1, maybe 2 or 3 lab leaks later

We don’t know the COVID-19 pandemic originated with an accidental laboratory leak. It’s a possibility and as Matt Ridley’s slightly inappropriate haiku thread points out, it’s plausible.

We do know the Delta variant leaked from a laboratory in Taiwan, mainly because Taiwan is civilised nation and kindly informed the world. This was not the origin of the Delta variant as the leak happened afterwards and the laboratory was studying the variant.

We can suspect that the Omicron variant originated with an accidental laboratory leak. Why? Because otherwise it would be weird.

Weirdness 1: The Phylogenetic Tree

First, look at the phylogenetic tree (it’s basically a family tree for viruses).

[…] But then look at omicron. It’s the red cluster in the upper right. It’s very, very different. It’s way off the “natural” family tree of descendants of the original SARS-CoV-2. What’s more, if you trace its “stalk” back (i.e., if you look where it branched off from the “family tree”), you see it sprang from an “ancestor” from sometime in Spring 2020.

So, how did that happen? How did it suddenly appear in November 2021, when its “forefather” was a version of the virus that was common in mid-2020?

And where is all the natural variation in between? Why is it not like the other variants, nested in that natural-looking spreading set of gradually mutating descendants?

[…]

Weirdness 2: The Proportion of the Mutations

[…] All viruses as they evolve develop mutations, all the time. That’s why you see, in the image above, that gradual wedge shape, as the virus gets more and more diverse over time. There’s more similarity on the left (fewer different versions of the virus) and more diversity on the right (more versions) as time goes by. The diversity occurs because mutations occur.

[…] Omicron has a lot of mutations, as you can see from that phylogenetic tree above. Because it has a lot of “useful” functional mutations, which seem to make it a very successful virus […], and because changes to any virus’s “recipe” are truly random if those changes occur in nature, you’d also expect to see many silent (unimportant) changes to its recipe.

In fact, based on all the other successful variants of SARS-CoV-2, scientists know the number of silent mutations they expect to see.

But they don’t find nearly enough of these silent mutations.

Weirdness 3: Its Remarkable Immune Evasion

As you may have heard, one of the most startling things about the omicron variant is its remarkable immune evasion. That means, for example, that our existing vaccines and the monoclonal antibodies we’ve been using to treat COVID patients are much less effective against it.

[…] “It’s not just evolutionary pressure. It’s extreme evolutionary pressure on preventing antibody binding to the spike in a very short time. (Very few silent mutations, which act like a clock, indicate it was frozen for close to 1 year.) It’s either a synthetic polymutant or bred in presence of extremely well-tuned sequence of different convalescent/vaccination sera or recombinant antibodies. That many resistances can’t come from one or few immunocompromised patients, which usually have B cell deficiencies, let alone animals, which initially don’t have antibodies.”

Weirdness 4: The Fact that It Seems to Have Come from a Mouse (in Some Form)

— “Lab Leak 2.0

I think there’s a compelling argument that we should stop doing gain-of-function experiments.

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