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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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KP.3.1 + ∆29728-29776 (bigger s2m deletion) [485 seq, Aug 16] #2646

Closed ryhisner closed 1 month ago

ryhisner commented 3 months ago

Transferred from https://github.com/sars-cov-2-variants/lineage-proposals/issues/1573

Description Sub-lineage of: KP.3.1 (JN.1.11.1.3 = JN.1 + S:F456L, Q493E, V1104L) Earliest sequence: 2024-4-15, Australia, Victoria — EPI_ISL_19084514 Most recent sequence: 2024-5-6, Spain, Madrid — EPI_ISL_19144199 Continents circulating: Oceania (7), Asia (2), Europe (2) Countries circulating: Australia (5), New Zealand (2), Spain (2), China (1), Singapore (1) Number of Sequences: 11 GISAID Nucleotide Query: A1620G, G15372T, -G29734 CovSpectrum Query: Nextcladepangolineage:KP.3* & [2-of: A1620G, G15372T] & [1-of: 29729-, !29735-] Substitutions/Deletions on top of KP.3: ORF1a: E452G (NSP2_E282G) Nucleotide: G15372T, A19722G, A1620G, ∆29728-29733 + ∆29760-29776

Phylogenetic Order of Mutations: G15372T, A19722G → A1620G (ORF1a:E452G), ∆29728-29733 + ∆ 29760-29776

USHER Tree https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons2/main/KP.3_29728-29776.json?c=gt-ORF1ab_452&gmax=21555&gmin=266&label=id:node_2371524

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Evidence BA.2 was the first global variant to feature a deletion in s2m, a 3' UTR stem-loop that is highly conserved in sarbecoviruses. All Omicron since BA.1 have had ∆29734-29759. This sublineage adds 23 nucleotides to the standard Omicron s2m deletion with ∆29728-29776. When the s2m deletion is enlarged, this is the most common pattern. s2m's function is unknown, and the reason for its deletion in BA.2/4/5 is also a mystery.

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Genomes

Genomes EPI_ISL_19084514, EPI_ISL_19095989, EPI_ISL_19122535, EPI_ISL_19122574, EPI_ISL_19122576, EPI_ISL_19122578, EPI_ISL_19134818, EPI_ISL_19142295, EPI_ISL_19142321, EPI_ISL_19144199, EPI_ISL_19146486
aviczhl2 commented 3 months ago

This has a large S:K679R--S:L176F branch now. image

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice59_genome_test_5e445_fb01a0.json?label=id:node_5450611

FedeGueli commented 3 months ago

This has a large S:K679R--S:L176F branch now. image

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice59_genome_test_5e445_fb01a0.json?label=id:node_5450611

Query: C14216T, A23598G,T3565C

FedeGueli commented 2 months ago

It is now 213 with 37 with S:K679R and 15 with further S:L176F cc @ryhisner @corneliusroemer

ryhisner commented 1 month ago

Still around in decent numbers, but not growing fast, Closing.