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KP.2.3 subbranch with S:del185-189(21 sequences, 3 countries) 8% in Chile in September #2003

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Over-There-Is opened this issue Sep 10, 2024 · 6 comments
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KP.2.3 subbranch with S:del185-189(21 sequences, 3 countries) 8% in Chile in September #2003

Over-There-Is opened this issue Sep 10, 2024 · 6 comments
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DeFLiRT S:S31/F32-+S:R346T+S:F456L Deletions between S:180-190 it is an umbrella that collects lineages with mutations in the S:180-190 area of the NTD Emerged in an undersampled area Actual infection toll may be much larger than number of sequences suggest High local prevalence Lineage that apparently gained high prevalence in one country or region KP.2.3 S:146 S:1104

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@Over-There-Is
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Over-There-Is commented Sep 10, 2024 •
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KP.2.3> C28714T> C18555T> G12208A> C878T, del22114-22128(S:del185-189)
Query: C878T, G12208A, C18555T

Earliest sequence: 07-15 Texas, USA PQ147847.1
Latest sequence: 08-26 Punta Arenas, Magallanes, Chile EPI_ISL_19390712
Regions detected: US 9(1 not on GISAID, 1 airport pooled), Chile 3, UK 1

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_5b00e_5a600.json?c=country&label=id:node_11644620
image

image

This lineage is found with a modified version of @aviczhl2 's tool:
https://github.com/aviczhl2/usher_analyse_tool/blob/Over-There-Is-1/analyse-modified.py
image

Sequences:
EPI_ISL_19307745, EPI_ISL_19316820, EPI_ISL_19335234,
EPI_ISL_19335490, EPI_ISL_19342392, EPI_ISL_19347439,
EPI_ISL_19349121, EPI_ISL_19349319, EPI_ISL_19349993,
EPI_ISL_19390712, EPI_ISL_19390746, EPI_ISL_19390749,
PQ147847.1
@Mydtlwn Mydtlwn mentioned this issue Sep 10, 2024
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@Over-There-Is Over-There-Is changed the title KP.2.3 subbranch with S:del185-189(12 sequences, 3 countries) KP.2.3 subbranch with S:del185-189(13 sequences, 3 countries) Sep 10, 2024
@Over-There-Is
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label:"Deletions between S:180-190" @aviczhl2 @FedeGueli

@FedeGueli FedeGueli added Deletions between S:180-190 it is an umbrella that collects lineages with mutations in the S:180-190 area of the NTD S:1104 S:146 DeFLiRT S:S31/F32-+S:R346T+S:F456L KP.2.3 labels Sep 10, 2024
@Over-There-Is Over-There-Is changed the title KP.2.3 subbranch with S:del185-189(13 sequences, 3 countries) KP.2.3 subbranch with S:del185-189(14 sequences, 3 countries) Sep 18, 2024
@FedeGueli FedeGueli changed the title KP.2.3 subbranch with S:del185-189(14 sequences, 3 countries) KP.2.3 subbranch with S:del185-189(20 sequences, 3 countries) Sep 26, 2024
@FedeGueli
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New batch of recent samples from Chile bringing the total to 20

@FedeGueli FedeGueli changed the title KP.2.3 subbranch with S:del185-189(20 sequences, 3 countries) KP.2.3 subbranch with S:del185-189(20 sequences, 3 countries) 8% in Chile in September Sep 26, 2024
@FedeGueli FedeGueli added the High local prevalence Lineage that apparently gained high prevalence in one country or region label Sep 26, 2024
@DailyCovidCases
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Currently still no new seqs

@FedeGueli
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Chile has not uploaded anything since

@FedeGueli FedeGueli added Emerged in an undersampled area Actual infection toll may be much larger than number of sequences suggest and removed Rapid review needed labels Oct 11, 2024
@DailyCovidCases
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Close this issue @Over-There-Is

@FedeGueli
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No one in the last batch from Chile

@FedeGueli FedeGueli closed this as not planned Won't fix, can't repro, duplicate, stale Nov 17, 2024
@Over-There-Is Over-There-Is changed the title KP.2.3 subbranch with S:del185-189(20 sequences, 3 countries) 8% in Chile in September KP.2.3 subbranch with S:del185-189(21 sequences, 3 countries) 8% in Chile in September Nov 23, 2024
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DeFLiRT S:S31/F32-+S:R346T+S:F456L Deletions between S:180-190 it is an umbrella that collects lineages with mutations in the S:180-190 area of the NTD Emerged in an undersampled area Actual infection toll may be much larger than number of sequences suggest High local prevalence Lineage that apparently gained high prevalence in one country or region KP.2.3 S:146 S:1104
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