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JD.1.1.1/JN.1.1 recombinant(53 seqs, 4 countries, 11% Brazil) #2477

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aviczhl2 opened this issue Jan 28, 2024 · 9 comments
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JD.1.1.1/JN.1.1 recombinant(53 seqs, 4 countries, 11% Brazil) #2477

aviczhl2 opened this issue Jan 28, 2024 · 9 comments

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@aviczhl2
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aviczhl2 commented Jan 28, 2024 •
edited

From sars-cov-2-variants/lineage-proposals#1250

JD.1.1.1--JN.1.1

Breakpoint between 11043 and 11726

image

Additional mutations:
C2668T

C2668T from a JD.1.1.1 branch.
There are other XBB.1.5.102* seqs with C2668T, however they have other mutations, so excluded.

Some seqs do not have C2668T, however they're missing coverage on that place, no seq have 2668C.

GISAID query: A405G, C6896T, C11747T,C28958A
No. of seqs: 22(Denmark 1 Spain 3 Canada 1 Brazil 17)

First, EPI_ISL_18572639, Brazil, 2023-11-8
Latest: EPI_ISL_18803970, Canada, 2024-1-11

usher

image
@FedeGueli
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It appears very fast maybe founder effect maybe something else.

@FedeGueli
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ping @corneliusroemer i suggest fast designation of this one.

@FedeGueli
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41 now! ping @corneliusroemer

@FedeGueli
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over 7% of brazilian sampels after December 16. Note : Multiple states

@aviczhl2
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Yeah +19 Brazil crazy.

@aviczhl2 aviczhl2 changed the title JD.1.1.1/JN.1.1 recombinant(22 seqs, 4 countries) JD.1.1.1/JN.1.1 recombinant(41 seqs, 4 countries, 7% Brazil) Jan 29, 2024
@aviczhl2 aviczhl2 changed the title JD.1.1.1/JN.1.1 recombinant(41 seqs, 4 countries, 7% Brazil) JD.1.1.1/JN.1.1 recombinant(44 seqs, 4 countries, 7% Brazil) Jan 30, 2024
@aviczhl2 aviczhl2 changed the title JD.1.1.1/JN.1.1 recombinant(44 seqs, 4 countries, 7% Brazil) JD.1.1.1/JN.1.1 recombinant(53 seqs, 4 countries, 7% Brazil) Feb 1, 2024
@aviczhl2
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aviczhl2 commented Feb 1, 2024

15/137=11% in 2024-1 Brazil samples.

@aviczhl2 aviczhl2 changed the title JD.1.1.1/JN.1.1 recombinant(53 seqs, 4 countries, 7% Brazil) JD.1.1.1/JN.1.1 recombinant(53 seqs, 4 countries, 11% Brazil) Feb 1, 2024
@FedeGueli
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ping @corneliusroemer this should be designated!

@Mike-Honey
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I think this was designated as XDR?

@aviczhl2
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aviczhl2 commented Feb 6, 2024

I think this was designated as XDR?

Yeah

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@Mike-Honey @aviczhl2 @FedeGueli