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Slack / Private Message Drop, p.443 [SLACK_000657] · slack_pm:msg:04582

Date: 2021-01-23 17:16
Type: chat message · slack
recipient: Robert F. Garry, Edward C. Holmes, Andrew Rambaut
speaker: Kristian G. Andersen

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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.

In context

A single line often inverts meaning once you see what it answers, so neighbouring messages are always shown.

2021-01-23 17:12 Andrew Rambaut open

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

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.
2021-01-23 17:17 Kristian G. Andersen open

I think the UK lineage is likely a weird example of a chronic infection that took off, while the BRA/RSA lineages are just a result of selection on the population.
2021-01-23 17:17 Andrew Rambaut open

The plastic ones could have just been hitchhiking in the generating individual
2021-01-23 17:17 Kristian G. Andersen open

True
2021-01-23 17:19 Andrew Rambaut open

Trevor has been going around saying the RSA lineage arose in sequence based on some genomes with only some of the mutations but they are not old sequences and I have heard that Tulio uses some weird homebrew bioinformatics that may call for reference occasionally.

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