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Repository for suggesting new lineages that should be added to the current scheme
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XDT: BA.2.86.4/GK.1 recombinant from Ireland, England and Scotland, 28 samples #2485

Closed JosetteSchoenma closed 5 months ago

JosetteSchoenma commented 5 months ago

Originally proposed by @DeepakPhuyal, see https://github.com/sars-cov-2-variants/lineage-proposals/issues/1183

Description:BA.2.86.4/GK.1 recombinant, First and biggest part (incl. from Spike) from BA.2.86.4 Private mutations: Really private:C1601T, T4654C, T7633C, C9661T and A19326G (thanks @Over-There-Is ) From BA.2.86.4: T5767C, A8633G From GK.1: T25496C, G27014A Breakpoint: between nucleotide 23673 and 24378 (Spike 704 and 939) Earliest sequence: 2023-11-13 from Ireland Most recent sequence: 2024-01-22 from England Countries circulating: Ireland 20, England 7, Scotland 1 GISAID query: A18492G, C23604G, A25045G, C25658T or C897A, A7842G, C1601T, A8633G found by @aviczhl2 CovSpectrum query: https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?nucMutations=C25658T&pangoLineage=BA.2.86.4*& Usher tree: image Nextclade: image Nextclade comparison: image

Note: I recommend designating this one, since right now half of the BA.2.86.4 sequences found are actually this recombinant. Plus, BA.2.86.4 seems to have stopped growing, while this recombinant has not. image

JosetteSchoenma commented 5 months ago

EPI_ISL_18729417 EPI_ISL_18521215 EPI_ISL_18636423 EPI_ISL_18636413 EPI_ISL_18636425 EPI_ISL_18636426 EPI_ISL_18722271 EPI_ISL_18722272 EPI_ISL_18722273 EPI_ISL_18722278 EPI_ISL_18722281 EPI_ISL_18737403 EPI_ISL_18754827 EPI_ISL_18737405 EPI_ISL_18763509 EPI_ISL_18815885 EPI_ISL_18784536 EPI_ISL_18784537 EPI_ISL_18800867 EPI_ISL_18822220 EPI_ISL_18822217 EPI_ISL_18815827 EPI_ISL_18822222 EPI_ISL_18822230 EPI_ISL_18822231 EPI_ISL_18832275 EPI_ISL_18854665 EPI_ISL_18839063

aviczhl2 commented 5 months ago

35 now. It is not slow.

FedeGueli commented 5 months ago

ping @corneliusroemer this should be designated. again we see BA.2.86 re - gaining some fitness via recombination with FLip lineages , i think it is the third with this trend.

JosetteSchoenma commented 5 months ago

XDT

Over-There-Is commented 5 months ago

And G29778A is also inherited from that GK.1 branch.

JosetteSchoenma commented 5 months ago

And G29778A is also inherited from that GK.1 branch.

I am not sure about that. Almost half of the samples do not have it. And I believe the matching GK.1's do not have it either, but I should check that further.