pango designation v1.19

Release notes

e531938 - Cornelius Roemer, Wed Mar 29 21:10:18 2023 +0200 : Added lineage FJ.1 (CH.1.1.19 with ORF1a:A1204V) with 180 designations
c78e249 - InfrPopGen, Wed Mar 29 15:42:30 2023 +0100 : Merge pull request #1818 from InfrPopGen/master
2a62dcf - InfrPopGen, Wed Mar 29 15:40:59 2023 +0100 : Added new lineage CH.1.1.22 from #1670 with 7 new sequence designations, and 9 updated from CH.1.1
f692d76 - Cornelius Roemer, Wed Mar 29 01:36:55 2023 +0200 : Added CH.1.1.21 (S:N481Y) from #1799, 50 designations
c578f47 - Cornelius Roemer, Tue Mar 28 23:30:31 2023 +0200 : fix: move "taxon,lineage" back to top
19170f5 - Angie Hinrichs, Tue Mar 28 14:19:23 2023 -0700 : #1776 was for XBB.2.3.2 not XBB.2.3, thanks @Over-There-Is, fixes #1803.
5cf9cd0 - InfrPopGen, Tue Mar 28 16:45:08 2023 +0100 : Merge pull request #1815 from InfrPopGen/master
bac15e0 - InfrPopGen, Tue Mar 28 16:42:35 2023 +0100 : Added new recombinant lineage XBZ from #1666 with 0 new sequence designations, and 238 updated designations
4a522cb - Angie Hinrichs, Mon Mar 27 11:35:36 2023 -0700 : Added 995 designations for the part of BA.5.1.15 that doesn't have C10183T (#1039). Many were previously designated BA.5.1; 20 were previously designated BA.5.1.22, 8 were BA.5.1.3 and 2 were BA.5.1.25 due to having both the defining mutations for those respective lineages and the defining mutation for BA.5.1.15 (C10790T).
385e78d - Cornelius Roemer, Mon Mar 27 04:43:37 2023 +0200 : Added lineage XBB.1.5.39 (ORF1a:M3684T) with 800 designations
37fb661 - Cornelius Roemer, Mon Mar 27 04:40:58 2023 +0200 : Added lineage FH.1 (XBB.1.5.17 with S:T883I) with 140 designations
773437b - Cornelius Roemer, Mon Mar 27 04:36:54 2023 +0200 : Added lineage XBB.1.5.38 (S:I666V, ORF1a:T403I) with 150 designations
7bfbd46 - Cornelius Roemer, Mon Mar 27 04:24:15 2023 +0200 : Added lineage FD.2 (XBB.1.5.15 with S:Q146K) from #1600 with 1000 designations
1d92447 - Cornelius Roemer, Mon Mar 27 04:21:09 2023 +0200 : Added lineage XBB.1.5.37 (S:K1045R) with 300 designations
ea6f34a - Cornelius Roemer, Fri Mar 24 21:11:20 2023 +0100 : Fix typo in lineage notes for mutation of CM.8.1.4 (thanks @FedeGueli)
411700b - Cornelius Roemer, Fri Mar 24 21:06:57 2023 +0100 : Added related issues to lineage notes, thanks @FedeGueli
1ee797a - Cornelius Roemer, Fri Mar 24 21:02:10 2023 +0100 : Add helper scripts to make designation more ergonomic
6dae4b8 - Cornelius Roemer, Fri Mar 24 20:56:54 2023 +0100 : Added lineage BF.5.5 (S:K147N) with 250 designations
0225b01 - Cornelius Roemer, Fri Mar 24 20:53:31 2023 +0100 : Added lineage XBB.2.7.1 (S:Y453F, S:K478Q, Singapore, #1725)
d6fed05 - Cornelius Roemer, Fri Mar 24 20:46:29 2023 +0100 : Added lineage XBB.2.8 (C6968T) with 250 designations
0ce4960 - Cornelius Roemer, Fri Mar 24 20:43:20 2023 +0100 : Added lineage DN.1.1.4 (S:N481S) with 70 designations
1ea0850 - Cornelius Roemer, Fri Mar 24 20:41:37 2023 +0100 : Added lineage DN.1.1.3 (S:S704L) with 100 designations
