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EG.5.1.1/non-EG.5 recombinant involving S:I1114T (186 seqs, 23 countries, 181 with Flip, 3% Malaysia 3% Gansu) #2351

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xz-keg opened this issue Oct 30, 2023 · 25 comments
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EG.5.1.1/non-EG.5 recombinant involving S:I1114T (186 seqs, 23 countries, 181 with Flip, 3% Malaysia 3% Gansu) #2351

xz-keg opened this issue Oct 30, 2023 · 25 comments
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@xz-keg
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xz-keg commented Oct 30, 2023 •
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From sars-cov-2-variants/lineage-proposals#914

EG.5.1.1+T29625C(Orf10:F23S rev)+C15981T,T24903C(S:I1114T)

EG.5.1.1--anything non-EG.5
Breakpoint before 25573 and 29624, range depend on donor

T29625C(rev) from anything non-EG.5
one of C15981T,T24903C come from an EG.5.1.1 branch, the other is private.

GISAID query: C15981T,T24903C
No. of seqs: 25(UK 1 France 6 Iceland 1 Malaysia 1 Norway 1 Sweden 3 Switzerland 2 China 10)

First: EPI_ISL_18111103, Yunnan, 2023-7-30
Latest: EPI_ISL_18439950, UK, 2023-10-16

GISAID query for branch with S:L455F: C15981T,T24903C,G22927T (23 seqs)

usher
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@xz-keg
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xz-keg commented Nov 3, 2023

27, Germany

@xz-keg xz-keg changed the title EG.5.1.1 recomb involving S:I1114T(25 seqs, 8 countries, 23 with Flip) EG.5.1.1 recomb involving S:I1114T(27 seqs, 9 countries, 25 with Flip) Nov 3, 2023
@xz-keg xz-keg changed the title EG.5.1.1 recomb involving S:I1114T(27 seqs, 9 countries, 25 with Flip) EG.5.1.1 recomb involving S:I1114T(30 seqs, 9 countries, 28 with Flip) Nov 7, 2023
@xz-keg xz-keg changed the title EG.5.1.1 recomb involving S:I1114T(30 seqs, 9 countries, 28 with Flip) EG.5.1.1 recomb involving S:I1114T(31 seqs, 9 countries, 29 with Flip) Nov 11, 2023
@xz-keg
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xz-keg commented Nov 15, 2023 •
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34, Mauritius, Denmark

@xz-keg xz-keg changed the title EG.5.1.1 recomb involving S:I1114T(31 seqs, 9 countries, 29 with Flip) EG.5.1.1 recomb involving S:I1114T(34 seqs, 12 countries, 32 with Flip) Nov 15, 2023
@xz-keg xz-keg changed the title EG.5.1.1 recomb involving S:I1114T(34 seqs, 12 countries, 32 with Flip) EG.5.1.1 recomb involving S:I1114T(39 seqs, 12 countries, 37 with Flip) Nov 21, 2023
@xz-keg
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xz-keg commented Nov 21, 2023

It seems that there's 13 additional CLIMB seqs not on GISAID now.

image

@xz-keg xz-keg changed the title EG.5.1.1 recomb involving S:I1114T(39 seqs, 12 countries, 37 with Flip) EG.5.1.1 recomb involving S:I1114T(52 seqs, 12 countries, 50 with Flip) Nov 21, 2023
@xz-keg
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xz-keg commented Nov 21, 2023 •
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While losing Orf10:S23F through recomb, the newly uploaded UK branch regains Orf10:R24C. @FedeGueli @ryhisner @corneliusroemer

@FedeGueli
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Thx @aviczhl2 interesting!

@xz-keg xz-keg changed the title EG.5.1.1 recomb involving S:I1114T(52 seqs, 12 countries, 50 with Flip) EG.5.1.1 recomb involving S:I1114T(55 seqs, 12 countries, 53 with Flip) Nov 23, 2023
@FedeGueli
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FedeGueli commented Nov 27, 2023 •
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Flip up to 74 now. (76 tot)

@xz-keg
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xz-keg commented Nov 27, 2023

New country of Singapore

@xz-keg xz-keg changed the title EG.5.1.1 recomb involving S:I1114T(55 seqs, 12 countries, 53 with Flip) EG.5.1.1 recomb involving S:I1114T(76 seqs, 12 countries, 74 with Flip) Nov 27, 2023
@xz-keg
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xz-keg commented Dec 1, 2023 •
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89, New Zealand, Spain, USA
This one seems fast. Accelerating

