New DeFLiRT : JN.1.16.1 with S:S31del and Orf8:Q29* emerged recently in France (53 seqs, 12 countries )

FedeGueli commented 2 weeks ago

Transferred from https://github.com/sars-cov-2-variants/lineage-proposals/issues/1590

JN.1.16.1>> N:R385K (G29427A) > Orf1a:T4368I (C13368T) > Orf1a:G519S (G1820A) > S:S31del (del21653_55), G8824A, Orf8:Q29* (C27978T ) Query:C13368T,del21653, G1820A Samples: 21 Countries: France (5 different regions), Italy , Spain, NYC, Qatar (via GBW), Canada , UK First collected on 2024-04-16 IDs: EPI_ISL_19157165, EPI_ISL_19162603, EPI_ISL_19166117, EPI_ISL_19166138, EPI_ISL_19173792, EPI_ISL_19174164, EPI_ISL_19175832, EPI_ISL_19179051, EPI_ISL_19184850, EPI_ISL_19187673, EPI_ISL_19189739, EPI_ISL_19189743-19189744, EPI_ISL_19189754, EPI_ISL_19189770, EPI_ISL_19189772, EPI_ISL_19190899, EPI_ISL_19191421, EPI_ISL_19191423, EPI_ISL_19191441, EPI_ISL_19191525

Tree:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_5525e_992c90.json?label=id:node_7140940

FedeGueli commented 2 weeks ago

ping @corneliusroemer @AngieHinrichs interesting one due the comeback of an Orf8 truncation on a competitive DeFLiRT backbone. Orf8:Q29stop came together with S:S31del in the same node.

FedeGueli commented 2 weeks ago

+2 from 2 different region of Spain

FedeGueli commented 1 week ago

32 now also in French Guyana. ping @corneliusroemer

FedeGueli commented 1 week ago

46 now with recent samples coming from France , Spain and Qatar (via GBW) ping @corneliusroemer i suggest to designate it

FedeGueli commented 4 days ago

53 expanding in multiple countries.

aviczhl2 commented 1 day ago

Designated LF.4.1

FedeGueli commented 1 day ago

Designated LF.4.1 via https://github.com/cov-lineages/pango-designation/commit/6c579b80861260450f670f8d640e6d193f7679e0

cov-lineages / pango-designation

New DeFLiRT : JN.1.16.1 with S:S31del and Orf8:Q29* emerged recently in France (53 seqs, 12 countries ) #2652