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

[NkRMnZr]

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]

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]

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]

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

[FedeGueli]

8 Austria new country

[ryhisner]

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]

i would add Or7ab expression ablated in the headline

[FedeGueli]

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

[FedeGueli]

Sorry already designated JR.1.1 via bd9a2f7