Release notes
beca95e - Angie Hinrichs, 2025-04-02 09:45:43 -0700 : Merge pull request #2929 from xz-keg/master
39a6a83 - Cornelius Roemer, 2025-04-02 20:51:36 +0200 : Designate XFJ from #2928
32f8da2 - Xu Zou, 2025-04-03 07:55:31 +0800 : manual fix for JH.2
97794f6 - Angie Hinrichs, 2025-04-02 16:58:56 -0700 : Merge pull request #2930 from xz-keg/master
50636af - Cornelius Roemer, 2025-04-06 20:05:51 +0200 : Designate XFK and XEC.5.1
864eea0 - Cornelius Roemer, 2025-04-11 12:25:40 +0200 : Designate a bunch of lineages
3bd9ff1 - Cornelius Roemer, 2025-04-11 12:53:28 +0200 : Designate XFL
0276761 - Cornelius Roemer, 2025-04-14 17:23:46 +0200 : Designate a few lineages from issues
33179fa - Cornelius Roemer, 2025-04-14 17:25:33 +0200 : Add issue to notes
b8a85b4 - Cornelius Roemer, 2025-04-14 17:52:35 +0200 : Designate a bunch of lineages
428c44b - Angie Hinrichs, 2025-04-15 14:38:30 -0700 : Change LP.8.1.6 designations with other LP.8.1.* mutations -- recurrent S:T22N. Change designations of LP.8.1 + C28674T (N:A134V, LP.8.1.8-defining) + C21627A (S:T22N, LP.8.1.6-defining) from LP.8.1.6 to LP.8.1.8 because S:T22N seems more likely recurrent than N:A134V. Similarly, change designations of LP.8.1 + C3096T (ORF1a:S944L) + C21627A from LP.8.1.6 to LP.8.1 because there is an undesignated branch with C3096T and S:T22N seems more likely recurrent. HT @FedeGueli for pointing out that LP.8.1.6 is attracting these recurrences of S:T22N as well as NY.7 in the UShER tree.
46a8086 - Walde1nsamkeit, 2025-04-20 21:57:56 +0800 : Update lineage_notes.txt
39ae964 - Cornelius Roemer, 2025-04-23 22:41:03 +0200 : Designate NA.2, add more LF.7.6.2 designations
e64ee34 - Cornelius Roemer, 2025-04-24 14:08:42 +0200 : Desigante a bunch of XEC branches
0e4ab3a - Cornelius Roemer, 2025-04-27 17:21:12 +0200 : Designate XFM, splitting away from XFJ
7cf5892 - Angie Hinrichs, 2025-04-28 14:07:49 -0700 : Merge pull request #2934 from AngieHinrichs/reduceLP.8.1.6
05dba24 - Angie Hinrichs, 2025-04-28 14:11:32 -0700 : Merge pull request #2935 from Walde1nsamkeit/patch-17
b7c3c31 - Walde1nsamkeit, 2025-05-03 20:01:42 +0800 : Update lineage_notes.txt
76286b2 - Walde1nsamkeit, 2025-05-03 20:48:06 +0800 : Update lineage_notes.txt
3036ffe - Cornelius Roemer, 2025-05-04 17:10:04 +0200 : Designate some XFG and NL sublineages
d8d6c2b - Angie Hinrichs, 2025-05-09 17:45:37 -0700 : Merge pull request #2950 from Walde1nsamkeit/patch-18
e491440 - xz, 2025-05-13 11:10:54 +0800 : add_23_autoref
3210b9b - Angie Hinrichs, 2025-05-13 10:40:30 -0700 : Merge pull request #2957 from xz-keg/master
4f39d17 - Cornelius Roemer, 2025-05-14 13:25:06 +0200 : Designate LF.7.9.1/2 and XFJ.1
1e7d885 - Cornelius Roemer, 2025-05-14 18:13:30 +0200 : Designate some NL sublineages
e3e7b9d - Cornelius Roemer, 2025-05-15 00:32:28 +0200 : Designate some LF.7 sublineages
de6fe22 - Cornelius Roemer, 2025-05-15 01:09:28 +0200 : Designate some XEC, MC.10.1, JN.1.23.1 sublineages
d3c361f - Cornelius Roemer, 2025-05-15 17:01:06 +0200 : Designate PL.1 (LF.7.1.10 with S:A475V), XEC.2.4, XEC.38
76308e8 - Federico Gueli, 2025-05-15 17:18:34 +0200 : NL.6.1 added a frameshifting deletion in orf7b that is in all the sequences
115e852 - Cornelius Roemer, 2025-05-16 10:49:19 +0200 : Designate XFJ.2
a307cc3 - Cornelius Roemer, 2025-05-16 11:20:44 +0200 : Designate a bunch of XEC.4.1 and XEC.4 sublineages
