KP.2.3 subbranch with Orf3d-2:K6* (215 sequences, 11 or 12 countries, mainly in US-TX)

[Over-There-Is]

Transferred from sars-cov-2-variants/lineage-proposals#2025
KP.2.3> C28714T> T7438C> T18438C> A25983T(Orf3d-2:K6*)
Query: C8293T, T18438C, A25983T
Query for sequences without T18438C: -T18438C, A25983T, C28714T

Earliest sequence: 05-18 England, United Kingdom EPI_ISL_19187747
Latest sequence: 09-01 Nebraska, USA EPI_ISL_19407519
Regions detected:
US 123(Texas 69, Nebraska 10, New York 10, Ohio 7, California 4, Florida 4, Louisiana 3, Arizona 2, Illinois 2, Nevada 2, Pennsylvania 2, Utah 2, Arkansas 1, Colorado 1, Oklahoma 1, Oregon 1, Virginia 1, West Virginia 1, 7 not on GISAID), Canada 5(Alberta 2, BC 2, Ontario 1);
UK 5(England 4, Scotland 1), Italy 3(Emilia-Romagna 1, Lazio 1, Lombardy 1), France 1(Ile-de-France);
Brazil 3, Chile 1;
Japan 1(from US or Mexico)

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_22e96_af8400.json?c=country&label=id:node_7149230

Sequences:

EPI_ISL_19187747, EPI_ISL_19210644, EPI_ISL_19216695,
EPI_ISL_19216697, EPI_ISL_19224979, EPI_ISL_19239302,
EPI_ISL_19251198, EPI_ISL_19259887, EPI_ISL_19262428,
EPI_ISL_19264026, EPI_ISL_19268485, EPI_ISL_19270034,
EPI_ISL_19286922, EPI_ISL_19295163, EPI_ISL_19295173,
EPI_ISL_19295198, EPI_ISL_19295243, EPI_ISL_19301092,
EPI_ISL_19306322, EPI_ISL_19311032, EPI_ISL_19311537,
EPI_ISL_19311543, EPI_ISL_19314519, EPI_ISL_19317627,
EPI_ISL_19317653, EPI_ISL_19317681, EPI_ISL_19317749,
EPI_ISL_19317889, EPI_ISL_19318121, EPI_ISL_19318528,
EPI_ISL_19318925, EPI_ISL_19324448, EPI_ISL_19325512,
EPI_ISL_19332212, EPI_ISL_19334693, EPI_ISL_19334850,
EPI_ISL_19334890, EPI_ISL_19334913, EPI_ISL_19334930,
EPI_ISL_19334954, EPI_ISL_19335070, EPI_ISL_19335373,
EPI_ISL_19335394, EPI_ISL_19335403, EPI_ISL_19335429-19335430,
EPI_ISL_19335502, EPI_ISL_19335841, EPI_ISL_19337557,
EPI_ISL_19337610, EPI_ISL_19339715, EPI_ISL_19343445,
EPI_ISL_19343849, EPI_ISL_19344142, EPI_ISL_19346021,
EPI_ISL_19346982, EPI_ISL_19347453, EPI_ISL_19347800,
EPI_ISL_19347811, EPI_ISL_19347825, EPI_ISL_19347829,
EPI_ISL_19347845, EPI_ISL_19347848, EPI_ISL_19348774,
EPI_ISL_19348831, EPI_ISL_19348858, EPI_ISL_19349216,
EPI_ISL_19349257, EPI_ISL_19349411, EPI_ISL_19349436,
EPI_ISL_19349447, EPI_ISL_19349453, EPI_ISL_19349567,
EPI_ISL_19350758, EPI_ISL_19353743, EPI_ISL_19354122,
EPI_ISL_19354456, EPI_ISL_19354507, EPI_ISL_19359829,
EPI_ISL_19360071, EPI_ISL_19360132, EPI_ISL_19360301,
EPI_ISL_19360444, EPI_ISL_19362229, EPI_ISL_19362545,
EPI_ISL_19362589, EPI_ISL_19362790, EPI_ISL_19365550,
EPI_ISL_19365623, EPI_ISL_19365635, EPI_ISL_19365672,
EPI_ISL_19365695, EPI_ISL_19365985, EPI_ISL_19365997,
EPI_ISL_19366091, EPI_ISL_19366144, EPI_ISL_19366151,
EPI_ISL_19366177, EPI_ISL_19366223, EPI_ISL_19367932,
EPI_ISL_19368802, EPI_ISL_19379243, EPI_ISL_19379403,
EPI_ISL_19379588, EPI_ISL_19382464, EPI_ISL_19382790,
EPI_ISL_19382797, EPI_ISL_19382804, EPI_ISL_19383697,
EPI_ISL_19383792, EPI_ISL_19385720-19385721, EPI_ISL_19385870,
EPI_ISL_19387459, EPI_ISL_19391161, EPI_ISL_19392559,
EPI_ISL_19392576, EPI_ISL_19392580, EPI_ISL_19392586,
EPI_ISL_19392596, EPI_ISL_19394669, EPI_ISL_19407519,
EPI_ISL_19408610, EPI_ISL_19408636, EPI_ISL_19411733,
EPI_ISL_19411741, EPI_ISL_19411940, EPI_ISL_19413034,
EPI_ISL_19414159, EPI_ISL_19414168, EPI_ISL_19414203,
EPI_ISL_19414404, EPI_ISL_19415703, EPI_ISL_19419104,
EPI_ISL_19419530, PQ041158.1, PQ108265.1,
PQ147929.1, PQ212289.1, PQ242812.1,
PQ242883.1, PQ289413.1

