KP.3.3+Orf1b:A1603S+Orf10 frameshift, S:F59S(184 seqs, 12 countries, 13% South Korea 5% New Zealand)

[xz-keg]

From https://github.com/sars-cov-2-variants/lineage-proposals/issues/1919

KP.3.3+G18274T(Orf1b:A1603S)+del29581(Orf10 frameshift)+T21738C(S:F59S)

GISAID query: G18274T,T21738C,G28884C No. of seqs: 35(USA 4(1 from South Korea 2 from China 1 from France) New Zealand 2 South Korea 29)

First: EPI_ISL_19215354, USA from France,2024-6-11 Latest: EPI_ISL_19362989, New Zealand, 2024-8-14

usher

[Over-There-Is]

All with del29581(Orf10:8fs), seems coming before Orf1b:A1603S and S:F59S @ryhisner

[Over-There-Is]

ATG GGC TAT ATA AAC GTT TTC GC-T TTC CGT TTA CGA TAT ATA GTC TAC TCT TGT GCA GAA TGA Original Orf10: MGYINVFAFPFTIYSLLLCRMNSRNYIAQVDVVNFNLT (38 aa) Shifted Orf10: MGYINVFAFRLRYVYSCAE(19aa)

[FedeGueli]

interestingly it could be creating also an Orf10b from Orf10:D31Mbut the TRS doesnt seem to be there.

[FedeGueli]

51 Scotland

[xz-keg]

52, Japan

[FedeGueli]

73 after a South Korean batch

[xz-keg]

84, Australia

[FedeGueli]

97

[xz-keg]

129, Argentina, Netherlands, Thailand

[FedeGueli]

13% in South Korea after September 15 , 5% in NZL

[FedeGueli]

133

[FedeGueli]

157 now with SK Jap Aus NZL as places of the most recent samples

[FedeGueli]

@corneliusroemer i suggest to designate this one not too fast but significant in eastern Asia and Oceania https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nextcladePangoLineage=KP.3.1.1*&nucMutations1=G18274T%2CT21738C%2CG28884C&analysisMode=CompareToBaseline&

[DailyCovidCases]

@corneliusroemer This branch is worth designation now

[FedeGueli]

178

[xz-keg]

184, Sweden

[FedeGueli]

One from Sweden found with T23943C, T27910C ,C3602T has also S:T22N and S:I794T

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_test_41cad_211200.json?c=userOrOld&label=id:node_7251780

[Over-There-Is]

186