EG.5.1.1 with S:L455F via G22927C (171 seqs, 13 countries) #2250

NkRMnZr · 2023-09-03T11:50:12Z

Taken from Branch 5 of Multitask sars-cov-2-variants/lineage-proposals#537, another proposal to feature G22927C rather than HK.3's G22927T, after #2194

Defining Mutations: EG.5.1.1 > G22927C(S:L455F)
Query: C6541T, G22927C, -C745T, -C3653T, -C6317T, -G6320A, -C6327T, -A6659G, -T7111C, -C8074T, -G8768A, -C10702T, -C11779T, -C13968A, -T17811C, -A21137G, -T21748C, -C22482T, -C24023T, -C27741T, -G29734T
Earliest seq: 2023-07-08 (EPI_ISL_18012368, Sichuan, China)
Latest seq: 2023-08-27 (EPI_ISL_18213371, Qinghai, China)
Sampled Countries: China (9: Shanghai/5; Liaoning/1; Qinghai/1; Sichuan/1; Taiwan/1), Australia (1: Queensland), USA (1, New York)

Genomes:

EPI_ISL_18012368, EPI_ISL_18074450, EPI_ISL_18105834, EPI_ISL_18108480, EPI_ISL_18122582, EPI_ISL_18138248, EPI_ISL_18146109, EPI_ISL_18160385, EPI_ISL_18164789, EPI_ISL_18208589, EPI_ISL_18213371

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_790d_46dd70.json?f_userOrOld=uploaded%20sample&label=id:node_6947948

Trivia:

Different nuc change of S:L455F to HK.3, probably artifact, but it could also be real. G>T has higher frequency than G>C.

The text was updated successfully, but these errors were encountered:

corneliusroemer · 2023-09-04T12:49:43Z

Don't think we should create more issues with potentially artefactual mutations.

Please open one when it's clear that it isn't an artefact. This one here looks similar to the other one with mostly Shanghai sequences, very suspicious.

FedeGueli · 2023-09-04T13:20:37Z

restart tracking in the other issue pls @NkRMnZr we will repropose once 50

NkRMnZr · 2023-09-12T10:45:13Z

25 now, at least 6 countries

UShER:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_a653_3c030.json?label=id:node_6964138

NkRMnZr · 2023-09-18T09:45:38Z

NOW 62 SAMPLES , 11 COUNTRIES , DOUBLING IN 8 OR 9 DAYS AS HK.3 PING @corneliusroemer PLEASE REOPEN IT.

I forgot to update the filters to the query, should be less than that. It is still tracked and updated on original issue from the other repo.

FedeGueli · 2023-09-18T10:16:49Z

NOW 62 SAMPLES , 11 COUNTRIES , DOUBLING IN 8 OR 9 DAYS AS HK.3 PING @corneliusroemer PLEASE REOPEN IT.

I forgot to update the filters to the query, should be less than that. It is still tracked and updated on original issue from the other repo.

Thank you deleted the posts indeed

NkRMnZr · 2023-09-26T13:50:58Z

updated query, should have 68 now

UShER:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1c23a_2e02c0.json?f_userOrOld=uploaded%20sample&label=id:node_6976398

NkRMnZr · 2023-09-27T13:45:00Z

73 now with newly emerged S:F797L, S:D1153H branch, noticed by @olias120676

UShER:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1a929_430cf0.json?f_userOrOld=uploaded%20sample

now detected in 8 different countries @FedeGueli @corneliusroemer

FedeGueli · 2023-09-27T22:01:47Z

This is becoming interesting @corneliusroemer i suggest to designate the biggest among this EG.5.1+FLip lineages

FedeGueli · 2023-10-02T08:28:53Z

@corneliusroemer please reopen and designate this, important SPIKE DIVERSITY:

As you can see above a subbranch of this one accumulated: S:F797L, S:D1153H first and then splitted in two branches one with S:Q14R convergently with JG.3 (the fastest lineage) counting 3 in China and the other with a new mutation S:Q474K counting 4 seqs in Uk

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_1e22a_a7d600.json?c=userOrOld&label=id:node_3664367

This subbranch was spotted first by Dave McNally

S:473 was identified by Bloom and Dadonaite as a strong escape residue: https://x.com/jbloom_lab/status/1696727571386311023?s=20

FedeGueli · 2023-10-02T10:00:53Z

Thank you

NkRMnZr · 2023-10-04T12:16:02Z

10-04, 30 seqs from Australia, Austria, China, Finland, Japan, UK and USA

UShER:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_33332_d55d60.json?f_userOrOld=uploaded%20sample&label=id:node_3650837

