DV.7 with ORF1b:A520V (nsp12_A529V), ORF3a:A72T (120 seqs, 10 countries)

[NkRMnZr]

Main proposal transferred to cov-lineages/pango-designation#2038

Original Main Proposal:

Defining mutations: (On top of CH.1.1.1's C25721T(ORF3a:A110V) > T4402A, that is, sibling to DV.1/2/3/5/6) > C10908T(ORF1a:A3548V) > C24134A(S:L858I) >
Query parental lineage : C25721T, T4402A, C10908T, C24134A, 200 seqs total, EDITED
Earliest seq: 2023/1/19 (EPI_ISL_16812642, Germany)
Latest seq: 2023/5/14 (EPI_ISL_17721803, UK)
Countries: UK (96, All England), Germany (20), Australia (4, All SA), Spain (2), Netherlands (1), France (1), USA (1, California)

Genomes:

EPI_ISL_16812642, EPI_ISL_16812860, EPI_ISL_16879358, EPI_ISL_16879359, EPI_ISL_16879366, EPI_ISL_16879382, EPI_ISL_16879413, EPI_ISL_16879424, EPI_ISL_16879488, EPI_ISL_16879496, EPI_ISL_16879517, EPI_ISL_16911716, EPI_ISL_16911849, EPI_ISL_16911869, EPI_ISL_16924619, EPI_ISL_16924695, EPI_ISL_16978857, EPI_ISL_16985870, EPI_ISL_17005111, EPI_ISL_17006309, EPI_ISL_17006458, EPI_ISL_17007332, EPI_ISL_17007827, EPI_ISL_17016847, EPI_ISL_17032222, EPI_ISL_17071230, EPI_ISL_17095132, EPI_ISL_17098110, EPI_ISL_17098122, EPI_ISL_17098152, EPI_ISL_17098168, EPI_ISL_17098236, EPI_ISL_17098239, EPI_ISL_17098389, EPI_ISL_17153388, EPI_ISL_17153397, EPI_ISL_17153447, EPI_ISL_17153515, EPI_ISL_17153530, EPI_ISL_17153589, EPI_ISL_17153681, EPI_ISL_17153906, EPI_ISL_17164896, EPI_ISL_17164960, EPI_ISL_17175404, EPI_ISL_17178096, EPI_ISL_17184404, EPI_ISL_17184440, EPI_ISL_17188128, EPI_ISL_17209872, EPI_ISL_17210134, EPI_ISL_17210169, EPI_ISL_17218851, EPI_ISL_17231442, EPI_ISL_17232517, EPI_ISL_17232626, EPI_ISL_17232679, EPI_ISL_17245402, EPI_ISL_17245457, EPI_ISL_17245886, EPI_ISL_17254450, EPI_ISL_17255538, EPI_ISL_17255547, EPI_ISL_17255862, EPI_ISL_17263234, EPI_ISL_17267206, EPI_ISL_17267252, EPI_ISL_17267272, EPI_ISL_17267288, EPI_ISL_17267322, EPI_ISL_17273926, EPI_ISL_17273949, EPI_ISL_17296374, EPI_ISL_17298882, EPI_ISL_17317110, EPI_ISL_17317206, EPI_ISL_17317254, EPI_ISL_17317308, EPI_ISL_17317316, EPI_ISL_17348275, EPI_ISL_17349096, EPI_ISL_17350760, EPI_ISL_17372926, EPI_ISL_17381502, EPI_ISL_17381686, EPI_ISL_17381954, EPI_ISL_17398424, EPI_ISL_17400589, EPI_ISL_17406860, EPI_ISL_17407849, EPI_ISL_17409545, EPI_ISL_17416805, EPI_ISL_17426979, EPI_ISL_17464260, EPI_ISL_17469827, EPI_ISL_17484800, EPI_ISL_17502280, EPI_ISL_17506823, EPI_ISL_17541789, EPI_ISL_17541854, EPI_ISL_17542173, EPI_ISL_17548038, EPI_ISL_17548813, EPI_ISL_17598847, EPI_ISL_17598889, EPI_ISL_17606372, EPI_ISL_17606576, EPI_ISL_17606643, EPI_ISL_17622521, EPI_ISL_17622662, EPI_ISL_17623124, EPI_ISL_17640241, EPI_ISL_17666230, EPI_ISL_17666261, EPI_ISL_17666461, EPI_ISL_17685527, EPI_ISL_17692299, EPI_ISL_17692520, EPI_ISL_17692649, EPI_ISL_17692821, EPI_ISL_17693048, EPI_ISL_17710132, EPI_ISL_17721674, EPI_ISL_17721690, EPI_ISL_17721803