19d4246 - Cornelius Roemer, Fri Mar 24 19:26:18 2023 +0100 : Added lineage CM.8.1.4 (ORF1a:N2890D) with 86 designations
8ab5b25 - Cornelius Roemer, Fri Mar 24 19:23:35 2023 +0100 : Added lineage CM.8.1.3 (S:Y1272H) with 48 designations
e3c981f - Cornelius Roemer, Fri Mar 24 19:20:30 2023 +0100 : Added lineage CH.1.1.20 (S:T299I, S:R403K, S:D1165G) from #1736
6f71f0c - Cornelius Roemer, Fri Mar 24 19:17:22 2023 +0100 : Added lineage CH.1.1.19 (C2773) with 450 designations
0947ed6 - Cornelius Roemer, Fri Mar 24 19:15:38 2023 +0100 : Added lineage FG.3 (S:I934V) with 75 designations
1cd5d3b - Cornelius Roemer, Fri Mar 24 19:14:29 2023 +0100 : Added lineage FG.2 (S:D178N) with 80 designations
a8a99b5 - Cornelius Roemer, Fri Mar 24 19:12:58 2023 +0100 : Added lineage FG.1 (XBB.1.5.16.1 with S:T284I, S:R403K, S:L513F) from #1751
fb4e8b2 - Cornelius Roemer, Fri Mar 24 19:09:27 2023 +0100 : Added lineage XBF.9 (ORF1b:S1003G) with 90 designations
3dd84ab - Cornelius Roemer, Fri Mar 24 19:06:08 2023 +0100 : Added lineage BQ.1.26.2 (S:F157L) with 90 designations
73062bf - Cornelius Roemer, Fri Mar 24 19:01:46 2023 +0100 : Added lineage BL.1.5 (S:A475V) with 120 designations
fa0fb80 - Cornelius Roemer, Fri Mar 24 18:56:09 2023 +0100 : Added lineage XBB.1.5.36 (C9442T) with 240 designations
2a3dec1 - Cornelius Roemer, Fri Mar 24 18:53:47 2023 +0100 : Added lineage XBB.1.5.35 (S:N978S, USA, from #1699) with 400 designations
8032c82 - Cornelius Roemer, Fri Mar 24 18:46:07 2023 +0100 : Added lineage XBB.1.30 (ORF1b:K2557R) with 150 designations
086bc4f - Cornelius Roemer, Fri Mar 24 18:39:38 2023 +0100 : Added lineage XBB.1.5.34 (ORF1a:T1754I) with 430 designations
94ecd67 - Cornelius Roemer, Fri Mar 24 18:36:59 2023 +0100 : Added lineage XBB.1.29 (ORF1a:L3829F, S:A292S) with 50 designations
5fdd9b0 - Cornelius Roemer, Fri Mar 24 18:33:34 2023 +0100 : Added lineage XBB.1.28 (S:R403K) with 13 designations
884b1f7 - Cornelius Roemer, Fri Mar 24 18:02:06 2023 +0100 : Added lineage CH.1.1.18 (S:K187T) with 150 designations, from #1747
4267069 - Cornelius Roemer, Fri Mar 24 17:58:40 2023 +0100 : Added lineage XBB.2.3 (S:G184V, ORF1a:R2159W) with 50 designations from #1776
c49a12a - Cornelius Roemer, Fri Mar 24 17:57:05 2023 +0100 : Added lineage XBB.2.3.1 (S:D80Y) with 80 designations
b4fb9dd - Cornelius Roemer, Fri Mar 24 17:52:32 2023 +0100 : Added lineages XBB.1.5.31, XBB.1.5.32, XBB.1.5.33
cdcebd4 - Cornelius Roemer, Thu Mar 23 23:42:16 2023 +0100 : Added lineage BN.1.3.9 (S:V83F) with 70 designations
d39dc6f - InfrPopGen, Thu Mar 23 19:22:10 2023 +0000 : Merge pull request #1793 from InfrPopGen/master
7b26841 - InfrPopGen, Thu Mar 23 19:20:43 2023 +0000 : Added new lineage CP.8.1 from #1627 with 0 new sequence designations, and 17 updated from CP.8, and 15 from BA.5.2.6
367c6fb - Cornelius Roemer, Thu Mar 23 18:06:49 2023 +0100 : feat: remove non-GISAID strainnames in deduplicate scripts
034686c - Angie Hinrichs, Wed Mar 22 15:41:25 2023 -0700 : Removed a few more INSDC accessions, all have COG-UK names already in lineages.csv.
