KP.2.3+S:A1174V (296 seqs, >10 places) 27% in Brazil ,Sep

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From sars-cov-2-variants/lineage-proposals#1843

KP.2.3(with 31del)+C28714T+C11518T+C25083T(S:A1174V)

GISAID query: C28714T, C11518T, C25083T
No. of seqs: 104(Belgium 1 Brazil 18 Canada 3 Denmark 1 UK 8 France 8 Ireland 4 Italy 3 Japan 1 Netherlands 5 New Zealand 1 Spain 23 Sweden 4 USA 24(1 from Nether;ands 1 from Spain 2 from Japan))

First: EPI_ISL_19276081, France, 2024-5-14
Latest: EPI_ISL_19386429,Canada, 2024-8-22

9/71 in Brazil seqs from 2024/8/1

usher

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107,Chile

[FedeGueli]

ping @corneliusroemer S:A1174X (V,T) seems convergent right now for unknown reason seem to confer some additional advantage. Maybe worth designating this and see if the other will follow the path or fade away as it happens frequently

[FedeGueli]

191 now with a striking 25% in Brazil in September close to 30% in Rio after August 1,
Ping @corneliusroemer
On S:A1174X i have found some interesting references:
In this study https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10290734/ authors (Yamamoto et al) grew different variants along wioth plasma from patients with different immunity, S:A1174T has been acquired quite quickly and showed strong resistnace to vaccinated people serum.

cc @ryhisner @aviczhl2 @thomasppeacock

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49/184=27% prevalence in Brazilian Sep seqs.

[FedeGueli]

201 and apparently (and unexpectedly) competitive vs Kp.3.1.1 baseline, maybe due to high prevalence in Brazil

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232 seqs now.

[FedeGueli]

ping @corneliusroemer this needs a designation

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250, Mexico,Germany

[FedeGueli]

This is consistently slighty faster than Kp.3.1.1 baseline that for a KP.2.3 is quite a thing.

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This is consistently slighty faster than Kp.3.1.1 baseline that for a KP.2.3 is quite a thing.

I have a feeling that KP.2.3 is more advanterous in some regions than KP.3.1.1.
Recent batches from China also show a quite unexpected rise of KP.2.2 and KP.2.3 while KP.3.1.1 decays.

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267, Ukraine, Argentina, Luxembourg

[FedeGueli]

Around 20% in Brazil after September 15 sampled in 3 states and in a passenger from Brazil via GBW

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296 seqs now, also in Austria

[FedeGueli]

Designated KP.2.3.12

[Over-There-Is]

it seems there are some sequences without 11518.

[FedeGueli]

it seems there are some sequences without 11518.

yeah 382>>404 i didnt check if all of them belongs really to this but it could be.thx . Brazil prevalences seems going down to 20% after September 20 and furter down but with small sample size after Oct 1. still interesting to see how 1174X suddenly became convergent an d beneficial

[FedeGueli]

30% after October 15 in brazil

[FedeGueli]

There have been 4 independent emergence of S:R190Son KP.2.3.12 all in Paraiba Brazil
I leave it here to keep trace of them

Tree:
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_test_20323_f1c00.json?f_userOrOld=uploaded%20sample&label=id:node_7401475