There are many more interesting mutations under this branch, e.g. S:S494P, S:T573I, there are only small clusters at the moment. There's another branch got S:G213V and S:S408R reversions. While keeping eyes on those, there's one cluster seems to grow quickly, which follows:

Defining mutations: (On top of the branch proposed above) > T4036A > C2227T, T25959C > C15026T(ORF1b:A520V) > G25606A(ORF3a:A72T) >
Query: C15026T, G25606A, T25959C, -G22927T [77 seqs]
Earliest seq: 2023-03-04 (EPI_ISL_17284442, UK)
Latest seq: 2023-05-22 (EPI_ISL_17762415, Spain)
Countries: UK (60: England/54, Wales/3, Scotland/3), USA (8, Minnesota, Iowa, Tennessee, North Carolina, Hawaii, Massachusetts, New Jersey, New York), France (4), Portugal (2), Spain (2), Italy (1), Canada (1, Quebec), Finland (1)

Genomes:

EPI_ISL_17246478, EPI_ISL_17284226, EPI_ISL_17284442, EPI_ISL_17293454, EPI_ISL_17299371, EPI_ISL_17350701, EPI_ISL_17350729, EPI_ISL_17381280, EPI_ISL_17381494, EPI_ISL_17381790, EPI_ISL_17382127, EPI_ISL_17382583, EPI_ISL_17400449, EPI_ISL_17400456, EPI_ISL_17400522, EPI_ISL_17400548, EPI_ISL_17400579, EPI_ISL_17400720, EPI_ISL_17400897, EPI_ISL_17400937, EPI_ISL_17400975, EPI_ISL_17417072, EPI_ISL_17426715, EPI_ISL_17426936, EPI_ISL_17426984, EPI_ISL_17434242, EPI_ISL_17464270, EPI_ISL_17464339, EPI_ISL_17464381, EPI_ISL_17465603, EPI_ISL_17470438, EPI_ISL_17484534, EPI_ISL_17484559, EPI_ISL_17484566, EPI_ISL_17484588, EPI_ISL_17484785, EPI_ISL_17513801, EPI_ISL_17534559, EPI_ISL_17541980, EPI_ISL_17542291, EPI_ISL_17542424, EPI_ISL_17549184, EPI_ISL_17549262, EPI_ISL_17549277, EPI_ISL_17587456, EPI_ISL_17598855, EPI_ISL_17598875, EPI_ISL_17598887, EPI_ISL_17598964, EPI_ISL_17606927, EPI_ISL_17608712, EPI_ISL_17614114, EPI_ISL_17614327, EPI_ISL_17617451, EPI_ISL_17626604, EPI_ISL_17666331, EPI_ISL_17666414, EPI_ISL_17666472, EPI_ISL_17666744, EPI_ISL_17666971, EPI_ISL_17677194, EPI_ISL_17692657, EPI_ISL_17692697, EPI_ISL_17692712, EPI_ISL_17700357, EPI_ISL_17704723, EPI_ISL_17705027, EPI_ISL_17715855, EPI_ISL_17716346, EPI_ISL_17720128, EPI_ISL_17720165, EPI_ISL_17721623, EPI_ISL_17726537, EPI_ISL_17732072, EPI_ISL_17736987, EPI_ISL_17762415, EPI_ISL_17763228, EPI_ISL_17776850, EPI_ISL_17776922

There's a seq with long branch of mutations from England, EPI_ISL_17666331 with mutations like:

Saltation:

nuc	unique	T1114C, G2089A, G3284A, C3634T, C7231T, G7940A, C8419T, G8844A, G9116A, G9575A, A11017G, G11204A, C11442T, G12067A, G12223A, G12265A, C12415T, G15448A, C16101T, G17149A, C19113T, A20297G, G21375A, C22127T, G27420A, C27847T, C28783T, A28983G
nuc	homoplasies	T202C, C3267T, C10747T, C11668T, C13366T, C15240T, T21198C
ORF1ab	unique	E1007K, V2559I, R2860K, D2951N, V3104I, V3647I, A3726V, M3934I, G5062S, V5629M, K6678R
ORF1ab	homoplasies	T1001I
S	unique	L189F
ORF7b	unique	S31L
N	unique	K237R

QC check

so far it's only 1 seq so it may not be a big deal yet, just keep an eye on it.

