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Slack / Private Message Drop, pp.442-443 [SLACK_000656] · slack_pm:msg:04578

Date: 2021-01-23 17:12
Type: chat message · slack
recipient: Kristian G. Andersen, Robert F. Garry, Edward C. Holmes
speaker: Andrew Rambaut

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Here is a full list of variants in B.1.1.7 on sites with mutation seen in P.1 and B.1.351 (and not originally in B.1.1.7):```Gene Mutation Original lineage Seen in B.1.1.7ORF1ab S1188L P.1 A/L/P 1/4/2 genomesK1655N B.1.351 M/N 1/3 genomesE5665D P.1 D 2 genomes spike L18F P.1/B.1.351 L 310 genomesT20I P.1 N 17 genomesP26S P.1 H/L/S 1/2/5 genomesD80A B.1.351 Y 4 genomesD138Y P.1 G/H 1/75 genomesR190S P.1 M/S 2/2 genomesD215G B.1.351 B/N/Y 1/1/8R246I B.1.351 K 4 genomesE484K P.1/B.1.351 G/K 1/10 genomesH655Y P.1 Y 7 genomesP681R R 10 genomesA701V B.1.351 V 25 genomesE P71L B.1.351 H/L/S 3/5/2N P80R P.1 L 6 genomesT205I B.1.351 I/N 13/2 genomes```

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2021-01-23 16:50 Andrew Rambaut open

spike L18F is seen in 310 genomes within B.1.1.7 in the UK - more convergence
2021-01-23 17:08 Kristian G. Andersen open

For fuck sake! This is adding immune escape to the increased transmission. Just need to add E484K and L417N/T and we're good to go.
2021-01-23 17:12 Andrew Rambaut

Here is a full list of variants in B.1.1.7 on sites with mutation seen in P.1 and B.1.351 (and not originally in B.1.1.7):```Gene Mutation Original lineage Seen in B.1.1.7ORF1ab S1188L P.1 A/L/P 1/4/2 genomesK1655N B.1.351 M/N 1/3 genomesE5665D P.1 D 2 genomes spike L18F P.1/B.1.351 L 310 genomesT20I P.1 N 17 genomesP26S P.1 H/L/S 1/2/5 genomesD80A B.1.351 Y 4 genomesD138Y P.1 G/H 1/75 genomesR190S P.1 M/S 2/2 genomesD215G B.1.351 B/N/Y 1/1/8R246I B.1.351 K 4 genomesE484K P.1/B.1.351 G/K 1/10 genomesH655Y P.1 Y 7 genomesP681R R 10 genomesA701V B.1.351 V 25 genomesE P71L B.1.351 H/L/S 3/5/2N P80R P.1 L 6 genomesT205I B.1.351 I/N 13/2 genomes```
2021-01-23 17:13 Andrew Rambaut open

Probably some of them (particularly those with multiple residues) are probably just plastic.
2021-01-23 17:14 Andrew Rambaut open

Will need to see how often some of these occur outside the background of B.1.1.7
2021-01-23 17:15 Kristian G. Andersen open

Yeah. Very interesting to see how several of these are shared with BRA/RSA variants though - I find that a little confusing
2021-01-23 17:16 Kristian G. Andersen open

I thought the mutations observed in P.1 / B.1.351 were likely fixed in a single individual and then took off in the population. But seeing them pop up here suggest to me that that likely wasn't the case. Maybe immune selection in_the population_, not _intrahost_, actually fixed them in the first place.

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