10404d2 - Angie Hinrichs, Wed Mar 22 15:29:14 2023 -0700 : Replaced INSDC accessions with names, resolved duplicates. Also removed non-sequence-name "strain".
c0aa9f5 - InfrPopGen, Wed Mar 22 16:13:11 2023 +0000 : Merge pull request #1788 from InfrPopGen/master
f662df7 - InfrPopGen, Wed Mar 22 16:11:44 2023 +0000 : Added new lineage FF.1 from #1523 with 65 new sequence designations, and 0 updated
a354100 - Cornelius Roemer, Wed Mar 22 01:37:41 2023 +0100 : Added lineage XBB.1.5.30 (S:A348T) with 250 designations
1558fa9 - Cornelius Roemer, Wed Mar 22 01:35:08 2023 +0100 : Added lineage XBB.1.5.29 (S:A348V) with 25 designations
ae4a881 - Cornelius Roemer, Wed Mar 22 01:31:23 2023 +0100 : Added lineage FE.1 (XBB.1.18.1 with S:F456L) with 10 designations
9c8e360 - Cornelius Roemer, Wed Mar 22 01:21:33 2023 +0100 : Added lineage FD.1.1 (S:F456L) with 50 designations
eb0ca1d - Cornelius Roemer, Wed Mar 22 01:19:30 2023 +0100 : Added lineage FD.1 (XBB.1.5.15 with ORF7b:E3*) with 150 designations
2961a14 - Cornelius Roemer, Wed Mar 22 01:09:37 2023 +0100 : Added lineage FC.1 (BQ.1.1.72 with S:478R) with 80 designations
70571ac - Cornelius Roemer, Wed Mar 22 01:06:37 2023 +0100 : Added lineage BQ.1.1.72 (ORF1b:D100A) with 700 designations
c1c65a2 - Cornelius Roemer, Wed Mar 22 01:03:59 2023 +0100 : Added lineage FB.2 (S:478R) with 70 designations
80d74a9 - Cornelius Roemer, Wed Mar 22 01:02:25 2023 +0100 : Added lineage FB.1 (BQ.1.2.1 with S:D253G) with 25 designations
fbe7ed4 - Cornelius Roemer, Wed Mar 22 00:57:49 2023 +0100 : Added lineage DR.2 (BQ.1.1.3 with S:478R) with 70 designations
ff7b395 - Cornelius Roemer, Wed Mar 22 00:54:41 2023 +0100 : Added lineage FA.2 (BQ.1.1.10 with S:T323I) with 100 designations
92524ad - Cornelius Roemer, Wed Mar 22 00:53:35 2023 +0100 : Added lineage FA.1 (BQ.1.1.10 with S:478R) with 100 designations
115a58a - Cornelius Roemer, Wed Mar 22 00:49:51 2023 +0100 : Added lineage BE.13 (S:346T, S:478R) with 110 designations
df35dea - Cornelius Roemer, Wed Mar 22 00:46:41 2023 +0100 : Added lineage BE.12 (C10834T, T18975C, A29359G) with 300 designations
cc043ad - Cornelius Roemer, Wed Mar 22 00:42:03 2023 +0100 : Added lineage BE.11 (T3049C) with 1000 designations
af92f39 - Cornelius Roemer, Wed Mar 22 00:19:03 2023 +0100 : Added lineage XBB.1.5.28 (S:478R on 17124C polytomy) with 50 designations
29a8c5e - Cornelius Roemer, Wed Mar 22 00:15:20 2023 +0100 : Added lineage EK.2.1 (S:478R) with 35 designations
cb29522 - Cornelius Roemer, Wed Mar 22 00:13:29 2023 +0100 : Added lineage EK.3 (S:P251S) with 130 designations
