Xu Zou
Xu Zou
XDQ.1+A18184G(Orf1b:M1573V)+C3885T, A12709G, A26594T, C20320T, C20719T, C23277T, G29254A(Orf1a:P1207L, Orf1b:H2285Y, S:T572I) GISAID query: C23277T, A18184G, C28846T No. of seqs: 5(Japan) First:EPI_ISL_19053147, 2024-3-24 Latest: EPI_ISL_19053134, 2024-3-27 [usher](https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice5_genome_test_36051_241a20.json?label=id:node_6910379) 
JN.1+C1973T+A22012T(S:K150N) GISAID query: C1973T,A22012T,T3565C No. of seqs: 66(Australia 1 Canada 2 UK 15 USA 48) First: EPI_ISL_18723555, 2023-12-10,USA Latest: EPI_ISL_19027075, 2024-3-13,Australia [usher](https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice117_genome_test_26d9d_120a30.json?label=id:node_7065555) 
JN.1.4.6+G3052T, C6471T, C15720T, C17172T,G18163T, C19118T, T28297C, A28958C(rev) Orf1a:E929D, T2069I Orf1b:V1466L, A2284V Orf9b:I5T N:K229Q(rev) JN.1.4.6--anything with Orf9b:I5T (most likely XBB* ) Breakpoint between 27916 and 28296 G3052T,C15720T, C17172T,G18163T, C19118T from an...
There seems to be a side branch of [XDP](https://github.com/cov-lineages/pango-designation/issues/2451), either formed by recomb of any XBB* and XDP, or via FL.15/JN.1/FL.15 sandwich recomb. XDP+A405G,T774C(rev) Orf1a: K47R, I170T(rev) XBB*--XDP (likely) Breakpoint...
JN.1.18+G25606A(Orf3a:A72T)+A13288G+A28834G+A3558G,C15933T, A25359G(Orf1a:K1098R,S:K1266R)+C23277T, G26367T, C28651T, C29555T(S:T572I) Although there is a JN.1+G25606A branch, this mutation is a convergent one as it also appears in JN.1.1 and JN.1.4. So current placement under JN.1.18...
KR.1+T21737C(S:F59L) GISAID query: T21737C, C9142T, C28498T No. of seqs: 13(USA 4(2 from France, 2 from Phillipines), South Korea 9) First: EPI_ISL_18982351, 2024-2-19, South Korea Latest: EPI_ISL_19093675, 2024-4-23, USA from France...
XDP+A23523T(S:E654V) GISAID query: A23523T,C28846T,C18894T No. of seqs: 14(UK 12 USA 1 New Zealand 1) This query only finds 3, another 11 are either not on GISAID, or cannot be queried...
JN.1.11.1+C23280T(S:T573I) GISAID query: C23280T, G17334T, C7113T, G24872T,-19895 No. of seqs: 4(Japan 1 Australia 2 USA 1) First:EPI_ISL_19046823, Australia, 2024-3-18 Latest:EPI_ISL_19076765, USA, 2024-4-11 [usher](https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_56ef6_e03c90.json?gt=S.573I&label=id:node_6975604) 
Hi, I wrote an open-sourced usher analyse tool that can automatically highlight important lineages in usher-processed jsons. Hope it can help everyone find and analyse new lineages more quickly, especially...
JN.1.16 is JN.1+S:F456L(T22928C)+S:R346T, and there is an S:L456V(C22928G) branch under it.  Given it is a single-nuc mutation on 22928, it is very unlikely for this position to mutate so...