Lineages with S:403K to watch for growth

[corneliusroemer]

Looked at recent lineages with S:403K that may be worth designating. All undesignated ones were a bit small, but a few should be worth tracking:

• XBF.9 (4, England/Wales)
• XBB.2 (4, Spain, with 428Y, 484V, and 1159R)
• ~XBB.1.9 (8, Indonesia/Poland/Israel, with 570T)~ designated XBB.1.9.6
• ~XBB.1.5 (6, South Africa, with 140I, 584F)~ designated XBB.1.5.53
• CH.1.1.1 (10, England/Slovenia)
• CH.1.1 (40, Wales, with 1263L)
• CM.8.1 (10, Utah)

Feel free to comment with queries/trees for these, I don't have the time right now to create them but the list above should be a good start for what to watch.

[FedeGueli]

The CH.1.1 from Wales has been proposed in https://github.com/cov-lineages/pango-designation/issues/1812 Both XBB.1.9.6 and XBB.1.5.53 were proposed i have added the related issues to the commits. We were tracking since some weeks the CM.8.1 (Now Proposed in https://github.com/cov-lineages/pango-designation/issues/2075 )waiting for it to show out of Utah , but this still didnt happen. There were another XBB.1.9.1+403K but went stale (#1790) and also https://github.com/cov-lineages/pango-designation/issues/1791 from Himachal Pradesh likely gone extincted.

[Memorablea]

I suggest continuing to track sequences from the state of Himachal Pradesh , as we have already seen too many Indian Powerful COVID-19 mutant

Additionally, what will be the consequences of the occurrence of S: 403K?

[FedeGueli]

I suggest continuing to track sequences from the state of Himachal Pradesh , as we have already seen too many Indian Powerful COVID-19 mutant

Additionally, what will be the consequences of the occurrence of S: 403K?

I keep tracking also closed issues, even if with a slower rythm. S:403K is known to improve Ace2 binding.

[oobb45729]

There's one recently paper about R403K that gives results that are somewhat different from https://jbloomlab.github.io/SARS-CoV-2-RBD_DMS_Omicron/RBD-heatmaps/. from https://www.biorxiv.org/content/10.1101/2023.03.22.533805v1.full

It claims that R403K, R346T, K356T improves ACE2 affinity at a similar level on BA.2.75. For DS.1, R403K is not enough to make up for the ACE2 affinity loss from F486S.

[FedeGueli]

I m noticing the combo S:R403K, S:A344T popping up in different lineage. it was in one sequence of that undersampled now closed issue (#1791) in HP,India . wondering if it made it through recombining or just maybe a good combo for some unknown reason

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice4_genome_8d33_c186b0.json?c=gt-S_344,403&f_userOrOld=uploaded%20sample

Now all designated EG.9.1 EG.10.1 EG.10 EG.9

[FedeGueli]

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice7_genome_8d33_c186b0.json?label=id:node_6425143

@corneliusroemer the XBF.9 + S:R403K + S:D843G went on growing reaching 15 sequences mainly from its Welsh branch that had further acquired Orf3a:P262L and Orf10:Q29* , should i propose in the preprosal page or will you procede to direct designation?

13 seqs as 28/06 died off likely

[FedeGueli]

There is a quite interesting XBB.1 that gained S:R403K along with two other spike mutations and an orf8 mutation, it likely emerged in malaysia but has been exported then in czechia and more recently in Italy and England.

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice11_genome_4065_81c40.json?c=userOrOld&label=id:node_6687743

defining mutations: XBB.1 >> > C541T > C15951T > C8905T, S:R403K (G22770A), S:E619A)A23418C, S:N824S (A24033G), Orf8:Q27K (C27972A)

Gisaid query: G22770A,A23418C,A24033G,C27972A finds just 2 out of 3 sequences.

