LB.1.3 + S:K147E, Y660R (2-nuc) (31 seq, 12 countries, Aug 3)

[ryhisner]

Description Sub-lineage of: LB.1.3 (S:∆S31, Q183H, R346T, F456L) Earliest sequence: 2024-4-29, France - EPI_ISL_19166088 Most recent sequence: 2024-5-16, Switzerland - EPI_ISL_19185299 Continents circulating: Europe (2) Countries circulating: France (1), Switzerland (1) Number of Sequences: 2 GISAID Nucleotide Query: T23540C, A23541G, G27261T CovSpectrum Query: Nextcladepangolineage:LB.1* & [3-of: T23540C, A23541G, G27261T, C18131T] Substitutions on top of X: Spike: K147E, Y660R Nucleotide: A22001G, T23540C, A23541G, G27261T

USHER Tree https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons2/main/LB.1.3_Y660R.json?c=gt-S_660&gmax=25384&gmin=21563&label=id:node_7131969

Evidence I call LB.1.3 the "global" branch of LB.1 because it seems to come disproportionately from travel sequences. The xtremely unusual 2-nuc S:Y660R mutation caught my eye here. S:K147E has been advantageous in the past and is another mutation increasing NTD's negative charge, which is a trend that's been going on for a long time now and shows no signs of slowing.

The most closely related sequence is a travel sequence from Qatar collected in the US.

Genomes

Genomes

EPI_ISL_19166088, EPI_ISL_19185299, EPI_ISL_19189757, EPI_ISL_19192350, EPI_ISL_19193564, EPI_ISL_19195905, EPI_ISL_19195971, EPI_ISL_19198865, EPI_ISL_19202120,

[HynnSpylor]

1 more in France

[FedeGueli]

6, New samples coming from ENV-Germany, France and Denmark

New Tree:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_3d320_bdfde0.json?c=userOrOld&label=id:node_7140780

IDs: EPI_ISL_19166088, EPI_ISL_19185299, EPI_ISL_19189757, EPI_ISL_19192350, EPI_ISL_19193564, EPI_ISL_19193656,

Ping @corneliusroemer it could be a new thing.

[FedeGueli]

+2 in two travellers from Germany (same day but different samples)

[ryhisner]

One of these showed up in British Columbia, Canada, so this one's skipping oceans now.

[FedeGueli]

10 Seqs 6 countries not slow at all pleaase propose it: https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?%2FAllSamples%2FPast3M%2Fvariants%3FnextcladePangoLineage=JN.1*&nextcladePangoLineage=JN.1*&nucMutations1=T23540C%2CA23541G%2CG27261T&analysisMode=CompareToBaseline&

[FedeGueli]

+2 France one of them from a new region of France : Cholet (Loire)

[DailyCovidCases]

Still 12 seqs: nextclade

[FedeGueli]

20 seqs from 9 countries.

To be noticed that 5/9 french samples come from inpatients. could it be a BQ.1.2.2 thing?

[aviczhl2]

30 seqs now.

[FedeGueli]

31 with two branches one mainly from France, the other more international, still i don't think it is fast enough to compete. A couple of samples have no 147E

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_test_27d3b_e22670.json?f_userOrOld=uploaded%20sample&label=id:node_7239347