sars-cov-2-variants / lineage-proposals

Repository to propose and discuss lineages
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JN.1.16.1 (Usher places it under LR.1) plus S:T22N, S31P, K182R, R190S, K444R + ORF9b:I5T + ORF1a:S2535L (7 seq, 6 countries; Aug 13) #1758

Closed ryhisner closed 3 months ago

ryhisner commented 3 months ago

Description Sub-lineage of: JN.1.16.1 Earliest sequence: 2024-6-24, Senegal Most recent sequence: 2024-6-25, Senegal Continents circulating: Africa (2) Countries circulating: Senegal (2) Number of Sequences: 2 GISAID Nucleotide Query: C5239T, C7869T, C8818T, G12892A, T16600C CovSpectrum Query: Nextcladepangolineage:JN.1* & [4-of: C5239T, C7869T, C8818T, G12892A, T16600C] Substitutions on top of JN.1.16.1: Spike: T22N, S31P, K182R, R190S, K444R ORF1a: S2535L ORF9b: I5T Nucleotide: C5239T, C7869T, C8818T, G12892A, T16600C, C21627A, T21653C, A22107G, G22132T, C22792T, A22893G, C22993T, T28297C

USHER Tree https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_31267_ab1a70.json?label=id:node_11550501

image

Evidence Just doing a crappy, short proposal for now since it's 2 sequences. If it grows, I'll do a proper one.

Genomes

Genomes EPI_ISL_19273031, EPI_ISL_19273041
FedeGueli commented 3 months ago

Both the samples are imported from elsewhere, but their collection bodes well with the targeted sequencing, done by Senegal, of returning pilgrims from Mecca. So this lineage likely emerged in another country, noticeably it has similarities both with MA.1 and MB.1.1

ryhisner commented 3 months ago

One of these showed up in Canada, collection date July 23. EPI_ISL_19293986

NkRMnZr commented 3 months ago

EPI_ISL_19305721 England

ryhisner commented 3 months ago

Sequence from France today with an additional S:D228H.

image
FedeGueli commented 3 months ago

New sample of this from GBW .

But more interestingly now it has been placed under LR.1 (JN.1.58.1) as sublineage:

Screenshot 2024-08-13 alle 17 03 50

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice24_genome_test_468d1_b6c340.json?label=id:node_6968744

(scratch>>)Another annotation: it is very likely that all of them have Orf1b:K2557R being only the samples from Senegal missing it.

Scratch that, that one is a reversion Orf1b:R2557K and points at a misplacement by Usher for unknown reasons.

xz-keg commented 3 months ago

+1 Australia

FedeGueli commented 3 months ago

@ryhisner please propose it i bet @corneliusroemer will designate it soon.

corneliusroemer commented 3 months ago

oh yeah this one is a no brainer, thanks!

ryhisner commented 3 months ago

@ryhisner please propose it i bet corneliusroemer will designate it soon.

Done. https://github.com/cov-lineages/pango-designation/issues/2733

FedeGueli commented 3 months ago

Designated LF.7 via https://github.com/cov-lineages/pango-designation/commit/43d7733254e29c91714acb4ed0ea2003b2873551