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XDV.1.1 ( T4579A , S:S60P) with further S:H146Y, S:N185D (30 Taiwan Hubei Shanxi Hong Kong) #1820

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FedeGueli opened this issue Aug 3, 2024 · 13 comments
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XDV.1.1 ( T4579A , S:S60P) with further S:H146Y, S:N185D (30 Taiwan Hubei Shanxi Hong Kong) #1820

FedeGueli opened this issue Aug 3, 2024 · 13 comments
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Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. designated partially designated S:60 XDV
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XDV.1.1

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@FedeGueli
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FedeGueli commented Aug 3, 2024 •
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Credits : spotted and tracked first by @Memorablea in Memorablea/COVID-19-#102 (comment)

T4579A was the defining of FL.2 , now popped up and seems expanding recently on XDV.1 backbone and seems successful if compared with XDV.1 4579T.
Screenshot 2024-08-03 alle 18 01 29
it further gained a S:S60P sublineage convergently with JN.1 descendants.

Defining XDV.1 > T4579A > T9208G > S:S60P (T21740C) > Orf1a:R226K (G942A)> S:H146Y (C21998T) > S:N185D (A22115G)
Query for T4579A: T4579A, C1170T,C6501A,T22930A
Samples: 49, first collected on 2024-04-22 in Sichuan
Countries: 13
Query for S:S60P: T4579A,T9208G ,T21740
Samples: 17, first collected on 2024-04-27 in Yunnan
Countries: 6
Query for 60P + H146Y + N185D: T4579A, G942A, A22115G
Samples:7
Country: Hubei

Tree:
Screenshot 2024-08-03 alle 18 11 03
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_383e7_e50380.json?f_userOrOld=uploaded%20sample
@FedeGueli FedeGueli changed the title XDV.1 + T4579A (49seqs, 13 countries ) with a sublinege with S:S60P (17, 6 countries) XDV.1 + T4579A (66 seqs, 14 countries ) with a sublinege with S:S60P (31, 6 countries) Aug 7, 2024
@FedeGueli
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Big upload from three different regions of China 66/31

@FedeGueli FedeGueli changed the title XDV.1 + T4579A (66 seqs, 14 countries ) with a sublinege with S:S60P (31, 6 countries) XDV.1 + T4579A (66 seqs, 14 countries ) with a sublinege with S:S60P (31, 6 countries) and further S:N185D (7,Hubei) Aug 7, 2024
@FedeGueli FedeGueli changed the title XDV.1 + T4579A (66 seqs, 14 countries ) with a sublinege with S:S60P (31, 6 countries) and further S:N185D (7,Hubei) XDV.1 + T4579A (66 seqs, 14 countries ) with a sublinege with S:S60P (31, 6 countries) and further S:H146Y, S:N185D (7, Hubei) Aug 7, 2024
@FedeGueli FedeGueli changed the title XDV.1 + T4579A (66 seqs, 14 countries ) with a sublinege with S:S60P (31, 6 countries) and further S:H146Y, S:N185D (7, Hubei) XDV.1 + T4579A (68 seqs, 14 countries ) with a sublinege with S:S60P (32, 6 countries) and further S:H146Y, S:N185D (7, Hubei) Aug 8, 2024
@FedeGueli FedeGueli changed the title XDV.1 + T4579A (68 seqs, 14 countries ) with a sublinege with S:S60P (32, 6 countries) and further S:H146Y, S:N185D (7, Hubei) XDV.1 + T4579A (71 seqs, 14 countries ) with a sublinege with S:S60P (36, 6 countries) and further S:H146Y, S:N185D (7, Hubei) Aug 13, 2024
@FedeGueli
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+3 with 60P Gansu

This is really interesting cc @corneliusroemer

@xz-keg
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xz-keg commented Aug 15, 2024 •
edited by FedeGueli
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Designated XDV.1.1 for the S60P branch VIA cov-lineages/pango-designation@43d7733

@xz-keg xz-keg added this to the XDV.1.1 milestone Aug 15, 2024
FedeGueli referenced this issue in cov-lineages/pango-designation Aug 15, 2024
@corneliusroemer
Designate LF.7, LR.3, XDV.1.1-1.6
43d7733
@xz-keg xz-keg changed the title XDV.1 + T4579A (71 seqs, 14 countries ) with a sublinege with S:S60P (36, 6 countries) and further S:H146Y, S:N185D (7, Hubei) XDV.1 + T4579A , S:S60P (Designated XDV.1.1) with further S:H146Y, S:N185D (7, Hubei) Aug 15, 2024
@Memorablea
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should add "partially designated"

@FedeGueli
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i will close this for now.

