Andy Larsen: Here’s what we now know about omicron. Some of it is good news. Some is not so good.

Studies show more immune system escape, but less-severe disease.

(Sydelle Willow Smith for The New York Times) A laboratory in Cape Town, South Africa.

Last week in this space, we covered the emergence of a new coronavirus variant named omicron.

As promised, scientists around the world have spent the past week studying omicron and its spread. In those days, we’ve learned a significant amount about what to expect from the variant and what impact it’ll likely have on our lives.

Let’s get right to the scintillating lessons from seven days of science.

Spreading like wildfire

Different countries are in different stages of omicron spread. Omicron was first discovered in South Africa, where cases are spiking at speeds we just haven’t seen before.

Coronavirus cases in South Africa since the beginning of the pandemic. Clearly, a new wave is coming — but that most recent line is *steep*. (https://ourworldindata.org/coronavirus/country/south-africa)

In European countries like Denmark and the United Kingdom, omicron still makes up a minority of cases, but that share is growing quite quickly.

Closer to home, we have more than 20 states with omicron discovered — including Utah, which has found two cases so far. One Utah case was detected in southwestern Utah in a person who had recently traveled from South Africa, while the other was found in Utah County. Contact tracers have been unable to contact the second man, so we don’t know if they knew each other, or if the second man also recently traveled, and so on.

Using these various pictures of spread, we can get an idea of just how contagious omicron is. If one person gets omicron, how many people does it spread to on average? Trevor Bedford, a viral evolution specialist, showed that omicron’s growth in South Africa reflects a contagion coefficient of 3 to 4. Meanwhile, Alastair Grant, a U.K. researcher, found an estimated contagion coefficient of 3.47 for omicron cases in the U.K. in recent days.

That’s super high. In fact, it approximates what the contagion coefficient was for the original coronavirus at the beginning of the pandemic in the United States. But back then, remember, no one had immunity to this new coronavirus. That this one is spreading essentially at the same rate, even in countries with widespread immunity through vaccination and previous infection, is bad news bears.

Vaccine neutralization lowered

Last week, we told you to keep an eye out for experiments that tested how well antibodies created by the vaccine performed against the omicron virus. We now have seen some of those studies.

And? Well, the results aren’t great, but aren’t horrible. In one study, antibodies created by the vaccine resulted were 41 times less effective in stopping omicron than the original coronavirus. In this graph, the left dots are the neutralization efficacy of the antibodies against the original coronavirus; the right dots are those same antibodies against the omicron variant.

Results from one study on how well antibodies from Pfizer's vaccine neutralizes omicron (on the right) compared to the original coronavirus variant (on the left). (https://twitter.com/_b_meyer/status/1468319835012673549)

You’ll notice two colors in the graph, too: green and orange. Green dots are from people who had both been vaccinated and been infected at some point with the coronavirus. The orange dots are from people who had only been vaccinated. As you can see, the people with both types of immunity end up with significantly higher rates of neutralization against omicron than just the vaccinated people — a couple of whom ended up with near-zero immunity. But most still have at least some immunity.

Other studies found similar results.

That data, though, was from people who had received two doses of the Pfizer vaccine. Boosting increases antibodies a good amount, especially after they wane over time. On Wednesday, a small study from Pfizer found a thirtyfold reduction after two doses, but a 2.6-fold reduction after three doses. That makes sense. After all, getting a booster leads to more antibodies.

A small Pfizer study showed smaller reduction in omicron neutralization for boosted people than in unboosted people. (https://twitter.com/laoneill111/status/1468641497167900676)

So, OK, what do these numbers actually mean? How much worse off will our vaccines be against omicron?

One approach would be to look at analogous cases, where neutralization also dropped by around the same amount, to see how effective vaccines were in those cases. Disease ecologist A. Marm Kilpatrick is working on a paper that uses this approach; he estimates a 40% to 60% reduction in unboosted people in terms of symptomatic infection and a 10% to 14% reduction in unboosted vaccine efficacy against hospitalization.

In other words, in his estimation, two-dose receivers would have vaccine efficacies at 50% or below against infection, but still roughly 75% to 80% effective against hospitalizations. And again, from the Pfizer data above, three-dose receivers should be significantly more protected.

It’s worth noting that the tactic of relying only on previous infection is looking less effective than before. One analysis from the South African National Department of Health found that reinfections were approximately 2.4 times more likely than in earlier waves.

But wait. Is omicron less severe?

Here’s the good news: There has been a relative dearth of severity among these omicron cases. Financial Times writer John Burn-Murdoch has dug into the hospitalization data in South Africa and found a significantly lower percentage of cases that make it to intensive care or get put on a ventilator.

There also has been a reduction in length of stay among hospitalized COVID-19 cases.

So, the big question now is why? We have pretty good data showing that omicron is currently causing less-severe cases, but we also have significant confounding factors that make projecting that trend forward a little sketchy.

First, the portion of the population getting omicron now is less susceptible to severe disease than previous populations. In particular, one doctor’s analysis of the hospitalizations in the Tshwane district of South Africa found that over 80% of the hospitalizations it had recently seen were from people younger than 50 — folks who usually don’t get severe disease from COVID-19 anyway.

Secondly, a large percentage of South Africans had some sort of immunity, whether it was through vaccination or previous infection. While the estimates of how many actually had the disease vary, previous immunity could be allowing people’s immune systems to fight back more effectively than their untrained ones had in previous waves.

Or, it is legitimately possible that omicron’s mutations just make it less troublesome than previous variants. This is mostly just a footnote, but one of omicron’s mutations is actually an insertion of RNA code that matches the code of a common cold virus. Does that mean omicron will act like the common cold? No, that’s not really how it works, but it’s still interesting.

The most likely explanation is probably some combination of the above factors, but exactly which combination is going to have to be determined by more data from other countries.

Regardless of the severity, math is not really on our side here. Even though the cases have been less severe than before, cases have gone up by so much that hospitalizations have increased significantly, too.

Comparing cases, positive test rates, and hospitalizations in South Africa among coronavirus waves. (https://twitter.com/jburnmurdoch/status/1468310618226798595/photo/1)

Cases matter, but hospitalizations — and deaths — matter more. The biggest question now is simple: Will the decrease in omicron severity counterbalance the increase in contagiousness and immune escape? And, in particular, will hospitalizations spike enough to cause overflowing hospitals and rationing care, again?

The world is keeping a close eye on the problem. I get it, I get it; following coronavirus variant coverage again is exhausting. But if you’d like to protect yourself to the extent possible now, I strongly suggest getting a booster shot if you haven’t already.

Andy Larsen is a data columnist for The Salt Lake Tribune. You can reach him at alarsen@sltrib.com.