KP.3.1.1 subbranch with S:R34G, N:S33C, Orf9b:A29I (35, Scotland)

[Over-There-Is]

This was first highlighted on X by @UseBy2022 >> https://x.com/siamosolocani/status/1834735537837478299

KP.3.1.1> C673T, C21662G(S:R34G), G28361T(=G28370T, N:GERS>G30-33C = N:S33C=N:G30C, Orf9b:MENA>M26-29I = Orf9b:A29I =Orf9b:M26I) Query: C673T, C21662G 08-11~08-27, Scotland, United Kingdom 16

Tree: (updated after the bug was resolved)

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_50279_949320.json?label=id:node_11659193

Sequences: EPI_ISL_19372191, EPI_ISL_19412375-19412376, EPI_ISL_19412378, EPI_ISL_19412380, EPI_ISL_19412409-19412413, EPI_ISL_19412416, EPI_ISL_19412420-19412421, EPI_ISL_19412426, EPI_ISL_19412446-19412447

Note that Usher Gisaid Covspectrum Nextclade read N:G30C as N:S33C so that is how it will be called here. (same for Orf9b:A26I it is read as Orf9b:A29I and that will be the way we will call it here)

[FedeGueli]

Please use the common reading by the tools. u can add the correspondance as additional information.

This was spotted first by UseBy2022 " Future" on Twitter/X

[FedeGueli]

Interestingly BF.7 has S:N33F so it could be relevant

[FedeGueli]

Misplacement has been already highlighted to @angiehinrichs .

[Over-There-Is]

In my understanding, N:31-33ERS and Orf9b:27-30ENA are already deleted.

[FedeGueli]

In my understanding, N:31-33ERS and Orf9b:27-30ENA are already deleted.

it doesnt matter here what it matters is the comprehension and replicability, with N:G30C you dont get anything in any tool. So it is useless using it while interesting to highlight. using the same logic you should rename all the spike due to the 24-26 deletion, would it make any sense? quick answer no.

[FedeGueli]

Misplacement solved thx @angiehinrichs !

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_50279_949320.json?label=id:node_11659193

[FedeGueli]

it is massive but in Scotland only