Xu Zou

MC.9+Orf1a:K2029N, S:T76I (9 seqs, 2 countries)

3

KP.3.1.1+G25617T(Orf3a:K75N)+G17122T(Orf1a:A1219S)+G6352T, C21789T(Orf1a:K2029N,S:T76I) GISAID qurry: G6352T,C21789T, G25617T No. of seqs: 6(USA, 5 from Italy) First: EPI_ISL_19285214, USA, 2024-7-8 Latest: EPI_ISL_19289854, USA from Italy, 2024-7-16 [usher](https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice5_genome_test_46dfb_5e30a0.json?label=id:node_6266715) 

Multiple JN.1* sub-lineages with S:S31- and S:R190S, 10 ongoing unproposed branches as of 9/26

81

It seems that there is a new convergent mutation of S:R190S. It usually couples with S:S31del. Cov-spectrum shows its growth is negative with S:S31S, but large growth advantage with S:S31-....

KP.2.15.1 (KP.2.15 + 572I)+ S:G798S(39 seqs, 6 countries)

12

Original KP.2.15.1 proposal KP.2.15(DeFLiRT)+T12304C+A3580G, T9418C, C23277T(S:T572I), another FULL QUAD branch. GISAID query: C23277T, T12304C, A10861G, G17334T No. of seqs: 19(Denmark 4 Germany 1 Sweden 9 USA 5(1 from Germany)) First:...

JN.1.16.1+S:S60P+S:N185D(36 seqs, 6 countries)

2

JN.1.16.1+T21740C(S:S60P)+A22115G(S:N185D) GISAID query: T21740C, A22115G, T22928C,G22599C,-3913 No. of seqs: 9(UK 2 Canada 3 USA 3 Spain 1) First:EPI_ISL_19055535, 2024-4-3, UK Latest: EPI_ISL_19252406, 2024-7-2, Spain [usher](https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice139_genome_test_26a0_dfd560.json?label=id:node_5643291) 

KP.3.1.1+S:N1187H( 12 seqs, 8 countries)

1

KP.3.1.1+A25121C(S:N1187H) GISAID query: A25121C, C12616T, A13121T No. of seqs: 10(Spain 2 UK 2 France 2 USA 2(from Netherlands) Canada 1 Sweden 1) First: EPI_ISL_19267885,Spain, 2024-6-10 Latest: EPI_ISL_19329869, Canada, 2024-7-29 [usher](https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice37_genome_test_66c3b_ac5e80.json?label=id:node_5489701)...

KP.3.1+Orf6:I33V+S:P793S (22 seqs, 3 countries)

1

KP.3.1+A27298G(Orf6:I33V)+C23939T(S:P793S) GISAID query: A27298G, C23939T No. of seqs: 16(Spain 15 UK 1 ) First: EPI_ISL_19131032, Spain, 2024-5-3 Latest: EPI_ISL_19270855, Spain, 2024-6-30 [usher](https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice148_genome_test_14995_dc9a20.json?label=id:node_5465024) 

KP.1.1.3+S:P1263L(19 seqs, 5 countries)

2

KP.1.1.3+C3992T+C25350T(S:P1263L) GISAID query: C3992T, C4999T, C25350T,del21653 No. of seqs: 7(USA 5(2 from UK), Spain 1 UK 1 ) First: EPI_ISL_19153965, USA, 2024-5-3 Latest: EPI_ISL_19254598, USA from UK, 2024-6-24 [usher](https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice77_genome_test_2afe_dfd4e0.json?label=id:node_5482504) 

KP.1.1.3+S:M153I(130 seqs, >15 countries, 46 with S:C1247S)

5

KP.1.1.3+G22021T(S:M153I) GISAID query: C4999T,G22021T,G24872T GISAID query for S:C1247S branch: C4999T,G22021T,G24872T,G25302C No. of seqs: 20(France 1 India 1 UK 1 Canada 1 Sweden 1 Spain 1 USA 14(3 from UK)) First:...

KP.2+S:L56V (37 seqs, 14 countries)

3

Besides KP.2.11, there seems to be a direct KP.2+S:L56V branch KP.2+T21728G(S:L56V) GISAID query: G17334T, T21728G, G22599C, -6543,-24819 No. of seqs: 25(Australia 1 Canada 2 France 1 India 1 Ireland 1...

KP.2+S:F59L via T21739G(52 seqs, 8 countries)

2

S:F59L is usually achieved via T21737C, however, this branch gets it by T21739G. KP.2+T6844C, C28603T+T21739G(S:F59L) GISAID query: T6844C, C28603T, T21739G No. of seqs: 41(Australia 1 Canada 6 UK 2 Germany...