XEC/XEK spike diversity issue (Updated as of Dec 22) #2088

xz-keg · 2024-09-25T03:18:00Z

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 10 seqs from 2 places, or from 3 or more places (NEW)

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.

Tasks

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Branch 1,Designated XEC.4: XEC+Orf1a:A599T+S:T572I(54 seqs, >10 places) cov-lineages/pango-designation#2803
Branch 2: Designated XEC.12 XEC.12: XEC + S:G252S (39 in 17 places 6 countries ) cov-lineages/pango-designation#2837
Branch 3: Designated XEC.1, XEC + S:K182R (6 , 4 countries) #1869
Branch 4 : XEC+Orf1a:A599T+S:L1224F,Dead Query: G25234T,G2060A,C18657T,-24376, 29 seqs, Scotland, USA-OH , Denmark Artifact?
Branch 5: XEC.15+S:A688V,Query: G2060A,G20433T,C23625T, 29 seqs, France, Portugal,Netherlands,USA, Spain,Italy,Qatar,Germany
Branch 6: XEC subbranch with S:R346I on Orf1a:A599T branch (5 sequences, 3 countries) #2029
Branch 7: Dead By @cvejris, XEC.9+ S:S680F (C23601T). Query: G2060A,C7086T,C23601T, 11 seqs: Guadeloupe, US, France , Wales, Portugal
Branch 8: Designated XEC.10 XEC+Orf1a:A599T+S:G75R, Proposed in XEC+Orf1a:A599T+S:G75R(35 seqs, 10 places) cov-lineages/pango-designation#2839
Branch 9, Designated XEC.3: By @cvejris, XEC+Orf1a:A599T+C11020T+S:E1202Q, XEC + S:E1202Q (22 seqs, 6 countries) cov-lineages/pango-designation#2812
Branch 10, Designated XEC.11 XEC+Orf1a:A599T+C829T+S:K182N, Proposed in XEC+Orf1a:A599T+S:K182N(31 seqs, >10 places) cov-lineages/pango-designation#2840
Branch 11,Designated XEC.5 By @cvejris, XEC+Orf1a:A599T+S:G72R, Query: G2060A, G21776A,T3565C, XEC+S:G72R (22 seqs, 11 countries) cov-lineages/pango-designation#2819
Branch 12, Dead. By @FedeGueli, XEC+ Orf1a:A599T + S:P561H (C23244A) Query: C23244A,C18657T, C25006T, Samples: 4 Scotland , Sweden, Denmark,Norway (Slow)
Branch 13 by @FedeGueli , XEC +Orf1a:A599T+ C583T + S:I68F XEC +Orf1a:A599T+ S:I68F(69 seqs, >10 places) cov-lineages/pango-designation#2802
Branch 14, Designated XEC.13 XEC+Orf1a:A599T+S:S98F, XEC+Orf1a:A599T+S:S98F( 62 seqs, >10 places) cov-lineages/pango-designation#2830
Branch 15,Designated XEC.7 by @cvejris XEC+Orf1a:A599T>Orf1a:G59C ( G440T),S:W152R(T22016A),S:P1263Q (C25350A) Query: G440T,T22016A,C25350A,T21738C Samples: 14 Ireland,Singapore, Netherlands, France
Branch 16, by @JosetteSchoenma XEC+Orf1a:A599T+C3787T,S:I68T, Query: T21771C, G21770A,G2060A, 9 seqs, Netherlands, Germany,Austria, Canada, Finland,Hungary (slow)
Branch 17, XEC+Orf1a:A599T+G20292T+C25665T+S:I584V Query: G2060A,A23312G, 36 seqs, USA, France, Canada, New Zealand, Sweden
Branch 18, XEC+Orf1a:A599T+S:H49Y, Query: C21707T, G2060A, C19716T,20 seqs, Netherlands, Sweden, UK, USA,France,Poland, Canada, Australia,Finland,Finland
Branch 19, DEAD XEC+Orf1a:A599T+S:E1202K, Query: G25166A,G2060A, 16 seqs, USA, Canada (Slow)
branch 20, Dead XEC.2+T7168C+S:G75R, Query: T7168C, G21785C,A4364C, 9 seqs, UK, France,USA,Guadeloupe , Canada, France[1 with S:P174R (C>G) to be checked]
Branch 21, XEC+Orf1a:A599T+S:A262S, Query:G2060A,G22346T,C25006T, 13 seqs, Denmark, Italy,UK, USA (Slow)
