Closed ryhisner closed 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
One of these showed up in Canada, collection date July 23. EPI_ISL_19293986
EPI_ISL_19305721
England
Sequence from France today with an additional S:D228H.
New sample of this from GBW .
But more interestingly now it has been placed under LR.1 (JN.1.58.1) as sublineage:
(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.
+1 Australia
@ryhisner please propose it i bet @corneliusroemer will designate it soon.
oh yeah this one is a no brainer, thanks!
@ryhisner please propose it i bet corneliusroemer will designate it soon.
Done. https://github.com/cov-lineages/pango-designation/issues/2733
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
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