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KP.3.3+Orf1b:A1603S+Orf10 frameshift, S:F59S(172 seqs, 11 countries, 13% South Korea 5% New Zealand) #2771

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xz-keg opened this issue Sep 9, 2024 · 14 comments
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KP.3.3+Orf1b:A1603S+Orf10 frameshift, S:F59S(172 seqs, 11 countries, 13% South Korea 5% New Zealand) #2771

xz-keg opened this issue Sep 9, 2024 · 14 comments

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@xz-keg
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xz-keg commented Sep 9, 2024 •
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From sars-cov-2-variants/lineage-proposals#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

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@Over-There-Is
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Over-There-Is commented Sep 13, 2024 •
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All with del29581(Orf10:8fs), seems coming before Orf1b:A1603S and S:F59S @ryhisner

@Over-There-Is
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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
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interestingly it could be creating also an Orf10b from Orf10:D31Mbut the TRS doesnt seem to be there.

@xz-keg xz-keg changed the title KP.3.3+Orf1b:A1603S+S:F59S(35 seqs, 5 countries) KP.3.3+Orf1b:A1603S+Orf10 frameshift, S:F59S(35 seqs, 5 countries) Sep 13, 2024
@xz-keg xz-keg changed the title KP.3.3+Orf1b:A1603S+Orf10 frameshift, S:F59S(35 seqs, 5 countries) KP.3.3+Orf1b:A1603S+Orf10 frameshift, S:F59S(49 seqs, 5 countries) Sep 14, 2024
@FedeGueli
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51 Scotland

@xz-keg
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xz-keg commented Sep 24, 2024

52, Japan

@xz-keg xz-keg changed the title KP.3.3+Orf1b:A1603S+Orf10 frameshift, S:F59S(49 seqs, 5 countries) KP.3.3+Orf1b:A1603S+Orf10 frameshift, S:F59S(52 seqs, 6 countries) Sep 24, 2024
@FedeGueli
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73 after a South Korean batch

@xz-keg xz-keg changed the title KP.3.3+Orf1b:A1603S+Orf10 frameshift, S:F59S(52 seqs, 6 countries) KP.3.3+Orf1b:A1603S+Orf10 frameshift, S:F59S(73 seqs, 6 countries) Sep 27, 2024
@xz-keg xz-keg changed the title KP.3.3+Orf1b:A1603S+Orf10 frameshift, S:F59S(73 seqs, 6 countries) KP.3.3+Orf1b:A1603S+Orf10 frameshift, S:F59S(80 seqs, 7 countries) Oct 6, 2024
@xz-keg
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xz-keg commented Oct 11, 2024

84, Australia

@xz-keg xz-keg changed the title KP.3.3+Orf1b:A1603S+Orf10 frameshift, S:F59S(80 seqs, 7 countries) KP.3.3+Orf1b:A1603S+Orf10 frameshift, S:F59S(84 seqs, 8 countries) Oct 11, 2024
@FedeGueli
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97

@xz-keg
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xz-keg commented Oct 19, 2024

129, Argentina, Netherlands, Thailand

@xz-keg xz-keg changed the title KP.3.3+Orf1b:A1603S+Orf10 frameshift, S:F59S(84 seqs, 8 countries) KP.3.3+Orf1b:A1603S+Orf10 frameshift, S:F59S(129 seqs, 11 countries) Oct 19, 2024
@FedeGueli
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13% in South Korea after September 15 , 5% in NZL

@xz-keg xz-keg changed the title KP.3.3+Orf1b:A1603S+Orf10 frameshift, S:F59S(129 seqs, 11 countries) KP.3.3+Orf1b:A1603S+Orf10 frameshift, S:F59S(129 seqs, 11 countries, 13% South Korea 5% New Zealand) Oct 20, 2024
@FedeGueli
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133

@xz-keg xz-keg changed the title KP.3.3+Orf1b:A1603S+Orf10 frameshift, S:F59S(129 seqs, 11 countries, 13% South Korea 5% New Zealand) KP.3.3+Orf1b:A1603S+Orf10 frameshift, S:F59S(141 seqs, 11 countries, 13% South Korea 5% New Zealand) Oct 27, 2024
@xz-keg xz-keg changed the title KP.3.3+Orf1b:A1603S+Orf10 frameshift, S:F59S(141 seqs, 11 countries, 13% South Korea 5% New Zealand) KP.3.3+Orf1b:A1603S+Orf10 frameshift, S:F59S(145 seqs, 11 countries, 13% South Korea 5% New Zealand) Nov 1, 2024
@FedeGueli
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157 now with SK Jap Aus NZL as places of the most recent samples

@FedeGueli
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@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&

@xz-keg xz-keg changed the title KP.3.3+Orf1b:A1603S+Orf10 frameshift, S:F59S(145 seqs, 11 countries, 13% South Korea 5% New Zealand) KP.3.3+Orf1b:A1603S+Orf10 frameshift, S:F59S(157 seqs, 11 countries, 13% South Korea 5% New Zealand) Nov 5, 2024
@xz-keg xz-keg changed the title KP.3.3+Orf1b:A1603S+Orf10 frameshift, S:F59S(157 seqs, 11 countries, 13% South Korea 5% New Zealand) KP.3.3+Orf1b:A1603S+Orf10 frameshift, S:F59S(172 seqs, 11 countries, 13% South Korea 5% New Zealand) Nov 10, 2024
@DailyCovidCases
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@corneliusroemer This branch is worth designation now

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@xz-keg @Over-There-Is @FedeGueli @DailyCovidCases