Branch 22,Designated XEC.6 By @cvejris XEC + Orf1a: A599T (G2060A) + S:S680F (C23601T) Query: G2060A,23601T,-7086 15 seqs: 3xSpain, 1xNetherlands, 1xJapan
Branch 23, Dead XEC.14+S:V1228L, Query: G2060A,G677A,G25244T,C19716T, 8 seqs, France, Australia, Ireland, Denmark,USA
Branch 24, XEC+Orf1a:A599T+S:S940F Query: C24381T,G2060A,C18657T, 11 seqs, Canada, USA,Germany,Italy,France, Luxembourg
Branch 25, XEC+Orf1a:A599T+S:L822I, Query: C24026A,G2060A, 15 seqs, Japan, Germany, Italy, Ireland, Sweden, with a sub branch with C26942T +S:N137M S:138-141del, Query: C24026A,C26942T, A21766C, Samples: 10 , Japan with a further branch with S:P384S Query: C22712T,C12525T,G11161A,T3565C , 4 seqs, Japan (Niigata) by @Over-There-Is
Branch 26, XEC+Orf1a:A599T+S:G181V, Query: G2060A,G22104T,C18657T, 19 seqs, Denmark, Netherlands, Germany, Luxembourg with a branch with S:H445R,N:G215C Query:T224C, G28916T, C25710T,t3565C 1 seq, Canada
Branch 27, XEC+Orf1a:A599T+S:W152R(T22016C), Query: T22016C, G2060A,C18657T,C19716T, 21 seqs, UK,Germany, Sweden, Ireland,USA,Canada, Italy,Netherlands
Branch 28, XEC+Orf1a:A599T+S:H1101Y, Query: C24863T, G2060A,C18657T, 19 seqs,Sweden, Canada, USA, Australia, Germany, Netherlands (Slow)
Branch 29, XEC+Orf1a:A599T+S:P681H, Query: C23604A, G2060A,C18657T,C19716T,-C6312T,-A7381G,-C745T,-G15007A,-G8258A,-C18131T,-A12421G,-C10369T 23 seqs, Denmark, Us, France, Germany, Canada, Netherlands
Branch 30, XEC+Orf1a:A599T+C1102T+S:V1176F,Orf3a:T89I, Query: G25088T,C1102T,G2060A, 50 seqs, Italy, France, Canada, Russia,Norway,Denmark,Spain,Luxembourg,Germany, China, Slovenia,US (Slow)
Branch 31, XEC+Orf1a:A599T+S:L1143F,Orf1b:Q2069K,Query:C24989T, C19672A,C19716T, 18 seqs, Netherlands, Ireland,Norway,US
Branch 32, XEC+Orf1a:A599T,A486V,ORf1b:P2313S+S:C1235F, Query: G2060A,G25266T,C1722T, 28 seqs, Netherlands, USA, Germany, Croatia, Denmark,UK,Brazil
Branch 33, By @FedeGueli, XEC.8 (T24376C)+Orf1a:T2183I+S:Q173R,N:A211V, Query: C28905T,T24376C,T3565C 62 seqs, Canada (Clusters)
Branch 34 by @cvejris XEC+Orf1a:A599T+G13309A+S:S31F (C21654T), Query: C21654T,G2060A,C19716T,-24376,-C710T ,8 seqs, France, Germany, South Africa, Italy, Sweden sub-branch withS:D88G (A21825G) Query:C21654T,A21825G 2 Samples
Branch 35,XEC.2+S:Q1201K, Query: C25162A, C25163A, A4364C, 7 seqs, Slovenia, Austria, Spain, Germany, Netherlands
Branch 36, Now designated XEC.2.3.1 by @Fearuncle in XEC.2 + N:T379I (51 on Gisaid in 6 countries) 19 with S:G181V #2104 XEC.2.3.1(T7168C+N:T379I+S:G181V) sub-branch with S:S680Y, Orf7b:L19F (rev) Query: C23601A, T7168C,G22104T 11 seqs, Denmark, Netherlands
Branch 37, by @Over-There-Is, XEC+Orf1a:A599T+C25521T+S:K679R, Query: A23598G, C25521T, C27654T, 10 seqs, Sweden, Germany, USA,Netherlands sub-branch with S:I68F, Query: A23598G, C25521T, C27654T,G21770T, 3 seq
Branch 38 DEAD XEC + Orf1a:A599T+Orf1a:T2093I (C6543T)+S:K1073N (G24781T)+T27484C Query: C6543T, G24781T, T27484C, 7 Seqs, Sweden , Ohio, Colorado with a branch with S:L1224F,Orf6:I60V Query: A27379G,C6543T, G24781T 2 Seqs, Colorado, Ohio and another with S:K182E Query: A22106G,C6543T, G24781T 5 Seqs, Sweden (Slow)
