A flurry of info on the B.1.1.7 variant in the US in the last couple of hours.


This shows in orange where on the spike the B.1.1.7 mutations are, and in red, it shows the location of the top 10 natural antibodies after a COVID infection. None of the 10 overlap the mutations, so we should expect little or no impact.



Further evidence that B.1.1.7 won't be especially likely to reinfect people who had wildtype COVID.


Another angle of investigation, also suggesting wildtype COVID immunity should work fine against B.1.1.7.


2nd US case found in California today.



It's also remarkable the speed they can move. 21 hours from a routine positive test result, to genome sequencing and B.1.1.7 confirmation, to contact tracing under way. Just...wow.

By the way, this "S dropout" thing is cool. One of the mutations in B.1.1.7 is the deletion of amino acids 69 and 70. By a stroke of luck, that makes some of our PCR tests fail on one of the three sequences they look for.

I say fortunate, because we can now watch for routine PCR tests that return two hits but a miss on this one, flagging them as possible B.1.1.7 cases.

But there's also a downside. Because we can spot likely B.1.1.7 subjects, our sequencing data is going to show an unrepresentative number of B.1.1.7 variants in our screening. It's going to take some quick work to calibrate that back to a proper denominator. (If you mostly sequence probable B.1.1.7 results you're going to see a high rate, but you need to account for all the ones you decided not to look at.)

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