Multiple FL.1.5.1 branches with S:E554X

[NkRMnZr]

Multiple FL.1.5.1 branches with S:E554K or S:E554D

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1. Branch 1 Designated as HN.5 via cov-lineages/pango-designation@b16ba74 , phylogenetic order follows: FL.1.5.1 > G23222A(S:E554K) [Query: G20060T, C22995G, G23222A, -A6063C, -G20944A, -C21036T, -G28375A]
2. Branch 2 FL.1.5.1 > C703T, A6063C(ORF1a:D1933A), C18981T > C619T, A2071G > T25833C > C15656T(ORF1b:T730I), G23222A(S:E554K) [Query: C619T, A6063C, G23222A, 13 seqs, 10/23]
3. HN.1 + ORF1a:I1367V and S:E554D (77) represents 2.1% of cases in Sweden #825 , proposed by @Fearuncle , HN.1 > A4364G(ORF1a:I1367V) > G23224T(S:E554D) [Query: A4364G, C21036T, G23224T, 62 seqs, 10/23]

Branch 1: Designated as HN.5 via cov-lineages/pango-designation@b16ba74

Designated as HN.5

Defining Mutations: FL.1.5.1 > G23222A(S:E554K)
Query: G20060T, C22995G, G23222A, -A6063C, -G20944A, -C21036T, -G28375A
Earliest seq: 2023-05-26 (EPI_ISL_17964641, Nizwá, Oman)
Latest seq: 2023-10-02 (EPI_ISL_18362024, Singapore)
Sampled Countries: Germany (9), Switzerland (6), Finland (4), UK (4: EN/3; SC), US (4: NJ/3; NY), Canada (3: ON/2; BC), Denmark (2), Ireland (2), Israel (2), Singapore (2), Costa Rica (1), France (1), Greece (1), South Korea (1), Oman (1), Sweden (1)

Genomes:

EPI_ISL_17964641, EPI_ISL_18039197, EPI_ISL_18052725, EPI_ISL_18216685, EPI_ISL_18220207, EPI_ISL_18255968, EPI_ISL_18258846, EPI_ISL_18258853, EPI_ISL_18284327, EPI_ISL_18285604, EPI_ISL_18285606, EPI_ISL_18295175, EPI_ISL_18299611, EPI_ISL_18299615, EPI_ISL_18299617, EPI_ISL_18299626, EPI_ISL_18299628, EPI_ISL_18299633, EPI_ISL_18300173, EPI_ISL_18309263, EPI_ISL_18309369, EPI_ISL_18314607, EPI_ISL_18315392, EPI_ISL_18323383, EPI_ISL_18323399, EPI_ISL_18323401, EPI_ISL_18340102, EPI_ISL_18343447, EPI_ISL_18343547, EPI_ISL_18344918, EPI_ISL_18345629, EPI_ISL_18347795, EPI_ISL_18347824, EPI_ISL_18347876, EPI_ISL_18347934, EPI_ISL_18356133, EPI_ISL_18356689, EPI_ISL_18357972, EPI_ISL_18359854, EPI_ISL_18360430, EPI_ISL_18360435, EPI_ISL_18361779, EPI_ISL_18362024, EPI_ISL_18362302

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1b557_3f7c90.json?f_userOrOld=uploaded%20sample&label=id:node_3391285

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Branch 2

Defining Mutations: FL.1.5.1 > C703T, A6063C(ORF1a:D1933A), C18981T > C619T, A2071G > T25833C > C15656T(ORF1b:T730I), G23222A(S:E554K)
Query: C619T, A6063C, G23222A
Earliest seq: 2023-08-14 (EPI_ISL_18168343, Lisses, France)
Latest seq: 2023-09-18 (EPI_ISL_18357389, France)
Sampled Countries: France (8), Japan (1)

Genomes:

EPI_ISL_18168343, EPI_ISL_18220219-18220220, EPI_ISL_18221831, EPI_ISL_18221870, EPI_ISL_18258682, EPI_ISL_18280676, EPI_ISL_18306605, EPI_ISL_18357389

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_24e9c_3fa7e0.json?f_userOrOld=uploaded%20sample&label=id:node_3390952

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[FedeGueli]

branch 1 seems quite fast. branch 2 to me is slow.

[NkRMnZr]

Tracking updates

10-15, Branch 1 +25; Branch 2 +3

Branch 1, +25 from Austria, Canada, Denmark, Georgia, Israel, S. Korea, UK, USA (1 ex. Spain)
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2dc03_bdbe20.json?f_userOrOld=uploaded%20sample

EPI_ISL_18366502, EPI_ISL_18368552, EPI_ISL_18369112, EPI_ISL_18370391, EPI_ISL_18370640, EPI_ISL_18372427, EPI_ISL_18373672, EPI_ISL_18374050, EPI_ISL_18378326, EPI_ISL_18380867, EPI_ISL_18381338, EPI_ISL_18381361, EPI_ISL_18381405, EPI_ISL_18382049, EPI_ISL_18383209, EPI_ISL_18383666, EPI_ISL_18383757, EPI_ISL_18384108, EPI_ISL_18385294, EPI_ISL_18385302, EPI_ISL_18389257, EPI_ISL_18389276, EPI_ISL_18389369, EPI_ISL_18389467, EPI_ISL_18389496

Branch 2, +3 from France EPI_ISL_18378937-18378938, EPI_ISL_18388720

[FedeGueli]

G20060T, C22995G, G23222A, -A6063C, -G20944A, -C21036T, -G28375A

Propose branch 1 : https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nextcladePangoLineage=HK.3*&nucMutations1=G20060T%2CC22995G%2CG23222A%2C6063A%2C20944G%2C21036C%2C28375G&analysisMode=CompareToBaseline&

[FedeGueli]

Branch 1 designated HN.5 via cov-lineages/pango-designation@b16ba74

[NkRMnZr]

branch 2 seems slow, closing it for now

[FedeGueli]

Thank you

[FedeGueli]

the Orf9b:S63F branch of HN.5 could be the donor of XDA : look:

https://cov-spectrum.org/explore/World/AllSamples/from%3D2023-11-01%26to%3D2023-12-19/variants?nextcladePangoLineage=XDA*&nucMutations1=C28471T&nextcladePangoLineage1=HN.5*&analysisMode=CompareEquals&
@corneliusroemer

[FedeGueli]

the Orf9b:S63F branch of HN.5 could be the donor of XDA : look: https://cov-spectrum.org/explore/World/AllSamples/from%3D2023-11-01%26to%3D2023-12-19/variants?nextcladePangoLineage=XDA*&nucMutations1=C28471T&nextcladePangoLineage1=HN.5*&analysisMode=CompareEquals& @corneliusroemer

already shown by lineages note.