XDG: XBB.1.9.1 / EG.5.2 recombinant with S:K679R, Orf1a:A498V and T4579A (26 seq, 6 countries until 2023-11-24)

[Over-There-Is]

Transferred from sars-cov-2-variants/lineage-proposals#770

Credit to @NkRMnZr

XBB.1.9.1 / EG.5.2

Query: T4690C, A23598G

Earliest sequence: 08-21 Denmark EPI_ISL_18210614 Latest sequence: 10-30 Drôme, Auvergne-Rhône-Alpes, France EPI_ISL_18510031 Regions detected: US 11(California 5, NY 4, Minnesota 2), Italy 8(Sicily 4, Apulia 3, Veneto 1), Canada 2(BC 1, Ontario 1), France 3(ARA), Denmark 1, Greece 1(Central Greece)

Mutations Based on XBB.1.9+S:S486P: C547T, C1758T(Orf1a:A498V, Private), T4579A, T4690C, T4930C / C9693T(Orf1a:A3143V), C11518T, A16878T, T16905C, C22480T, T22930A(S:F456L), A23598G(S:K679R), A25744G(Orf3a:I118V), A27507C, C28754T(N:L161F), C29625T(Orf10:S23F)

Breakpoint: 6729\~9693 5' donor: XBB.1.9.1> C29614T> C547T> T15309C(85 seq)> T4690C, T4930C, G10540T(Orf1a:M3425I), C26054T(Orf3a:T221I) (2 seq, 1 seq has further T4579A) 3' donor: EG.5.2> A6729G(Orf1a:N2155S)> C11518T> C3602T(Orf1a:H1113Y)> A25744G(Orf3a:I118V, shared with EG.5.2.1)> A23598G(S:K679R, 32 seq)> C583T, T16905C (4 seq) The 5' donor has T4579A, but it's not FL.2. The 3' donor is on a sibling branch of EG.5.2.1.

https://nextstrain.org/fetch/github.com/Over-There-Is/subtreeAuspice/raw/main/subtreeAuspice_genome_20424_7b8a0.json?c=country&label=id:node_6946874

Sequences:

EPI_ISL_18210080, EPI_ISL_18210109, EPI_ISL_18210181, EPI_ISL_18210614, EPI_ISL_18218428, EPI_ISL_18300257, EPI_ISL_18314673, EPI_ISL_18330426, EPI_ISL_18344025, EPI_ISL_18357726, EPI_ISL_18363919, EPI_ISL_18364276, EPI_ISL_18368928, EPI_ISL_18389364, EPI_ISL_18394164, EPI_ISL_18404126, EPI_ISL_18419443, EPI_ISL_18419447, EPI_ISL_18419462, EPI_ISL_18419489, EPI_ISL_18422941, EPI_ISL_18433988, EPI_ISL_18440980, EPI_ISL_18502876, EPI_ISL_18510031, EPI_ISL_18533287

[Over-There-Is]

XDG