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Repository for suggesting new lineages that should be added to the current scheme
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KP.3.3+Orf1b:A1603S+Orf10 frameshift, S:F59S(157 seqs, 11 countries, 13% South Korea 5% New Zealand) #2771

Open xz-keg opened 2 months ago

xz-keg commented 2 months ago

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 image

Over-There-Is commented 1 month ago

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

Over-There-Is commented 1 month ago

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 commented 1 month ago

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

FedeGueli commented 1 month ago

51 Scotland

xz-keg commented 1 month ago

52, Japan

FedeGueli commented 1 month ago

73 after a South Korean batch

xz-keg commented 4 weeks ago

84, Australia

FedeGueli commented 3 weeks ago

97

xz-keg commented 3 weeks ago

129, Argentina, Netherlands, Thailand

FedeGueli commented 2 weeks ago

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

FedeGueli commented 2 weeks ago

133

FedeGueli commented 5 days ago

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

FedeGueli commented 5 days ago

@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&