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_30566_9135a0.json?c=pango_lineage&f_userOrOld=uploaded%20sample&label=id:node_7294302&showBranchLabels=all

Trivia:

• S:L858I (C24134A) is one of the definition mutations found in BA.2.39, CH.1.1.12, BQ.1.25.1, FZ.1.1 (XBB.1.5.47.1.1)
• ORF1b:A520V (C15026T, nsp3:A72V) is one one of the definition mutations found in XBC, BA.5.1.7
• ORF3a:A72T (G25606A) was once driven by some BQ.1.12, actually about a quarter of BQ.1.12 sequences has this mutation, quite a bit share of recent FD.1.1 seqs from Canada also has it.

[FedeGueli]

I think @ryhisner spotted this or something in this one last week, we have discussed a bit if it could be CH.1.1.12 but it cannot be.

[NkRMnZr]

I think @ryhisner spotted this or something in this one last week, we have discussed a bit if it could be CH.1.1.12 but it cannot be.

just added some info for EPI_ISL_17666331 35 nuc saltation

[ryhisner]

@NkRMnZr, thanks for proposing this. I thought this was probably a new lineage, but I was too lazy to investigate closely and write a proposal.

And that 35-nuc saltation is on my list of molnupiravir sequences. It's a no-doubter: 35/35 nuc mutations are transitions, with 14/35 (40%) G->A and 42.9% C->T.

[FedeGueli]

Pleasee propose the main branch while keep this open to monitor the sublineage.

[NkRMnZr]

Tracking updates:

Update 1, 23-06-17: 9 additional seqs since parent branch got designated

6 from Spain: EPI_ISL_17780925, EPI_ISL_17780999, EPI_ISL_17781006, EPI_ISL_17786000, EPI_ISL_17786016

2 from England: EPI_ISL_17803936, EPI_ISL_17808992

1 from Sweden (new entry): EPI_ISL_17809228

Update 2, 23-06-21, 7 seqs from 3 countries:

3 from England, UK: EPI_ISL_17813066, EPI_ISL_17813069, EPI_ISL_17813073

3 from Spain: EPI_ISL_17812745, EPI_ISL_17812757, EPI_ISL_17817737
1 from Michigan, USA: EPI_ISL_17815211

Of all the seqs, there are 12 from Spain that actually goes to #135 , query now filtered by -G22927T

a sub-branch of this one that acquired L455F+F456L combo now designated as DV.7.1:

cov-lineages/pango-designation@ed6f4b2

EPI_ISL_17726537, EPI_ISL_17762415, EPI_ISL_17780925, EPI_ISL_17780999, EPI_ISL_17781001, EPI_ISL_17781004, EPI_ISL_17781006, EPI_ISL_17786000, EPI_ISL_17786016, EPI_ISL_17812745, EPI_ISL_17812757, EPI_ISL_17817737

UShER tree after 3 updates:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_f1f3_974470.json?f_userOrOld=uploaded%20sample

Update 3, 23-06-27, 12 seqs from Canada:

all from Ontario:

EPI_ISL_17849074, EPI_ISL_17849076-17849079, EPI_ISL_17849123, EPI_ISL_17849127, EPI_ISL_17849130, EPI_ISL_17849149-17849150, EPI_ISL_17849213, EPI_ISL_17849215

Update 4, 23-06-29, 4 seqs from 2 countries:

2 from England: EPI_ISL_17884499, EPI_ISL_17884500

New entry:
2 from Japan: EPI_ISL_17881369, EPI_ISL_17882926

Update 5: 23-07-06, 5 seqs from 3 countries

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3cad2_6722d0.json?f_userOrOld=uploaded%20sample&showBranchLabels=all

1 from Italy: EPI_ISL_17949479
1 from England: EPI_ISL_17953433
1 from Scotland: EPI_ISL_17960326
2 from Ontario, Canada: EPI_ISL_17960583, EPI_ISL_17960588

[FedeGueli]

Please propose this one too in the main page.

[NkRMnZr]

Please propose this one too in the main page.

The problem is, its sub-branch with L455F+F456L combo already got designated recently as DV.7.1. The query of this one already filtered them out, but seems still growing.

[FedeGueli]

cov-lineages/pango-designation

So we can just close this one. Id sone specific lineage will pop up we will name 7.2 7.3 and so on

[NkRMnZr]

cov-lineages/pango-designation

So we can just close this one. Id sone specific lineage will pop up we will name 7.2 7.3 and so on

Agreed, closing it down to monitor it privately.