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LF.7 + Orf1a:R1225I (NSP4_R407I) + S:T572I (59, >10 places) 80% prevalence in Peru' after Dec 25, with a S:S1261P sub-branch (7, 3 Places) #2855

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FedeGueli opened this issue Jan 4, 2025 · 11 comments
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LF.7 + Orf1a:R1225I (NSP4_R407I) + S:T572I (59, >10 places) 80% prevalence in Peru' after Dec 25, with a S:S1261P sub-branch (7, 3 Places) #2855

FedeGueli opened this issue Jan 4, 2025 · 11 comments

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@FedeGueli
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FedeGueli commented Jan 4, 2025 •
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In the last few weeks side bey side to 475V emerged another strongly.convergent mutation on LF.7 backbone.
One of these branches has reached a high prevalence >50% in Peru' and surroundings in Deember

From Branch 1 of sars-cov-2-variants/lineage-proposals#2215

LF.7 >> Orf1a:R1225I (G3939T) > S:T572I (C23277T)
Query:C5239T, C7869T, G3939T,C23277T
Samples: 53
Places: Peru'(7+10GBW),NZL, NY, Germany, Italy, Colombia(GBW), Spain,US (8 States),Japan, Denmark

IDS: EPI_ISL_19484880, EPI_ISL_19589262, EPI_ISL_19608416, EPI_ISL_19622886, EPI_ISL_19624034, EPI_ISL_19624036-19624038, EPI_ISL_19624040-19624041, EPI_ISL_19624043, EPI_ISL_19636307, EPI_ISL_19639729, EPI_ISL_19643332, EPI_ISL_19644719-19644720, EPI_ISL_19644729

Sub Branches

Query for S:S1261P branch: C5239T, G3939T, T25343C
Samples: 7
Places: 3 Japan, NZL, US - 3 States

Query for S:A475V: C22986T,T6634A,C10594T
Samples: 1 FLA (2025)

Tree updated on Jan 25, 2025:
Image
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_test_2b5482_575e20.json?label=id:node_7183102
This was referenced Jan 4, 2025
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@FedeGueli FedeGueli changed the title LF.7 + Orf1a:R1225I (NSP4_R407I + S:T572I (17, 7 places) >50% in Peru' in December LF.7 + Orf1a:R1225I (NSP4_R407I + S:T572I (20, 7 places) >50% in Peru' in December Jan 8, 2025
@FedeGueli
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+3 GBW from Peru' plus NY and Utah

@FedeGueli FedeGueli mentioned this issue Jan 8, 2025
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@FedeGueli FedeGueli changed the title LF.7 + Orf1a:R1225I (NSP4_R407I + S:T572I (20, 7 places) >50% in Peru' in December LF.7 + Orf1a:R1225I (NSP4_R407I + S:T572I (20, 8 places) 60% prevalence in Peru' in December Jan 8, 2025
@FedeGueli FedeGueli changed the title LF.7 + Orf1a:R1225I (NSP4_R407I + S:T572I (20, 8 places) 60% prevalence in Peru' in December LF.7 + Orf1a:R1225I (NSP4_R407I + S:T572I (27, 8 places) 60% prevalence in Peru' in December Jan 11, 2025
@FedeGueli
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  • 7 with a bunch of GBW samples from Peru'. ping @corneliusroemer i suggest to designate this one

@FedeGueli FedeGueli changed the title LF.7 + Orf1a:R1225I (NSP4_R407I + S:T572I (27, 8 places) 60% prevalence in Peru' in December LF.7 + Orf1a:R1225I (NSP4_R407I + S:T572I (27, 8 places) 60% prevalence in Peru' in December [7/9 after Dec 15] Jan 11, 2025
@FedeGueli FedeGueli changed the title LF.7 + Orf1a:R1225I (NSP4_R407I + S:T572I (27, 8 places) 60% prevalence in Peru' in December [7/9 after Dec 15] LF.7 + Orf1a:R1225I (NSP4_R407I + S:T572I (29, 8 places) 60% prevalence in Peru' in December [7/9 after Dec 15] Jan 13, 2025
@FedeGueli
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+2 NZL