[FedeGueli]

NOW EG.7

Instead i m pre proposing this one: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice2_genome_4065_81c20.json?label=id:node_6733437 https://github.com/sars-cov-2-variants/lineage-proposals/issues/56

[FedeGueli]

Here another XBB.1.9.2 plus S:R403K and this time with S:A344T : https://github.com/sars-cov-2-variants/lineage-proposals/issues/57

designated EG.10

[FedeGueli]

New one from Spain Italy France: CM.7 : https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice11_genome_26c4_11ec90.json?label=id:node_7094192

Gisaid query: G14500T, C26801T,G656A, G22770A finds 12 (28-06) cc @corneliusroemer

[FedeGueli]

Another one in DV.6 in England: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice13_genome_26c4_11ec90.json?c=gt-S_403&label=id:node_7276223

15 sequences as 28/06/2023 EDITED: Query: T9723G, T21322G ,G22770A, C29420T see : https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice2_genome_test_d51d_c43ac0.json?c=userOrOld&label=id:node_7304656

proposing it now: https://github.com/sars-cov-2-variants/lineage-proposals/issues/270

[FedeGueli]

Here another one: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice3_genome_3b90_9964b0.json?c=userOrOld&label=id:node_7237008 with 4 spike mutations: F186L, R403K, A852V, S1147L

Gisaid query: G1264A, C3276T, G8561T, A18273G

this reached 7 after one months hyatus. last sequences from France (Gironde)

[FedeGueli]

Also : https://github.com/sars-cov-2-variants/lineage-proposals/issues/205:

gisaid: G24620T,C23855A, C21411T

[FedeGueli]

also wuth S:R403T found by @josetteshoenma: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice24_genome_test_160cc_c40760.json?label=id:node_7256174

Gisaid: C11103T, G11906A, G22770C

[FedeGueli]

Another branch of FL.5 got S:R403K:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice7_genome_test_c4f4_b5af40.json?c=gt-S_403&label=id:node_6686465

gisaid: C23188T, C2137T, G22770A, C29200T seqs 3

[NkRMnZr]

a singlet from EG.5.1.1 saltation EPI_ISL_17837041 got R403S [query: A22771C, G22344T] https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1019a_e0c1c0.json?f_userOrOld=uploaded%20sample

[FedeGueli]

a singlet from EG.5.1.1 saltation EPI_ISL_17837041 got R403S [query: A22771C, G22344T] https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1019a_e0c1c0.json?f_userOrOld=uploaded%20sample

Yes thanks i m tracking that one!

[FedeGueli]

Australian saltation with 340K and 403K : query:C3984T, A5627G, C8991T, count : 2 ****

[NkRMnZr]

CH.1.1.1 + R403K seems to be quite elusive, hard to use query to catch them all. Now there's at least 16 seqs, slowly but surely accumulating, sill within UK though.

it follows CH.1.1.1 [C25721T(ORF3a:A110V) > T4402A] > G15025T(ORF1b:A520S) > G11527A > G22770A(S:R403K)

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice57_genome_2e74b_ba0880.json?f_userOrOld=uploaded%20sample

Genomes:

``` England/BRBR-32710401/2023|EPI_ISL_17350880|2023-03-24 England/BRBR-3271043E/2023|EPI_ISL_17350860|2023-03-24 England/CLIMB-CM7YF5FS/2023|EPI_ISL_17989737|2023-06-30 England/CLIMB-CM7YKN7I/2023|EPI_ISL_18015636|2023-07-09 England/CLIMB-CM7YKY1W/2023|EPI_ISL_17989777|2023-06-07 England/CLIMB-CM7YRU96/2023|EPI_ISL_18015564|2023-07-01 England/PHEC-YYE3BW5/2023|EPI_ISL_17721627|2023-05-04 England/PHEC-YYE4ZIB/2023|OY290526.1|2023-06-01 England/PHEC-YYE5Q8F/2023|EPI_ISL_17838261|2023-06-05 England/PHEC-YYE5QM7/2023|EPI_ISL_17838270|2023-05-30 England/PHEC-YYEZIM6/2023|EPI_ISL_17666189|2023-05-05 England/PHEP-YYGOY4R/2023|EPI_ISL_17299227|2023-03-13 England/PHEP-YYGTBIM/2023|EPI_ISL_17400899|2023-03-18 England/PHEP-YYGTBWP/2023|EPI_ISL_17400910|2023-03-18 Northern_Ireland/NIRE-022098/2023|EPI_ISL_17964390|2023-06-02 Scotland/SCOT-31431/2023|EPI_ISL_17884623|2023-06-09 ```

It probably have ORF1a:82-86 deletion too

[Memorablea]

EG.5+S:R403K 1 NOW

[DailyCovidCases]

This branch is dead, please close this issue