COVID-19: Chapter 9 - OMGicron

Sounds like we’re almost certainly headed towards an Omicron-specific vaccine in a few months.

Yeah, and get that too when it’s available. If you have holistic, homeopathic friends, tell them it’s like accupuncture that actually works.

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So fun.

Interesting suggestion here. It sounds plausible but I have no idea how plausible.

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It’s not impossible, but I’m not even sure it’s falsifiable via any sort of practical means. As such, I can’t see worrying about it.

Think it is booster plus behavior change. We should all be going back to cautious and avoiding contact as much as possible for the near future. I’m probably going back to a very small Christmas and certainly not traveling.

real or onion?

https://thehill.com/changing-america/enrichment/arts-culture/584060-ufc-head-reveals-he-has-covid-19-and-asked-joe-rogan

The study discussed here may have some answers for you:

https://twitter.com/apsmunro/status/1466707676964995073?s=21

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It seems weird that Wuhan COVID would infect an animal, evolve for a year, then pop out as something as infectious or more infectious in humans than Delta, which had hundreds of millions of rounds of infecting humans to evolve on.

But it also seems weird that an infection in a single person would lurk for a year getting more and more contagious, then burst on to the scene.

The whole thing is pretty baffling.

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?

All of those things happen all the time, but in most cases the mutations/recombinations are disadvantageous and we never see the results.

Evolution is not really a process. It’s more of a scorecard. Variability happens and then selection determines the winners.

Billions of virus particles replicate million or billion fold per infection and then act on millions in population. Infection of animals probably happens all the time. The math is staggering for low frequency events to happen with some reasonable confidence. From their it’s a bit of luck and competition.

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I’m not sure we’re on the same page when you say that evolution is not really a process. The number of virus replications is large relative to the number of single mutations that could occur, but it’s tiny relative to the number of mutations separating Omicron from its last known human ancestor. COVID has 30k base pairs, so say 90k possible point mutations. Omicron has something like 50 mutations since its last known ancestor. If even 5 of those are “important,” that’s ~10^24. A human case of COVID is something like 10^11 viruses, so you’d need 10 trillion cases before you saw an Omicron (assuming each virus has exactly 5 random mutations from ancestral, which makes no sense but I’m rolling with for estimation).

Now maybe there are a bunch of 5-base-pair mutations that are as infectious as Omicron, but then why aren’t we surprised not to have seen Omicron emerge earlier in humans? Surely there’s more COVID replication going on in humans than animals, right? Plus there’s not an interspecies barrier to jump back across.

It seems like you really need the concept of iterative selection to make it tractable. Which is why it’s confusing to me if the evolution happened in animals rather than humans. It would sort of make sense if human COVID evolution got shunted down an evolutionary dead end that leads to Delta by one of the early mutations, while an animal population preserved the original strain long enough to stumble onto a moderately difficult mutation that leads to Omicron? IDK, biology is confusing.

The animal host theory seems very speculative aorn.

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Even so, my dog has suggested a global squirrel genocide. Just in case.

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More not exactly encouraging news out of Gauteng.

Basically hospitalisation data for the last week continues to be revised upwards (from 580 on Monday to 788 yesterday to 821 today). This week’s numbers sit at 1,130 with 3 days still to go + backfill through next week. Means the slope of Omicron in the 3rd graph @HueHuecoyotl posted above is even steeper. Still early days but hospitalisations now seem to be clearly outpacing all earlier trends.

This is in spite of the age profile of admissions being almost inverted . This was a screenshot from today’s press briefing comparing the age range of patients between Omicron and Delta (Tshwane metro only):

https://twitter.com/PeterBarabas1/status/1466721182309363712

Meanwhile Gauteng recorded 8,280 cases yesterday, which is clearly huge, but also came with a 34% positivity rate. Looking at HueHue’s 2nd graph I think that’s the highest positivity rate they’ve recorded and obviously indicates that infection is now outstripping their ability to effectively test.

Edit: And today Gauteng recorded 11,553 cases.

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I read that the symptoms had a lot more of a gastro component to it then delta. As a result, there are a lot of kids being admitted for short periods for IVs to treat dehydration.

What we know about Omicron so far (spoiler: not much!)

https://www.nature.com/articles/d41586-021-03614-z

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I guess that would be better than struggling to breathe. I’ve only seen descriptors like “unusual, but mild” with no more specific info provided.

It was just an anecdote, trying to find the article again, but would make the 0-4 stuff a bit less scary than if they were being hospitalized with typical COVID symptoms. We’ll have to see, should know more in the coming days.

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This. We’ve had the word spoken repeatedly in a pop culture show for 20 years now.

I had one two weeks ago. It sucked for that poor kid. Drilled into their bone.