Branch 39, XEC+Orf1a:A599T+S:V1264L, Query:G25352T, G2060A, C19716T,-22107, -T23104A (edited by fed) 24 seqs, Canada, Sweden, UK, Italy, USA, France, Ireland, Spain, Slovenia, Denmark
Branch 40 Dead XEC + Orf1a:A599T + T24022C + T1477C + C12043T, S:T470I (C22971T), ORF8:G77V(G28123T) Query:C12043T, G28123T 4 Seqs, Japan, Nevada, Canada
Branch 41, By @cvejris, Dead XEC.5+C10834T+A25590G+S:K182I, Query: A25590G,A22107T, C10834T, 3 seqs, Israel, USA,UK
Branch 42 DEAD XEC+ orf1a:A599T + G2272A + S:T572I (C23277T) Query: G2272A,C23277T,C18657T, 8 Samples, Scotland, Ireland , Germany
Branch 43, by @Fearuncle XEK+G16662A+S:M177I, Query: G16662A,G22093C,C593T, 5 seqs, France, USA
Branch 44, XEK+S:Y1155F, Query: 25026T, C593T, 4 seqs, Denmark, Slovenia, France , Sweden
Branch 45, XEC+Orf1a:A599T+S:A222V, Query: C22227T, G2060A,C18657T,-16461,-13338,-24376, 47 seqs, Canada, Japan, France,USA ,Netherlands(GBW) mostly clusters
Branch 46 by @cvejris XEC+Orf1a:A599T + C835T, T6607C,S:H146Y (C21998T), Query: C835T,T6607C,T21994C, 45 seqs, Germany,USA, Canada (Clusters)
Branch 47, XEK+A20453T,S:S680F,Designated XEK.4 Query: A20453T, C23601T, 46 seqs, USA,Canada (Clusters)
Branch 48, XEC.8 (T24376C)+ T27995C+Orf1a:K1981R+S:A688V, Query: T24376C,T27995C,C23625T, 4 seqs, USA, Sweden,
Branch 49, By @cvejris, XEC+Orf1a:A599T with C4009T, Orf1a:P3767L (C11565T), T14658A, C16428T, S:E1188D, Query: G2060A,G25126T,C4009T, 50 seqs, Canada (Clusters)
Branch 50 XEC + orf1a:A599T > S:E309Q (G22487C) Query: G22487C, G2060A,-C5974T , 10 Samples, Australia, Canada, Usa, Italy, Puertorico, Netherlands,, Chile
Branch 51 XEC +Orf1a:A599T> Orf1a:K3353R (A10323G) > C5974T > S:E309Q (G22487C) Query:A10323G,C5974T,G22487C, 4 Seqs, England,Canada,Australia
Branch 52 XEC + orf1a:A599T> C8146T >T18894C (rev Jn.1 def)>G7996T>ORF1a:I1848V(A5807G=PLPro_I285V),S:R190S(G22132T),S:A435S(G22865T) Query:G7996T,A5807G,G22132T 4 seqs Germany( 2 regions)
Branch 53 XEC + Orf1a:A>T599I (C2061T) > G598A, S:K444R (A22893G) Query:G598A,A22893G,T3565C 9 Seqs, Canada, Germany, NZL
Branch 54 XEC + orf1a:A599T > S:T678I (C23595T),Designated XEC.16 QUERY: C25006T, G2060A,C23595T,-G4144A,-C7420T,-G677A,-C2455T,-C19859T,-C25416T,-C28093T,-C6312T,-C4455T,-G7865T,-C27641T 15 seqs, Canada, Germany, Spain further branch with S:A475V query for it: C5310T,G2060A,C22986T,T3565C 2 seqs,Canada
Branch 55, XEC.11+Orf10:N5D+Orf1a:V2090F,S:V1264L, Query: G25352C,A29570,G2060, 32 seqs, Japan, Canada, USA
Branch 56 XEC + Orf1a:A599T > Orf1a:K513R (A1803G) > S:S514F (C23103T), Query: C23103T,A1803G, 5 samples, Scotland, Denmark
Branch 57, XEC.2+Orf1a:T1820A+S:R765L, Query: G23856T,A5723, 5 seqs, Denmark, USA, Canada
Branch 58, XEC.1+Orf1a:S2673G,S:A67V, Query:A21484G, C21762T,C22414T, 6 seqs, USA(3 states)
branch 59, by @Over-There-Is XEC.8 + S:A688V (II) Query:C23625T,C28603T,T3565C,-A11749T, 9 seqs, Slovenia,Italy,Spain,France
Branch 60, by @Over-There-Is XEC.2.2+T9508C+S:T572I, Query:C23277T, T9508C,A4364C,C19716T, 7 seqs, UK,Ireland,Australia,
Options

