FR.1.1 with S:82 reverted (115 seqs, 7 countries)

[xz-keg]

FR.1.1+T14961C+A3715G,C15960T, A21807C(S:P82H, reversion)

GISAID query: A3715G,C15960T,C1142T,T2372C,T14961C,C7318T,-21807

None of the seqs under A3715G,C15960T branch has S:H82P, none of them has S:82 masked, so on position 82 it is P.

No. of seqs: 61(Austria 1 Italy 2(from China), Singapore 2(1 from Italy, 1 from China), South Korea 1 USA 2 China 53)

First seq: EPI_ISL_17516758, 2023-4-6, Liaoning
Latest: EPI_ISL_17836899, 2023-6-13, Shanghai

It shares lots of FR.1.1 specific mutations (C1142T,T2372C, and T14961C on FR.1.1's main branch), so shall be FR.1.1+S:82 reversion. Which is a bit strange as S:P82H is FR.1.1's defining mutation and it immediately reverts back.

Another possibility is FR.1/FR.1.1 recombinant.

usher

[FedeGueli]

Hi @aviczhl2 for opening this one. I multiple times lost a lot of time trying tomunderstande the FR.1.1 tree.
I never was able to draw any conclusion but to me everything is messed by 337 C337T that undergoes multiple reversions in the proposed branch and outside.

cc @AngieHinrichs @corneliusroemer could you take a look please?

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice19_genome_317ce_9687c0.json?c=gt-nuc_337&label=id:node_7225110

[xz-keg]

Hi @aviczhl2 for opening this one. I multiple times lost a lot of time trying tomunderstande the FR.1.1 tree. I never was able to draw any conclusion but to me everything is messed by 337 C337T that undergoes multiple reversions in the proposed branch and outside.

I just ignore 337 and it turns out that without 337 it still shall belong to FR.1.1 due to shared C1142T,T2372C, and T14961C.

[FedeGueli]

Hi @aviczhl2 for opening this one. I multiple times lost a lot of time trying tomunderstande the FR.1.1 tree. I never was able to draw any conclusion but to me everything is messed by 337 C337T that undergoes multiple reversions in the proposed branch and outside.

I just ignore 337 and it turns out that without 337 it still shall belong to FR.1.1 due to shared C1142T,T2372C, and T14961C.

yeah but that doesnt explain why 337 makes flip flop around , without understanding that impossible to say anything on S:P82H >P

[xz-keg]

99 and in Japan