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FL.1 with ORF1a:T2300I (nsp3_T1482I), ORF1a:K4348R (nsp10_K95R), S:T478R and S:P521T (48 seqs, 14 countries) around 3% in Russia #1058

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NkRMnZr opened this issue Nov 5, 2023 · 5 comments
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FL.1 with ORF1a:T2300I (nsp3_T1482I), ORF1a:K4348R (nsp10_K95R), S:T478R and S:P521T (48 seqs, 14 countries) around 3% in Russia #1058

NkRMnZr opened this issue Nov 5, 2023 · 5 comments
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designated Emerged in an undersampled area Actual infection toll may be much larger than number of sequences suggest ORF9b S:478 S:521
Milestone
FL.1.8

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@NkRMnZr
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NkRMnZr commented Nov 5, 2023

Defining Mutations: FL.1 > C7164T(ORF1a:T2300I), A13308G(ORF1a:K4348R), C14877T > C22995G(S:T478R), C23123A(S:P521T) > G5917A, A26544G(M:I8V)
Query: C7164T, A13308G, C22995G
Earliest seq: 2023-08-02 (EPI_ISL_18129436, Wisconsin, USA)
Latest seq: 2023-10-29 (EPI_ISL_18464822, Israel)
Sampled Countries: Russia (10), UK (5: WS/3; EN/2), Israel (4), Netherlands (3), USA (3), Switzerland (2), Denmark (1), Japan (1), Kazakhstan (1)

Genomes:

EPI_ISL_18129436, EPI_ISL_18238370, EPI_ISL_18246964, EPI_ISL_18276299, EPI_ISL_18300085, EPI_ISL_18331416, EPI_ISL_18339107, EPI_ISL_18340038, EPI_ISL_18356282, EPI_ISL_18360490, EPI_ISL_18411854, EPI_ISL_18416719-18416720, EPI_ISL_18417199, EPI_ISL_18417425, EPI_ISL_18417580, EPI_ISL_18417602, EPI_ISL_18417629, EPI_ISL_18417689-18417690, EPI_ISL_18419982, EPI_ISL_18421296, EPI_ISL_18429135, EPI_ISL_18440409, EPI_ISL_18440434, EPI_ISL_18444569, EPI_ISL_18450591, EPI_ISL_18451030, EPI_ISL_18455020, EPI_ISL_18464822

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3c333_739010.json?label=id:node_3418797
image

Trivia:

  • Already seen a couple of recombinant with XBB.2.3* (placed at the bottom of the tree) : Russia/PRI-RII-MH145732S/2023|EPI_ISL_18417689|2023-09-14 and Russia/SPE-RII-MH145868S/2023|EPI_ISL_18416719|2023-10-03
@NkRMnZr NkRMnZr mentioned this issue Nov 5, 2023
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@FedeGueli FedeGueli added S:478 S:521 ORF9b Emerged in an undersampled area Actual infection toll may be much larger than number of sequences suggest labels Nov 6, 2023
@FedeGueli FedeGueli changed the title FL.1 with ORF1a:T2300I (nsp3_T1482I), ORF1a:K4348R (nsp10_K95R), S:T478R and S:P521T (30 seqs, 9 countries) FL.1 with ORF1a:T2300I (nsp3_T1482I), ORF1a:K4348R (nsp10_K95R), S:T478R and S:P521T (38 seqs, 13 countries) Nov 16, 2023
@FedeGueli
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Last Samples from Russia, Ireland, China England

@NkRMnZr
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NkRMnZr commented Dec 7, 2023

Tracking updates

11-17, 8 seqs from China, Greece, Ireland, Russia, UK: EPI_ISL_18486475, EPI_ISL_18487011, EPI_ISL_18487311, EPI_ISL_18487383, EPI_ISL_18487761, EPI_ISL_18491380, EPI_ISL_18491600, EPI_ISL_18505722
12-05, 10 seqs from Russia EPI_ISL_18559909, EPI_ISL_18561309, EPI_ISL_18561411, EPI_ISL_18561517, EPI_ISL_18579931, EPI_ISL_18579946, EPI_ISL_18579956, EPI_ISL_18580092, EPI_ISL_18580128, EPI_ISL_18580178

@NkRMnZr NkRMnZr changed the title FL.1 with ORF1a:T2300I (nsp3_T1482I), ORF1a:K4348R (nsp10_K95R), S:T478R and S:P521T (38 seqs, 13 countries) FL.1 with ORF1a:T2300I (nsp3_T1482I), ORF1a:K4348R (nsp10_K95R), S:T478R and S:P521T (48 seqs, 14 countries) Dec 7, 2023
@FedeGueli FedeGueli changed the title FL.1 with ORF1a:T2300I (nsp3_T1482I), ORF1a:K4348R (nsp10_K95R), S:T478R and S:P521T (48 seqs, 14 countries) FL.1 with ORF1a:T2300I (nsp3_T1482I), ORF1a:K4348R (nsp10_K95R), S:T478R and S:P521T (48 seqs, 14 countries) around 3% in Russia Dec 7, 2023
@FedeGueli
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please propose it.

@FedeGueli FedeGueli added the To be proposed Green light for proposal label Dec 7, 2023
@NkRMnZr NkRMnZr mentioned this issue Dec 15, 2023
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@NkRMnZr
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NkRMnZr commented Dec 15, 2023

Transferred to cov-lineages/pango-designation#2412

@NkRMnZr NkRMnZr closed this as completed Dec 15, 2023
@FedeGueli FedeGueli added designated and removed To be proposed Green light for proposal labels Dec 17, 2023
@FedeGueli FedeGueli added this to the FL.1.8 milestone Dec 17, 2023
@FedeGueli
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Designated FL.18 via cov-lineages/pango-designation@b89aa1c

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