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JN.11 (BA.2.86.1+S:V1104L)with S:L455S (25 sequences 8 countries) #1303

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xz-keg opened this issue Jan 16, 2024 · 13 comments
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JN.11 (BA.2.86.1+S:V1104L)with S:L455S (25 sequences 8 countries) #1303

xz-keg opened this issue Jan 16, 2024 · 13 comments
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BA.2.86 designated Emerged in an undersampled area Actual infection toll may be much larger than number of sequences suggest JN.1 Spike partially designated S:455 S:1104
Milestone
JN.11 JN.11.1

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@xz-keg
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xz-keg commented Jan 16, 2024 •
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It seems that there's another BA.2.86+S:V1104L branch likely emerged in SE Asia, with S:L455S it effectively reproduces the current fastest spike of JN.1.11.

BA.2.86.1+G24872T(S:V1104L)

GISAID query:A6183G,G24872T,-27810,-7528,-8456,-A405G
No. of seqs: 72(Australia 9 Canada 1 UK 1 France 6 Indonesia 3 Japan 6 Malaysia 1 Singapore 21(1 from Malaysia), South Korea 6 Sweden 1 USA 15(1 from UAE) China 1 Vietnam 1)

First: EPI_ISL_18499092, USA, 2023-10-3
Latest: EPI_ISL_18757342, USA, 2023-1-8

GISAID query for S:L455S branch: A6183G,G24872T,-27810,-7528,-8456,-A405G, ,-T3565C,T22926C (4 seqs, Singapore, Japan, USA)

usher
Note that some are on other artefact branches.

image
@FedeGueli
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+1 Thailand. great catch btw! it appears that S:V1104L is beneficial in BA.2.86
and it is predicted to be good by Bloom/Neher,
Screenshot 2024-01-16 alle 10 49 49
While Dadonaite/Bloom predicts it to affect ace2 binding.

@FedeGueli FedeGueli changed the title BA.2.86.1+S:V1104L(72 seqs,14 countries, 4 with S:L455S) BA.2.86.1+S:V1104L(73 seqs, 15 countries, 4 with S:L455S) Jan 16, 2024
@xz-keg xz-keg changed the title BA.2.86.1+S:V1104L(73 seqs, 15 countries, 4 with S:L455S) BA.2.86.1+S:V1104L(80 seqs, 15 countries, 5 with S:L455S) Jan 18, 2024
@xz-keg
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xz-keg commented Jan 18, 2024 •
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+1 USA airport seq on S:L455S branch , origin country unknown.

@corneliusroemer corneliusroemer added this to the JN.11 milestone Jan 21, 2024
@FedeGueli FedeGueli changed the title BA.2.86.1+S:V1104L(80 seqs, 15 countries, 5 with S:L455S) JN.11 (BA.2.86.1+S:V1104L)(with S:L455S (5 sequences) Jan 21, 2024
@FedeGueli FedeGueli changed the title JN.11 (BA.2.86.1+S:V1104L)(with S:L455S (5 sequences) JN.11 (BA.2.86.1+S:V1104L)with S:L455S (5 sequences) Jan 21, 2024
@xz-keg
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xz-keg commented Jan 22, 2024

Let's reopen this to track the S:L455S sub-branch

@xz-keg xz-keg reopened this Jan 22, 2024
@xz-keg xz-keg changed the title JN.11 (BA.2.86.1+S:V1104L)with S:L455S (5 sequences) JN.11 (BA.2.86.1+S:V1104L)with S:L455S (5 sequences 3 countries) Jan 22, 2024
@xz-keg xz-keg changed the title JN.11 (BA.2.86.1+S:V1104L)with S:L455S (5 sequences 3 countries) JN.11 (BA.2.86.1+S:V1104L)with S:L455S (6 sequences 3 countries) Jan 26, 2024
@xz-keg xz-keg changed the title JN.11 (BA.2.86.1+S:V1104L)with S:L455S (6 sequences 3 countries) JN.11 (BA.2.86.1+S:V1104L)with S:L455S (8 sequences 3 countries) Feb 2, 2024
@xz-keg
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xz-keg commented Feb 7, 2024

+1 India for S:L455S branch

@xz-keg xz-keg changed the title JN.11 (BA.2.86.1+S:V1104L)with S:L455S (8 sequences 3 countries) JN.11 (BA.2.86.1+S:V1104L)with S:L455S (10 sequences 4 countries) Feb 7, 2024
@xz-keg xz-keg changed the title JN.11 (BA.2.86.1+S:V1104L)with S:L455S (10 sequences 4 countries) JN.11 (BA.2.86.1+S:V1104L)with S:L455S (11 sequences 4 countries) Feb 14, 2024
@xz-keg xz-keg changed the title JN.11 (BA.2.86.1+S:V1104L)with S:L455S (11 sequences 4 countries) JN.11 (BA.2.86.1+S:V1104L)with S:L455S (14 sequences 4 countries) Feb 18, 2024
@xz-keg
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xz-keg commented Feb 23, 2024 •
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There seems to be some JN.1/JN.11 recombinant(with JN.1-5' and JN.11-3'), alter query to exclude them.