3291f7e - Cornelius Roemer, 2025-05-16 11:37:51 +0200 : Designate some XEC lineages
1e1129c - Cornelius Roemer, 2025-05-16 11:53:10 +0200 : Designate XEC.14.1(.1)
99d4304 - Cornelius Roemer, 2025-05-16 12:58:11 +0200 : Deignate NY.13, XEC.2.5, XEC.2.6
e301571 - Cornelius Roemer, 2025-05-16 13:21:56 +0200 : Designate some MC.11, XEK.1 and XFB sublineages
7fd8fc3 - Cornelius Roemer, 2025-05-16 13:40:09 +0200 : Designate PDs and MC.41
586b8d1 - Cornelius Roemer, 2025-05-16 14:04:44 +0200 : Designate some NY and KP.3.3.10
e5db294 - Cornelius Roemer, 2025-05-16 14:26:32 +0200 : Designate MC.10.2.2
bbcc3b1 - Walde1nsamkeit, 2025-05-18 02:42:06 +0800 : Update lineage_notes.txt
7f95ee0 - Walde1nsamkeit, 2025-05-18 02:46:43 +0800 : Update lineage_notes.txt
9b9ecb4 - Cornelius Roemer, 2025-05-18 12:56:53 +0200 : Designate PG.4-6
6c441f8 - Cornelius Roemer, 2025-05-18 13:49:48 +0200 : Designate KP.3.2.6 sublineages (PM), XDV.1.7.2
a719870 - Cornelius Roemer, 2025-05-18 13:58:22 +0200 : Designate PN.1 and XDV.1.7.3
b44fd25 - Cornelius Roemer, 2025-05-18 14:14:22 +0200 : Designate XDV.1.12
c56a43d - Cornelius Roemer, 2025-05-18 14:26:36 +0200 : Fix XDV.1.7.3, add XDV.1.7.5
4acc9c7 - Cornelius Roemer, 2025-05-18 18:10:33 +0200 : Require T25473C for MC.11.2
addc765 - Cornelius Roemer, 2025-05-18 18:26:18 +0200 : Fix #2965
e1bcc87 - Federico Gueli, 2025-05-19 01:03:29 +0200 : added the AA to the definig mutation of NL.6.1
c4bc7fd - Federico Gueli, 2025-05-19 02:03:53 +0200 : Adding the corresponding Alias to PN.1
b198259 - Angie Hinrichs, 2025-05-19 11:44:43 -0700 : Merge pull request #2966 from Walde1nsamkeit/patch-19
42827af - Angie Hinrichs, 2025-05-19 11:47:08 -0700 : Merge pull request #2963 from FedeGueli/patch-66
9a538e4 - Angie Hinrichs, 2025-05-19 11:48:07 -0700 : Merge pull request #2967 from FedeGueli/patch-67
b2b6f98 - Angie Hinrichs, 2025-05-19 11:49:32 -0700 : Merge pull request #2968 from FedeGueli/patch-68
edb91ee - Cornelius Roemer, 2025-05-20 13:01:06 +0200 : Designate some LP.8.1s and PP (LP.8.1.8.*)
a9d6e81 - Cornelius Roemer, 2025-05-20 13:12:50 +0200 : Consider S:T22N with ORF1a:S944L to be part of LP.8.1.6
731aa91 - Cornelius Roemer, 2025-05-20 13:29:50 +0200 : Designate PF.2 (LP.8.1.6 with ORF1a:S944L) and sublineages
d849c37 - Cornelius Roemer, 2025-05-20 14:05:30 +0200 : Designate a bunch of lineages, including NB.1.8.1s (PQ)
42c88a7 - Cornelius Roemer, 2025-05-20 15:09:19 +0200 : Narrow NY.7 to require ORF1b:A788V, C925T, C29708T as there's little evidence for proper LP.8.1.1 + just S:T22N
f3e887e - Josh Levy, 2025-05-22 11:16:53 -0700 : Update lineage_notes.txt
2837f66 - Angie Hinrichs, 2025-05-23 09:33:39 -0700 : Merge pull request #2972 from joshuailevy/patch-3
7ceb45c - Cornelius Roemer, 2025-05-29 03:08:41 +0200 : Designate NY.3 sublineages, NY.15
6b8e6fb - Cornelius Roemer, 2025-05-29 03:17:57 +0200 : Designate a few NWs
266c79c - Cornelius Roemer, 2025-05-29 03:31:07 +0200 : Designate LP.8.1.5 sublineages (PR), PA and MC.13.2 sublineages
1b719be - Cornelius Roemer, 2025-05-29 03:43:58 +0200 : Designate MV.1.1.1 sublineages, some MV.1s, PLs, MC.9.2
352f664 - Cornelius Roemer, 2025-05-29 11:39:45 +0200 : Designate some XEC.. lineages and XFN/XFP
7cfe28f - Cornelius Roemer, 2025-05-29 12:39:13 +0200 : Designate some NY, XEC, XFG