FedeGueli · 2024-09-25T09:22:30Z

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 · 2024-09-25T10:13:26Z

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 · 2024-09-26T17:18:23Z

Branch X: XEC+Orf1a:A599T+S:S680F (furin), 5seqs (1xFrance, 1xCanada, 3xUS). Arose 2x independently (all US sequences are separated on the Orf1a:T2274I subbranch = XEC.9, edited). All seqs less than 1 month old. Query: G2060A, C23601T

Mydtlwn · 2024-09-27T06:46:40Z

@corneliusroemer

cvejris · 2024-09-28T15:33:23Z

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

FedeGueli · 2024-09-28T17:23:59Z

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

cvejris · 2024-10-01T20:20:41Z

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

cvejris · 2024-10-01T20:25:00Z

Branch X: 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 · 2024-10-01T20:51:26Z

Branch X: 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 · 2024-10-01T21:16:38Z

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 · 2024-10-01T21:39:48Z

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

xz-keg · 2024-10-02T00:39:59Z

Branch X: 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 · 2024-10-02T06:38:44Z

Branch X: 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 · 2024-10-02T08:07:23Z

@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 · 2024-10-02T22:35:02Z

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

FedeGueli · 2024-10-03T22:27:45Z

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 · 2024-10-03T22:43:17Z

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 · 2024-10-04T15:28:25Z

Branch X: 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 · 2024-10-05T10:47:02Z

Branch X: 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 · 2024-10-06T03:05:48Z

G2060A, G21776A,T3565C

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

FedeGueli · 2024-10-06T14:14:50Z

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

FedeGueli · 2024-10-07T16:52:11Z

XEC+ Orf1a:A599T + S:P561H (C23244A)
Query: C23244A,C18657T, C25006T,
Samples: 2
Countries: 2 Scotland , Sweden

FedeGueli · 2024-10-09T09:50:48Z

Important (likely): XEC got S:I68F (by Gisiad correctly) ( read as S:-70F by USher, Covspectrum and Nextclade ) :
Xec> C583T > S:I68F (G21770T)
Query: C583T,G21770T,T3565C
Samples: 4
Countries 4 France, Rep Czech, Sweden , Egypt (via GBW)
Tree:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_18030_6500e0.json?c=userOrOld&label=id:node_11692317

