Multiple XBB.2.3.3* Lineages with S:T478X

[NkRMnZr]

Multiple XBB.2.3.3* Lineages with S:T478X Tracker

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1. Branch 1: GJ.1.2 (XBB.2.3.3.1.2) > C5869T > C22995G(S:T478R) [Query: C7819G, C5869T, C22995G, 55 seqs, 12/15]
2. Branch 2: Designated as GJ.1.2.7 via cov-lineages/pango-designation@d0c77a4 , phylogenetic order follows: GJ.1.2 > C3020T(ORF1a:H919Y) > T6511C > C22995G(S:T478R) [Query: C3020T, T6511C, C22995G]
3. Branch 3: Designated as GJ.1.2.6 via cov-lineages/pango-designation@0b7f46a , phylogenetic order follows: GJ.1.2 > T16456C(ORF1b:S997P) > C22995G(S:T478R) [Query: C7819G, T16456C, C22995G]
4. Branch 4: GJ.1.2 > T16456C(ORF1b:S997P) > C24210T(S:T883I) > A12571G, C22995T(S:T478I) [Query: T16456C, C22995T, C24210T, 22 seqs, 12/12] Slow
5. Branch 5: GJ.1.2 > C22995T(S:T478I) [Query: C7819G, G16795A, C22995T, -T16456C, 20 seqs, 12/05] Slow
6. Branch 6: GJ.1.2.4 > C4084T, G18049A(ORF1b:V1528I), C22995G(S:T478R), C29284T [Query: C3020T, C4084T, C22995G, 29 seqs, 12/08]
7. Branch 7: GJ.1.2 > T22197C(S:L212S) > C11669T(ORF1a:R3802C), C22995G(S:T478R), T26510G [Query: C7819G, T22197C, C22995G, 27 seqs, 12/12]
8. Branch 8: GJ.1.2 > C25708T(ORF3a:L106F) > C22995G(S:T478R), C26873T, T27499G(ORF7a:S36A [Query: C7819G, C22995G, C25708T, 53 seqs, 12/04]
9. Branch 10: GJ.1.2 > T16456C(ORF1b:S997P) > C1427T(ORF1a:H388Y) > T25458C > G22241A(S:V227I), C22995G(S:T478R), A27979T(ORF8:Q29L) [Query: C1427T, T16456C, C22995G, 8 seqs, 10/22] Slow
10. Branch 11: XBB.2.3.3 > C19884T > C3688T > T22195C(S:N211N) > A8088G(ORF1a:K2608R) > A9085G, T11463C(ORF1a:M3733T), A22996T(S:T478N) [Query: C3688T, A8088G, A22996T, 15, 11/13] Slow
11. Designated as GJ.5 via cov-lineages/pango-designation@897f423 from XBB.2.3.3 (S:K182N) acquired S:T478R in Thailand (3% prevalence in August) and it is spreading internationally (158 seq - 13 countries) cov-lineages/pango-designation#2181 proposed by @FedeGueli , follows: XBB.2.3.3 > C19884T > C13138T> A11794G, C22995G(S:T478R) [Query: A11794G, C13138T, C19884T]
12. XBB.2.3.3 Sublineage w/new S2' FCS—S:N450D, S:K478R, S:P812R, S:V1264L + 4x ORF1ab (6 countries, 48 seq, Jan 21) #656 proposed by @ryhisner , follows: XBB.2.3.3 > C19884T > C936T(ORF1a:T224I), G16396T(ORF1b:G977C), A17622G > A6326G(ORF1a:T2021A), A13021G, A22910G(S:N450D), C22995G(S:T478R), T23830C > G3620A(ORF1a:G1119S), C15540T, C23997G(S:P812R), G25352C(S:V1264L), C26936T [Query: T23830C, C23997G, 38 seqs, 12/04]
13. JE.1 (GJ.1.2.1.1/XBB.2.3.3.1.2.1.1), designated via cov-lineages/pango-designation@e58c620, follows phylogenetic order: GJ.1.2.1 > C22995G(S:T478R), [Query: C7819G, A22910G, C22995G]
14. GJ.1.2.2, formerly misplaced under GJ.1.2.1, Designated via cov-lineages/pango-designation@18177cf, follows phylogenetic order: GJ.1.2 > G3719T(ORF1a:G1152C), C22995G(S:T478R), T28297C(ORF9b:I5T), T29068C, [Query: G3719T, C7819G, C22995G, T28297C]

• Query for all XBB.2.3.3* with S:T478X minus designated ones: spike_T478, -spike_T478K, G6536A, A22108T, -G669A, -C1190T, -T1927A, -G3719T, -T4726C, -T6511C, -A6739G, -C8251T, -G9190T, -A11794G, -C13138T, -A22910G, -G23587C, 394 seqs, 12/14.

