Very Diverse Tree Indicating Collection of EG.5.1*+S:157L besides EG.5.1.6 and HK.3.1

[krosa1910]

Parent: EG.5.1( and sometimes its first descendents as EG.5.1.1 or else)

Gisaid Inquiry : -C5835T,-G22927T,C22033A,G21718T,C22480T (The latter two indicates EG.5.1, C22033A for F157L, and the first two removes potential EG.5.1.6 and HK.3.1* as they are already designated).

Sequences:96-8-9-1=78 total (7 England, 5 France, 1 Italy, 2 Japan, 2 Netherland, 2 Portugal, 11 Scotland, 3-1=2 South Korea, 2 Spain, 29-8-9=12 US, the rest 30 in various Chinese Provinces, of which Shanghai and Yunnan looks important) 8+9+1 seqs are removed as they are either EG.5.1.6*, or Spike-Only sequences. Earliest: EPI_ISL_18036594 Guangdong, China 06-18 Latest: EPI_ISL_18239743 France, 08-28 Usher Tree:https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_1d1df_e27e30.json?f_userOrOld=uploaded%20sample&label=id:node_3064067 Picture of it:

Note: I revived discussion of S:F157L in XBB when searching for potential BA.2.75/XBB recombinations (as S:F157L is sign of XBB), yet instead I see just how widespread and fast this mutation arises in general XBB population. After some works of other spotters and me, we spot and designate several lineages, and I thought it was over. And just today, I decided to check over my issues and see how much they grow. EG.5.1.6 was certainly beyond my expectation, yet I found a large crowd of EG.5.1+S:157L. The most noticible one is certainly the "flip" one-HK.3.1, but a lot of unclassified lineages seem to exist, and they are everywhere (across many major subdivisions of EG.5.1), as shown in the picture. And a lot of those are pretty new, I made a comparison between it, EG.5.1, and EG.5.1*+flip. It is almost as fast as Flip I guess.

I will try my best to get this part described. But help would be appreciated.

Update: Quite large uploads have increased total number of sequences to 109-8-10=91 now.

### Tasks
- [ ] Branch 1:EG.5.1->G670T ( universal reversion,questionable) C12439T, C22033A 22seqs, 3 countries  
      Gisaid Inquiry: C12439T,-C5835T,-G22927T,C22033A,G21718T,C22480T
- [ ] https://github.com/sars-cov-2-variants/lineage-proposals/issues/774

### Tasks
- [ ] #774
- [ ] Branch 2: EG.5.1* derivative with G670T, C12439T, C22033A

[krosa1910]

Lineage 1: Defining Mutations: G670T (orf1a_R135Srev=nsp1_R135Srev), C12439T on top of EG.5.1* I think this is weird because it is defined by a reversion and a silent mutation, but whatever it seemed the largest thing I could dig out from this pile. Also it appeared in four region/countries (depending on how to count England and Scotland), so a little higher credibility Gisaid Inquiry: C22033A,G21718T,C12439T,-T670G 18 sequences Earliest: EPI_ISL_18228064 Scotland 07-29 Latest: EPI_ISL_18239744 France 08-28

Lineage 2: Defining Mutations: S:S98F,S: F157L and some more on top of EG.5.1* I don't know why it only showed up 8 sequences on my side, seems more than that. This is covered by #774 So I would leave the job of tracking it to Ryan

This has grown pretty much just since I propose these lineages, I would try to regroup them sometime between today and tomorrow.

[FedeGueli]

ping @corneliusroemer have you already looked in S:F157L homoplasic in EG.5.1 and EG.5.1.1?

[krosa1910]

I now believe this has sustained population and steady growth because it has been uploaded everyday for the last 8 weekdays (that is the last week+ this week). Would try to sort out everything recognizable >5 to be a "lineage" (smaller will be sin/dou/tri/quadlet)

[FedeGueli]

Hi @krosa1910 could you provide a query please?

[FedeGueli]

the EG.5.1.1 top branch in your first tree now designated HK.19

[FedeGueli]

I am not sure if milestoning this one , cause the secific queries miss the ones analyzed by you. let me know.