EPI_ISL_18325618, EPI_ISL_18325919, EPI_ISL_18325924, EPI_ISL_18325995, EPI_ISL_18328631, EPI_ISL_18329495, EPI_ISL_18329528, EPI_ISL_18330281, EPI_ISL_18330286, EPI_ISL_18330339, EPI_ISL_18332111, EPI_ISL_18332125, EPI_ISL_18332259, EPI_ISL_18332813, EPI_ISL_18333060, EPI_ISL_18333475, EPI_ISL_18333479, EPI_ISL_18333701, EPI_ISL_18334020, EPI_ISL_18337115, EPI_ISL_18337472, EPI_ISL_18337479, EPI_ISL_18337725, EPI_ISL_18337861, EPI_ISL_18337882, EPI_ISL_18337885, EPI_ISL_18337889, EPI_ISL_18337892, EPI_ISL_18341777, EPI_ISL_18341809

NkRMnZr · 2023-10-08T16:42:31Z

10-08, 56 seqs from Australia, Canada, China, Iceland, S. Korea, New Zealand, Singapore, UK and USA

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_324d7_2d9670.json?f_userOrOld=uploaded%20sample&label=id:node_3449269

EPI_ISL_18346037, EPI_ISL_18346975, EPI_ISL_18347519, EPI_ISL_18347572, EPI_ISL_18349788, EPI_ISL_18349790, EPI_ISL_18349797, EPI_ISL_18349805, EPI_ISL_18350420, EPI_ISL_18353883, EPI_ISL_18354107, EPI_ISL_18354394, EPI_ISL_18354439, EPI_ISL_18355067-18355068, EPI_ISL_18355070, EPI_ISL_18355073, EPI_ISL_18355075-18355076, EPI_ISL_18355078-18355079, EPI_ISL_18355083-18355084, EPI_ISL_18355091, EPI_ISL_18355093, EPI_ISL_18355100, EPI_ISL_18355103, EPI_ISL_18355106-18355110, EPI_ISL_18355117-18355119, EPI_ISL_18355125, EPI_ISL_18355130, EPI_ISL_18356199, EPI_ISL_18356201, EPI_ISL_18356204, EPI_ISL_18356209, EPI_ISL_18357740, EPI_ISL_18357742, EPI_ISL_18357744-18357745, EPI_ISL_18358038, EPI_ISL_18358040-18358041, EPI_ISL_18358043, EPI_ISL_18358046, EPI_ISL_18358308, EPI_ISL_18360234, EPI_ISL_18360299, EPI_ISL_18360350

FedeGueli · 2023-10-09T09:25:52Z

This is becoming big . @corneliusroemer i suggest strongly to designate the two big FLip lineages with G22927C

FedeGueli · 2023-10-12T07:25:43Z

225 now it should be designated.

FedeGueli · 2023-10-12T07:31:37Z

@corneliusroemer here the growth advantage query : https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nextcladePangoLineage=HK.3*&nucMutations1=C6541T%2CG22927C%2C3653C%2CC6317C%2CG6320G%2CA6659A%2CT7111T%2CC8074C%2CC6327C%2CC745C%2CG8768G%2CC10702C%2CC11779C%2CC13968C%2CT17811T%2CA21137A%2CT21748T%2CC22482C%2CC24023C%2CC27741C&analysisMode=CompareToBaseline& it seems real.

FedeGueli · 2023-10-12T07:32:07Z

Look at direct comparison in Singapore: https://cov-spectrum.org/explore/Singapore/AllSamples/Past3M/variants?nextcladePangoLineage=HK.3*&nucMutations1=C6541T%2CG22927C%2C3653C%2CC6317C%2CG6320G%2CA6659A%2CT7111T%2CC8074C%2CC6327C%2CC745C%2CG8768G%2CC10702C%2CC11779C%2CC13968C%2CT17811T%2CA21137A%2CT21748T%2CC22482C%2CC24023C%2CC27741C&analysisMode=CompareToBaseline&

FedeGueli · 2023-10-12T07:41:43Z

@NkRMnZr you should add -C20132T cause there is an unrelated spanish sequence with that nuc.

corneliusroemer · 2023-10-12T08:12:13Z

Yes, I am convinced now the 22927X is real too, will designate, thanks!

…

On Thu, Oct 12, 2023, 09:31 Federico Gueli ***@***.***> wrote: @corneliusroemer <https://github.com/corneliusroemer> here the growth advantage query : https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nextcladePangoLineage=HK.3*&nucMutations1=C6541T%2CG22927C%2C3653C%2CC6317C%2CG6320G%2CA6659A%2CT7111T%2CC8074C%2CC6327C%2CC745C%2CG8768G%2CC10702C%2CC11779C%2CC13968C%2CT17811T%2CA21137A%2CT21748T%2CC22482C%2CC24023C%2CC27741C&analysisMode=CompareToBaseline& it seems real. — Reply to this email directly, view it on GitHub <#2250 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AF77AQP2AAOCJFZWYBC4RNDX66MGJANCNFSM6AAAAAA4JIKER4> . You are receiving this because you were mentioned.Message ID: ***@***.***>

…378T, A24604G)