@FedeGueli FedeGueli changed the title LF.7 + Orf1a:R1225I (NSP4_R407I + S:T572I (29, 8 places) 60% prevalence in Peru' in December [7/9 after Dec 15] LF.7 + Orf1a:R1225I (NSP4_R407I + S:T572I (35, 8 places) 60% prevalence in Peru' in December [7/9 after Dec 15] Jan 14, 2025
@FedeGueli
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35 again Peru' via Gbw and three differen American States

@FedeGueli FedeGueli changed the title LF.7 + Orf1a:R1225I (NSP4_R407I + S:T572I (35, 8 places) 60% prevalence in Peru' in December [7/9 after Dec 15] LF.7 + Orf1a:R1225I (NSP4_R407I + S:T572I (35, 8 places) 60% prevalence in Peru' in December [8/10) after Dec 15] Jan 14, 2025
@FedeGueli FedeGueli changed the title LF.7 + Orf1a:R1225I (NSP4_R407I + S:T572I (35, 8 places) 60% prevalence in Peru' in December [8/10) after Dec 15] LF.7 + Orf1a:R1225I (NSP4_R407I + S:T572I (36, 9 places) 60% prevalence in Peru' in December [8/10) after Dec 15] with a singlet with S:A475V Jan 15, 2025
@FedeGueli
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36 now Denmark.
I just added a S:475V singlet from Florida collected in 2025

@FedeGueli FedeGueli mentioned this issue Jan 15, 2025
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@FedeGueli FedeGueli changed the title LF.7 + Orf1a:R1225I (NSP4_R407I + S:T572I (36, 9 places) 60% prevalence in Peru' in December [8/10) after Dec 15] with a singlet with S:A475V LF.7 + Orf1a:R1225I (NSP4_R407I + S:T572I (37, >10 places) 60% prevalence in Peru' in December [8/10) after Dec 15] with a singlet with S:A475V Jan 17, 2025
@FedeGueli
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+1 Japan

@FedeGueli FedeGueli changed the title LF.7 + Orf1a:R1225I (NSP4_R407I + S:T572I (37, >10 places) 60% prevalence in Peru' in December [8/10) after Dec 15] with a singlet with S:A475V LF.7 + Orf1a:R1225I (NSP4_R407I + S:T572I (43, >10 places) 60% prevalence in Peru' in December [8/10) after Dec 15] with a singlet with S:A475V Jan 20, 2025
@FedeGueli
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+6 : 4 Spain (Madrid 3, Sevilla 1), NY, Singapore

ping @corneliusroemer

@FedeGueli FedeGueli changed the title LF.7 + Orf1a:R1225I (NSP4_R407I + S:T572I (43, >10 places) 60% prevalence in Peru' in December [8/10) after Dec 15] with a singlet with S:A475V LF.7 + Orf1a:R1225I (NSP4_R407I + S:T572I (46, >10 places) 60% prevalence in Peru' in December [8/10) after Dec 15] with a singlet with S:A475V Jan 22, 2025
@FedeGueli
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46 with Pennsylvania, and Peru' (GBW) and Argentina (GBW)

@FedeGueli FedeGueli changed the title LF.7 + Orf1a:R1225I (NSP4_R407I + S:T572I (46, >10 places) 60% prevalence in Peru' in December [8/10) after Dec 15] with a singlet with S:A475V LF.7 + Orf1a:R1225I (NSP4_R407I + S:T572I (47, >10 places) 60% prevalence in Peru' in December [8/10) after Dec 15] with a singlet with S:A475V Jan 22, 2025
@FedeGueli
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+1 Spain

@FedeGueli FedeGueli changed the title LF.7 + Orf1a:R1225I (NSP4_R407I + S:T572I (47, >10 places) 60% prevalence in Peru' in December [8/10) after Dec 15] with a singlet with S:A475V LF.7 + Orf1a:R1225I (NSP4_R407I + S:T572I (53, >10 places) 60% prevalence in Peru' in December [8/10) after Dec 15] with a singlet with S:A475V Jan 25, 2025
@FedeGueli
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53 now with one more GBW from Peru' and two samples from California in a branch with S:S1261P that i am going to add to the proposal and further S:W1217L in just these two Californian samples.

