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cov-lineages / pango-designation

Repository for suggesting new lineages that should be added to the current scheme
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LB.1.3 + S:K147E, Y660R (2-nuc) (16 seq, 7 countries, Jun 28) #2662

Open ryhisner opened 1 week ago

ryhisner commented 1 week ago

Transferred from https://github.com/sars-cov-2-variants/lineage-proposals/issues/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

image

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.

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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 commented 1 week ago

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 commented 1 week ago

13 ses in total with T23540C, A23541G, G27261T