XEC spike diversity issue

[xz-keg]

It seems that there is, and will be a lot of spike diversity in XEC. Better gather them in one issue.
Only count for branches with more than 2 places.

GPT Model trained on August data(seqs before XEC appears) predicts 4 spike mutations for XEC on top potential mutation list: S:T572I, S:R346T, S:N185D, S:A688V.

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1. Branch 1: XEC+Orf1a:A599T+S:T572I (10 seqs, 6 places) #2087
2. Branch 2: XEC + S:G252S on the ORF1a:A599T branch (19 in 4 countries - 6 on Gisaid)  #1993
3. Branch 3: Designated XEC.1, XEC + S:K182R (6 , 4 countries) #1869
4. Branch 4: XEC+Orf1a:A599T+S:L1224F, Query: G25234T,G2060A,C18657T, 5 seqs, Scotland, USA-OH
5. Branch 5: XEC+Orf1a:A599T+Orf1b:M2322I+S:A688V,Query: G2060A,G20433T,C23625T, 2 seqs, France, Portugal
6. Branch 6: XEC subbranch with S:R346I on Orf1a:A599T branch (5 sequences, 3 countries) #2029
7. Branch 7: By @cvejris, XEC+Orf1a:A599T+S:S680F,splited to 2 usher branches but can be convergent C7086T Query: G2060A, C23601T, 9 seqs, Canada, France, USA, Peru' (via GBW), UK, sub-branch with S:T259I, Query: G2060A, C23601T,C22338T, 3 seqs.
8. Branch 8: XEC+Orf1a:A599T+S:G75R, Query: G21785C,G2060A,-G1681A , 5 seqs, USA, France, Spain,Germany
9. Branch 9: By @cvejris, XEC+Orf1a:A599T+S:E1202Q, Query: G2060A,C11020T,G25166C, 2 seqs, France , Ireland.
10. Branch 10, XEC+Orf1a:A599T+S:K182N, Query: G2060, A22108T, C829, 6 seqs, USA, Canary Islands, Netherlands, UK
11. Branch 11, By @cvejris, XEC+Orf1a:A599T+S:G72R, Query: G2060A, G21776A,T3565C, 5 seqs, Canada, France, Denmark, Netherlands, Mexico, USA,

[FedeGueli]

Very good idea, i will try to help. do u prefer direct editing or highlighting in the comments?

I would require also that the lineage has to be sampled at least once in September ( or last 30 days) to avoid dead ends
If you agree .

[xz-keg]

Very good idea, i will try to help. do u prefer direct editing or highlighting in the comments?

I would require also that the lineage has to be sampled at least once in September ( or last 30 days) to avoid dead ends If you agree .

Sure, you can do direct editing.

[cvejris]

Branch 7: XEC+Orf1a:A599T+S:S680F (furin), 5seqs (1xFrance, 1xCanada, 3xUS). Arose 2x independently (all US sequences are separated on the Orf1a:T2274I subbranch). All seqs less than 1 month old. Query: G2060A, C23601T

[Mydtlwn]

@corneliusroemer

[cvejris]

Branch 9: XEC+Orf1a:A599T+S:E1202Q, 2 seqs, France + Ireland. Query: G2060A,C11020T,G25166C

[FedeGueli]

Br.7 went to 8 with three GBW samples from Peru' (2 patients)

[cvejris]

Branch 10/11: XEC+S:W152R (defining for Centaurus) arose convergently: Branch 10 via T22016A (1xNL, 1xFR). Branch 11 via T22016C (1xIR, 1xUSA). All seqs sampled in September

[cvejris]

Branch 12: XEC+S:T678I (C23595T), furin-adjacent. 4xCAN, 2xFR, 2xUSA. Convergent: one on the Orf1a:I1367L, the rest on the Orf1a:A599T polytomy. All seqs sampled in September

[cvejris]

Branch 13: XEC+S:P1263Q(C25350A): 3xSW,1xFR,1xNL. Convergent (Swedish seqs on the C27630T subbranch of Orf1a:A599T, the rest on the Orf1a:A599T polytomy).
Interestingly, most XEC with P1263Q harbor other "promising" mutations

[xz-keg]

Branch 10: XEC+S:W152R (defining for Centaurus) arose convergently: i. via T22016A (1xNL, 1xFR) ii. via T22016C (1xIR, 1xUSA). All seqs sampled in September

Please separate these branches and ensure every branch is monoplyetic.

