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XBB.1.9.1 with S:V6L and S:E554Q (48 seqs, 9 countries) with further sublineage got S:F456L (22 seqs, 4 countries) #719

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NkRMnZr opened this issue Aug 30, 2023 · 6 comments
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XBB.1.9.1 with S:V6L and S:E554Q (48 seqs, 9 countries) with further sublineage got S:F456L (22 seqs, 4 countries) #719

NkRMnZr opened this issue Aug 30, 2023 · 6 comments
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combo It has a couple of mutation in RBD designated S:456 S:554
Milestone
FL.32 FL.32.1

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@NkRMnZr
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NkRMnZr commented Aug 30, 2023

Defining Mutations: XBB.1.9.1 > C21952T > G21578C(S:V6L), G23222C(S:E554Q), C28657T > G7331A(ORF1a:V2356I/nsp3_V1538I)
Query: G21578C, C21952T, G23222C

Defining Mutations for Further S:F456L sub-branch: main proposal > T13339C, C19961T(ORF1b:T2165M) > T22928C(S:F456L), C25572T
Query for further S:F456L: G7331A, T13339C, T22928C

Earliest seq: 2023-04-30 (EPI_ISL_17627824, Washington, USA)
Latest seq: 2023-08-16 (EPI_ISL_18144424, New York, USA)
Sampled Countries: USA (16: NY/7; CA/4; NJ/1; TX/1; UT/1; WA/1), Australia (3), France (2), Canada (1), Greece (1), Ireland (1), Italy (1), Sweden (1)

Genomes:

EPI_ISL_17627824, EPI_ISL_17743571, EPI_ISL_17802036, EPI_ISL_17802259, EPI_ISL_17802866, EPI_ISL_17809594, EPI_ISL_17818647, EPI_ISL_17819979, EPI_ISL_17952310, EPI_ISL_17976781, EPI_ISL_18042611, EPI_ISL_18053301, EPI_ISL_18058566, EPI_ISL_18072721, EPI_ISL_18079428, EPI_ISL_18080087, EPI_ISL_18096113, EPI_ISL_18115323, EPI_ISL_18119324, EPI_ISL_18121778, EPI_ISL_18126492, EPI_ISL_18129811, EPI_ISL_18144424, EPI_ISL_18144990, EPI_ISL_18145277, EPI_ISL_18146903

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_21ad6_f75b40.json?label=id:node_6924449
details
@NkRMnZr NkRMnZr changed the title XBB.1.9.1 with S:V6L and S:E554Q (26 seqs, 8 countries) with further sublineage got S:F456L (5, 3 countries) XBB.1.9.1 with S:V6L and S:E554Q (26 seqs, 8 countries) with further sublineage got S:F456L (5 seqs, 3 countries) Aug 30, 2023
@NkRMnZr NkRMnZr mentioned this issue Aug 30, 2023
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@FedeGueli FedeGueli added S:456 S:554 Rapid review needed combo It has a couple of mutation in RBD labels Aug 30, 2023
@FedeGueli
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Thank you very good spot

@NkRMnZr
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NkRMnZr commented Sep 2, 2023 •
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Tracking updates

09-02, 2 seqs from UK and USA EPI_ISL_18207204, EPI_ISL_18209217
09-08, 9 seqs from France, Ireland, UK and USA

@NkRMnZr NkRMnZr changed the title XBB.1.9.1 with S:V6L and S:E554Q (26 seqs, 8 countries) with further sublineage got S:F456L (5 seqs, 3 countries) XBB.1.9.1 with S:V6L and S:E554Q (28 seqs, 9 countries) with further sublineage got S:F456L (6 seqs, 4 countries) Sep 2, 2023
@NkRMnZr
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NkRMnZr commented Sep 9, 2023

09-08, 9 seqs from France, Ireland, UK and USA

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_25c95_c4f210.json?f_userOrOld=uploaded%20sample&label=id:node_6935454
image

EPI_ISL_18220278, EPI_ISL_18221403, EPI_ISL_18222305, EPI_ISL_18222638, EPI_ISL_18223061, EPI_ISL_18223407, EPI_ISL_18224946, EPI_ISL_18232832, EPI_ISL_18240879

@NkRMnZr NkRMnZr changed the title XBB.1.9.1 with S:V6L and S:E554Q (28 seqs, 9 countries) with further sublineage got S:F456L (6 seqs, 4 countries) XBB.1.9.1 with S:V6L and S:E554Q (37 seqs, 9 countries) with further sublineage got S:F456L (12 seqs, 4 countries) Sep 9, 2023
@ryhisner
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ryhisner commented Sep 15, 2023 •
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Seven sequences from California today in the F456L branch, along with four from two days ago (Sept 12). All but one are from Helix, so the quality is pretty low. One of the four from Sept 12 was a US sequence with travel from Peru, so this could be circulating there.
EPI_ISL_18252054, EPI_ISL_18252688, EPI_ISL_18252710, EPI_ISL_18252809, EPI_ISL_18260388, EPI_ISL_18260548, EPI_ISL_18260652, EPI_ISL_18260811, EPI_ISL_18260833, EPI_ISL_18261260, EPI_ISL_18261327

@NkRMnZr NkRMnZr changed the title XBB.1.9.1 with S:V6L and S:E554Q (37 seqs, 9 countries) with further sublineage got S:F456L (12 seqs, 4 countries) XBB.1.9.1 with S:V6L and S:E554Q (48 seqs, 9 countries) with further sublineage got S:F456L (21 seqs, 4 countries) Sep 15, 2023
@FedeGueli
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now 22 , it seems pretty fast . please propose when it reaches 50

@FedeGueli FedeGueli changed the title XBB.1.9.1 with S:V6L and S:E554Q (48 seqs, 9 countries) with further sublineage got S:F456L (21 seqs, 4 countries) XBB.1.9.1 with S:V6L and S:E554Q (48 seqs, 9 countries) with further sublineage got S:F456L (22 seqs, 4 countries) Sep 18, 2023
Over-There-Is referenced this issue in cov-lineages/pango-designation Sep 21, 2023
@corneliusroemer
Designate FL.32 (XBB.1.9.1.32, S:E554Q, S:V6L) with 60 seqs
73afbe1
@NkRMnZr
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NkRMnZr commented Sep 22, 2023

@FedeGueli need milestone for this

@NkRMnZr NkRMnZr closed this as completed Sep 22, 2023
@FedeGueli FedeGueli added this to the FL.32 milestone Sep 22, 2023
@FedeGueli FedeGueli modified the milestones: FL.32, FL.32 FL.32.1 Sep 22, 2023
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combo It has a couple of mutation in RBD designated S:456 S:554
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@ryhisner @FedeGueli @NkRMnZr