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XBB.1.5 sublineage with S:N978S - 378 sequences mainly in North America #1699

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FedeGueli opened this issue Feb 26, 2023 · 4 comments
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XBB proposed sublineage of XBB

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@FedeGueli
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FedeGueli commented Feb 26, 2023

Starting to propose some of the biggest lineage with spike mutations detected in #1510

First i want to propose S:N978S
It is accumulating sequences sligthy faster than XBB.1.5 meaning it can compete with its fastest sublineage.
Schermata 2023-02-26 alle 11 50 16

https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?nextcladePangoLineage=XBB.1.5*&aaMutations1=S%3AN978S&nextcladePangoLineage1=XBB.1.5*&analysisMode=CompareToBaseline&
And this is clearer looking at Us sequences only
Schermata 2023-02-26 alle 11 50 56

Defining mutations: XBB.1.5 > > S:N978S (A24495G) it represents a branch stemming out directly from the XBB.1.5 politomy so this is one more reason to designate it.

Looking at Usher tree is easy to spot a branch with S:D198G but it seems slower than the main lineage
Schermata 2023-02-26 alle 11 54 18
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_13548_b1f810.json?c=userOrOld&label=id:node_7665336

Gisaid Query: A24495G,T17124C,T23018C

Sequences : 160

Expand for EPI_ISLs EPI_ISL_16307277, EPI_ISL_16307699, EPI_ISL_16322834, EPI_ISL_16363920, EPI_ISL_16398754, EPI_ISL_16416180, EPI_ISL_16479076, EPI_ISL_16533535, EPI_ISL_16533542, EPI_ISL_16533549, EPI_ISL_16629155, EPI_ISL_16641390, EPI_ISL_16650623, EPI_ISL_16652310, EPI_ISL_16654157, EPI_ISL_16659558, EPI_ISL_16663083, EPI_ISL_16664348, EPI_ISL_16664593, EPI_ISL_16664754, EPI_ISL_16664934, EPI_ISL_16665408, EPI_ISL_16665763, EPI_ISL_16667917, EPI_ISL_16668422-16668423, EPI_ISL_16670266, EPI_ISL_16682101, EPI_ISL_16709857, EPI_ISL_16710980, EPI_ISL_16729557, EPI_ISL_16729749, EPI_ISL_16735387, EPI_ISL_16748220, EPI_ISL_16752332, EPI_ISL_16753380, EPI_ISL_16757046, EPI_ISL_16762901, EPI_ISL_16817673, EPI_ISL_16819209-16819210, EPI_ISL_16824034, EPI_ISL_16835085, EPI_ISL_16835121, EPI_ISL_16835222, EPI_ISL_16836016, EPI_ISL_16836142, EPI_ISL_16838754-16838755, EPI_ISL_16850903, EPI_ISL_16851014, EPI_ISL_16851032, EPI_ISL_16859458, EPI_ISL_16859645, EPI_ISL_16869693, EPI_ISL_16869791, EPI_ISL_16869821, EPI_ISL_16889474, EPI_ISL_16891148, EPI_ISL_16892984, EPI_ISL_16893455, EPI_ISL_16894051, EPI_ISL_16894057, EPI_ISL_16894067, EPI_ISL_16894072, EPI_ISL_16894074, EPI_ISL_16894100, EPI_ISL_16896068, EPI_ISL_16896126, EPI_ISL_16906511, EPI_ISL_16906718, EPI_ISL_16906926, EPI_ISL_16907180, EPI_ISL_16907434, EPI_ISL_16907508, EPI_ISL_16915704, EPI_ISL_16915792-16915793, EPI_ISL_16916007, EPI_ISL_16916017, EPI_ISL_16916026, EPI_ISL_16916085, EPI_ISL_16916132, EPI_ISL_16916134, EPI_ISL_16916631, EPI_ISL_16916804, EPI_ISL_16917099, EPI_ISL_16918275, EPI_ISL_16918423, EPI_ISL_16919406, EPI_ISL_16944786, EPI_ISL_16945711, EPI_ISL_16945853, EPI_ISL_16945915, EPI_ISL_16946139, EPI_ISL_16946186, EPI_ISL_16946621, EPI_ISL_16947206, EPI_ISL_16947221, EPI_ISL_16947241, EPI_ISL_16947262, EPI_ISL_16947273, EPI_ISL_16947280, EPI_ISL_16947286, EPI_ISL_16957513, EPI_ISL_16957596, EPI_ISL_16957610, EPI_ISL_16957713, EPI_ISL_16958232, EPI_ISL_16980623, EPI_ISL_16980637, EPI_ISL_16982422, EPI_ISL_16982424, EPI_ISL_16982428, EPI_ISL_16982432, EPI_ISL_16982459, EPI_ISL_16982495, EPI_ISL_16982501, EPI_ISL_16987888, EPI_ISL_16987951, EPI_ISL_16992804, EPI_ISL_16992923, EPI_ISL_16993096, EPI_ISL_16993159, EPI_ISL_16993166, EPI_ISL_17001163, EPI_ISL_17001166, EPI_ISL_17001174, EPI_ISL_17001197, EPI_ISL_17009067, EPI_ISL_17009285, EPI_ISL_17013018, EPI_ISL_17013035, EPI_ISL_17013071, EPI_ISL_17013075, EPI_ISL_17013083, EPI_ISL_17013085, EPI_ISL_17013095, EPI_ISL_17013118, EPI_ISL_17013124, EPI_ISL_17013129, EPI_ISL_17019381, EPI_ISL_17019394, EPI_ISL_17019415, EPI_ISL_17019632, EPI_ISL_17019762, EPI_ISL_17019781, EPI_ISL_17019825, EPI_ISL_17019952, EPI_ISL_17022932, EPI_ISL_17022979, EPI_ISL_17023614, EPI_ISL_17024145, EPI_ISL_17024888, EPI_ISL_17024935-17024936, EPI_ISL_17024945, EPI_ISL_17024971, EPI_ISL_17024986, EPI_ISL_17025149
@thomasppeacock thomasppeacock added the XBB proposed sublineage of XBB label Feb 27, 2023
@FedeGueli FedeGueli changed the title XBB.1.5 sublineage with S:N978S - 160 sequences XBB.1.5 sublineage with S:N978S - 165 sequences Mar 1, 2023
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179 seqs as today

@FedeGueli FedeGueli changed the title XBB.1.5 sublineage with S:N978S - 165 sequences XBB.1.5 sublineage with S:N978S - 179 sequences Mar 4, 2023
@FedeGueli FedeGueli changed the title XBB.1.5 sublineage with S:N978S - 179 sequences XBB.1.5 sublineage with S:N978S - 228 sequences mainly in North America Mar 8, 2023
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228 sequences as today.
It seems spreading in Switzerland too.

@FedeGueli FedeGueli changed the title XBB.1.5 sublineage with S:N978S - 228 sequences mainly in North America XBB.1.5 sublineage with S:N978S - 308 sequences mainly in North America Mar 13, 2023
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308 Sequences mainly north american lineage.

@FedeGueli
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378 sequences as today

@FedeGueli FedeGueli changed the title XBB.1.5 sublineage with S:N978S - 308 sequences mainly in North America XBB.1.5 sublineage with S:N978S - 378 sequences mainly in North America Mar 19, 2023
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