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LF.3.1 sub-branch with S:D745A ( 110 seqs, 13 countries, 4 of them in South America) #2697

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FedeGueli opened this issue Jul 23, 2024 · 12 comments
Closed

LF.3.1 sub-branch with S:D745A ( 110 seqs, 13 countries, 4 of them in South America) #2697

FedeGueli opened this issue Jul 23, 2024 · 12 comments

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@FedeGueli
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This is the sibling lineage of LF.3.1.1 previously described as Branch 2 in sars-cov-2-variants/lineage-proposals#1558.
It is still a small lineage but having been sampled in or from three South American countries this could be quite widespread
LF.3.1 [Jn.1.16.1> C5581A, C7594T, Orf1a:A4285V (C13119T) > S:V>H445P ( T>A22896C)] > S:D745A (A23796C)
Query: T22896C,A23796C,T3565C
Samples: 20
Countries : 6 (including : Peru', Colombia, Ecuador)
IDs: EPI_ISL_19101707, EPI_ISL_19135408, EPI_ISL_19136576,
EPI_ISL_19148755, EPI_ISL_19195661, EPI_ISL_19195708,
EPI_ISL_19195728, EPI_ISL_19210403, EPI_ISL_19221376,
EPI_ISL_19253469, EPI_ISL_19259535, EPI_ISL_19260233,
EPI_ISL_19262880, EPI_ISL_19262909, EPI_ISL_19269271,
EPI_ISL_19271577, EPI_ISL_19273633, EPI_ISL_19273850,
EPI_ISL_19279807, EPI_ISL_19280173

Tree:
Screenshot 2024-07-23 alle 23 52 09
Screenshot 2024-07-23 alle 23 52 36
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice18_genome_test_abdd_fdb2d0.json?label=id:node_7206124
@FedeGueli FedeGueli mentioned this issue Jul 23, 2024
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@ryhisner
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There were four sequences from New Zealand uploaded yesterday with S:D745E, and of course there's MK.1 (KP.3.1.6.1) that has S:D745G. This is looking like it could be a new site for convergent mutations.

@FedeGueli FedeGueli changed the title LF.3.1 subranch with S:D745A (20 Seqs, 6 countries, 3 of them in South America) LF.3.1 sub-branch with S:D745A (36 Seqs, 8 countries, 3 of them in South America) Aug 3, 2024
@FedeGueli
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still around now at 26

@xz-keg
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xz-keg commented Aug 22, 2024 •
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58 seqs now. It seems prevalent in Peru in Apr and May (seqs recently uploaded)

@FedeGueli FedeGueli changed the title LF.3.1 sub-branch with S:D745A (36 Seqs, 8 countries, 3 of them in South America) LF.3.1 sub-branch with S:D745A (58 Seqs, 10 countries, 3 of them in South America) Aug 22, 2024
@FedeGueli
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Thx!

@xz-keg
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xz-keg commented Aug 25, 2024

67 After adding another Peru/Chile batch

@FedeGueli FedeGueli changed the title LF.3.1 sub-branch with S:D745A (58 Seqs, 10 countries, 3 of them in South America) LF.3.1 sub-branch with S:D745A (67 Seqs, 10 countries, 3 of them in South America) Aug 25, 2024
@FedeGueli FedeGueli changed the title LF.3.1 sub-branch with S:D745A (67 Seqs, 10 countries, 3 of them in South America) LF.3.1 sub-branch with S:D745A (69 Seqs, 12 countries, 4 of them in South America) Aug 30, 2024
@FedeGueli
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69 now with samples coming from Chile, new country the 4th in South America. To be noticed thast one GBW sample is from India.

@FedeGueli FedeGueli changed the title LF.3.1 sub-branch with S:D745A (69 Seqs, 12 countries, 4 of them in South America) LF.3.1 sub-branch with S:D745A ( 78 seqs, 12 countries, 4 of them in South America) Sep 9, 2024
@FedeGueli
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78 ping @corneliusroemer this although not super fast deserves a designation due to its spread in Southern America

@FedeGueli FedeGueli changed the title LF.3.1 sub-branch with S:D745A ( 78 seqs, 12 countries, 4 of them in South America) LF.3.1 sub-branch with S:D745A ( 82 seqs, 12 countries, 4 of them in South America) Sep 11, 2024
@FedeGueli FedeGueli changed the title LF.3.1 sub-branch with S:D745A ( 82 seqs, 12 countries, 4 of them in South America) LF.3.1 sub-branch with S:D745A ( 86 seqs, 12 countries, 4 of them in South America) Sep 19, 2024
@DailyCovidCases
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Tree now:
usher
Tracked in issue2697
Screenshot (236)

@FedeGueli FedeGueli changed the title LF.3.1 sub-branch with S:D745A ( 86 seqs, 12 countries, 4 of them in South America) LF.3.1 sub-branch with S:D745A ( 91 seqs, 13 countries, 4 of them in South America) Sep 24, 2024
@FedeGueli
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91, greece

@FedeGueli FedeGueli changed the title LF.3.1 sub-branch with S:D745A ( 91 seqs, 13 countries, 4 of them in South America) LF.3.1 sub-branch with S:D745A ( 94 seqs, 13 countries, 4 of them in South America) Sep 26, 2024
@DailyCovidCases
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DailyCovidCases commented Oct 9, 2024 •
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Now 96 seqs
@FedeGueli This branch has slowed down a lot. You can close this issue now

@FedeGueli FedeGueli changed the title LF.3.1 sub-branch with S:D745A ( 94 seqs, 13 countries, 4 of them in South America) LF.3.1 sub-branch with S:D745A ( 100 seqs, 13 countries, 4 of them in South America) Oct 9, 2024
@FedeGueli FedeGueli closed this as not planned Won't fix, can't repro, duplicate, stale Oct 9, 2024
@Over-There-Is
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110 now

@FedeGueli FedeGueli changed the title LF.3.1 sub-branch with S:D745A ( 100 seqs, 13 countries, 4 of them in South America) LF.3.1 sub-branch with S:D745A ( 110 seqs, 13 countries, 4 of them in South America) Oct 14, 2024
Over-There-Is referenced this issue Oct 21, 2024
@corneliusroemer
Designate XEL (Recombinant lineage of KS.1.1.2, JN.1 (breakpoint: 229…
d247018 
…29-24820), from #2751)

Resolves #2751
@FedeGueli
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Designated LF.3.1.2 via d247018#commitcomment-148151048

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@xz-keg @ryhisner @Over-There-Is @FedeGueli @DailyCovidCases