@FedeGueli FedeGueli changed the title LF.7 + Orf1a:R1225I (NSP4_R407I + S:T572I (53, >10 places) 60% prevalence in Peru' in December [8/10) after Dec 15] with a singlet with S:A475V LF.7 + Orf1a:R1225I (NSP4_R407I + S:T572I (53, >10 places) 60% prevalence in Peru' in December [8/10) after Dec 15] with a S:S1261P sub-branch ( 7, 3 Places) Jan 25, 2025
@FedeGueli FedeGueli changed the title LF.7 + Orf1a:R1225I (NSP4_R407I + S:T572I (53, >10 places) 60% prevalence in Peru' in December [8/10) after Dec 15] with a S:S1261P sub-branch ( 7, 3 Places) LF.7 + Orf1a:R1225I (NSP4_R407I + S:T572I (53, >10 places) 80% prevalence in Peru' in December [8/10) after Dec 25] with a S:S1261P sub-branch ( 7, 3 Places) Jan 25, 2025
@FedeGueli FedeGueli changed the title LF.7 + Orf1a:R1225I (NSP4_R407I + S:T572I (53, >10 places) 80% prevalence in Peru' in December [8/10) after Dec 25] with a S:S1261P sub-branch ( 7, 3 Places) LF.7 + Orf1a:R1225I (NSP4_R407I) + S:T572I (53, >10 places) 80% prevalence in Peru' in December after Dec 25, with a S:S1261P sub-branch (7, 3 Places) Jan 25, 2025
@FedeGueli FedeGueli changed the title LF.7 + Orf1a:R1225I (NSP4_R407I) + S:T572I (53, >10 places) 80% prevalence in Peru' in December after Dec 25, with a S:S1261P sub-branch (7, 3 Places) LF.7 + Orf1a:R1225I (NSP4_R407I) + S:T572I (53, >10 places) 80% prevalence in Peru' after Dec 25, with a S:S1261P sub-branch (7, 3 Places) Jan 25, 2025
@FedeGueli FedeGueli changed the title LF.7 + Orf1a:R1225I (NSP4_R407I) + S:T572I (53, >10 places) 80% prevalence in Peru' after Dec 25, with a S:S1261P sub-branch (7, 3 Places) LF.7 + Orf1a:R1225I (NSP4_R407I) + S:T572I (56, >10 places) 80% prevalence in Peru' after Dec 25, with a S:S1261P sub-branch (7, 3 Places) Jan 27, 2025
@FedeGueli
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56 Spain

@FedeGueli FedeGueli changed the title LF.7 + Orf1a:R1225I (NSP4_R407I) + S:T572I (56, >10 places) 80% prevalence in Peru' after Dec 25, with a S:S1261P sub-branch (7, 3 Places) LF.7 + Orf1a:R1225I (NSP4_R407I) + S:T572I (57, >10 places) 80% prevalence in Peru' after Dec 25, with a S:S1261P sub-branch (7, 3 Places) Jan 28, 2025
@FedeGueli FedeGueli changed the title LF.7 + Orf1a:R1225I (NSP4_R407I) + S:T572I (57, >10 places) 80% prevalence in Peru' after Dec 25, with a S:S1261P sub-branch (7, 3 Places) LF.7 + Orf1a:R1225I (NSP4_R407I) + S:T572I (59, >10 places) 80% prevalence in Peru' after Dec 25, with a S:S1261P sub-branch (7, 3 Places) Feb 1, 2025
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