EG.5.1.1 with S:L455F on C11173T branch (708 seqs, 25 countries)

[NkRMnZr]

Taken from Branch 10 of multitask sars-cov-2-variants/lineage-proposals#537

Defining Mutations: EG.5.1.1 > C11173T > G22927T(S:L455F) Query: C11173T, G13627A, G22927T, -T10837G, -T15042C, -T22228C, -C27406T, -T28157C Earliest seq: 2023-07-16 (EPI_ISL_18049850, Qinghai, OR 2023-03-26, EPI_ISL_18398063, Veneto, Italy, probably collection date error) Latest seq: 2023-10-15 (EPI_ISL_18409252, Gansu) Sampled Countries: China (47: SC/21; LN/12; SH/12; HB/9; FJ/4; GS/2; QH/2; XJ/2; AH/1; HK/1; SX/1; YN/1), USA (16: NY/12; CA/1; CO/1; HI/1; VA:1), Singapore (14), Canada (7: AB/3; ON/3; BC), Japan (5), South Korea (5), Australia (4: NSW), Denmark (4), Sweden (3), Israel (2), Italy (2), Austria (1), France (1), Germany (1)

Genomes:

`EPI_ISL_18049850, EPI_ISL_18108872, EPI_ISL_18114762, EPI_ISL_18116311, EPI_ISL_18133939, EPI_ISL_18133980, EPI_ISL_18138175, EPI_ISL_18146058, EPI_ISL_18166202, EPI_ISL_18208650, EPI_ISL_18213226, EPI_ISL_18243494, EPI_ISL_18245834, EPI_ISL_18246273, EPI_ISL_18246285-18246286, EPI_ISL_18246309, EPI_ISL_18254261, EPI_ISL_18261471-18261472, EPI_ISL_18261475, EPI_ISL_18261479, EPI_ISL_18268212, EPI_ISL_18268407, EPI_ISL_18273291, EPI_ISL_18277184, EPI_ISL_18284700, EPI_ISL_18284819, EPI_ISL_18284933, EPI_ISL_18284992, EPI_ISL_18285023, EPI_ISL_18285060, EPI_ISL_18292657, EPI_ISL_18303672, EPI_ISL_18303890, EPI_ISL_18304224, EPI_ISL_18304268, EPI_ISL_18304968, EPI_ISL_18306651, EPI_ISL_18306986, EPI_ISL_18307196, EPI_ISL_18308182, EPI_ISL_18313142, EPI_ISL_18313204, EPI_ISL_18313516, EPI_ISL_18320692, EPI_ISL_18320708, EPI_ISL_18320715-18320716, EPI_ISL_18320766, EPI_ISL_18320812, EPI_ISL_18320839, EPI_ISL_18320847, EPI_ISL_18324953, EPI_ISL_18330207, EPI_ISL_18330267, EPI_ISL_18330274, EPI_ISL_18330287, EPI_ISL_18331069, EPI_ISL_18345058, EPI_ISL_18345633, EPI_ISL_18345667, EPI_ISL_18346284, EPI_ISL_18346390, EPI_ISL_18346567, EPI_ISL_18354959, EPI_ISL_18356763, EPI_ISL_18359746, EPI_ISL_18359823, EPI_ISL_18359866, EPI_ISL_18360499, EPI_ISL_18360553, EPI_ISL_18361709, EPI_ISL_18361920, EPI_ISL_18361963, EPI_ISL_18362021, EPI_ISL_18362089, EPI_ISL_18363972, EPI_ISL_18365935, EPI_ISL_18366368, EPI_ISL_18375870, EPI_ISL_18376451, EPI_ISL_18376476-18376477, EPI_ISL_18376491, EPI_ISL_18376500, EPI_ISL_18376539, EPI_ISL_18376546, EPI_ISL_18376562, EPI_ISL_18376637, EPI_ISL_18378092, EPI_ISL_18381319, EPI_ISL_18382192, EPI_ISL_18382557, EPI_ISL_18383822, EPI_ISL_18388934, EPI_ISL_18388939, EPI_ISL_18388947, EPI_ISL_18389049, EPI_ISL_18389217, EPI_ISL_18389272, EPI_ISL_18389442, EPI_ISL_18389499, EPI_ISL_18389623, EPI_ISL_18391198, EPI_ISL_18393878, EPI_ISL_18393880, EPI_ISL_18393894, EPI_ISL_18397233, EPI_ISL_18397369, EPI_ISL_18397511, EPI_ISL_18397636, EPI_ISL_18397640, EPI_ISL_18398063, EPI_ISL_18401943, EPI_ISL_18401958, EPI_ISL_18402558, EPI_ISL_18404379, EPI_ISL_18405125, EPI_ISL_18406328, EPI_ISL_18408840, EPI_ISL_18409093, EPI_ISL_18409235, EPI_ISL_18409245, EPI_ISL_18409252, EPI_ISL_18409269, EPI_ISL_18409295, EPI_ISL_18409297-18409298, EPI_ISL_18410663, EPI_ISL_18411535, EPI_ISL_18411563, EPI_ISL_18411596`

UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_6d28_46d7b0.json?c=gt-S_455&gmax=25384&gmin=21563&label=id:node_6951068

view from EG.5.1.1's C11173T branch

details

[corneliusroemer]

Too small, there are already many sister lineages with this genotype, let's wait which ones become big otherwise we end up with 10s of lineages with the same genotype most of which never become big

[FedeGueli]

The sense of the proposals was exactly the opposite to designate them after being tracked briefly here to avoid a lot of confusion: @corneliusroemer we are actually tracking 63 sublineages/douplets/singlets of EG.5.1 with S:L455F 15 above 3 seqs the vast so prepare yourself it will be the mess now or one month it doesnt change the fact that an unprecedented evolution happening in China.

[FedeGueli]

@NkRMnZr please restart the tracking in the other page we will raise the threeshold to be proposed to 50 seqs , it will be reopenened here when reached.

[AngieHinrichs]

63 sublineages/douplets/singlets of EG.5.1 with S:L455F

That sounds crazy! I wonder if dropout or primer-overlap or other problems are causing that position to be inconsistently detected... that could potentially cause that kind of weirdness. I will take a closer look later.

[FedeGueli]

63 sublineages/douplets/singlets of EG.5.1 with S:L455F

That sounds crazy! I wonder if dropout or primer-overlap or other problems are causing that position to be inconsistently detected... that could potentially cause that kind of weirdness. I will take a closer look later.

i dont think so cause in 1/3 of cases they went to 3 seqs in more than half they arrived to 2. i didnt check how many are from the same lab but we have seen in the biggest ones that they expand to other areas/labs. To me is something from an evolutionary point of view very significant happening here.

[aviczhl2]

67 now. Not small.

[FedeGueli]

@corneliusroemer pls reopen this one showing further spike diversity (even if not very successful as 335F or 105F) as S:Q607R https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_2a402_e74280.json?label=id:node_3997756

[FedeGueli]

82 now

[FedeGueli]

96 now @corneliusroemer i suggest to reopem this one. although slower than Hk.3 is faster than many leading lineages so it could go on expanding: https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nextcladePangoLineage=HK.3*&nucMutations1=C11173T%2CG13627A%2CG22927T&analysisMode=CompareToBaseline&

[FedeGueli]

@corneliusroemer please reopen this one.

[Over-There-Is]

seems only 2 has A17267G(ORF1b:D1267G).

[Over-There-Is]

A7150C(Orf1a:L2295F), G28212T(~Orf8:D107Y~) branch seems recombined with FL.2.4(or FE.1?).

[FedeGueli]

seems only 2 has A17267G(ORF1b:D1267G).

Thanks for noticing @NkRMnZr please change the proposal to C11173T only. It is still Branch 10.

[NkRMnZr]

Thanks @Over-There-Is and @FedeGueli that A17267G(ORF1b:D1267G) seems to be artifactual and UShER already removes that, it is now EG.5.1.1 > C11173T > G22927T(S:L455F) and luckily it doesn't affect the query. And most importantly, the "tasklist" on sars-cov-2-variants/lineage-proposals#537 already fixed it.

There is only a doublet with A17267G(ORF1b:D1267G) under this branch.

Completely overhauled the proposal with updates.

[FedeGueli]

Thank you @NkRMnZr , all credit to @Over-There-Is i only rechecked if it has been merged to other trees in the meanwhile.

[Over-There-Is]

328, UK, Brunei, Costa Rica

[FedeGueli]

495

[Over-There-Is]

565?

[FedeGueli]

@corneliusroemer this is quite big a pity to leave it out from a designation, not urgent nor important but still...

[aviczhl2]

668 seqs now. @corneliusroemer