Gauteng's Omicron Wave Is Already Peaking. Why?

[marmar]

(New York magazine) In Gauteng, South Africa’s Omicron epicenter, the wave seems to be cresting. In other parts of the country, too, the terrifyingly fast rise of the new variant appears already to be slowing and even receding. This is very encouraging, since it suggests that Omicron waves elsewhere in the world may also be, if disorientingly fast, also mercifully short. But it is also a bit confusing, given that the wave has peaked well before anything like it had fully penetrated the local population, and given that everything we know about the new variant is that neither infection-acquired immunity nor two vaccine doses do much at all to stop transmission.

But this is not a phenomenon peculiar to Omicron. At earlier stages of the pandemic, in sometimes less dramatic ways, other waves have crested and declined much before crude models might’ve suggested the vulnerable population had been exhausted. Sometimes, this has led to premature predictions of early herd immunity: Last summer, Youyang Gu, who’d distinguished himself as a modeler of the pandemic, suggested that in parts of the U.S., at least, communities could be reaching “temporary herd immunity” with exposure levels between 10 percent and 35 percent. More recently, Philippe Lemoine has argued that population structure is a hugely underappreciated factor in pandemic spread, and that we shouldn’t keep turning back to models based on simple inputs like doubling time (how long it takes caseloads to grow by a factor of two) or Rt (how many people each infected person infects, on average).

On Friday, I spoke with Trevor Bedford, of Seattle’s Fred Hutchinson Cancer Research Center, about how to make sense of this phenomenon, and how comfortably we can count on the Omicron waves taking a similar turn, on a similar timetable, elsewhere in the world.

I’m curious to talk to you about the state of play generally, but I wanted to start with what we’re seeing in Gauteng, where the wave already appears to be cresting, though many fewer people appear to have been infected than are vulnerable — especially when you consider that, while people who’ve been infected or vaccinated already may be protected against severe disease, there is hardly any protection against infection per se. Which means, in terms of infection, this is almost a virgin population, so to speak. How do you understand that?

Yeah, it’s a really good question. I’ve been looking into this a bit. The basic idea is that we can measure Rt, and there’s a very simple equation that will convert Rt into your population attack rate: how many people will be infected in the entire epidemic wave. That projection is quite linear. With Delta and the Delta Rt of 1.5 — when it was coming in — I was able to convert that to an attack rate that ultimately matched what we saw. I did that by assuming it would really be mostly targeting the people that aren’t vaccinated or infected previously.

With Omicron, and its initial Rt being three-ish, that same equation should give you something like 90 percent of the population infected. But from what we’ve seen in South Africa, it seems like the wave is crashing well before that. So something is going on. .............(more)

https://nymag.com/intelligencer/2021/12/the-south-africa-omicron-wave-is-already-peaking-why.html

[Bernardo de La Paz]

1. Interesting interview. Thank you for posting. . . nt

[Delphinus]

2. Thank you

I heard Trevor on Andy Slavitt just this week - he seems to have a good grasp of what is happening.

[NickB79]

3. COVID has behaved differently in Africa the entire pandemic

If Delta behaved elsewhere like it did in much of Africa, the pandemic would be almost over by now, and the death toll would be a quarter what it is today. Instead, it crushed Europe and the US.

There's something about the environment and populace of sub-Saharan Africa that keeps Covid low, and science hasn't found an answer yet.

[roamer65]

4. Genetics.

It’s all in the genes, possibly past exposure to a similar coronavirus.

That’s my theory.

[PoindexterOglethorpe]

6. You may well be right.

All during this pandemic I have been struck over and over by the vast differences in responses to the disease and to the vaccines.

I do happen to be someone with a very strong immune system, although I cheerfully got the vaccine and recently a booster. But in normal times I simply never get sick. I can be very annoying that way. Other people get everything that goes around.

I do wish that the huge variance in response both to the disease and to the vaccines will trigger research into individual immune systems. Maybe there are patterns, or some finite number and versions of immune systems, and if they can be studied and labelled, we could all benefit.

[NickB79]

7. It is interesting that the only African nation with some European genetics got hit hardest

Nigeria has 200 million people and only a thousand documented deaths, while South Africa has the tens of thousands dead with a smaller population.

[PoindexterOglethorpe]

5. Absolutely fascinating.

Omicron really does seem to be vastly milder than the earlier versions, and especially milder than Delta. That was actually obvious from the very beginning, even though we kept on being told, and are still being told, that it's too early to know. Nope, it's not too early. Hospitalizations from Omicron were immediately vastly lower than from Delta.

The relative mildness of Omicron is important. "And if, on average, you’ve reduced the severity of cases, there’d be a lot of people that don’t bother to come to the hospital or to get tested." Which is exactly what's happening.

I will compare this to smallpox. Smallpox had been around for thousands of years, killed many millions of people and scarred millions more. In fact, it was so common, and the scarring was so common, that anyone not scarred was automatically considered beautiful or handsome, regardless of their appearance.

In the late 19th century, in two different parts of the world, Africa and North America, variola major, smallpox, mutated to become variola minor. Still smallpox, but in the minor version, people were not as sick in the first place, meaning they were able to be up and around and spread the disease much better. They rarely died, and never scarred. Basically, smallpox in the variola minor form was becoming a childhood disease that most people would get and recover from, and then be immune forever to smallpox in either form. Right at that time the smallpox vaccine became common and widespread, and eventually smallpox was completely eradicated, essentially because it only lived in humans. Any early or original animal version was long since gone.

[Turbineguy]

8. That might make it more difficult

for the anti-vaxxer / anti-maskers to draw it out.