Sub-lineage of: JN.1.7 (BA.2.86.1.1.7)
Earliest sequence: 2023-12-4, USA, Nevada — EPI_ISL_18663699
Most recent sequence: 2024-1-30, USA, California — EPI_ISL_18866056 + 1 other
Continents circulating: North America (127), Europe (6)
Countries circulating: USA (123), Canada (3), Spain (3), England (2), Costa Rica (1), Netherlands (1),
Number of Sequences: 133
GISAID Nucleotide Query: C10448T, C25566T, C23277T, -A405G, -G13427A
CovSpectrum Query: Nextcladepangolineage:JN.1.7* & [1-of: C10448T] & [exactly-0-of: A405G, G13427A]
Substitutions on top of JN.1:ORF1a: H3395Y (NSP5_H132Y)
Nucleotide: C10448T
Evidence
NSP5_P132H/ORF1a:P3395H has been universal ever since Omicron first appeared. It's one of the very rare NSP5 mutations to stick around (the major other one being the conservative NSP5_K90R/ORF1a:K3353R). This creates three nucleotides in a row different from wild-type. It appears to be growing quickly, but is probably just riding the JN.1.7 wave. It doesn't appear, at the moment, to be growing any faster than JN.1.7 as a whole.
The excluded mutations in the GISAID query were needed in order to filter out the usual garbage from Ginkgo Bozoworks.
Transferred from https://github.com/sars-cov-2-variants/lineage-proposals/issues/1374
Description
Sub-lineage of: JN.1.7 (BA.2.86.1.1.7) Earliest sequence: 2023-12-4, USA, Nevada — EPI_ISL_18663699 Most recent sequence: 2024-1-30, USA, California — EPI_ISL_18866056 + 1 other Continents circulating: North America (127), Europe (6) Countries circulating: USA (123), Canada (3), Spain (3), England (2), Costa Rica (1), Netherlands (1), Number of Sequences: 133 GISAID Nucleotide Query: C10448T, C25566T, C23277T, -A405G, -G13427A CovSpectrum Query: Nextcladepangolineage:JN.1.7* & [1-of: C10448T] & [exactly-0-of: A405G, G13427A] Substitutions on top of JN.1: ORF1a: H3395Y (NSP5_H132Y) Nucleotide: C10448T
USHER Tree https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons2/main/JN.1.7__NSP5_H132Y.json?label=id:node_2330313
Evidence NSP5_P132H/ORF1a:P3395H has been universal ever since Omicron first appeared. It's one of the very rare NSP5 mutations to stick around (the major other one being the conservative NSP5_K90R/ORF1a:K3353R). This creates three nucleotides in a row different from wild-type. It appears to be growing quickly, but is probably just riding the JN.1.7 wave. It doesn't appear, at the moment, to be growing any faster than JN.1.7 as a whole.
The excluded mutations in the GISAID query were needed in order to filter out the usual garbage from Ginkgo Bozoworks.
Genomes
Genomes
EPI_ISL_18663699, EPI_ISL_18690123, EPI_ISL_18690219, EPI_ISL_18692386, EPI_ISL_18692393, EPI_ISL_18699555, EPI_ISL_18715819, EPI_ISL_18729111, EPI_ISL_18729224, EPI_ISL_18731542, EPI_ISL_18731573, EPI_ISL_18743038, EPI_ISL_18743089, EPI_ISL_18743147, EPI_ISL_18743224, EPI_ISL_18743289, EPI_ISL_18743307-18743308, EPI_ISL_18743358, EPI_ISL_18743364, EPI_ISL_18743725, EPI_ISL_18746315, EPI_ISL_18746595, EPI_ISL_18750499, EPI_ISL_18755407, EPI_ISL_18757185, EPI_ISL_18773899, EPI_ISL_18773986, EPI_ISL_18776757, EPI_ISL_18776770, EPI_ISL_18776789, EPI_ISL_18778793, EPI_ISL_18778829, EPI_ISL_18778908, EPI_ISL_18780003, EPI_ISL_18780601, EPI_ISL_18780937, EPI_ISL_18780939, EPI_ISL_18781117-18781118, EPI_ISL_18782632, EPI_ISL_18800578, EPI_ISL_18804730, EPI_ISL_18808559, EPI_ISL_18809125, EPI_ISL_18809264, EPI_ISL_18809288, EPI_ISL_18813810, EPI_ISL_18816363, EPI_ISL_18816409, EPI_ISL_18816500, EPI_ISL_18816581, EPI_ISL_18816607, EPI_ISL_18816671, EPI_ISL_18816673, EPI_ISL_18816711, EPI_ISL_18816724, EPI_ISL_18816774, EPI_ISL_18816896, EPI_ISL_18816978, EPI_ISL_18817086, EPI_ISL_18818136, EPI_ISL_18818701, EPI_ISL_18818735-18818736, EPI_ISL_18826214, EPI_ISL_18826232, EPI_ISL_18826515, EPI_ISL_18826537, EPI_ISL_18826888, EPI_ISL_18827014, EPI_ISL_18827470, EPI_ISL_18827483, EPI_ISL_18827583, EPI_ISL_18827969, EPI_ISL_18834080, EPI_ISL_18834515, EPI_ISL_18834902, EPI_ISL_18835016, EPI_ISL_18835116, EPI_ISL_18835261, EPI_ISL_18835495, EPI_ISL_18835603, EPI_ISL_18835722, EPI_ISL_18837093, EPI_ISL_18837179, EPI_ISL_18838470, EPI_ISL_18838903, EPI_ISL_18839852, EPI_ISL_18840042, EPI_ISL_18841487, EPI_ISL_18846848, EPI_ISL_18846852, EPI_ISL_18846888, EPI_ISL_18846891, EPI_ISL_18847425, EPI_ISL_18847931, EPI_ISL_18848809, EPI_ISL_18849585, EPI_ISL_18849602, EPI_ISL_18849666, EPI_ISL_18852302, EPI_ISL_18853644, EPI_ISL_18856303, EPI_ISL_18859084, EPI_ISL_18859156, EPI_ISL_18859214, EPI_ISL_18859524, EPI_ISL_18859532, EPI_ISL_18859718, EPI_ISL_18859760, EPI_ISL_18859783, EPI_ISL_18859795, EPI_ISL_18860709, EPI_ISL_18861703, EPI_ISL_18861778, EPI_ISL_18861791, EPI_ISL_18861810, EPI_ISL_18861847, EPI_ISL_18862092, EPI_ISL_18863752, EPI_ISL_18864010, EPI_ISL_18866028, EPI_ISL_18866056, EPI_ISL_18866111, EPI_ISL_18867919, EPI_ISL_18868254, EPI_ISL_18868260, EPI_ISL_18868538, EPI_ISL_18868707, EPI_ISL_18869217, EPI_ISL_18869622, EPI_ISL_18871787