NkRMnZr · 2023-10-13T10:14:43Z

Designated as HK.13 via 49cdcb4

NkRMnZr mentioned this issue Sep 3, 2023

Multiple EG.5.1* Lineages with S:L455F sars-cov-2-variants/lineage-proposals#537

Closed

corneliusroemer closed this as completed Sep 4, 2023

NkRMnZr changed the title ~~EG.5.1.1 with S:L455F via G22927C (11 seqs, mainly in China, 3 countries)~~ EG.5.1.1 with S:L455F via G22927C (12 seqs, China, Australia, Singapore, Canada) Sep 9, 2023

NkRMnZr changed the title ~~EG.5.1.1 with S:L455F via G22927C (12 seqs, China, Australia, Singapore, Canada)~~ EG.5.1.1 with S:L455F via G22927C (25 seqs, China, Australia, USA, Japan, Singapore, Canada) Sep 12, 2023

NkRMnZr changed the title ~~EG.5.1.1 with S:L455F via G22927C (25 seqs, China, Australia, USA, Japan, Singapore, Canada)~~ EG.5.1.1 with S:L455F via G22927C (30 seqs, China, Australia, USA, Japan, Singapore, Canada) Sep 13, 2023

NkRMnZr changed the title ~~EG.5.1.1 with S:L455F via G22927C (30 seqs, China, Australia, USA, Japan, Singapore, Canada)~~ EG.5.1.1 with S:L455F via G22927C (44 seqs, China, Australia, USA, Japan, Singapore, Canada) Sep 16, 2023

NkRMnZr changed the title ~~EG.5.1.1 with S:L455F via G22927C (44 seqs, China, Australia, USA, Japan, Singapore, Canada)~~ EG.5.1.1 with S:L455F via G22927C (51 seqs, China, Australia, USA, Japan, Singapore, Canada, UK) Sep 20, 2023

NkRMnZr changed the title ~~EG.5.1.1 with S:L455F via G22927C (51 seqs, China, Australia, USA, Japan, Singapore, Canada, UK)~~ EG.5.1.1 with S:L455F via G22927C (53 seqs, China, Australia, USA, Japan, Singapore, Canada, UK, France) Sep 23, 2023

NkRMnZr changed the title ~~EG.5.1.1 with S:L455F via G22927C (53 seqs, China, Australia, USA, Japan, Singapore, Canada, UK, France)~~ EG.5.1.1 with S:L455F via G22927C (68 seqs, China, Australia, USA, Japan, Singapore, Canada, UK, France) Sep 26, 2023

NkRMnZr changed the title ~~EG.5.1.1 with S:L455F via G22927C (68 seqs, China, Australia, USA, Japan, Singapore, Canada, UK, France)~~ EG.5.1.1 with S:L455F via G22927C (73 seqs, China, Australia, USA, Japan, Singapore, Canada, UK, France) Sep 27, 2023

NkRMnZr changed the title ~~EG.5.1.1 with S:L455F via G22927C (73 seqs, China, Australia, USA, Japan, Singapore, Canada, UK, France)~~ EG.5.1.1 with S:L455F via G22927C (85 seqs, China, Australia, USA, Japan, Singapore, Canada, UK, France) Sep 29, 2023

corneliusroemer reopened this Oct 2, 2023

NkRMnZr changed the title ~~EG.5.1.1 with S:L455F via G22927C (85 seqs, China, Australia, USA, Japan, Singapore, Canada, UK, France)~~ EG.5.1.1 with S:L455F via G22927C (115 seqs, China, Australia, USA, Japan, Singapore, Canada, UK, France, Austria, Finland) Oct 4, 2023

NkRMnZr changed the title ~~EG.5.1.1 with S:L455F via G22927C (115 seqs, China, Australia, USA, Japan, Singapore, Canada, UK, France, Austria, Finland)~~ EG.5.1.1 with S:L455F via G22927C (171 seqs, 13 countries) Oct 8, 2023

FedeGueli mentioned this issue Oct 12, 2023

HK.13.2 (S:F797L, S:D1153H) with further rare mutations: S:Q474K, ORF9b:A57V, ORF1b:Y1648C (18 seq, England, 2023-10-13) EDITED sars-cov-2-variants/lineage-proposals#943

Closed

Over-There-Is referenced this issue Oct 13, 2023

Designate HK.13 (S:L455F (G22927C), China, 250 seqs) and HK.13.1 (C13…

49cdcb4

…378T, A24604G)

NkRMnZr closed this as completed Oct 13, 2023

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EG.5.1.1 with S:L455F via G22927C (171 seqs, 13 countries) #2250

EG.5.1.1 with S:L455F via G22927C (171 seqs, 13 countries) #2250

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NkRMnZr commented Oct 13, 2023

EG.5.1.1 with S:L455F via G22927C (171 seqs, 13 countries) #2250

EG.5.1.1 with S:L455F via G22927C (171 seqs, 13 countries) #2250

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