Branch 1

Defining Mutations: GJ.1.2 > C5869T > C22995G(S:T478R)
Query: C7819G, C5869T, C22995G
Earliest seq: 2023-06-22 (EPI_ISL_17956860, Shanghai Customs, with travel history to The United Arab Emirates)
Latest seq: 2023-08-05 (EPI_ISL_18145390, California)
Sampled Countries: USA(4: CA/3; HI/1), China (1, ex. UAE)

Genomes:

EPI_ISL_17956860, EPI_ISL_18060602, EPI_ISL_18120714, EPI_ISL_18120993, EPI_ISL_18145390

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_33228_5ab10.json?f_userOrOld=uploaded%20sample&label=id:node_7377446

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Branch 2

Defining Mutations: GJ.1.2 > C3020T(ORF1a:H919Y) > T6511C > C22995G(S:T478R)
Query: C3020T, T6511C, C22995G
Earliest seq: 2023-06-26 (EPI_ISL_18030811, South Korea)
Latest seq: 2023-07-28 (EPI_ISL_18117817, South Korea)
Sampled Countries: South Korea (11)

Genomes:

EPI_ISL_18030811, EPI_ISL_18031062, EPI_ISL_18031253, EPI_ISL_18031280, EPI_ISL_18031484, EPI_ISL_18031541, EPI_ISL_18031862, EPI_ISL_18038938, EPI_ISL_18111724, EPI_ISL_18116390, EPI_ISL_18117817

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_33228_5ab10.json?f_userOrOld=uploaded%20sample&label=id:node_7375561

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Branch 3

Defining Mutations: GJ.1.2 > T16456C(ORF1b:S997P) > C22995G(S:T478R)
Query: C7819G, T16456C, C22995G
Earliest seq: 2023-05-26 (EPI_ISL_17816375, South Korea)
Latest seq: 2023-08-23 (EPI_ISL_18151210, Ontario, Canada)
Sampled Countries: USA (3: NJ; NY; WA), Canada (1: ON), South Korea

Genomes:

EPI_ISL_17816375, EPI_ISL_18072746, EPI_ISL_18121338, EPI_ISL_18121459, EPI_ISL_18151210

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_33228_5ab10.json?f_userOrOld=uploaded%20sample&label=id:node_7376202

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Branch 4

Defining Mutations: GJ.1.2 > T16456C(ORF1b:S997P) > C24210T(S:T883I) > A12571G, C22995T(S:T478I)
Query: T16456C, C22995T, C24210T
Earliest seq: 2023-07-29 (EPI_ISL_18108094, Hawaii)
Latest seq: 2023-08-14 (EPI_ISL_18144783, California)
Sampled Countries: USA (5: HI/3; CA/1; WA/1); Spain (1)

Genomes:

EPI_ISL_18095691, EPI_ISL_18104044, EPI_ISL_18108094, EPI_ISL_18143300, EPI_ISL_18144109, EPI_ISL_18144783

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1cad4_730b0.json?label=id:node_7376622

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Branch 5

Defining Mutations: GJ.1.2 > C22995T(S:T478I)
Query: C7819G, G16795A, C22995T, -T16456C
Earliest seq: 2023-07-28 (EPI_ISL_18094135, Iceland)
Latest seq: 2023-08-09 (EPI_ISL_18148013, USA)
Sampled Countries: Iceland (5), USA (1: DC)

Genomes:

EPI_ISL_18094135, EPI_ISL_18094136, EPI_ISL_18094141, EPI_ISL_18094147, EPI_ISL_18094152, EPI_ISL_18148013

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_23dab_77270.json?f_userOrOld=uploaded%20sample&label=id:node_7377691

