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GK.1 sublineage with ORF3a:V50I (>160 seq in 19 countries. Maybe originated in Colombia) and a further sublineage with ORF1a:I114V and S:A475V (18 seq. Spain, Colombia, USA, Germany, Israel, Australia, Italy, Canada) #2304

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oobb45729 opened this issue Oct 1, 2023 · 3 comments
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GK.1 sublineage with ORF3a:V50I (>160 seq in 19 countries. Maybe originated in Colombia) and a further sublineage with ORF1a:I114V and S:A475V (18 seq. Spain, Colombia, USA, Germany, Israel, Australia, Italy, Canada) #2304

oobb45729 opened this issue Oct 1, 2023 · 3 comments

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@oobb45729
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Defining mutations:
GK.1 then nuc:C853T+ORF3a:V50I(G25540A)
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https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_13bdd_8bc040.json?c=gt-S_475&gmax=25384&gmin=21563&label=id:node_3914667
5
https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=nextcladePangoLineage%3AGK.1*%26ORF3a%3AV50I&
The first sequence of this sublineage is from Colombia. (Up till now, it hasn't shown up in Brazil yet.) Colombia does not upload many sequences. However, considering how widespread this lineage is, it likely did well somewhere (maybe in Colombia or nearby countries).
@oobb45729 oobb45729 mentioned this issue Oct 1, 2023
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@FedeGueli
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former cluster 9 in sars-cov-2-variants/lineage-proposals#643

@FedeGueli
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Gisaid query: A605G,C22986T finds 11 samples

@FedeGueli
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14 now

@oobb45729 oobb45729 changed the title GK.1 sublineage with ORF3a:V50I (>110 seq in 19 countries. Maybe originated in Colombia) and a further sublineage with ORF1a:I114V and S:A475V (10 seq. Spain, Colombia, USA, German, Israel, Australia) GK.1 sublineage with ORF3a:V50I (>120 seq in 19 countries. Maybe originated in Colombia) and a further sublineage with ORF1a:I114V and S:A475V (10 seq. Spain, Colombia, USA, German, Israel, Australia, Italy) Oct 7, 2023
@oobb45729 oobb45729 changed the title GK.1 sublineage with ORF3a:V50I (>120 seq in 19 countries. Maybe originated in Colombia) and a further sublineage with ORF1a:I114V and S:A475V (10 seq. Spain, Colombia, USA, German, Israel, Australia, Italy) GK.1 sublineage with ORF3a:V50I (>120 seq in 19 countries. Maybe originated in Colombia) and a further sublineage with ORF1a:I114V and S:A475V (16 seq. Spain, Colombia, USA, German, Israel, Australia, Italy) Oct 7, 2023
@oobb45729 oobb45729 changed the title GK.1 sublineage with ORF3a:V50I (>120 seq in 19 countries. Maybe originated in Colombia) and a further sublineage with ORF1a:I114V and S:A475V (16 seq. Spain, Colombia, USA, German, Israel, Australia, Italy) GK.1 sublineage with ORF3a:V50I (>120 seq in 19 countries. Maybe originated in Colombia) and a further sublineage with ORF1a:I114V and S:A475V (16 seq. Spain, Colombia, USA, Germany, Israel, Australia, Italy) Oct 7, 2023
@oobb45729 oobb45729 changed the title GK.1 sublineage with ORF3a:V50I (>120 seq in 19 countries. Maybe originated in Colombia) and a further sublineage with ORF1a:I114V and S:A475V (16 seq. Spain, Colombia, USA, Germany, Israel, Australia, Italy) GK.1 sublineage with ORF3a:V50I (>120 seq in 19 countries. Maybe originated in Colombia) and a further sublineage with ORF1a:I114V and S:A475V (18 seq. Spain, Colombia, USA, Germany, Israel, Australia, Italy, Canada) Oct 12, 2023
@oobb45729 oobb45729 changed the title GK.1 sublineage with ORF3a:V50I (>120 seq in 19 countries. Maybe originated in Colombia) and a further sublineage with ORF1a:I114V and S:A475V (18 seq. Spain, Colombia, USA, Germany, Israel, Australia, Italy, Canada) GK.1 sublineage with ORF3a:V50I (>160 seq in 19 countries. Maybe originated in Colombia) and a further sublineage with ORF1a:I114V and S:A475V (18 seq. Spain, Colombia, USA, Germany, Israel, Australia, Italy, Canada) Oct 12, 2023
Over-There-Is referenced this issue Oct 15, 2023
@corneliusroemer
Designate GK.1.6 (XBB.1.5.70.1.6, ORF3a:V50I, Colombia) with 150 seqs
ab068f9
FedeGueli referenced this issue Oct 15, 2023
@corneliusroemer
Designate GK.1.6.1 (XBB.1.5.70.1.6.1, S:A475V, ORF1a:I114V, Colombia)…
8e45078 
… with 15 seqs
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@FedeGueli @oobb45729