Now added as branch 13

Ping @corneliusroemer here something to watch

FedeGueli · 2024-10-10T15:44:38Z

Important (likely): XEC got S:I68F (by Gisiad correctly) ( read as S:-70F by USher, Covspectrum and Nextclade ) : Xec> C583T > S:I68F (G21770T) Query: C583T,G21770T,T3565C Samples: 4 Countries 4 France, Rep Czech, Sweden , Egypt (via GBW)
Now added as branch 13

Jumped to 7 with a batch from France, 2 different provinces

xz-keg · 2024-10-12T04:27:37Z

Important (likely): XEC got S:I68F (by Gisiad correctly) ( read as S:-70F by USher, Covspectrum and Nextclade ) : Xec> C583T > S:I68F (G21770T) Query: C583T,G21770T,T3565C Samples: 4 Countries 4 France, Rep Czech, Sweden , Egypt (via GBW)
Now added as branch 13

Jumped to 7 with a batch from France, 2 different provinces

+3 GBW from Turkey, you can propose it to main.

FedeGueli · 2024-12-15T22:42:55Z

the XEC+475V + orf3a:S60F + Orf6:L52F Ontario cluster grew to 14 and recent samples. One to watch if it manages to exit the cluster. (Q: C6582T, T19230C, C22522T,)

FedeGueli · 2024-12-15T22:44:27Z

Br 17 went to 34
updated everything some more are dead some growing interestingly. still too ealry to propose in my view

FedeGueli · 2024-12-16T00:08:52Z

A former Scottish cluster now found also in Denmark with S:S514F
query: C23103T,A1803G
Samples: 5 all from november
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_test_1f349_f6f260.json?label=id:node_7264304

should i add it? cc @xz-keg

xz-keg · 2024-12-16T00:31:19Z

A former Scottish cluster now found also in Denmark with S:S514F query: C23103T,A1803G Samples: 5 all from november https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_test_1f349_f6f260.json?label=id:node_7264304

should i add it? cc @xz-keg

yeah pls

FedeGueli · 2024-12-16T08:44:12Z

A former Scottish cluster now found also in Denmark with S:S514F query: C23103T,A1803G Samples: 5 all from november https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_test_1f349_f6f260.json?label=id:node_7264304
should i add it? cc @xz-keg

yeah pls

Br.56 now

FedeGueli · 2024-12-16T09:51:57Z

Br.25 , formerly thought dead now jumped to 15 with a batch from Japan , 4 of the new samples have S:P384S that is predicted by J Bloom to be a hotspot for immuno escape.,

Over-There-Is · 2024-12-16T14:46:39Z

Br.25 , formerly thought dead now jumped to 15 with a batch from Japan , 4 of the new samples have S:P384S that is predicted by J Bloom to be a hotspot for immuno escape.,

also NDPFL137-141M

Over-There-Is · 2024-12-16T14:50:32Z

All 10 Japanese sequences of Branch 25 have C21997T.

FedeGueli · 2024-12-16T16:26:54Z

All 10 Japanese sequences of Branch 25 have C21997T.

yeah i saw that and the deletion even a bit messy on nextclade, i will re fromulate the br.25 to include all the nodes (it is hard to specify for sub brannches in multiple lineages proposalS) thx for checking

FedeGueli · 2024-12-16T16:42:47Z

Br.25 , formerly thought dead now jumped to 15 with a batch from Japan , 4 of the new samples have S:P384S that is predicted by J Bloom to be a hotspot for immuno escape.,

also NDPFL137-141M

to me it is
S:N137M + 138-141del D142D V143V 144del
or
S:137-140del S:L141M D142D V143V 144del

xz-keg · 2024-12-18T05:20:11Z

branch 17 is now 35 @FedeGueli I'll propose it?

corneliusroemer · 2024-12-18T20:49:01Z

Thoughts on this branch in XEC.8?

