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FL.13 with ORF1a:T1000I (nsp3_T182I), ORF1a:L2527M (nsp3_L1709M) and S:F456L (34 seqs, mainly in Chile - 5% prevalence, 8 countries) #692

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NkRMnZr opened this issue Aug 26, 2023 · 8 comments
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FL.13 with ORF1a:T1000I (nsp3_T182I), ORF1a:L2527M (nsp3_L1709M) and S:F456L (34 seqs, mainly in Chile - 5% prevalence, 8 countries) #692

NkRMnZr opened this issue Aug 26, 2023 · 8 comments
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designated 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 S:456
Milestone
FL.13.5

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@NkRMnZr
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NkRMnZr commented Aug 26, 2023

Defining Mutations: FL.13 > C27297T > C3264T(ORF1a:T1000I), A3754G, T4507C > C7844A(ORF1a:L2527M), T21976C, T22928C(S:F456L), C23929T
Query: C3264T, G4354A, T22928C
Earliest seq: 2023-07-26 (EPI_ISL_18137360, Hidalgo, Mexico)
Latest seq: 2023-08-15 (EPI_ISL_18124553, Ontario, Canada)
Sampled Countries: Canada (5, Ontario), Mexico (1), Singapore (1)

Genomes:

EPI_ISL_18124416-18124417, EPI_ISL_18124484, EPI_ISL_18124486, EPI_ISL_18124553, EPI_ISL_18127460, EPI_ISL_18137360

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice65_genome_8efa_9dfcf0.json?c=gt-S_456&label=id:node_6883987
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@NkRMnZr NkRMnZr mentioned this issue Aug 26, 2023
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@FedeGueli FedeGueli added S:456 Rapid review needed Emerged in an undersampled area Actual infection toll may be much larger than number of sequences suggest labels Aug 26, 2023
@NkRMnZr
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NkRMnZr commented Sep 2, 2023 •
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Tracking updates

09-02, 2 seqs from Argentina and USA: EPI_ISL_18147533, EPI_ISL_18207808
09-15, 2 seqs from Spain
09-23, 2 seqs from Spain and USA
09-27, 2 seqs from Argentina
10-03, 17 seqs from Chile, France and USA
10-08, 2 seqs from Argentina EPI_ISL_18359389, EPI_ISL_18359421

@NkRMnZr NkRMnZr changed the title FL.13 with ORF1a:T1000I (nsp3_T182I), ORF1a:L2527M (nsp3_L1709M) and S:F456L (7 seqs, Canada, Mexico and Singapore) FL.13 with ORF1a:T1000I (nsp3_T182I), ORF1a:L2527M (nsp3_L1709M) and S:F456L (9 seqs, 5 countries) Sep 2, 2023
@NkRMnZr
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NkRMnZr commented Sep 15, 2023

09-15, 2 seqs from Spain EPI_ISL_18244200, EPI_ISL_18258220

@NkRMnZr NkRMnZr changed the title FL.13 with ORF1a:T1000I (nsp3_T182I), ORF1a:L2527M (nsp3_L1709M) and S:F456L (9 seqs, 5 countries) FL.13 with ORF1a:T1000I (nsp3_T182I), ORF1a:L2527M (nsp3_L1709M) and S:F456L (11 seqs, 6 countries) Sep 15, 2023
@FedeGueli
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FedeGueli commented Sep 15, 2023 •
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adding a growth tracker : https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nextcladePangoLineage=HK.3*&nucMutations1=C3264T%2CG4354A%2CT22928C&analysisMode=CompareToBaseline&

@NkRMnZr NkRMnZr changed the title FL.13 with ORF1a:T1000I (nsp3_T182I), ORF1a:L2527M (nsp3_L1709M) and S:F456L (11 seqs, 6 countries) FL.13 with ORF1a:T1000I (nsp3_T182I), ORF1a:L2527M (nsp3_L1709M) and S:F456L (13 seqs, 6 countries) Sep 24, 2023
@NkRMnZr
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NkRMnZr commented Sep 24, 2023

09-23, 2 seqs from Spain and USA EPI_ISL_18266311, EPI_ISL_18273167

@NkRMnZr
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NkRMnZr commented Sep 27, 2023

09-27, 2 seqs from Argentina EPI_ISL_18309064, EPI_ISL_18309069

@NkRMnZr NkRMnZr changed the title FL.13 with ORF1a:T1000I (nsp3_T182I), ORF1a:L2527M (nsp3_L1709M) and S:F456L (13 seqs, 6 countries) FL.13 with ORF1a:T1000I (nsp3_T182I), ORF1a:L2527M (nsp3_L1709M) and S:F456L (15 seqs, 6 countries) Sep 27, 2023
@NkRMnZr NkRMnZr changed the title FL.13 with ORF1a:T1000I (nsp3_T182I), ORF1a:L2527M (nsp3_L1709M) and S:F456L (15 seqs, 6 countries) FL.13 with ORF1a:T1000I (nsp3_T182I), ORF1a:L2527M (nsp3_L1709M) and S:F456L (32 seqs, mainly in Chile, 8 countries) Oct 3, 2023
@NkRMnZr
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NkRMnZr commented Oct 3, 2023

10-03, 17 seqs from Chile, France and USA

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_7e2c_bdc410.json?f_userOrOld=uploaded%20sample&label=id:node_3535157
image

EPI_ISL_18321845, EPI_ISL_18326725, EPI_ISL_18334935, EPI_ISL_18334938, EPI_ISL_18334942, EPI_ISL_18334969, EPI_ISL_18334999-18335000, EPI_ISL_18335002, EPI_ISL_18335008, EPI_ISL_18335011, EPI_ISL_18335015, EPI_ISL_18335017, EPI_ISL_18335021, EPI_ISL_18335041, EPI_ISL_18335049, EPI_ISL_18335069

@FedeGueli FedeGueli changed the title FL.13 with ORF1a:T1000I (nsp3_T182I), ORF1a:L2527M (nsp3_L1709M) and S:F456L (32 seqs, mainly in Chile, 8 countries) FL.13 with ORF1a:T1000I (nsp3_T182I), ORF1a:L2527M (nsp3_L1709M) and S:F456L (32 seqs, mainly in Chile - 5% prevalence, 8 countries) Oct 3, 2023
@FedeGueli
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this seems to have a 5% of prevalence recently in Chile.

@FedeGueli FedeGueli added the High local prevalence Lineage that apparently gained high prevalence in one country or region label Oct 3, 2023
@NkRMnZr NkRMnZr changed the title FL.13 with ORF1a:T1000I (nsp3_T182I), ORF1a:L2527M (nsp3_L1709M) and S:F456L (32 seqs, mainly in Chile - 5% prevalence, 8 countries) FL.13 with ORF1a:T1000I (nsp3_T182I), ORF1a:L2527M (nsp3_L1709M) and S:F456L (34 seqs, mainly in Chile - 5% prevalence, 8 countries) Oct 15, 2023
Over-There-Is referenced this issue in cov-lineages/pango-designation Oct 15, 2023
@corneliusroemer
Designate FL.13.5 (XBB.1.9.1.13.5, S:F456L (T22928C), ORF1a:T1000I, O…
73069df 
…RF1a:L2527M, Chile/Argentina)
@FedeGueli FedeGueli added this to the FL.13.5 milestone Oct 15, 2023
@FedeGueli
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Designated FL.13.5 via cov-lineages/pango-designation@73069df

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