Seqs belonging to this branch shall be 8, with countries USA,Japan,Singapore, Vietnam

@xz-keg xz-keg changed the title JN.11 (BA.2.86.1+S:V1104L)with S:L455S (14 sequences 4 countries) JN.11 (BA.2.86.1+S:V1104L)with S:L455S (8 sequences 4 countries) Feb 23, 2024
@FedeGueli FedeGueli added the Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. label Mar 3, 2024
@FedeGueli
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the 455S branch seems slow

@FedeGueli FedeGueli changed the title JN.11 (BA.2.86.1+S:V1104L)with S:L455S (8 sequences 4 countries) JN.11 (BA.2.86.1+S:V1104L)with S:L455S (10 sequences 5 countries) Mar 4, 2024
@FedeGueli
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FedeGueli commented Mar 4, 2024 •
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+2 Japan and South Korea

@xz-keg
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xz-keg commented Mar 9, 2024

+3 Thailand

@xz-keg xz-keg changed the title JN.11 (BA.2.86.1+S:V1104L)with S:L455S (10 sequences 5 countries) JN.11 (BA.2.86.1+S:V1104L)with S:L455S (14 sequences 6 countries) Mar 9, 2024
@xz-keg
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xz-keg commented Mar 14, 2024

+1 China

@xz-keg xz-keg changed the title JN.11 (BA.2.86.1+S:V1104L)with S:L455S (14 sequences 6 countries) JN.11 (BA.2.86.1+S:V1104L)with S:L455S (15 sequences 7 countries) Mar 14, 2024
@xz-keg xz-keg changed the title JN.11 (BA.2.86.1+S:V1104L)with S:L455S (15 sequences 7 countries) JN.11 (BA.2.86.1+S:V1104L)with S:L455S (16 sequences 7 countries) Mar 21, 2024
@FedeGueli FedeGueli changed the title JN.11 (BA.2.86.1+S:V1104L)with S:L455S (16 sequences 7 countries) JN.11 (BA.2.86.1+S:V1104L)with S:L455S (17 sequences 7 countries) Mar 26, 2024
@FedeGueli
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17 now

@xz-keg xz-keg changed the title JN.11 (BA.2.86.1+S:V1104L)with S:L455S (17 sequences 7 countries) JN.11 (BA.2.86.1+S:V1104L)with S:L455S (18 sequences 7 countries) Mar 31, 2024
@FedeGueli
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Slowed down lets keep this open due to Fujan sample from March for a bit more.

@xz-keg
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xz-keg commented Apr 2, 2024

20, GBW from Qatar

@xz-keg xz-keg changed the title JN.11 (BA.2.86.1+S:V1104L)with S:L455S (18 sequences 7 countries) JN.11 (BA.2.86.1+S:V1104L)with S:L455S (20 sequences 8 countries) Apr 2, 2024
@FedeGueli FedeGueli added Emerged in an undersampled area Actual infection toll may be much larger than number of sequences suggest and removed Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. labels Apr 16, 2024
@xz-keg xz-keg changed the title JN.11 (BA.2.86.1+S:V1104L)with S:L455S (20 sequences 8 countries) JN.11 (BA.2.86.1+S:V1104L)with S:L455S (21 sequences 8 countries) Apr 24, 2024
@xz-keg xz-keg changed the title JN.11 (BA.2.86.1+S:V1104L)with S:L455S (21 sequences 8 countries) JN.11 (BA.2.86.1+S:V1104L)with S:L455S (22 sequences 8 countries) May 5, 2024
@xz-keg xz-keg changed the title JN.11 (BA.2.86.1+S:V1104L)with S:L455S (22 sequences 8 countries) JN.11 (BA.2.86.1+S:V1104L)with S:L455S (25 sequences 8 countries) May 11, 2024
@xz-keg
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xz-keg commented May 16, 2024 •
edited by FedeGueli
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Designated JN.11.1 VIA cov-lineages/pango-designation@79d6afb

@xz-keg xz-keg closed this as completed May 16, 2024
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BA.2.86 designated Emerged in an undersampled area Actual infection toll may be much larger than number of sequences suggest JN.1 Spike partially designated S:455 S:1104
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