[Over-There-Is]

Greece

[FedeGueli]

@corneliusroemer this is certainly faster than KP.2.3 baseline , for unknown reasons ( the orf3d mutation is all to be verified for having an impact, but apparently here it has. @ryhisner : any thougth on Orf3D and this mutation?)

[FedeGueli]

@Over-There-Is could you add a reference for the Orf3D sequence? is there a paper with it?
When referring not to Consensus it is useful to mention sources.

[FedeGueli]

New batch from Chile Uploaded today weirdly the count is still 155+3

[ryhisner]

@corneliusroemer this is certainly faster than KP.2.3 baseline , for unknown reasons ( the orf3d mutation is all to be verified for having an impact, but apparently here it has. @ryhisner : any thougth on Orf3D and this mutation?)

I've not seen any evidence that ORF3d is expressed at all, so if A25983T is relevant, I don't think it would be because it changes ORF3d.

[FedeGueli]

@corneliusroemer this is certainly faster than KP.2.3 baseline , for unknown reasons ( the orf3d mutation is all to be verified for having an impact, but apparently here it has. @ryhisner : any thougth on Orf3D and this mutation?)

I've not seen any evidence that ORF3d is expressed at all, so if A25983T is relevant, I don't think it would be because it changes ORF3d.

Thanks Ryan. It should have something different because it has an advantage over KP.2.3 baseline (so including all the evovled descendants) : https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nextcladePangoLineage=KP.2.3*&nucMutations1=C8293T%2CT18438C%2CA25983T&analysisMode=CompareToBaseline&

[FedeGueli]

And the advantage is the same also looking at US only where it is mostly sampled so it should not be a gographical effect/Sequencing intensity thing : https://cov-spectrum.org/explore/United%20States/AllSamples/Past3M/variants?nextcladePangoLineage=KP.2.3*&nucMutations1=C8293T%2CT18438C%2CA25983T&analysisMode=CompareToBaseline&

[DailyCovidCases]

Now 160 seqs, this branch has slowed down a lot

[Over-There-Is]

1 Sweden via US-NJ, 1 AU-NSW

[Over-There-Is]

EPI_ISL_19471571 A25983T dropout
C8293T, A8965T, T18438C, -A25983T

[Over-There-Is]

10 not on gisaid now.

[FedeGueli]

15/192 from Spetember likely dying off