JN.1+S:T22N,F456L,Q493E(Designated JN.1.16.5)+S:S31P( 120 seqs, 10 countries, 12 with S:T1273I)

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From branch 115 of sars-cov-2-variants/lineage-proposals#1253

JN.1+C23039G, T22928C, C21627A(S:T22N, F456L, Q493E)

Or JN.1.16+C23039G,C21627A(S:T22N,Q493E)

Now usher put some of them under JN.1.16.1+S:Q493E+S:T22N Flip-Flop branch and some under JN.1.16+S:Q493E+S:T22N.

GISAID query: C23039G, T22928C, C21627A,-17334,-24872
GISAID query for S:S31P sub-branch: C3923T, T21653C
GISAID query for S:T1273I further branch: C3923T, T21653C,C25380T
No. of seqs: 6(USA 2(1 from Turkey), Sweden 2 Netherlands 1 Israel 1 )

First: EPI_ISL_19254779, 2024-6-5,Sweden
Latest: EPI_ISL_19300799, 2024-7-23, Israel

usher

[FedeGueli]

8 Japan

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A sub-branch with S:S31P appears in this lineage, usher places it under JN.1.40.

[corneliusroemer]

This one is interesting but still a bit weird with few, scattered sequences, let's wait a bit more - it should grow if it's real

[FedeGueli]

+1 Sweden

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This is now 18 seqs, misplaced under JN.1.16.1 and having one S:R346T sample.
There are also some samples without S:T22N, they have S:R346T and shall not be related to this branch.

@AngieHinrichs

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Designated JN.1.16.5

[FedeGueli]

Designated JN.1.16.5 via 56fe08a

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S:S31P branch is now 13 seqs in Sweden, re-open.

[FedeGueli]

Now there is a singlet with S:F59L ( not in the s:s31P branch tough)
Query: G6879A, C8692T, A9353T (potential)
Tree:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice2_genome_test_37285_e60e30.json?label=id:node_11619447

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+1 UK

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+1 Denmark

[FedeGueli]

ping @corneliusroemer designating this could help it is one of the few fast things and not too small still missing a name

[JosetteSchoenma]

Subbranch with S31P (C3923T, T21653C), +2 from the Netherlands, +1 Wales, total 36

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It seems to gain further S:T1273I, followed by S:A871V recently

[FedeGueli]

This should be designated it is one of the half dozen lineages showing a growth advantage superior to KP.3.1.1

[Over-There-Is]

46 now, Sweden +5

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54, France

[FedeGueli]

This is in the group of the fastest lineages placed between XEC and Kp.3.1.1 ping @corneliusroemer

[DailyCovidCases]

73 seqs now
Tree:
usher


@corneliusroemer This lineage should be designated since it's growing very rapidly now

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81, Ireland

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89, Singapore, Germany

[FedeGueli]

4% in Swedish recent samples

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107-12 now.

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120,Luxembourg, Spain

[FedeGueli]

4 seqs now with further S:G72W from England and Wales

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designated NF.1

[FedeGueli]

designated NF.1

via eabf495