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Branch 6

Defining Mutations: GJ.1.2 > C4084T, G18049A(ORF1b:V1528I), C22995G(S:T478R), C29284T
Query: C3020T, C4084T, C22995G
Earliest seq: 2023-08-22 (EPI_ISL_18141232, Singapore)
Latest seq: 2023-08-26 (EPI_ISL_18213433, Israel)
Sampled Countries: Israel (2), Singapore (1)

Genomes:

EPI_ISL_18141232, EPI_ISL_18213393, EPI_ISL_18213433

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3aec7_5762f0.json?f_userOrOld=uploaded%20sample&label=id:node_7381704

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Branch 7

Defining Mutations: GJ.1.2 > T22197C(S:L212S) > C11669T(ORF1a:R3802C), C22995G(S:T478R), T26510G
Query: C7819G, T22197C, C22995G
Earliest seq: 2023-08-08 (EPI_ISL_18156338, North Carolina)
Latest seq: 2023-08-25 (EPI_ISL_18232940, Washington)
Sampled Countries: USA (4: OR/2; NC; WA)

Genomes:

EPI_ISL_18156338, EPI_ISL_18211184, EPI_ISL_18225600, EPI_ISL_18232940

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1ad03_c66440.json?label=id:node_7401263

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Branch 8

Defining Mutations: GJ.1.2 > C25708T(ORF3a:L106F) > C22995G(S:T478R), C26873T, T27499G(ORF7a:S36A)
Query: C7819G, C22995G, C25708T
Earliest seq: 2023-08-08 (EPI_ISL_18130721, England)
Latest seq: 2023-09-04 (EPI_ISL_18258432, Bouches-du-Rhône)
Sampled Countries: France (2: PAC), UK (2: EN)

Genomes:

EPI_ISL_18130721, EPI_ISL_18216039, EPI_ISL_18258378, EPI_ISL_18258432

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_8477_44d570.json?label=id:node_10878890

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Branch 10

Defining Mutations: GJ.1.2 > T16456C(ORF1b:S997P) > C1427T(ORF1a:H388Y) > T25458C > G22241A(S:V227I), C22995G(S:T478R), A27979T(ORF8:Q29L)
Query: C1427T, T16456C, C22995G
Earliest seq: 2023-09-14 (EPI_ISL_18300158, Israel)
Latest seq: 2023-10-11 (EPI_ISL_18417835, Israel)
Sampled Countries: Israel (7), France (1)

Genomes:

EPI_ISL_18300158-18300159, EPI_ISL_18338276, EPI_ISL_18374009, EPI_ISL_18374027, EPI_ISL_18403037, EPI_ISL_18417833, EPI_ISL_18417835

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_38359_ec36c0.json?label=id%3Anode_4019050

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Branch 11

Defining Mutations: XBB.2.3.3 > C19884T > C3688T > T22195C(S:N211N) > A8088G(ORF1a:K2608R) > A9085G, T11463C(ORF1a:M3733T), A22996T(S:T478N)
Query: C3688T, A8088G, A22996T
Earliest seq: 2023-09-04 (EPI_ISL_18315891, Gujarat, India)
Latest seq: 2023-11-03 (EPI_ISL_18497346, England, UK)
Sampled Countries: India (5: GJ), USA (4: CO; IA; NY; WY), UK (3: EN), Israel (1), Mauritius (1), Spain (1)

Genomes:

EPI_ISL_18315891, EPI_ISL_18337673, EPI_ISL_18357572, EPI_ISL_18420442, EPI_ISL_18420465, EPI_ISL_18451036, EPI_ISL_18457714, EPI_ISL_18457717, EPI_ISL_18457726, EPI_ISL_18457731, EPI_ISL_18457739-18457740, EPI_ISL_18469918, EPI_ISL_18497346, EPI_ISL_18498369

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice6_genome_38359_ec36e0.json?label=id%3Anode_4024961

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---

Notable singlets

• USA/CA-CDPH-500126515/2023|EPI_ISL_18555769|2023-09-19
  GJ.1.2 > T16456C(ORF1b:S997P) > C5758T > C11102A(ORF1a:P3613T), G14050A(ORF1b:V195I) > C1884T(ORF1a:A540V), A4717G, T14796C, G22319T(S:D253C), G22331T(S:G257C), G22927A(S:L455L), C22995G(S:T478R), C26110T(ORF3a:P240S), T26573C, C29614T [Query: C5758T, C11102A, C22995G, 11/28]

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Don't be confused with #236

[FedeGueli]

AH this is a new one i was opening all the way the notification and thinking i have answered yesterday where is my answer?? sorry a little burn out in these days. great work. Lets propose each of them when they reach 35 if it is before 30 september.

