Multiple XBB.1.5.51 branches with S:T478R (99/19/2)

[NkRMnZr]

### Multiple XBB.1.5.51 branches with S:T478R
- [ ] Branch 1: Transferred to cov-lineages/pango-designation#2186 XBB.1.5.51 > C22995G(**S:T478R**)
- [ ] Branch 2: XBB.1.5.51 > A3379G > C1875T(ORF1a:A537V), C14529T, C22498T, C22995G(**S:T478R**), C27600T [Query:`C14529T, C22498T, C22995G`, 22 seqs, 09/01]
- [ ] Branch 3: XBB.1.5.51 > A3379G > T14658A > T26430C > C9559T > C22995G(**S:T478R**) [Query: `A3379G, C22995G, T26430C`, 2 seqs, 07/18]
- [ ] _Further step_ with **S:F456L** from **Branch 1**: XBB.1.5.51 > C22995G(**S:T478R**) > A28025G > A507G(ORF1a:H81R) > C28507T(ORF9b:A75V) > G10523C(ORF1a:V3420L), A19134G, C21597A(**S:S12Y**), T22928C(**S:F456L**), C27920T [Query: `C21597A, T22928C, C27920T`, 4 seqs, 07/10]
- [ ] _Further step_ with **S:Q613H** from **Branch 2**: XBB.1.5.51 > A3379G > C1875T(ORF1a:A537V), C14529T, C22498T, C22995G(**S:T478R**), C27600T > T6274C, C11094T(ORF1a:A3610V), C11824T, T12175C, C13957T(ORF1b:R164C), C21855T(**S:S98F**), G23401T(**S:Q613H**) [Query: `T12175C, C21855T, G23401T`, 9 seqs, 09/01]

Branch 1:

Transferred

_Transferred to cov-lineages/pango-designation#2186_ **Defining Mutations:** `XBB.1.5.51` > `C22995G(S:T478R)` **Query:** `A9291C, C25553T, C22995G, -T19209G, -A3379G` **Earliest seq:** 2023-01-24 (`EPI_ISL_16892598`, South Carolina, USA) **Latest seq:** 2023-07-08 (`EPI_ISL_18008689`, Oregon, USA) **Sampled Countries:** USA (48), Spain (12), Mexico (7), Austria (4), France (3), Germany (3), Netherlands (2), Belgium (1), Chile (1), India (1), Ireland (1), Peru (1), Sweden (1), UK (1, England)

Genomes:

`EPI_ISL_16892598, EPI_ISL_16944857, EPI_ISL_16945621, EPI_ISL_16992959, EPI_ISL_17127174, EPI_ISL_17170239, EPI_ISL_17201936, EPI_ISL_17250533, EPI_ISL_17278361, EPI_ISL_17279062, EPI_ISL_17384922, EPI_ISL_17384974, EPI_ISL_17411502, EPI_ISL_17412225, EPI_ISL_17417735, EPI_ISL_17417866, EPI_ISL_17430300, EPI_ISL_17446687, EPI_ISL_17465568, EPI_ISL_17467427, EPI_ISL_17471954, EPI_ISL_17476429, EPI_ISL_17477756, EPI_ISL_17497548, EPI_ISL_17519071, EPI_ISL_17546901, EPI_ISL_17554337, EPI_ISL_17588627, EPI_ISL_17591119, EPI_ISL_17591193, EPI_ISL_17591344, EPI_ISL_17597795, EPI_ISL_17612881, EPI_ISL_17651419, EPI_ISL_17664377, EPI_ISL_17664408, EPI_ISL_17664436, EPI_ISL_17665628-17665629, EPI_ISL_17667805, EPI_ISL_17712119, EPI_ISL_17723015, EPI_ISL_17765412, EPI_ISL_17782135, EPI_ISL_17785442, EPI_ISL_17788559, EPI_ISL_17791848, EPI_ISL_17791890, EPI_ISL_17797810, EPI_ISL_17805062, EPI_ISL_17814403, EPI_ISL_17833149, EPI_ISL_17839169, EPI_ISL_17842452, EPI_ISL_17844518, EPI_ISL_17845937, EPI_ISL_17853478, EPI_ISL_17861254, EPI_ISL_17880945, EPI_ISL_17880985, EPI_ISL_17881020, EPI_ISL_17885008, EPI_ISL_17950861, EPI_ISL_17950930, EPI_ISL_17956100, EPI_ISL_17956377, EPI_ISL_17966204, EPI_ISL_17971535, EPI_ISL_17971542, EPI_ISL_17972220, EPI_ISL_17976115, EPI_ISL_17976128, EPI_ISL_17976408, EPI_ISL_17976649, EPI_ISL_17976744, EPI_ISL_17978844, EPI_ISL_17987408, EPI_ISL_17990370, EPI_ISL_17997687, EPI_ISL_17997727, EPI_ISL_18008689, EPI_ISL_18011891, EPI_ISL_18026796, EPI_ISL_18038146, EPI_ISL_18042399`

