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XBB.1.9.1 with ORF1a:E637K (Side branch of FL.15) with S:T478R and S:Q613H (87 seqs, mainly in Russia, 11 countries) #1001

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NkRMnZr opened this issue Oct 22, 2023 · 4 comments
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XBB.1.9.1 with ORF1a:E637K (Side branch of FL.15) with S:T478R and S:Q613H (87 seqs, mainly in Russia, 11 countries) #1001

NkRMnZr opened this issue Oct 22, 2023 · 4 comments
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designated Emerged in an undersampled area Actual infection toll may be much larger than number of sequences suggest S:478 S:613
Milestone
FL.38

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@NkRMnZr
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NkRMnZr commented Oct 22, 2023

Defining Mutations: XBB.1.9.1 > C28846T > G2174A(ORF1a:E637K/nsp2_E457K) > C25482T > A2821G, C14670T, C22995G(S:T478R), T23158C(S:N532), G23401T(S:Q613H)
Query: G2174A, A2821G, C14670T
Earliest seq: 2023-07-09 (EPI_ISL_18023444, Saint Petersburg, Russia)
Latest seq: 2023-10-04 (EPI_ISL_18403129, Ghent, Belgium)
Sampled Countries: Russia (37: SPE/24; TAM/9; TYU/3; MOW/1), UK (3: EN), Belgium (1), Italy (1), South Korea (1), Netherlands (1), Slovenia (1), USA (1: CA)

Genomes:

EPI_ISL_18023444, EPI_ISL_18110993, EPI_ISL_18238332, EPI_ISL_18293557, EPI_ISL_18299851, EPI_ISL_18301623, EPI_ISL_18301633, EPI_ISL_18325223, EPI_ISL_18331900, EPI_ISL_18375598, EPI_ISL_18386800, EPI_ISL_18402749, EPI_ISL_18403129, EPI_ISL_18416898, EPI_ISL_18416913, EPI_ISL_18416919, EPI_ISL_18416924, EPI_ISL_18416926, EPI_ISL_18416928, EPI_ISL_18416964, EPI_ISL_18416966-18416967, EPI_ISL_18416969-18416970, EPI_ISL_18416972, EPI_ISL_18416974-18416975, EPI_ISL_18416978, EPI_ISL_18417109, EPI_ISL_18417118, EPI_ISL_18417123-18417124, EPI_ISL_18417128, EPI_ISL_18417134, EPI_ISL_18417153, EPI_ISL_18417163, EPI_ISL_18417166, EPI_ISL_18417190, EPI_ISL_18417198, EPI_ISL_18417338, EPI_ISL_18417412, EPI_ISL_18417434-18417435, EPI_ISL_18417596, EPI_ISL_18417599, EPI_ISL_18417628

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2a62d_4c6c30.json?label=id:node_3338399

view from XBB.1.9.1's C28846T branch, the upper one with S:F456L is FL.15
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@NkRMnZr NkRMnZr mentioned this issue Oct 22, 2023
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@NkRMnZr NkRMnZr changed the title XBB.1.9.1 with ORF1a:E637K (Side branch of FL.15) with S:T478R and S:Q613H (46 seqs, mainly in Russia, countries) XBB.1.9.1 with ORF1a:E637K (Side branch of FL.15) with S:T478R and S:Q613H (46 seqs, mainly in Russia, 8 countries) Oct 23, 2023
@FedeGueli FedeGueli changed the title XBB.1.9.1 with ORF1a:E637K (Side branch of FL.15) with S:T478R and S:Q613H (46 seqs, mainly in Russia, 8 countries) XBB.1.9.1 with ORF1a:E637K (Side branch of FL.15) with S:T478R and S:Q613H (74 seqs, mainly in Russia, 10 countries) Nov 16, 2023
@FedeGueli
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2,5% in Russia at the end of October

@FedeGueli FedeGueli added the Emerged in an undersampled area Actual infection toll may be much larger than number of sequences suggest label Nov 16, 2023
@NkRMnZr NkRMnZr changed the title XBB.1.9.1 with ORF1a:E637K (Side branch of FL.15) with S:T478R and S:Q613H (74 seqs, mainly in Russia, 10 countries) XBB.1.9.1 with ORF1a:E637K (Side branch of FL.15) with S:T478R and S:Q613H (76 seqs, mainly in Russia, 11 countries) Dec 5, 2023
@NkRMnZr
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NkRMnZr commented Dec 5, 2023 •
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Tracking updates

11-17, 28 seqs from France, Israel, Russia

EPI_ISL_18417868, EPI_ISL_18486918, EPI_ISL_18486950, EPI_ISL_18486963, EPI_ISL_18486988, EPI_ISL_18487009, EPI_ISL_18487018, EPI_ISL_18487021, EPI_ISL_18487026, EPI_ISL_18487126, EPI_ISL_18487187, EPI_ISL_18487237-18487238, EPI_ISL_18487317, EPI_ISL_18487339, EPI_ISL_18487400, EPI_ISL_18487415, EPI_ISL_18487439, EPI_ISL_18487453, EPI_ISL_18487516, EPI_ISL_18487559, EPI_ISL_18487581, EPI_ISL_18487604, EPI_ISL_18487606, EPI_ISL_18487759, EPI_ISL_18487764, EPI_ISL_18487778, EPI_ISL_18499506

12-04, 8 seqs from Russia and Lithuania EPI_ISL_18561345, EPI_ISL_18579391, EPI_ISL_18580021, EPI_ISL_18580025, EPI_ISL_18580032, EPI_ISL_18580036, EPI_ISL_18580039, EPI_ISL_18580079

12-16, 5 seqs from Russia EPI_ISL_18638493, EPI_ISL_18638594, EPI_ISL_18638839, EPI_ISL_18638878, EPI_ISL_18638914

@FedeGueli
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2% in St Petersburg

@NkRMnZr NkRMnZr changed the title XBB.1.9.1 with ORF1a:E637K (Side branch of FL.15) with S:T478R and S:Q613H (76 seqs, mainly in Russia, 11 countries) XBB.1.9.1 with ORF1a:E637K (Side branch of FL.15) with S:T478R and S:Q613H (82 seqs, mainly in Russia, 11 countries) Dec 6, 2023
@NkRMnZr NkRMnZr changed the title XBB.1.9.1 with ORF1a:E637K (Side branch of FL.15) with S:T478R and S:Q613H (82 seqs, mainly in Russia, 11 countries) XBB.1.9.1 with ORF1a:E637K (Side branch of FL.15) with S:T478R and S:Q613H (87 seqs, mainly in Russia, 11 countries) Dec 17, 2023
FedeGueli referenced this issue in cov-lineages/pango-designation Dec 17, 2023
@corneliusroemer
Designate FL.38 (S:K478R, S:Q613H, C25482T, Russia)
7f94a43
@FedeGueli FedeGueli added this to the FL.38 milestone Dec 17, 2023
@FedeGueli
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Designated FL.38 via cov-lineages/pango-designation@7f94a43

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designated Emerged in an undersampled area Actual infection toll may be much larger than number of sequences suggest S:478 S:613
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