Fearuncle

KP.2 + ORF3a:T221K (56 Seq. in 5 countries)

1

  Tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2d006_71aa00.json?c=gt-ORF3a_221&gmax=26220&gmin=25393&label=id:node_6956477 First Seq: 2024-03-02 Most Recent: 2024-03-17 Gisaid Query: C26054A, A22556G EPI_ISL_18983710 EPI_ISL_19011001 EPI_ISL_19002254 EPI_ISL_19010984

KS.1+ N:P383L, ORF3a:H78Y (15 in Canada)

1

 tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_830a_883d10.json?c=gt-N_383&gmax=29533&gmin=28274&label=id:node_7014539 First Seq: 2024-04-05 Most Recent: 2024-04-15 Gisaid Query: C25624T, C29421T, T22917G, A29510C EPI_ISL_19051389 EPI_ISL_19051392 EPI_ISL_19063897 EPI_ISL_19051397 EPI_ISL_19051384 EPI_ISL_19051345 EPI_ISL_19051439 EPI_ISL_19063905 EPI_ISL_19063953 EPI_ISL_19063901 EPI_ISL_19051447 EPI_ISL_19051451 EPI_ISL_19051438 EPI_ISL_19051440

BA.1.1 saltation branch with 26 aa mutations (3 seqs in Nebraska, US)

4

  tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_234d6_ccb720.json?c=gt-nuc_160&gmax=1160&label=id:node_2493993 First Seq: 2024-03-09 Most Recent: 2024-03-14 Gisaid query: G160T, G2494T, C4230T, G5180A EPI_ISL_19009131 EPI_ISL_19009123 Mutations: Orf1a: E743D, T1322I, A1420V, D1639N, T2300I, S2500F, L3060F, A3697V, Y3765H, L3829P,...

KP.3.1.1/XDV.1 recombinant (3 seqs. 3 countries)

2

 Tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_59bc_ed67e0.json?c=gt-N_204&gmax=29533&gmin=28274&label=id:node_7036069 Seq: 2024-07-28 Mutations: ORF1a:K47R, ORF1a:D211A (R), ORF1a:S302F, ORF1a:L1056V (R), ORF1a:T1322I, ORF3a:N82D, N:R204Q Gisaid: C4230T, A25636G EPI_ISL_19324526 EPI_ISL_19324633 EPI_ISL_19324816

KP.3.1.1 + ORF9b:I5T + S:Q677H (10 in NY and 1 in Pennsylvania) 3 with S:R346T

1

 tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_8c90_35ca60.json?f_userOrOld=uploaded%20sample First Seq: 2024-08-16 Most Recent: 2024-09-19 Gisaid: G23593T, T28297C, T27484C PQ387629.1 PQ409687.1 PQ426798.1 EPI_ISL_19423728 EPI_ISL_19447378 EPI_ISL_19447146 PQ277259.1 PQ409794.1 EPI_ISL_19423829 PQ386731.1 PQ363340.1

XEC.2 + ORF7a:T14I (9, 4 places including Kosovo)

1

 tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_ddd4_354fa0.json?f_userOrOld=uploaded%20sample First seq: 2024-09-04 Most Recent: 2024-09-20 Gisaid: A4364C,-G2060A,C27434T ,C897A (Edited) CovSpectrum advanced query :A4364C & !G2060A & C27434T & C897A EPI_ISL_19450989 EPI_ISL_19457124 EPI_ISL_19448898 EPI_ISL_19430765 EPI_ISL_19451006 EPI_ISL_19433936 EPI_ISL_19451014

KP.1.1.1 + S:F59S,T22N (18 seqs) with a S:K478T+M153I branch (14) and further S:H445R (2, India, GBW)

18

_This was spotted first by @aviczhl2 in the groups (edited)_ Proposal edited by mod on November 17 KP.1.1.1 > S:F59S (T21738C) > S:T22N (C21627A) >> S:K478T (A22995C) > Orf1a:F2321L (T7226C)...

LB.1.3/KP.3.3 recombinant (5 in 2 countries)

6

 Updated tree:  tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_18d07_b8c250.json It adds S:S31-, S:Q183H, S:R346T, ORF1b:T1555I First Seq: 2024-07-26 Most Recent: 2024-08-07 Query: C16111T, G22111T, G22599C, C7113T PQ214083.1 Scotland/CLIMB-CM7Y8EO6/2024

 tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_15460_b3e3f0.json?f_userOrOld=uploaded%20sample First Seq: 2024-07-19 Most Recent: 2024-08-29 Query: A23592T, C6310T, C21627A EPI_ISL_19386660 EPI_ISL_19375525 EPI_ISL_19411044 EPI_ISL_19416613

KP.2.14 (with S:22N) + ORF1a:T2183I + ORF1a:S443T + S:A435S (12)

2

  tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_10035_20b050.json?f_userOrOld=uploaded%20sample First Seq: 2024-07-12 Most Recent: 2024-08-19 Gisaid: C24700T, G22865T PQ211668.1 PQ237420.1 EPI_ISL_19301636 PQ147761.1 PQ237609.1 PQ061078.1 PQ237497.1