@xz-keg xz-keg changed the title EG.5.1.1 recomb involving S:I1114T(76 seqs, 12 countries, 74 with Flip) EG.5.1.1 recomb involving S:I1114T(89 seqs, 14 countries, 87 with Flip) Dec 1, 2023
@xz-keg xz-keg changed the title EG.5.1.1 recomb involving S:I1114T(89 seqs, 14 countries, 87 with Flip) EG.5.1.1 recomb involving S:I1114T(89 seqs, 15 countries, 87 with Flip) Dec 1, 2023
@FedeGueli
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Yes it well over other designated lineages: https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nextcladePangoLineage=JN.1*&nucMutations1=C15981T%2CT24903C&analysisMode=CompareToBaseline&

@FedeGueli
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98 @corneliusroemer i suggest t designate this one

@xz-keg xz-keg changed the title EG.5.1.1 recomb involving S:I1114T(89 seqs, 15 countries, 87 with Flip) EG.5.1.1 recomb involving S:I1114T(100 seqs, 15 countries, 98 with Flip) Dec 6, 2023
@xz-keg xz-keg changed the title EG.5.1.1 recomb involving S:I1114T(100 seqs, 15 countries, 98 with Flip) EG.5.1.1 recomb involving S:I1114T(111 seqs, 15 countries, 109 with Flip) Dec 10, 2023
@xz-keg
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xz-keg commented Dec 10, 2023

111 now. @corneliusroemer @InfrPopGen

@FedeGueli
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one of the fastest not Ba.2.86 lineage

@xz-keg xz-keg changed the title EG.5.1.1 recomb involving S:I1114T(111 seqs, 15 countries, 109 with Flip) EG.5.1.1/(XBB.1.9.2+S:I1114T) recombinant(111 seqs, 15 countries, 109 with Flip) Dec 10, 2023
@xz-keg xz-keg changed the title EG.5.1.1/(XBB.1.9.2+S:I1114T) recombinant(111 seqs, 15 countries, 109 with Flip) EG.5.1.1 recombinant involving S:I1114T (111 seqs, 15 countries, 109 with Flip) Dec 10, 2023
@xz-keg xz-keg changed the title EG.5.1.1 recombinant involving S:I1114T (111 seqs, 15 countries, 109 with Flip) EG.5.1.1/non-EG.5 recombinant involving S:I1114T (111 seqs, 15 countries, 109 with Flip) Dec 10, 2023
@xz-keg
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xz-keg commented Dec 10, 2023 •
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Wait I find a way to express this recomb to 0 private mutations. We can view it as recomb between XBB.1.9.2+S:1114T and EG.5.1.1+C15981T. Maybe this is a better way? This view increases 1 explained mutation and reduces private mutations from 1 to 0.

Sorry this one cannot happen as there's no XBB.1.9.2+S:I1114T having C25572T. Breakkpoint shall be after 25573 though

@xz-keg
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xz-keg commented Dec 14, 2023

128, Italy

@xz-keg xz-keg changed the title EG.5.1.1/non-EG.5 recombinant involving S:I1114T (111 seqs, 15 countries, 109 with Flip) EG.5.1.1/non-EG.5 recombinant involving S:I1114T (128 seqs, 16 countries, 126 with Flip) Dec 14, 2023
@xz-keg
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xz-keg commented Dec 16, 2023

130, Finland

@xz-keg xz-keg changed the title EG.5.1.1/non-EG.5 recombinant involving S:I1114T (128 seqs, 16 countries, 126 with Flip) EG.5.1.1/non-EG.5 recombinant involving S:I1114T (130 seqs, 17 countries, 128 with Flip) Dec 16, 2023
@xz-keg xz-keg changed the title EG.5.1.1/non-EG.5 recombinant involving S:I1114T (130 seqs, 17 countries, 128 with Flip) EG.5.1.1/non-EG.5 recombinant involving S:I1114T (130 seqs, 17 countries, 127 with Flip) Dec 16, 2023
@xz-keg xz-keg mentioned this issue Dec 18, 2023
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@xz-keg
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xz-keg commented Dec 19, 2023 •
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141, Netherlands, Japan.

Also 5/333(1.5%) in the 12-19 Singapore batch of local cases.

@xz-keg xz-keg changed the title EG.5.1.1/non-EG.5 recombinant involving S:I1114T (130 seqs, 17 countries, 127 with Flip) EG.5.1.1/non-EG.5 recombinant involving S:I1114T (141 seqs, 19 countries, 138 with Flip) Dec 19, 2023
@xz-keg xz-keg changed the title EG.5.1.1/non-EG.5 recombinant involving S:I1114T (141 seqs, 19 countries, 138 with Flip) EG.5.1.1/non-EG.5 recombinant involving S:I1114T (141 seqs, 19 countries, 138 with Flip, 1.5% Singapore) Dec 19, 2023
@FedeGueli
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@corneliusroemer this is increasing its share in Singapore, still low numbers so it could be biased , but still i think it is worth designating. i noticed that nextclade assigns it to multiple different lineages
Schermata 2023-12-19 alle 11 28 06
maybe better designating and keep it tracked.

