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XDJ: HK.3.1/XBB.1.16.6 recombinant(17 seqs, 6 countries, 2 with S:L582H, 2 with S:S704L) #997

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aviczhl2 opened this issue Oct 21, 2023 · 10 comments
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XDJ: HK.3.1/XBB.1.16.6 recombinant(17 seqs, 6 countries, 2 with S:L582H, 2 with S:S704L) #997

aviczhl2 opened this issue Oct 21, 2023 · 10 comments
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designated FLip = S:L455F / S:F456L recombinant S:52 s:157 XDJ
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XDJ

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@aviczhl2
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aviczhl2 commented Oct 21, 2023 •
edited

XBB.1.16.6 from 1 to 14856, HK.3.1 from 14857 to end.

Additional mutations: G29081T,A29700G
N:T270I

image

Using the Slovenia seq as ref but it has S:455,456 masked so not exactly accurate. It is HK.3.1-Spike(Flip+52+157)

XBB.1.16.6--HK.3.1
Breakpoint between 14857 and 16877
G29081T,A29700G from an HK.3.1 branch

GISAID query: G29081T,C29625T,A14856G
No. of seqs: 3(France 2 Slovenia 1)

EPI_ISL_18396986, France, 2023-10-2
EPI_ISL_18412837, France, 2023-10-3
EPI_ISL_18402814, Slovenia, 2023-10-11

usher

image

usher for HK.3.1 donor
image
@aviczhl2 aviczhl2 changed the title HK.3.1/XBB.1.16.6 recombinant(3 seqs, 2 countries) HK.3.1/XBB.1.16.6 recombinant(3 seqs, France, Slovenia) Oct 21, 2023
@aviczhl2 aviczhl2 changed the title HK.3.1/XBB.1.16.6 recombinant(3 seqs, France, Slovenia) HK.3.1/XBB.1.16.6 recombinant(5 seqs, France, Slovenia) Oct 25, 2023
@aviczhl2 aviczhl2 changed the title HK.3.1/XBB.1.16.6 recombinant(5 seqs, France, Slovenia) HK.3.1/XBB.1.16.6 recombinant(7 seqs, France, Slovenia) Nov 8, 2023
@aviczhl2 aviczhl2 changed the title HK.3.1/XBB.1.16.6 recombinant(7 seqs, France, Slovenia) HK.3.1/XBB.1.16.6 recombinant(8 seqs, France, Slovenia) Nov 14, 2023
@FedeGueli
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One month from last sample has been collected it seems slow

@FedeGueli FedeGueli added Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. and removed Rapid review needed labels Nov 16, 2023
@aviczhl2
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+2 Italy

@aviczhl2 aviczhl2 changed the title HK.3.1/XBB.1.16.6 recombinant(8 seqs, France, Slovenia) HK.3.1/XBB.1.16.6 recombinant(10 seqs, 3 countries) Nov 21, 2023
@FedeGueli FedeGueli removed the Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. label Nov 21, 2023
@aviczhl2
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+1 Denmark

@aviczhl2 aviczhl2 changed the title HK.3.1/XBB.1.16.6 recombinant(10 seqs, 3 countries) HK.3.1/XBB.1.16.6 recombinant(11 seqs, 4 countries) Nov 26, 2023
@aviczhl2 aviczhl2 changed the title HK.3.1/XBB.1.16.6 recombinant(11 seqs, 4 countries) HK.3.1/XBB.1.16.6 recombinant(14 seqs, 4 countries) Nov 28, 2023
@aviczhl2 aviczhl2 changed the title HK.3.1/XBB.1.16.6 recombinant(14 seqs, 4 countries) HK.3.1/XBB.1.16.6 recombinant(14 seqs, 4 countries, 2 with S:L582H) Nov 28, 2023
@aviczhl2
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aviczhl2 commented Dec 7, 2023

+1 Netherlands

@aviczhl2 aviczhl2 changed the title HK.3.1/XBB.1.16.6 recombinant(14 seqs, 4 countries, 2 with S:L582H) HK.3.1/XBB.1.16.6 recombinant(15 seqs, 5 countries, 2 with S:L582H) Dec 7, 2023
@aviczhl2 aviczhl2 changed the title HK.3.1/XBB.1.16.6 recombinant(15 seqs, 5 countries, 2 with S:L582H) HK.3.1/XBB.1.16.6 recombinant(16 seqs, 5 countries, 2 with S:L582H) Dec 12, 2023
@aviczhl2
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+1 Australia

@aviczhl2 aviczhl2 changed the title HK.3.1/XBB.1.16.6 recombinant(16 seqs, 5 countries, 2 with S:L582H) HK.3.1/XBB.1.16.6 recombinant(17 seqs, 6 countries, 2 with S:L582H) Dec 16, 2023
@FedeGueli
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While not fast in November it expanded itself to new countries

@aviczhl2 aviczhl2 changed the title HK.3.1/XBB.1.16.6 recombinant(17 seqs, 6 countries, 2 with S:L582H) HK.3.1/XBB.1.16.6 recombinant(17 seqs, 6 countries, 2 with S:L582H, 2 with S:S704L) Dec 17, 2023
@aviczhl2
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While not fast in November it expanded itself to new countries

Seems it is getting S:S704L independently.

@corneliusroemer
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Just found this independently and it's not super small so I think it's worth designating as it is clearly a recombinant.

@corneliusroemer
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It's currently on quite a recombinant branch - but all the others are doublets or at most triplets
image

@corneliusroemer
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XDJ

@aviczhl2 aviczhl2 changed the title HK.3.1/XBB.1.16.6 recombinant(17 seqs, 6 countries, 2 with S:L582H, 2 with S:S704L) XDJ: HK.3.1/XBB.1.16.6 recombinant(17 seqs, 6 countries, 2 with S:L582H, 2 with S:S704L) Dec 17, 2023
@aviczhl2 aviczhl2 added this to the XDJ milestone Dec 17, 2023
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@aviczhl2 @corneliusroemer @FedeGueli