[NkRMnZr]

Tracking updates

09-04, adding Branch 6 from former singlet
09-08, adding Branch 7
09-15, adding branch 8, 9
09-29
10-09

[FedeGueli]

1 , 2 , 3 seems slow 4 and 5 could be good 6 likely quite fast but too soon.

[NkRMnZr]

09-08

Branch 1, +1 (NL) EPI_ISL_18238207
Branch 2, +5 (JP, KR) EPI_ISL_18226607, EPI_ISL_18235792, EPI_ISL_18236876, EPI_ISL_18239270, EPI_ISL_18239503
Branch 3, +2 (CA, US) EPI_ISL_18239035, EPI_ISL_18240798
Branch 4, +3 (ES, US) EPI_ISL_18215662, EPI_ISL_18225064, EPI_ISL_18225076
Branch 5, +2 (SE, US) EPI_ISL_18221487, EPI_ISL_18222058
Branch 6, +1 (US) EPI_ISL_18225103

Adding Branch 7 from former doublet

[Over-There-Is]

Branch 6 is sublineage of GJ.1.2.4 now.

[FedeGueli]

///Also branch 2 is now a sublineage of GJ.1.2.4// Scratch this is the same branch but GJ.1.2.4 starts deeper in the tree.
( already recorrected the task)

While GJ.1.2.2 has been designated with S:T478R and Orf9b:I5T it was misplaced in GJ.1.2.1 tree so likely we didnt see it for that reason. But super interesting lineage with 3 mutations to Cysteine in the NSP2 and NSP3 via cov-lineages/pango-designation@18177cf

[NkRMnZr]

09-15

Branch 1, +5 (California; Noord-Brabant; Zagreb) EPI_ISL_18241664-18241666, EPI_ISL_18244831, EPI_ISL_18257854
Branch 3, +8 (Dublin; Israel; Singapore; Texas; Western Australia) EPI_ISL_18243337, EPI_ISL_18243342, EPI_ISL_18243446, EPI_ISL_18243981, EPI_ISL_18246941, EPI_ISL_18254314, EPI_ISL_18256049, EPI_ISL_18256073
Branch 4, +2 (Geneva, Hawaii) EPI_ISL_18241268, EPI_ISL_18258858
Branch 5, +1 (Bucharest) EPI_ISL_18262041
Branch 6, +3 (California; Israel) EPI_ISL_18246945, EPI_ISL_18246950, EPI_ISL_18261147

Adding Branch 8 from former doublet with 2 seqs from Bouches-du-Rhône
Adding Branch 9 from former quartlet with 3 seqs from Israel and California

[FedeGueli]

Branch 9 looks interesting with 554K in a subbranch thx

[FedeGueli]

@NkRMnZr the threshold to become a branch is three?

[NkRMnZr]

@FedeGueli
the threshold to become a branch is three?

Ah I forgot it's not FLip, maybe set it to 10? I'll fix that when new batch of seqs come in.

[FedeGueli]

Thank you. Still all quite fast so i think we can leave it at 3 or five as u prefer

[FedeGueli]

Branch 6 has been independently spotted and proposed i #830 i let that open i ve added credit to your work @NkRMnZr if it is ok for you.

[FedeGueli]

i have:
B1 = 18 (G.A)
B2 = 19 (G.A)
B3 = 18 (G.A.)
B4 = 11 (G.A.)
B5 = 18 (G.A.)
B6 = 8
B7 = 5
B8 = 5
B9 = 8

[NkRMnZr]