---

Branch 2

Defining Mutations: XBB.1.5.51 > A3379G > C1875T(ORF1a:A537V), C14529T, C22498T, C22995G(S:T478R), C27600T Query: C14529T, C22498T, C22995G Earliest seq: 2023-03-07 (EPI_ISL_17249468, Maryland, USA) Latest seq: 2023-07-04 (EPI_ISL_17997281, Hongkong, China) Sampled Countries: USA (8, many with travel history to: Ghana), Ireland (3), Bulgaria (1), China (1, Hongkong), Finland (1), Germany (1), UK (1, England)

Genomes:

`EPI_ISL_17249468, EPI_ISL_17428406, EPI_ISL_17428527, EPI_ISL_17468642, EPI_ISL_17669173, EPI_ISL_17716722, EPI_ISL_17716765, EPI_ISL_17716835, EPI_ISL_17812678, EPI_ISL_17820969, EPI_ISL_17958969-17958970, EPI_ISL_17960218, EPI_ISL_17974335, EPI_ISL_17997281, EPI_ISL_18033613`

---

Branch 3

Defining Mutations: Branch 3: XBB.1.5.51 > A3379G > T14658A> T26430C > C9559T> C22995G(S:T478R) Query: A3379G, C22995G, T26430C Earliest seq: 2023-06-08 (EPI_ISL_17954550, Guatemala) Latest seq: 2023-07-11 (EPI_ISL_17996882, Ontario, Canada) Sampled Countries: Guatemala (1), Canada (1)

Genomes:

`EPI_ISL_17954550, EPI_ISL_17996882`

UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1dc96_24c530.json?c=gt-nuc_3379&f_userOrOld=uploaded%20sample

view from XBB.1.5.51 polytomy

details for Branch 1


details for Branch 2 & 3

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_304a6_256a90.json?c=gt-S_478,613&f_userOrOld=uploaded%20sample 

[FedeGueli]

Very good catch

[NkRMnZr]

Tracking updates:

08-01, 3 seqs on Branch 1 from USA; 2 seqs on Branch 2 from UK and Iceland

Branch 1, 3 seqs from USA: `EPI_ISL_18045070, EPI_ISL_18045407, EPI_ISL_18053721` Branch 2, 2 seqs from England, UK and Iceland: `EPI_ISL_18044170, EPI_ISL_18052596`, the latter has S:Q613H

08-05, 3 seqs from USA (Texas, Puerto Rico) on Branch 1

08-08, 4 seqs from USA on Branch 1

08-13, Branch 1, +3 (USA); Branch 2, +1 (Canada)

[NkRMnZr]

08-05, 3 seqs from USA (Texas, Puerto Rico) on Branch 1: EPI_ISL_18057108, EPI_ISL_18059991, EPI_ISL_18060006

[NkRMnZr]

08-08: Branch 1, +4 seqs from USA: EPI_ISL_18071339, EPI_ISL_18071343, EPI_ISL_18071349, EPI_ISL_18074162

[NkRMnZr]

08-13, Branch 1, +3 (USA); Branch 2, +1 (Canada) Branch 1, +3 from USA: EPI_ISL_18079516, EPI_ISL_18079822, EPI_ISL_18095389 Branch 2, +1 from Canada: EPI_ISL_18081741

[FedeGueli]

Please propose branch 1 on the main pango page.