NL.6 with Orf7b frameshift in Denmark recently(113 seqs, 9 Places) prevalence down to 15% in April

[FedeGueli]

Transferred from sars-cov-2-variants/lineage-proposals#2532

Frameshifting deletions in Orf7b seem being back recently,
Here we document a NL.6 sublineage rising in. prevalence in Denmark after getting the new orf7b
Interesting this time is a little bit different than in the XBB era, because here we have two nucleotides removed (del27795 and del27796) and it starts from Orf7b:F13- that is replaced by TTT so it maintains F as first AA of the frameshifted ORF7b after Orf7b:F13- for this reason Gisaid sees it del27795-96 and not del27792-93 as nextclade does)

The new orf7b resulting from the frameshift is:
Orf7b:1MIELSLIDFYLCFSLSATPCFNYAYYLLVLT32stop
instead of
Orf7b:1MIELSLIDFYLCFLAFLLLLVLIMLIIFWFSLELQDHNETCHA44stop

@corneliusroemer please consider that:

1. this represents most of NL.6: 106/136
2. most of the samples of this has also ORF1a:L3754F(G11527T), T19725G : 93/106
3. It has been sampled in 5 different countries and in the US in 5 different states, so clearly real

NL.6>> Orf7b:F14-(del27795_27796) > ORF1a:L3754F(G11527T), T19725G
Query:C18526T, G25088T, del27795_27796
Samples: 106
First sampled on 2024-09-30 in Den
Places: Denmark 74, US 24(MN 17,IA,MI 2,RI,OH 3),Netherlands 4, Ireland 2, England 2
Tree:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_1e9c78_35e8a0.json?label=id:node_7144649

IDs:
EPI_ISL_19498087, EPI_ISL_19498232, EPI_ISL_19531541,
EPI_ISL_19534317, EPI_ISL_19540417, EPI_ISL_19545137,
EPI_ISL_19555465, EPI_ISL_19562781, EPI_ISL_19602794,
EPI_ISL_19602851, EPI_ISL_19605403, EPI_ISL_19615098,
EPI_ISL_19615855, EPI_ISL_19652444, EPI_ISL_19652471,
EPI_ISL_19652530, EPI_ISL_19652573, EPI_ISL_19658852,
EPI_ISL_19664449, EPI_ISL_19666998, EPI_ISL_19667114,
EPI_ISL_19667126, EPI_ISL_19667139, EPI_ISL_19667198,
EPI_ISL_19670022, EPI_ISL_19679917, EPI_ISL_19690720,
EPI_ISL_19692157, EPI_ISL_19695096, EPI_ISL_19695140,
EPI_ISL_19695154, EPI_ISL_19695993, EPI_ISL_19696049,
EPI_ISL_19702930, EPI_ISL_19703645, EPI_ISL_19708110,
EPI_ISL_19711262, EPI_ISL_19716137, EPI_ISL_19722398,
EPI_ISL_19722414, EPI_ISL_19722423, EPI_ISL_19722433,
EPI_ISL_19722454, EPI_ISL_19722466, EPI_ISL_19722484,
EPI_ISL_19734938, EPI_ISL_19734996, EPI_ISL_19735059,
EPI_ISL_19751849, EPI_ISL_19751858-19751859, EPI_ISL_19751908,
EPI_ISL_19751910, EPI_ISL_19751920, EPI_ISL_19751923,
EPI_ISL_19770915, EPI_ISL_19776503-19776504, EPI_ISL_19776511,
EPI_ISL_19776522, EPI_ISL_19776548, EPI_ISL_19776578,
EPI_ISL_19776583, EPI_ISL_19793546, EPI_ISL_19793582,
EPI_ISL_19795981, EPI_ISL_19796006, EPI_ISL_19796019,
EPI_ISL_19796023-19796024, EPI_ISL_19796026, EPI_ISL_19796050,
EPI_ISL_19796052, EPI_ISL_19796061-19796062, EPI_ISL_19821482,
EPI_ISL_19822774, EPI_ISL_19822777, EPI_ISL_19822782,
EPI_ISL_19822786, EPI_ISL_19822793-19822795, EPI_ISL_19822803,
EPI_ISL_19822806, EPI_ISL_19822811, EPI_ISL_19822815,
EPI_ISL_19822818, EPI_ISL_19822824, EPI_ISL_19822833,
EPI_ISL_19822839, EPI_ISL_19822844, EPI_ISL_19831788,
EPI_ISL_19832203, EPI_ISL_19852999, EPI_ISL_19853173,
EPI_ISL_19854628-19854629, EPI_ISL_19854634, EPI_ISL_19854637-19854638,
EPI_ISL_19854640, EPI_ISL_19854644, EPI_ISL_19854648,
EPI_ISL_19854650, EPI_ISL_19854658

[FedeGueli]

I just discovered that most of NL.10 has exactly the same deletion of this proposed lineage and smae Orf7b frameshifted consequently:

Query:,del27795,C15763T,C1387T,T3565C
Samples: 108
Places: 13 American States + 3 exportations
Tree:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_1e3352_1ac8c0.json?label=id:node_7141739

[xz-keg]

designated NL.6.1