32848ee - Cornelius Roemer, Wed Mar 22 00:09:05 2023 +0100 : Added lineage XBB.1.5.27 (S:K478R) with 60 designations
39015b3 - Cornelius Roemer, Wed Mar 22 00:06:10 2023 +0100 : Added lineage XBB.1.16.1 (S:T547I) with 60 designations
3ba50f5 - Cornelius Roemer, Wed Mar 22 00:04:09 2023 +0100 : Added lineage XBB.1.27 (S:478R, S:A890V) with 20 designations
42f97a9 - Cornelius Roemer, Tue Mar 21 23:54:35 2023 +0100 : Added lineage EZ.1 (BQ.1.1.43 with S:S247N, S:Y248S) with 50 designations
764d273 - Cornelius Roemer, Tue Mar 21 23:50:56 2023 +0100 : Added lineage EY.1 (EF.1.1.1 with S:Q613H) with 150 designations
911be60 - Cornelius Roemer, Tue Mar 21 23:42:28 2023 +0100 : Added lineage EW.3 (S:A348S) with 50 designations
c433f46 - Cornelius Roemer, Tue Mar 21 23:40:10 2023 +0100 : Added lineage EW.2 (S:A701V) with 200 designations
49a6cbb - Cornelius Roemer, Tue Mar 21 23:38:17 2023 +0100 : Added lineage EW.1 (BQ.1.1.38 with S:478R) with 80 designations
bd69c9c - Cornelius Roemer, Tue Mar 21 23:34:53 2023 +0100 : Added lineage EV.1 (BQ.1.1.71 with S:248H) with 15 designations
6419f4a - Angie Hinrichs, Mon Mar 20 15:45:07 2023 -0700 : Removing incomplete sequence name.
f19893e - Angie Hinrichs, Mon Mar 20 15:15:28 2023 -0700 : Updating some names that have been updated in GISAID and removing some resulting duplicates.
f10c6f5 - Angie Hinrichs, Mon Mar 20 15:00:36 2023 -0700 : Removing non-sequence-name words (gene names and "strain" column header).
27a04d8 - Angie Hinrichs, Mon Mar 20 14:58:23 2023 -0700 : Replaced INSDC accessions with names, resolved duplicates.
0339b26 - Angie Hinrichs, Mon Mar 20 14:18:59 2023 -0700 : Resolved 853 duplicates introduced with recently added lineages e.g. XBB.1.5.23, XBB.1.5.24, CP.8, XBB.1.17.1
15464b9 - Angie Hinrichs, Mon Mar 20 13:19:44 2023 -0700 : Merge pull request #1774 from AngieHinrichs/addSequences_2023-03-16
b487aa6 - Angie Hinrichs, Fri Mar 17 17:02:49 2023 -0700 : Added 894 sequences (900 random minus dups) for BQ.1.1.22
cfe80c6 - Angie Hinrichs, Fri Mar 17 17:01:27 2023 -0700 : Added 3966 sequences (4000 random minus dups) for BA.5.2.6
14e413e - Angie Hinrichs, Fri Mar 17 16:59:32 2023 -0700 : Correcting 5 designations from BA.5.2 to BA.5.2.6.
536f5f2 - Angie Hinrichs, Fri Mar 17 16:53:23 2023 -0700 : Added 1982 sequences (2000 random minus dups) for BR.2.1
ccbe5c7 - Angie Hinrichs, Fri Mar 17 16:51:40 2023 -0700 : Added 2480 sequences (2500 random minus dups) for XBF
cc686e1 - Angie Hinrichs, Fri Mar 17 16:46:56 2023 -0700 : Added 9885 sequences (10000 random minus dups) for BF.7
b30321e - Angie Hinrichs, Fri Mar 17 16:39:50 2023 -0700 : Correcting 48 designations from BA.5.2.1 to BF.7.