@xz-keg
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xz-keg commented Dec 19, 2023

@corneliusroemer this is increasing its share in Singapore, still low numbers so it could be biased , but still i think it is worth designating. i noticed that nextclade assigns it to multiple different lineages ![Schermata 2023-12-19 alle 11 28 06]

I don't find any sub-branch having S:Q14H or S:T883I. Why is it assigned to HK.2.1 or HK.4?

@xz-keg
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xz-keg commented Dec 24, 2023

153, Austria , Greece

@xz-keg xz-keg changed the title EG.5.1.1/non-EG.5 recombinant involving S:I1114T (141 seqs, 19 countries, 138 with Flip, 1.5% Singapore) EG.5.1.1/non-EG.5 recombinant involving S:I1114T (153 seqs, 21 countries, 149 with Flip, 1.5% Singapore) Dec 24, 2023
@FedeGueli
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162 now with a 2% prevlaence in Gansu, China. @corneliusroemer i suggest a designation of this one being big enough and enough widespread.
Its growth disadvantage vs JN.1 is clear but not super huge: https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nucMutations=C15981T%2CT24903C&nextcladePangoLineage1=JN.1*&analysisMode=CompareToBaseline&

@xz-keg xz-keg changed the title EG.5.1.1/non-EG.5 recombinant involving S:I1114T (153 seqs, 21 countries, 149 with Flip, 1.5% Singapore) EG.5.1.1/non-EG.5 recombinant involving S:I1114T (162 seqs, 21 countries, 157 with Flip, 1.5% Singapore 2% Gansu) Dec 26, 2023
@xz-keg xz-keg changed the title EG.5.1.1/non-EG.5 recombinant involving S:I1114T (162 seqs, 21 countries, 157 with Flip, 1.5% Singapore 2% Gansu) EG.5.1.1/non-EG.5 recombinant involving S:I1114T (162 seqs, 21 countries, 157 with Flip, 1.5% Singapore 3% Gansu) Dec 26, 2023
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xz-keg commented Dec 26, 2023

5/175 in the 12-24 Gansu batch

@xz-keg xz-keg changed the title EG.5.1.1/non-EG.5 recombinant involving S:I1114T (162 seqs, 21 countries, 157 with Flip, 1.5% Singapore 3% Gansu) EG.5.1.1/non-EG.5 recombinant involving S:I1114T (174 seqs, 21 countries, 169 with Flip, 1.5% Singapore 3% Gansu) Dec 30, 2023
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xz-keg commented Dec 30, 2023

11/387 in Malaysia seqs from 2023.11.1

@xz-keg xz-keg changed the title EG.5.1.1/non-EG.5 recombinant involving S:I1114T (174 seqs, 21 countries, 169 with Flip, 1.5% Singapore 3% Gansu) EG.5.1.1/non-EG.5 recombinant involving S:I1114T (174 seqs, 21 countries, 169 with Flip, 3% Malaysia 3% Gansu) Dec 30, 2023
@xz-keg xz-keg changed the title EG.5.1.1/non-EG.5 recombinant involving S:I1114T (174 seqs, 21 countries, 169 with Flip, 3% Malaysia 3% Gansu) EG.5.1.1/non-EG.5 recombinant involving S:I1114T (182 seqs, 22 countries, 174 with Flip, 3% Malaysia 3% Gansu) Jan 4, 2024
@xz-keg xz-keg changed the title EG.5.1.1/non-EG.5 recombinant involving S:I1114T (182 seqs, 22 countries, 174 with Flip, 3% Malaysia 3% Gansu) EG.5.1.1/non-EG.5 recombinant involving S:I1114T (182 seqs, 22 countries, 177 with Flip, 3% Malaysia 3% Gansu) Jan 4, 2024
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xz-keg commented Jan 4, 2024

182, Poland

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xz-keg commented Jan 8, 2024

186, Australia

@xz-keg xz-keg changed the title EG.5.1.1/non-EG.5 recombinant involving S:I1114T (182 seqs, 22 countries, 177 with Flip, 3% Malaysia 3% Gansu) EG.5.1.1/non-EG.5 recombinant involving S:I1114T (186 seqs, 23 countries, 181 with Flip, 3% Malaysia 3% Gansu) Jan 8, 2024
@corneliusroemer corneliusroemer added this to the XDL milestone Jan 8, 2024
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XDL

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