09-29

Branch 1, +8 (Denmark; USA) EPI_ISL_18263986, EPI_ISL_18267318, EPI_ISL_18269914, EPI_ISL_18270009, EPI_ISL_18280411, EPI_ISL_18280427, EPI_ISL_18308154, EPI_ISL_18316206
Branch 2, +12 (Australia, Belgium, Canada, Singapore, South Korea) EPI_ISL_18242692, EPI_ISL_18272248, EPI_ISL_18272284, EPI_ISL_18285264, EPI_ISL_18293166, EPI_ISL_18293259, EPI_ISL_18293268, EPI_ISL_18293589, EPI_ISL_18300734, EPI_ISL_18306982, EPI_ISL_18308914, EPI_ISL_18312930
Branch 3, +9 (Australia, Canada, Ireland, Israel, UK and USA) EPI_ISL_18267525, EPI_ISL_18273777, EPI_ISL_18280421, EPI_ISL_18300158-18300159, EPI_ISL_18300294, EPI_ISL_18302987, EPI_ISL_18305516, EPI_ISL_18324443
Branch 4, +2 (USA) EPI_ISL_18283153, EPI_ISL_18299595
Branch 5, +3 (Belgium, France, USA) EPI_ISL_18288017, EPI_ISL_18299675, EPI_ISL_18314194
Branch 7, +4 (USA) EPI_ISL_18267578, EPI_ISL_18274582, EPI_ISL_18305824, EPI_ISL_18322461
Branch 8, +9 (France and US) EPI_ISL_18273740, EPI_ISL_18281389, EPI_ISL_18281417, EPI_ISL_18295356, EPI_ISL_18301660, EPI_ISL_18302081, EPI_ISL_18302091, EPI_ISL_18302187, EPI_ISL_18314205
Branch 9, +3 (USA) EPI_ISL_18278433, EPI_ISL_18317692, EPI_ISL_18318849

[FedeGueli]

Branch 2 designated GJ.1.2.7 via cov-lineages/pango-designation@d0c77a4

[FedeGueli]

Branch 3 GJ.1.2.6 via cov-lineages/pango-designation@0b7f46a

[NkRMnZr]

10-09

Branch 1, +4 (Denmark, Singapore, USA) EPI_ISL_18335175, EPI_ISL_18337245, EPI_ISL_18352912, EPI_ISL_18355166
Branch 4, +2 (Spain, USA) EPI_ISL_18329498, EPI_ISL_18356383
Branch 7, +5 (US) EPI_ISL_18329623, EPI_ISL_18335620, EPI_ISL_18335631, EPI_ISL_18340169, EPI_ISL_18351787
Branch 8, +4 (France, Japan, UK) EPI_ISL_18325869, EPI_ISL_18326029, EPI_ISL_18354781, EPI_ISL_18357267

[FedeGueli]

Please propose branch 5 with S:T478I closing it now ( the other are not slow but unlikely to survive in this form)

[FedeGueli]

Branch 9 seems now growing at 22 and with 3/36 samples from Philippines it seems to have a relevant share there.

[FedeGueli]

also branch 8 grew to 46 managing to give birth to an outbreak in Canada but also exported in Ireland.

Ping @corneliusroemer on Branch 8 and Branch 9 if you can consider to designation or not.

[NkRMnZr]

12-02

Branch 1, +7 (US) EPI_ISL_18550258, EPI_ISL_18555841-18555842, EPI_ISL_18555889, EPI_ISL_18555903, EPI_ISL_18556037, EPI_ISL_18569999
Branch 6, +5 (SI; US) EPI_ISL_18546079, EPI_ISL_18546085, EPI_ISL_18546182-18546183, EPI_ISL_18555059
Branch 8, +6 (DE; ES; IT; PH; UK) EPI_ISL_18531523, EPI_ISL_18540562, EPI_ISL_18552349, EPI_ISL_18552356, EPI_ISL_18553011, EPI_ISL_18553190
Branch 9, +5 (SI; US) EPI_ISL_18546079, EPI_ISL_18546085, EPI_ISL_18546182-18546183, EPI_ISL_18555059

[NkRMnZr]

these are slowing down again

[NkRMnZr]

A sequence from Branch 6 got further S:L455F and S:F456S USA/CA-HLX-STM-GK9RARFYU/2023|EPI_ISL_18774385|2023-12-04

[FedeGueli]

A sequence from Branch 9 got further S:L455F and S:F456S USA/CA-HLX-STM-GK9RARFYU/2023|EPI_ISL_18774385|2023-12-04

query for it: C17985T ,C13011T,A26612T