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New XBB.1.5.57 + N:S194P sublineage with S:F456L appeared in Spain (14 sequences ) #10

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FedeGueli opened this issue May 6, 2023 · 4 comments
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Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. Convergent evolution Lineages with convergent mutations S:456

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@FedeGueli
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FedeGueli commented May 6, 2023

I mentioned this one briefly in the main pango github page : cov-lineages/pango-designation#1949 ith @krosa1910, but it has grown further since so a pre proposal is deserved:

Def muts: XBB.1.5.57 + A18333G, N_S194P (T28853C) >> C26681T > C1594T > Orf1a:L2620I (C8123A) >Orf1a:G934S (G3065A) > C1853T, S:F456L (T22928C)

Gisaid Query : N_S194P, Spike_F456L

Sequences: EPI_ISL_17469836, EPI_ISL_17469840, EPI_ISL_17504402,
EPI_ISL_17504404-17504406, EPI_ISL_17505609, EPI_ISL_17505611,
EPI_ISL_17540248, EPI_ISL_17597796, EPI_ISL_17597801,

Tree:
Schermata 2023-05-06 alle 19 39 08

Schermata 2023-05-06 alle 19 39 27

Schermata 2023-05-06 alle 19 39 46

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_395c0_68f9e0.json?c=gt-S_456&label=id:node_5921924

Note that XBB.1.5.57 is in the pre T17124C branch of XBB.1.5 and it is likely the parental lineage of XBL

@krosa1910
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Is this the new platform to submit issues?
If so could someone help relocate my issue 1984 in the original respitory here?

@FedeGueli
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hi @krosa1910 this repo is for very small, uncertain, low priority or artefact dubious lineages or for discussions on everything is linked tona lineage/mutation spotted.

This helps to keep the designation work lighter.
Obviously if something is growing and will be highlighted by the community that will be open in the main page by the author and closed here.
It is like a two tiers system.

Just copy and paste here the link to the issue in the main pango github. and the title..

This is for lineages with less chance to be fast designated , or without spike mutations or without already known significant mutation or alteady clear growth (for an example : a small.intetesting lineage from a very slow sequencer countr

@FedeGueli FedeGueli added Convergent evolution Lineages with convergent mutations S:456 labels May 7, 2023
@FedeGueli FedeGueli changed the title New XBB.1.5.57 + N:S194P sublineage with S:F456L appeared in Spain (11 sequences all from April ahead) New XBB.1.5.57 + N:S194P sublineage with S:F456L appeared in Spain (12 sequences all from April ahead) May 12, 2023
@FedeGueli
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No new sequences as today. ill keep this open till next week

@FedeGueli FedeGueli added the Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. label May 17, 2023
@FedeGueli
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Closing this for now

@FedeGueli FedeGueli closed this as not planned Won't fix, can't repro, duplicate, stale May 23, 2023
@FedeGueli FedeGueli changed the title New XBB.1.5.57 + N:S194P sublineage with S:F456L appeared in Spain (12 sequences all from April ahead) New XBB.1.5.57 + N:S194P sublineage with S:F456L appeared in Spain (14 sequences ) Jun 26, 2023
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