Phylogenetics rundown on the new UK Covid mutation.


So I've been reading a bunch on the new viral strain in the UK. My initial understanding from the maddeningly vague reporting was that this was the Spanish strain that has been spreading for months. It's not, it's something new.

Key take-aways, then some more detail, plus a very good paper linked above.

1) This is new, it's been FOUND in the UK and 4 other countries. Because relatively few positive tests are followed with sequencing (required to ID the strain) I suspect it is in far more countries, including the US by now. (If they've sequenced nearly 2000 cases of this variant, there are many tens of thousands out and about.)

2) They believe it spreads faster. I haven't been able to find any detailed analysis on this yet, and it's a surprisingly difficult thing to nail down with a super-spreader driven virus. (Is it more contagious, or did it just get lucky with a few super-spreaders?) Should become a lot clearer in the coming weeks. I'd treat this as a "best guess" for now.
3) No data or reason to believe it will respond differently to the vaccines. Good reasons to believe it will be the same.

There is something unusual about this variant, that takes a bit of explaining...and it has a very likely answer.

When SARS-CoV-2 jumps from one person to another, there's about a 50/50 chance that a mutation will be introduced somewhere in the virus's RNA. That is, if Alice infects Bob, there's a 50% chance that the RNA in Bob's virus is exactly the same, and about 50% that there's a single change somewhere. If Bob infects Carol, and Carol infects David, and David infects Emily...odds are that Emily's virus probably has about 2 mutations compared to Alice's original. (Maybe 1, maybe 3, but as the chain goes on things average out.)

What this means for the epidemic overall is that as the months go by, the number of differences from the original strain tend to go up by one or two mutations per month. So most of the currently circulating strains have a handful of changes that differ from the original.

What's interesting about this new strain shows up in the image below. B.1.1.7 (the branch containing all cases of this new variant) show quite a few more mutations than other variants. In fact, it's roughly double, but it appears to be adding mutations at the normal rate.

What would cause this? Almost certainly it's from a sequence of events like this:

An immunocompromised patient has COVID-19 and can't shake it, with the infection going at high levels for many weeks. Among other treatments, convalescent plasma is administered two or three times. Then, the surviving virus infects somebody else and starts to spread.

A patient with a sustained high load of virus can end up with a virtual zoo of different strains. Convalescent plasma and other treatments can then act as a selective filter, killing off some strains but leaving others to thrive. This can end up with a series of unique mutations in one patient, far faster than a normal transmission chain would generate.

It's very likely that such a patient in England was the source of this new variant. Many of the mutations have arisen independently in multiple locations around the globe, but this strain is unusual in having so many differences from the original.

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