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MC.9+S:T76I (18 seqs, 4 countries) #1788

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xz-keg opened this issue Jul 28, 2024 · 12 comments
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MC.9+S:T76I (18 seqs, 4 countries) #1788

xz-keg opened this issue Jul 28, 2024 · 12 comments
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Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. KP.3.1.1 S:76

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@xz-keg
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xz-keg commented Jul 28, 2024 •
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KP.3.1.1+G25617T(Orf3a:K75N)+G17122T(Orf1a:A1219S)+C21789T(S:T76I)

GISAID qurry: G17122T,C21789T, G25617T
No. of seqs: 6(USA, 5 from Italy)

First: EPI_ISL_19285214, USA, 2024-7-8
Latest: EPI_ISL_19289854, USA from Italy, 2024-7-16

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@FedeGueli
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I saw that too! it should remove N74 Glycan

@ryhisner
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It's always been a deleterious mutation in the past. By far the biggest lineage with it was BA.5.5, the slowest of all BA.5* lineages.

@xz-keg xz-keg changed the title KP.3.1.1+Orf3a:K75N+Orf1a:A1219S,K2029N, S:T76I (6 seqs, 2 countries) KP.3.1.1+Orf3a:K75N+Orf1a:A1219S,K2029N, S:T76I (8 seqs, 2 countries) Aug 12, 2024
@xz-keg xz-keg changed the title KP.3.1.1+Orf3a:K75N+Orf1a:A1219S,K2029N, S:T76I (8 seqs, 2 countries) MC.9+Orf1a:K2029N, S:T76I (8 seqs, 2 countries) Aug 15, 2024
@FedeGueli
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Parent is now MC.9

FedeGueli referenced this issue in cov-lineages/pango-designation Aug 15, 2024
@corneliusroemer
Designate MC.5-11.1
610a2f5
@xz-keg xz-keg changed the title MC.9+Orf1a:K2029N, S:T76I (8 seqs, 2 countries) MC.9+Orf1a:K2029N, S:T76I (9 seqs, 2 countries) Aug 15, 2024
@xz-keg
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xz-keg commented Sep 2, 2024

No new seqs

@xz-keg xz-keg closed this as not planned Won't fix, can't repro, duplicate, stale Sep 2, 2024
@xz-keg
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xz-keg commented Sep 6, 2024

11, Sweden

@xz-keg xz-keg reopened this Sep 6, 2024
@xz-keg xz-keg changed the title MC.9+Orf1a:K2029N, S:T76I (9 seqs, 2 countries) MC.9+Orf1a:K2029N, S:T76I (11 seqs, 3 countries) Sep 6, 2024
@FedeGueli FedeGueli added the Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. label Sep 7, 2024
@FedeGueli
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There is another S:t76I sublineage under KP.3.1.1 : it got S:t76I after S:L1143F and Orf1a:T812I
Query:C2700T ,C24989T,T2230C
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_59968_96d600.json?label=id:node_7024542
Screenshot 2024-09-17 alle 13 57 17

very recent but just a Canadian cluster i suppose.

@xz-keg xz-keg changed the title MC.9+Orf1a:K2029N, S:T76I (11 seqs, 3 countries) MC.9+Orf1a:K2029N, S:T76I (12 seqs, 3 countries) Sep 22, 2024
@xz-keg
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xz-keg commented Sep 27, 2024

15, Spain

@xz-keg xz-keg changed the title MC.9+Orf1a:K2029N, S:T76I (12 seqs, 3 countries) MC.9+Orf1a:K2029N, S:T76I (15 seqs, 4 countries) Sep 27, 2024
@FedeGueli
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No chance to compete better closing this

@FedeGueli
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no recent samples closing it

@FedeGueli FedeGueli closed this as not planned Won't fix, can't repro, duplicate, stale Sep 30, 2024
@Over-There-Is
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some has no K2029N.

@Over-There-Is
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18 now

@xz-keg xz-keg changed the title MC.9+Orf1a:K2029N, S:T76I (15 seqs, 4 countries) MC.9+Orf1a:K2029N, S:T76I (16 seqs, 4 countries) Oct 14, 2024
@FedeGueli FedeGueli changed the title MC.9+Orf1a:K2029N, S:T76I (16 seqs, 4 countries) MC.9+Orf1a:K2029N, S:T76I (18 seqs, 4 countries) Oct 14, 2024
@FedeGueli
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dead

@xz-keg xz-keg changed the title MC.9+Orf1a:K2029N, S:T76I (18 seqs, 4 countries) MC.9+S:T76I (18 seqs, 4 countries) Oct 14, 2024
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Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. KP.3.1.1 S:76
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@xz-keg @ryhisner @Over-There-Is @FedeGueli