LF.7.1 subbranch with S:V>H445P(40, 11 countries), 2 subbranches with further S:ins16IPLF(26, 6) or S:A475V(14, 9)

[Walde1nsamkeit]

Transferred from sars-cov-2-variants/lineage-proposals#2480
LF.7.1> C16767T, A22896C(S:H445P)
Query: C6310T, C8293T, C16767T (1 uncaught)
Query for S:ins16IPLF branch: C6310T, C8293T, C16767T, -C26873T
Query for S:A475V branch: C6310T, C8293T, C16767T, C26873T and C12115T, C22986T, C26873T by @FedeGueli (each with 1 uncaught)

https://nextstrain.org/fetch/genome.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice2_genome_217541_20c5b0.json?c=country&label=id:node_7158228

All sequences are under following 2 subbranches:

LF.7.1> C16767T, A22896C(S:H445P)> C8980T, ins21608TCATTCCGCTGT(S:ins16IPLF, M>I)

Earliest sequence: 10-07 Kiryandongo, Uganda EPI_ISL_19767094
Latest sequence: 04-03 New Jersey, United States EPI_ISL_19829203
Regions detected: US 14, Uganda 5, Thailand 1, UK 1, Australia 1

ins21608TCATTCCGCTGT is misinterpreted as ins21606TGTTCATTCCGC(S:ins16HSAV) in Ugandan sequences. These sequences have too many artefactual reversions and are unable to be placed on tree by usher.

Sequence	Mutation path
Uganda/UVRI_KIL0771/2024|EPI_ISL_19767090|2024-10-10	> A19291T(Orf1b:S1942C), T29492C> G22380T(S:R237M)?
Uganda/UVRI_KIL0833/2024|EPI_ISL_19767093|2024-10-09	> A19291T(Orf1b:S1942C), T29492C
Uganda/UVRI_KIL0866/2024|EPI_ISL_19767094|2024-10-07	> G22380T(S:R237M)
Uganda/KIL1043/2025|EPI_ISL_19848747|2025-01-20	> C8950T, A23147G(S:K529E)
Uganda/UVRI_KIL0875/2024|EPI_ISL_19767095|2024-10-14

Sequences:
EPI_ISL_19603040, EPI_ISL_19695296, EPI_ISL_19754951,
EPI_ISL_19767090, EPI_ISL_19767093-19767095, EPI_ISL_19771553,
EPI_ISL_19772151, EPI_ISL_19780364, EPI_ISL_19792869,
EPI_ISL_19792904, EPI_ISL_19802291, EPI_ISL_19809824,
EPI_ISL_19809904, EPI_ISL_19811926, EPI_ISL_19820133,
EPI_ISL_19825243, EPI_ISL_19826622, EPI_ISL_19829203,
EPI_ISL_19848747, EPI_ISL_19849630

LF.7.1> C16767T, A22896C(S:H445P)> C12115T, C22986T(S:A475V), C26873T

Earliest sequence: 03-03 Halland, Sweden EPI_ISL_19810699
Latest sequence: 04-10 Ontario, Canada EPI_ISL_19853346
Regions detected: Australia 1, Canada 1, France 1, Luxembourg 1, Sweden 1, US 1(from Saudi Arabia)

Sequences:
EPI_ISL_19803310, EPI_ISL_19810699, EPI_ISL_19813372,
EPI_ISL_19831768, EPI_ISL_19833051, EPI_ISL_19853346,

[FedeGueli]

Ahha i was just writing on the other repo about the 475V Ins16MPLF branch! https://nextstrain.org/fetch/genome.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice22_genome_26d786_161780.json?label=id:node_7158228

[FedeGueli]

the 475V is up to 9 ( with your query @Walde1nsamkeit ) or 10 with C12115T, C22986T, C26873T (which are simply last node of the branch )

very interestingly the last one is a GBW sample from Egypt, when the first sample was a GBW from Saudi A.

cc @corneliusroemer @xz-keg i suggest to designate this.

[Walde1nsamkeit]

A475V: UK, Egypt

[FedeGueli]

33 for the 445P branch
23 for the insertion branch +1. Hawaii
11 for the 475V +1 NY interestingly it has also S:T345S (Query: C9778T, G14874T ,C22596G,C12115T, Samples: 3 , Places: NY, Wales, Saudi A.(GBW)

cc @corneliusroemer worth designating this one.

[FedeGueli]

12 now for the 475V branch with +1 from England ( with further S:680F and S:G798S)

[FedeGueli]

26 for the insertion branch

[FedeGueli]

cc @corneliusroemer the 475V seems fast