’s what we know, and what we don’t.

We should be concerned, but a porous travel ban makes little sense.

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The World Health Organization announced today that SARS-CoV-2 B.1.1.529 has been elevated to a “variant of concern” and will be known as Omicron. (In recent days, many had speculated that the Greek letter Nu would be used; the Greek letter Omicron was felt to be less confusing, because “Nu” and “new” sound too similar). Shortly after, the United States announced restrictions on travelers from South Africa and at least 7 other nations so far. The rules do not apply to US citizens or permanent US residents.

Here’s what we know and do not know right now.

1. Omicron has over 30 mutations in the spike protein an unusually large number of mutations. This suggests that the variant may have emerged from a single patient whose body could not clear the infection, remaining contagious for far longer than most patients. The longer an infection persists, the more mutations one virus can accumulate. This is known to occur in people with profoundly compromised immune systems.

2. Spike protein mutations may make it easier for the virus to enter a host cell where it can replicate. Some mutations, however, might have the opposite effect. Also, some mutations may help the virus more easily evade our existing acquired immunity, whether from prior infection or vaccines.

3. We have no evidence suggesting Omicron causes worse disease than its ancestors nor that it does so more frequently.

4. We do not have direct evidence to suggest that Omicron is either markedly less vulnerable to our existing immunity or is more contagious in any clinically meaningful way, at least so far. This, however, could change, and that’s the crux of everything. While these spike mutations and the prevalence of Omicron in Southern Africa raise these as genuine possibilities (and therefore warrant attention and resource-intensive investigations), those outcomes are not guaranteed.

Let’s focus in on immune “escape” and contagiousness.

First, is Omicron more contagious than prior variants? The WHO implies that they think so; otherwise B.1.1.529 would just be a variant of “interest” rather than of “concern. (To my knowledge, none of the other criteria for elevating a variant from being one of “interest” to one of “concern” have been met).

However, I simply have not seen public data that supports or proves that Omicron is more contagious. The WHO also stated that concerns regarding an increased likelihood of “reinfection” were partially behind their choice to designate Omicron as a variant of concern. Again, I’m aware of no data on this, other than perhaps from anecdotal reports. (A CDC official I spoke to did not indicate that my impression was incorrect.) So, it’s possible that the WHO and others have important data on these issues. But nobody I know has seen those data. If they exist, they should be shared now. The WHO has either gotten ahead of this (some would say “jumped the gun”), in which case we may soon be able to de-escalate if our worst fears do not play out, or they are withholding data that we desperately need to see. It’s unlikely that the WHO is withholding data. So we should watch things unfold with open minds. This could go in any direction.

In fact, given what we know, there are two important and realistic possibilities to explain Omicron’s dominance in some parts of Southern Africa. The first is that Omicron truly is more contagious. For now, we should assume that’s the case. But the second possibility not yet ruled out is that Omicron is actually not more contagious. If that’s the case, what we are seeing in South Africa and a few other regions could be an example of what is known as the “founder effect.”

The founder effect occurs when there is no disease in a certain area and a new outbreak occurs. Over a few weeks, one case spreads to dozens, then hundreds, and then thousands. Any genetic analysis on any these thousands of cases would show similar results: in this instance, all Omicron, all the time. But that’s because literally every case tracks back to the same “index patient” that started a particular outbreak. This scenario remains possible, since Omicron apparently emerged from regions of Southern Africa where there has apparently been very little Covid-19 recently. That said, surveillance there might not be adequate and the fact that Omicron has started showing up elsewhere is worrying. On the other hand, if Omicron took over regions where a fair number of Delta variant infections were simultaneously circulating, that would suggest the newer variant is indeed more contagious.

So far, we do not know which of these possibilities is true, though again it makes sense to assume that Omicron is more contagious until we know more. But if what we are seeing is all “founder effect” and Omicron us truly not more contagious than Delta, the worries (including a market spook) may be unfounded. As I write this, I remain of mixed mind. Part of me wants more data and part of me acknowledges that my colleagues across the world are seeing something that worries them, and we should pay attention.

Next, let’s turn to immune evasion. Is Omicron able to escape immunity that individuals have, either from prior infection or vaccination? That’s unknown. While it is quite likely to (in some degree), the difference could range from inconsequential to devastating. It’s easy to imagine that a variant which our immune systems have more trouble attacking might represent a doomsday scenario. But even with 30 mutations or more, our immune systems are likely to be able to keep up, for the most part. In fact, if the mutations amounted to a new version of the coronavirus spike protein that was so very different than previous versions, such changes could actually backfire for the virus, making it harder to invade our cells. Some mutations hurt us, some help us, most do nothing.

It is possible, and perhaps even likely, that Omicron partially lowers our vaccines’ effectiveness against infection (and also protection from prior infections)—but not against severe disease. If so, we should again be reminded that increases in mild breakthrough infections would not be nearly as worrisome as increases in breakthrough severe disease would be. We should get very worried if we learn that Omicron breakthrough infections are more likely to cause severe illnesses. During the Delta era, we’ve almost exclusively seen breakthrough severe illnesses in older populations, (which is why I remain in favor of boosting older people in particular).

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What should we do right now? Does the United States’ new quasi-travel restriction for non-US citizens from Southern Africa starting three days from now make sense?

That depends, but probably not. The current policy is either hopelessly permeable or, in the best case opposite scenario, completely unnecessary. With respect to travel restrictions, we should go big, or go home. In fact, in general, limiting travel bans to countries where new variants were first detected disincentivizes nations to be transparent with the WHO and other global partners.

If Omicron is more contagious, but not more deadly for the vaccinated (or even the unvaccinated), a leaky travel ban would slow things down a bit but the outcome would be the same; the unvaccinated will suffer the consequences of their choices sooner. That is unless Omicron scares a few people on the fence into finally vaccinating. That’s one upside of early alarmism.

If the worst-case scenario emerges, and Omicron renders our vaccines far less effective or even useless against severe disease, hospitalization, and death, a far more restrictive (and perhaps universal) travel ban to keep out new source patients could be a good move, but only insofar as it would be buying us time.

Time to do what, exactly? At that point, we would need to acknowledge why we were instituting such a ban: to buy time for Pfizer, Moderna, and Johnson & Johnson to pump out hundreds of millions of doses of a modified vaccine while we essentially shut down all over again and wait.

It must be said, Omicron is probably already here. So if Omicron sets us back to the pre-vaccine era, any successful travel ban would have to be far-more extensive and less porous than the measly one rolled out today. In that scenario, in order to work, a comprehensive travel ban would likely have to be accompanied by a return to major disruptions in daily life while we re-vaccinate everyone from scratch. Anyone who says a shutdown is off the table right now is either not paying attention, or is in denial.

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