XBB.1.16 with ORF1a:A3889T, S:F456L then saltation with ORF1a:G963D, ORF1a:K2045R, S:E554K and ORF3a:M260T (171 seqs, mainly in France, 19 countries)

[NkRMnZr]

Transferred from sars-cov-2-variants/lineage-proposals#922

Defining Mutations: XBB.1.16 > G11930A(ORF1a:A3889T/nsp7_A30T) > T22928C(S:F456L) > G3153A(ORF1a:G963D/nsp3_G145D), A6399G(ORF1a:K2045R/nsp3_K1227R), C7720T, T12673C, T19065G, T20484C, C20628T, G23222A(S:E554K), T26171C(ORF3a:M260T), A28984G
Query: A6399G, G11930A, T22928C
Earliest seq: 2023-08-07 (EPI_ISL_18147969, Bouches-du-Rhône, France)
Latest seq: 2023-10-12 (EPI_ISL_18422743, Auvergne-Rhône-Alpes, France)
Sampled Countries: France (85), UK (6: EN), Austria (2), Croatia (1), Ireland (1), Israel (1), Poland (1), Switzerland (1), USA (4: NY/2; ex. United Arab Emirates/2)

Genomes:

EPI_ISL_18147969, EPI_ISL_18215130-18215131, EPI_ISL_18221730, EPI_ISL_18228747, EPI_ISL_18228846, EPI_ISL_18228979, EPI_ISL_18229085, EPI_ISL_18229098, EPI_ISL_18229239, EPI_ISL_18229335, EPI_ISL_18229340, EPI_ISL_18229633, EPI_ISL_18229636, EPI_ISL_18229643, EPI_ISL_18258298, EPI_ISL_18258365, EPI_ISL_18258376, EPI_ISL_18258418, EPI_ISL_18258447, EPI_ISL_18258455, EPI_ISL_18258462, EPI_ISL_18258467, EPI_ISL_18258469, EPI_ISL_18258821, EPI_ISL_18273211, EPI_ISL_18280744, EPI_ISL_18280782, EPI_ISL_18295375, EPI_ISL_18295530, EPI_ISL_18295558, EPI_ISL_18295566, EPI_ISL_18295578, EPI_ISL_18295592, EPI_ISL_18295594, EPI_ISL_18295615, EPI_ISL_18300169, EPI_ISL_18309232, EPI_ISL_18313720, EPI_ISL_18314249, EPI_ISL_18322392, EPI_ISL_18326506, EPI_ISL_18326563, EPI_ISL_18326583, EPI_ISL_18326937, EPI_ISL_18326958, EPI_ISL_18327135, EPI_ISL_18327153, EPI_ISL_18327249, EPI_ISL_18327291, EPI_ISL_18327315, EPI_ISL_18327420, EPI_ISL_18331883, EPI_ISL_18332023, EPI_ISL_18352495, EPI_ISL_18354516, EPI_ISL_18355964, EPI_ISL_18356924, EPI_ISL_18356972, EPI_ISL_18356979, EPI_ISL_18357095, EPI_ISL_18357173, EPI_ISL_18357257, EPI_ISL_18357266, EPI_ISL_18357270, EPI_ISL_18357272, EPI_ISL_18357280, EPI_ISL_18357347, EPI_ISL_18357390, EPI_ISL_18361686, EPI_ISL_18363481, EPI_ISL_18369422, EPI_ISL_18370608, EPI_ISL_18375993, EPI_ISL_18385116, EPI_ISL_18385568, EPI_ISL_18386598, EPI_ISL_18386602, EPI_ISL_18387057, EPI_ISL_18387152, EPI_ISL_18387605, EPI_ISL_18387673, EPI_ISL_18387737, EPI_ISL_18387741, EPI_ISL_18396767, EPI_ISL_18396864, EPI_ISL_18396926, EPI_ISL_18396938, EPI_ISL_18412674, EPI_ISL_18421168, EPI_ISL_18422676, EPI_ISL_18422697, EPI_ISL_18422712, EPI_ISL_18422743, EPI_ISL_18422794, EPI_ISL_18422802, EPI_ISL_18422866, EPI_ISL_18422925, EPI_ISL_18422953, EPI_ISL_18423059, EPI_ISL_18423109, EPI_ISL_18423163

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1cdcb_75e340.json?f_userOrOld=uploaded%20sample&label=id:node_3246965

[NkRMnZr]

Tracking updates

10-29, 16 seqs from Belgium, Denmark, France, Italy and Switzerland

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_325bd_f2e630.json?f_userOrOld=uploaded%20sample&label=id:node_3249091

EPI_ISL_18428362, EPI_ISL_18437864, EPI_ISL_18438858, EPI_ISL_18440879, EPI_ISL_18440900, EPI_ISL_18440915, EPI_ISL_18440924-18440925, EPI_ISL_18440969, EPI_ISL_18441009, EPI_ISL_18441020-18441021, EPI_ISL_18441174, EPI_ISL_18441980, EPI_ISL_18442844, EPI_ISL_18443747

11-05, 13 seqs from Australia, Bulgaria, France, Italy, Poland and UK

EPI_ISL_18447146, EPI_ISL_18447215, EPI_ISL_18447218, EPI_ISL_18450597, EPI_ISL_18452054, EPI_ISL_18453671-18453672, EPI_ISL_18454527, EPI_ISL_18457752, EPI_ISL_18457754, EPI_ISL_18458576, EPI_ISL_18462386, EPI_ISL_18462403

11-18, 39 seqs from Australia, Denmark, France, Italy, South Korea, New Zealand, Spain, Sweden, Türkiye, UK and USA

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2d20_a2ce10.json?f_userOrOld=uploaded%20sample&label=id:node_3252244

EPI_ISL_18466732, EPI_ISL_18468678, EPI_ISL_18468695, EPI_ISL_18468707, EPI_ISL_18468728, EPI_ISL_18468958, EPI_ISL_18469620, EPI_ISL_18469790, EPI_ISL_18472844, EPI_ISL_18473084, EPI_ISL_18473208, EPI_ISL_18488390, EPI_ISL_18489761, EPI_ISL_18489767, EPI_ISL_18489780, EPI_ISL_18491903, EPI_ISL_18491928, EPI_ISL_18492025, EPI_ISL_18492034, EPI_ISL_18492084, EPI_ISL_18492102, EPI_ISL_18492380, EPI_ISL_18493386, EPI_ISL_18494347, EPI_ISL_18494393, EPI_ISL_18496507, EPI_ISL_18496728, EPI_ISL_18497002, EPI_ISL_18498705, EPI_ISL_18499441, EPI_ISL_18499552, EPI_ISL_18500940, EPI_ISL_18503463, EPI_ISL_18507035, EPI_ISL_18510423, EPI_ISL_18511228, EPI_ISL_18513659, EPI_ISL_18518758, EPI_ISL_18518881

[NkRMnZr]

Designated as XBB.1.16.27 via f38283e