It looks like it could be a KP.2.3--(3506-?22k?)-XEC.8 recombinant, where the donor on KP.2.3 side is the German/Dutch branch from KP.2.3 with 593T and 3505

query for recombinant: C593T, C3505T, G24193T

query for minor donor: C593T, C3505T, A15402G

Timeline and location fits a recombination event in Germany around July/August 2024.

xz-keg · 2024-12-19T00:00:15Z

branch 47 designated XEK.4 via cov-lineages/pango-designation@7cb9d21

branch 54 designated XEC.16 via cov-lineages/pango-designation@4256d9b

… XEC.16 (S:T678I)

xz-keg · 2024-12-19T01:58:29Z

Thoughts on this branch in XEC.8?

It looks like it could be a KP.2.3--(3506-?22k?)-XEC.8 recombinant, where the donor on KP.2.3 side is the German/Dutch branch from KP.2.3 with 593T and 3505

query for recombinant: C593T, C3505T, G24193T

query for minor donor: C593T, C3505T, A15402G

Timeline and location fits a recombination event in Germany around July/August 2024.

C593T and C3505T are XEK specific, likely XEK/XEC.8 recombinant given XEK is much more prevalent than its KP.2.3 parent.
wait it also have C28291A rev which is weird since 28884 is not reverted so this part is unlikely due to recomb.

FedeGueli · 2024-12-19T17:19:23Z

There is an interesting branch of XEC that in its least branch evolved S:T33K and S:141-144del:
Query: G12749A,C27972A (5/6 with 141-144del, 4/6 w T33K)
tree:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_test_2eafc_4541e0.json?c=userOrOld&label=id:node_7256969

For now just a cluster.

FedeGueli · 2024-12-20T20:17:04Z

Br.53 (444R) one more from NZL (new)

xz-keg · 2024-12-22T06:10:42Z

Add branch 57 (XEC.2+R765L)
branch 58 (XEC.1+A67V)

raise threshold for 2 place branches to 10 seqs. (still no threshold if detected in 3 different places)

FedeGueli · 2024-12-22T12:07:01Z

Br.55 appears to be fast.- everything just updated

FedeGueli · 2024-12-22T12:13:29Z

Added several -s to Br.29 (681H)

Over-There-Is · 2024-12-24T17:34:25Z

C8146T,T2803C,G25249T M1229I CA-ON

Over-There-Is · 2024-12-24T17:37:38Z

XEC.2.2 + T572I T1104C, T9508C, C23277T 3 UK, Ireland

Over-There-Is · 2024-12-24T17:59:18Z

Another XEC.8+S:A688V, C23625T,C28603T, not on T27995C branch

FedeGueli · 2024-12-25T23:45:58Z

Another XEC.8+S:A688V, C23625T,C28603T, not on T27995C branch

added as branch 59

xz-keg · 2024-12-26T03:21:04Z

branch 55 is 32 now.

xz-keg · 2024-12-26T04:44:57Z

XEC.2.2 + T572I T1104C, T9508C, C23277T 3 UK, Ireland

added as branch 60.

FedeGueli added Multiple lineages spike diversity XEC Interesting diversity in the tree the tree shows multiple interesting branches labels Sep 25, 2024

xz-keg pinned this issue Sep 26, 2024

FedeGueli changed the title ~~XEC/XEK spike diversity issue (Updated as of Dec 10)~~ XEC/XEK spike diversity issue (Updated as of Dec 15) Dec 15, 2024

FedeGueli referenced this issue in cov-lineages/pango-designation Dec 19, 2024

Designate a few extra lineages

7cb9d21

FedeGueli referenced this issue in cov-lineages/pango-designation Dec 19, 2024

Designate NU.1 (JN.1.55.2 + S:R346T, S:Q677H, ORF3a:L52F, Brazil) and…

4256d9b

… XEC.16 (S:T678I)

xz-keg mentioned this issue Dec 19, 2024

XEU:XEK/XEC.8 recombinant(16 seqs, >10 places) #2298

Closed

FedeGueli changed the title ~~XEC/XEK spike diversity issue (Updated as of Dec 15)~~ XEC/XEK spike diversity issue (Updated as of Dec 22) Dec 22, 2024

XEC/XEK spike diversity issue (Updated as of Dec 22) #2088

XEC/XEK spike diversity issue (Updated as of Dec 22) #2088

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