LB.1.3 + S:K147E, Y660R (2-nuc) (26 seq, 12 countries, Aug 9)

[ryhisner]

Transferred from sars-cov-2-variants/lineage-proposals#1601
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 (9), Asia (1), North America (1)
Countries circulating: France (5), Germany (2—both travel to USA), Canada (1), Denmark (1), Qatar (1—travel to USA), Sweden (1), Switzerland (1)
Number of Sequences: 12
GISAID Nucleotide Query: T23540C, A23541G, G27261T
CovSpectrum Query: Nextcladepangolineage:LB.1* & [3-of: T23540C, A23541G, G27261T, C18131T]
Substitutions on top of LB.1.3:
Spike: K147E, Y660R
Nucleotide: A22001G, T23540C, A23541G, G27261T

USHER Tree
https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons2/main/Y660R_at_9_seq.json?c=gt-S_660&gmax=25384&gmin=21563&label=id:node_7145835

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, EPI_ISL_19205790, EPI_ISL_19205796, EPI_ISL_19210286,

[ryhisner]

Today a sequence from Qatar in a traveler to the USA showed up. Collection date June 11. Given the relatively small amount of diversity, the recent collection dates, and the wide geographical spread, I think there's a chance this lineage is pretty fit.

Right now it seems like Qatar and Germany are the top two candidates for being its epicenter. The most closely related sequence not in this lineage is a sequence from a traveler to the US from Qatar, collected May 15. Germany itself basically does no surveillance at all, and there are two sequences from German travelers to the US. Also, S:Y660R showed up in one of the German wastewater samples uploaded to GISAID.

[FedeGueli]

13 ses in total with T23540C, A23541G, G27261T

[FedeGueli]

23 now with Netherlands and UAE (via GBW) as new countries

[FedeGueli]

In France 5/11 samples are from Inpatients while the average of sequences labeled as hospitalized there is 1/5 - 1/6 in June: i think we should keep an eye on this.

[FedeGueli]

24 samples from 11 countries now, last sample came from Iceland

cc @corneliusroemer

[FedeGueli]

26 from 12 countries including two middle eastern countries cc @ryhisner please update the count!
@corneliusroemer worth deisgnating this although not very fast

[ryhisner]

Interesting lineage but appears to be dead. Closing