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LF.7.3 + S:D228E ( 8 Seqs, Kenya, Canada, NY) 10% Prevalence in Kenya after Nov 15 #2386

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FedeGueli opened this issue Jan 26, 2025 · 0 comments
Open

LF.7.3 + S:D228E ( 8 Seqs, Kenya, Canada, NY) 10% Prevalence in Kenya after Nov 15 #2386

FedeGueli opened this issue Jan 26, 2025 · 0 comments
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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 LF.7 S:228

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FedeGueli commented Jan 26, 2025 •
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Just found in the last batch from Kenya, dominated by LF.7 descendants with a prevalence over 80% there, a branch with S:D228E widespread there and already exported to Canada

LF.7.3>> C22855T > Orf1a:I1398V (A4457G) > S:D228E (T22246G)
Query: A4457G,T22246G
Samples: 8
First collected on 2024-11-14 in Kenya
Places: Kenya (4) , Canada (3), NY (1)
Tree:
Image
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_test_3ed672_6bd760.json?label=id:node_7183344

In the updated version of the so called Neher-Bloom calculator S:D228E scores good:

Image
@FedeGueli FedeGueli changed the title LF.7.3 + S:D228E ( 8 Seqs, Kenya, Canada, NY) LF.7.3 + S:D228E ( 8 Seqs, Kenya, Canada, NY) 10% Prevalence in Kenya after Nov 15 Jan 26, 2025
@FedeGueli FedeGueli added Emerged in an undersampled area Actual infection toll may be much larger than number of sequences suggest LF.7 S:228 High local prevalence Lineage that apparently gained high prevalence in one country or region labels Jan 26, 2025
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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 LF.7 S:228
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