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Repository for suggesting new lineages that should be added to the current scheme
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KP.2.3+S:A1174V (296 seqs, >10 places) 27% in Brazil ,Sep #2765

Closed xz-keg closed 1 week ago

xz-keg commented 1 month ago

From https://github.com/sars-cov-2-variants/lineage-proposals/issues/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 image

xz-keg commented 1 month ago

107,Chile

FedeGueli commented 1 month ago

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 commented 1 month ago

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

xz-keg commented 1 month ago

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

FedeGueli commented 1 month ago

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

xz-keg commented 4 weeks ago

232 seqs now.

FedeGueli commented 3 weeks ago

ping @corneliusroemer this needs a designation

xz-keg commented 3 weeks ago

250, Mexico,Germany

FedeGueli commented 2 weeks ago

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

xz-keg commented 2 weeks ago

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.

xz-keg commented 2 weeks ago

267, Ukraine, Argentina, Luxembourg

FedeGueli commented 2 weeks ago

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

xz-keg commented 1 week ago

296 seqs now, also in Austria

FedeGueli commented 1 week ago

Designated KP.2.3.12