@FedeGueli FedeGueli closed this as not planned Won't fix, can't repro, duplicate, stale Aug 22, 2024
@FedeGueli FedeGueli changed the title XDV.1 + T4579A , S:S60P (Designated XDV.1.1) with further S:H146Y, S:N185D (7, Hubei) XDV.1.1 ( T4579A , S:S60P) with further S:H146Y, S:N185D (20 Hubei) Sep 8, 2024
@FedeGueli
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XDV.1.1 is one of the fastest lineage circulating with a small disadvantage vs KP.3.1.1 , now the branch with 146Y and 185D reached 20. i m reopening it.

Another mini branch of XDV.1.1 has now acquired S:D420N query: G22820A , G942A,C1387T

@FedeGueli FedeGueli reopened this Sep 8, 2024
@FedeGueli FedeGueli changed the title XDV.1.1 ( T4579A , S:S60P) with further S:H146Y, S:N185D (20 Hubei) XDV.1.1 ( T4579A , S:S60P) with further S:H146Y, S:N185D (21 Hubei) Sep 17, 2024
@xz-keg xz-keg changed the title XDV.1.1 ( T4579A , S:S60P) with further S:H146Y, S:N185D (21 Hubei) XDV.1.1 ( T4579A , S:S60P) with further S:H146Y, S:N185D (24 Hubei) Sep 26, 2024
@xz-keg
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xz-keg commented Sep 26, 2024 •
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The S:H146Y,N185D branch seems to be spread all over Hubei in Xiaogan, Xiantao,Wuhan, Huangshi, Enshi, Jingzhou, Yichang, Qianjiang and Ezhou. It also spreads to Shanxi.

It shall not be a cluster, but just underrepresented due to the lack of survellience in other Chinese provinces.

@xz-keg xz-keg changed the title XDV.1.1 ( T4579A , S:S60P) with further S:H146Y, S:N185D (24 Hubei) XDV.1.1 ( T4579A , S:S60P) with further S:H146Y, S:N185D (24 Hubei Shanxi) Sep 26, 2024
@FedeGueli FedeGueli changed the title XDV.1.1 ( T4579A , S:S60P) with further S:H146Y, S:N185D (24 Hubei Shanxi) XDV.1.1 ( T4579A , S:S60P) with further S:H146Y, S:N185D (25 Hubei Shanxi) Oct 1, 2024
@FedeGueli
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+1 Hubei

@FedeGueli FedeGueli changed the title XDV.1.1 ( T4579A , S:S60P) with further S:H146Y, S:N185D (25 Hubei Shanxi) XDV.1.1 ( T4579A , S:S60P) with further S:H146Y, S:N185D (26 Hubei Shanxi) Oct 10, 2024
@FedeGueli FedeGueli changed the title XDV.1.1 ( T4579A , S:S60P) with further S:H146Y, S:N185D (26 Hubei Shanxi) XDV.1.1 ( T4579A , S:S60P) with further S:H146Y, S:N185D (26 Hubei Shanxi Hong Kong) Oct 10, 2024
@FedeGueli
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+1 HK

@FedeGueli FedeGueli changed the title XDV.1.1 ( T4579A , S:S60P) with further S:H146Y, S:N185D (26 Hubei Shanxi Hong Kong) XDV.1.1 ( T4579A , S:S60P) with further S:H146Y, S:N185D (28 Hubei Shanxi Hong Kong) Oct 18, 2024
@FedeGueli
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no chance to compete closing this

@FedeGueli FedeGueli closed this as not planned Won't fix, can't repro, duplicate, stale Oct 28, 2024
@xz-keg
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xz-keg commented Nov 4, 2024

+1 Taiwan

@xz-keg xz-keg changed the title XDV.1.1 ( T4579A , S:S60P) with further S:H146Y, S:N185D (28 Hubei Shanxi Hong Kong) XDV.1.1 ( T4579A , S:S60P) with further S:H146Y, S:N185D (29 Taiwan Hubei Shanxi Hong Kong) Nov 4, 2024
@FedeGueli FedeGueli reopened this Nov 4, 2024
@FedeGueli
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+1 Taiwan

super recent one, reopening for a while

@FedeGueli FedeGueli added Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. and removed Rapid review needed labels Nov 4, 2024
@FedeGueli FedeGueli changed the title XDV.1.1 ( T4579A , S:S60P) with further S:H146Y, S:N185D (29 Taiwan Hubei Shanxi Hong Kong) XDV.1.1 ( T4579A , S:S60P) with further S:H146Y, S:N185D (30 Taiwan Hubei Shanxi Hong Kong) Nov 26, 2024
@FedeGueli
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one only recent is not enough to keep this open

@FedeGueli FedeGueli closed this as not planned Won't fix, can't repro, duplicate, stale Nov 26, 2024
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Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. designated partially designated S:60 XDV
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