[cvejris]

Branch 14: XEC+S:P1263L(C25350T), same site as branch 13. 1xSW,1xPL.

[xz-keg]

Branch 13: XEC+S:P1263Q(C25350A): 3xSW,1xFR,1xNL. Interestingly, most XEC with P1263Q harbor other "promising" mutations

Please check with usher before proposing. They seem to be on different usher branches.
https://genome-test.gi.ucsc.edu/cgi-bin/hgPhyloPlace

If they are on different usher branches it is likely they emerge separately and shouldn't be treated as one. Unless you provide reason (artifact, usher-flip flop, convergent other mutations like branch 7, etc. ) to merge them.

[cvejris]

Branch 13: XEC+S:P1263Q(C25350A): 3xSW,1xFR,1xNL. Interestingly, most XEC with P1263Q harbor other "promising" mutations

Please check with usher before proposing. They seem to be on different usher branches. https://genome-test.gi.ucsc.edu/cgi-bin/hgPhyloPlace

If they are on different usher branches it is likely they emerge separately and shouldn't be treated as one. Unless you provide reason (artifact, usher-flip flop, convergent other mutations like branch 7, etc. ) to merge them.

IMO, at present the relatively low number of XEC seqs makes it hard to correctly assess the phylogeny, the resolution is still insufficient. The total XEC Usher tree still places most seqs on polytomy.
My contributions should not be treated as lineage proposals. I look for mutations which may be beneficial for the virus. They might be i. founder mutations for a monophyletic lineage which spread to different countries, or ii. the same AA substitution arising independently on different background in different countries. It does not make that much difference - both scenarios may in theory indicate selective advantage conferred by the mutations.
I edited my contributions by adding notes about convergence for the mutations where I think there was one :)

[FedeGueli]

@aviczhl2 i think soon we will be force to raise the parameters to three places and 10 seqs, i tell this because in my previous experience with spike diversity issues it rapidly becomes very mess or too long with the opposite effect to risk hiding something fast instead of highlighting it. It is not yet the moment but we shopuld think about it.

[cvejris]

Branch 15: XEC+Orf1a:A599T+S:K182N. 3xNL, 1xENG, 1xCanary Islands (with additional S:M153I). Monophyletic, query: C829T, A22108T

[FedeGueli]

Not a Branch but worth tracking: XEC + Orf1a:A599T+ S:A475V
Query:T8416C,C22986T,T3565C
Samples: 3
Places: Netherlands, 2 regions (Gelderman, Zuit Holland)

[FedeGueli]

Solved 5 now from Br.8 also from Germany it looks interesting

Deleted for mistake the query of BR.8 i m re building it ( i fear it is not monophyletic though)

[cvejris]

Branch 16: XEC+Orf1a:A599T+S:G72R. 5 seqs, 5 countries: Denmark, Netherlands, France (with S:K113R), Canada, GBW from Mexico. Query: G2060A, G21776A,T3565C (edited)

[FedeGueli]

Branch 16: XEC+Orf1a:A599T+S:G72R. 5 seqs, 5 countries: Denmark, Netherlands, France (with S:K113R), Canada, GBW from Mexico. Query: G2060A, G21776A,T3565C (edited)

i ve added T3565C to exclude old samples.

[xz-keg]

G2060A, G21776A,T3565C

You can directly edit the task list. But be cautious on cvejris proposals that may not be monophyletic.

[FedeGueli]

G2060A, G21776A,T3565C

You can directly edit the task list. But be cautious on cvejris proposals that may not be monophyletic.

yeah i m a bit confused about the branch numbering . @cvejris i suggest just to add the lineage you find without a branch number