EG.5.1 with S:K182Q, S:T478R, ORF3a:Y91C, ORF1a:L450F, ORF1b:G2510C and S:L455F via G22927C (9 seqs, 8 countries) - Githubissues

cov-lineages / pango-designation

Repository for suggesting new lineages that should be added to the current scheme

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EG.5.1 with S:K182Q, S:T478R, ORF3a:Y91C, ORF1a:L450F, ORF1b:G2510C and S:L455F via G22927C (9 seqs, 8 countries) #2296

Closed NkRMnZr closed 1 year ago

NkRMnZr commented 1 year ago

Taken from Branch 44 of multitask sars-cov-2-variants/lineage-proposals#537

Defining Mutations: EG.5.1 > A22106C(S:K182Q) > C22995G(S:T478R), A25664G(ORF3a:Y91C) > C1613T(ORF1a:L450F), G20995T(ORF1b:G2510C), G22927C(S:L455F), A27388C Query: A22106C, G22927C, C22995G Earliest seq: 2023-08-14 (EPI_ISL_18160020, Denmark, OR EPI_ISL_18278998, Singapore) Latest seq: 2023-09-13 (EPI_ISL_18295307, SFO airport, California, USA with travel history to: Japan) Sampled Countries: Denmark (2), France (1), Singapore (1), USA (1, ex. Japan)

Genomes:

`EPI_ISL_18160020, EPI_ISL_18243476, EPI_ISL_18278998, EPI_ISL_18295307, EPI_ISL_18314088`

UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice2_genome_ec32_42b9b0.json?label=id:node_6951991

Trivia:

Another S:L455F via G22927C, branching from a seemingly hiatus S:T478R sublineage from Indonesia, where doesn't have much sequences available since June.
A27388C is ORF7a TRS related.

FedeGueli commented 1 year ago

Ping @corneliusroemer i suggest a close monitor of this one: 1) The tree roots could suggest it emerged in Indonesia ( we have only 4 travellers sample for Indonesia = 200M for september) 2) the mutational profile combines FLip to 478R and with 182 residue mutated to Q that is N in XBB.2.3.3 and it is associated usually to fit lineages. 3) 5 samples 4 countries considering that French sample in a young woman the danish is recent two from Singapore with two different age and the one intercepted in Us airports is in a traveller coming from Japan.

NkRMnZr commented 1 year ago

Tracking updates

09-29, 1 from NSW: EPI_ISL_18324922 10-02, 1 from Basque EPI_ISL_18331861 10-06, 1 from Vienna EPI_ISL_18354495 10-11, 1 from Hyogo EPI_ISL_18376275

FedeGueli commented 1 year ago

7 Spain (new country) 7 seqs 6 countries 4 continents

FedeGueli commented 1 year ago

8 Austria new country

ryhisner commented 1 year ago

Worth noting that the A27388C in this branch spoils the ORF7a/ORF7b TRS. There's probably almost no ORF7a or ORF7b expression in this lineage.

FedeGueli commented 1 year ago

i would add Or7ab expression ablated in the headline

FedeGueli commented 1 year ago

This is now a sublineage of JR.1 (EG.5.1.11.1)

FedeGueli commented 1 year ago

Sorry already designated JR.1.1 via https://github.com/cov-lineages/pango-designation/commit/bd9a2f7e2cc8baf43ae8317b9105c62673cacd63