e5017a1 - Cornelius Roemer, 2025-05-29 13:30:46 +0200 : Designate a few more
0938974 - Cornelius Roemer, 2025-05-29 13:33:24 +0200 : Designate NL.8.1
9757214 - Cornelius Roemer, 2025-05-30 14:03:18 +0200 : Designate some NLs
c32057a - Cornelius Roemer, 2025-05-30 14:17:54 +0200 : Designate NM.3
60db47b - Cornelius Roemer, 2025-05-30 14:26:01 +0200 : Designate some XEKs
fef5076 - Federico Gueli, 2025-05-30 18:17:33 +0200 : XEK.7 added mutation in the insertion as defining
b08ae3f - Josh Levy, 2025-05-30 11:05:00 -0700 : Update alias_key.json
4b233f0 - Mike Honey, 2025-05-31 11:03:12 +1000 : deleted duplicate row for MV.1.1.1
9c89842 - Angie Hinrichs, 2025-06-02 09:54:20 -0700 : Merge pull request #2980 from FedeGueli/patch-70
5d162c2 - Angie Hinrichs, 2025-06-02 09:54:54 -0700 : Merge pull request #2981 from joshuailevy/patch-4
33c4257 - Angie Hinrichs, 2025-06-02 09:56:53 -0700 : Merge pull request #2982 from Mike-Honey/patch-1
ce52e27 - Cornelius Roemer, 2025-06-04 20:55:16 +0200 : Add extra BA.3.2 designations
720d7dc - Josh Levy, 2025-06-05 11:21:15 -0700 : XFP missing from key, update alias_key.json
a12eade - Angie Hinrichs, 2025-06-05 13:11:36 -0700 : Merge pull request #2986 from joshuailevy/patch-5
c2af815 - Cornelius Roemer, 2025-06-06 10:51:10 +0200 : Designate BA.3.2.1 (S:H681R, S:P1162R) and BA.3.2.2 (S:K356T, S:A575S)
50ef261 - Andrew Rambaut, 2025-06-06 11:50:22 +0100 : Storing Pango rules here
b17dcf9 - Andrew Rambaut, 2025-06-06 11:53:30 +0100 : Rename pango_rules.md to docs/pango_rules.md
58278bf - Andrew Rambaut, 2025-06-06 11:55:51 +0100 : Create index.html
7875baa - Andrew Rambaut, 2025-06-06 11:57:16 +0100 : Rename index.html to index.md
1bb577d - Cornelius Roemer, 2025-06-06 13:17:44 +0200 : Designate XFJ.4
f90e5f0 - Cornelius Roemer, 2025-06-06 16:37:22 +0200 : Designate LS.2.1 and LS.2.1.1 to make XFJ/XFP/XFM donors more specific
5bebd58 - Cornelius Roemer, 2025-06-07 08:13:53 +0200 : Designate some PQs
7d44ea2 - Cornelius Roemer, 2025-06-07 08:34:01 +0200 : Designate PAs, MCs and XEC.18s
6d87670 - Cornelius Roemer, 2025-06-07 08:51:02 +0200 : Designate LF.7.9.2s (PW) and LF.7.9.3
b88ed38 - Cornelius Roemer, 2025-06-07 09:10:56 +0200 : Designate PYs (LF.7.9.1)
0aca838 - Cornelius Roemer, 2025-06-07 13:20:57 +0200 : Designate some PCs
aa25918 - Cornelius Roemer, 2025-06-07 15:02:45 +0200 : NY.7 seems to have been broadly annotated on Usher
4ff5531 - Cornelius Roemer, 2025-06-07 15:04:33 +0200 : Designate NY.17(.1/.2)
b1852f9 - Cornelius Roemer, 2025-06-07 18:20:38 +0200 : Designate NB.1.6.1, NB.1.7.1, XFF.1
6357f98 - Cornelius Roemer, 2025-06-08 11:17:06 +0200 : Designate some PQs with plausible 478T sublineages
4ded79b - Walde1nsamkeit, 2025-06-08 17:28:03 +0800 : Update lineage_notes.txt (#2984)
73cd53e - Federico Gueli, 2025-06-08 11:28:49 +0200 : I ve added S:S680P to PC.2.2 defining mutation (#2976)
5cb3dee - Cornelius Roemer, 2025-06-08 11:30:25 +0200 : Add dependabot to update workflows
4223bb8 - Cornelius Roemer, 2025-06-08 11:38:06 +0200 : Designate more PQ branches with potential 478T sublineages
7a8ac46 - Cornelius Roemer, 2025-06-11 11:38:25 +0200 : Clean up NY.7 to remove non-22N
f7b1b4b - Angie Hinrichs, 2025-06-11 12:16:28 -0700 : Broadening NY.7 to just S:T22N; the more restrictive definition is NY.7.1.