f7aa78d - Angie Hinrichs, Fri Mar 17 16:31:49 2023 -0700 : Added 994 sequences (1000 random minus dups) for CL.1
143dcb6 - Angie Hinrichs, Fri Mar 17 16:29:27 2023 -0700 : Added 879 sequences (900 random minus dups) for CK.2.1
801bcd6 - Angie Hinrichs, Fri Mar 17 16:21:55 2023 -0700 : Added 2383 sequences (2400 random minus dups) for BN.1.2
ceeb126 - Angie Hinrichs, Fri Mar 17 16:19:26 2023 -0700 : Added 5965 sequences (6000 random minus dups) for XBB.1
e5f31e5 - Angie Hinrichs, Fri Mar 17 15:58:49 2023 -0700 : Added 299 sequences (300 random minus dups) for BN.3.1
d70a6d1 - Angie Hinrichs, Fri Mar 17 15:45:14 2023 -0700 : Added 2954 sequences (3000 random minus dups) for BQ.1.1.4
ede7164 - Angie Hinrichs, Fri Mar 17 15:43:37 2023 -0700 : Added 1968 sequences (2000 random minus dups) for BQ.1.5
1211b1e - Angie Hinrichs, Fri Mar 17 15:42:35 2023 -0700 : Added 196 sequences (200 random minus dups) for DB.1
d587e89 - Angie Hinrichs, Fri Mar 17 15:41:50 2023 -0700 : Added 146 sequences (150 random minus dups) for BQ.1.26
3eae2e6 - Angie Hinrichs, Fri Mar 17 15:40:47 2023 -0700 : Added 2460 sequences (2500 random minus dups) for BF.14
fe381dd - Angie Hinrichs, Fri Mar 17 15:39:36 2023 -0700 : Added 1480 sequences (1500 random minus dups) for BN.1.3.1
8e36d35 - Angie Hinrichs, Fri Mar 17 15:38:39 2023 -0700 : Added 397 sequences (400 random minus dups) for BN.1.2.1
7c5a841 - Angie Hinrichs, Fri Mar 17 15:37:02 2023 -0700 : Added 3453 sequences (3500 random minus dups) for BN.1.3
a0511ad - Angie Hinrichs, Fri Mar 17 15:36:06 2023 -0700 : Added 296 sequences (300 random minus dups) for BR.2
4a48e5c - Angie Hinrichs, Fri Mar 17 15:34:44 2023 -0700 : Added 2475 sequences (2500 random minus dups) for BQ.1.8
25691e5 - Angie Hinrichs, Fri Mar 17 15:33:43 2023 -0700 : Added 2952 sequences (3000 random minus dups) for BF.7.4.1
7426dd2 - Angie Hinrichs, Fri Mar 17 15:32:43 2023 -0700 : Added 2471 sequences (2500 random minus dups) for BQ.1.12
bde8a9f - Angie Hinrichs, Fri Mar 17 15:28:18 2023 -0700 : Added 2367 sequences (2400 random minus dups) for BQ.1.14
e54d8a2 - Angie Hinrichs, Fri Mar 17 15:27:02 2023 -0700 : Added 593 sequences (600 random minus dups) for XBB.1.4.1
3bc1aca - Angie Hinrichs, Fri Mar 17 15:25:10 2023 -0700 : Added 593 sequences (600 random minus dups) for BA.2.75.5
9c5fbcf - Angie Hinrichs, Fri Mar 17 15:15:45 2023 -0700 : Don't add blank line at end of file.
969f3ab - Angie Hinrichs, Fri Mar 17 15:12:56 2023 -0700 : Added 294 sequences (300 random minus dups) for BM.1.1
ff51501 - Angie Hinrichs, Fri Mar 17 15:11:56 2023 -0700 : Added 2480 sequences (2500 random minus dups) for CH.1.1.1
60100c5 - Angie Hinrichs, Fri Mar 17 15:10:30 2023 -0700 : Added 597 sequences (600 random minus dups) for CQ.2
87eaa56 - Angie Hinrichs, Fri Mar 17 15:09:21 2023 -0700 : Added 992 sequences (1000 random minus dups) for BQ.1.1.2
ddcd45d - Angie Hinrichs, Fri Mar 17 15:08:16 2023 -0700 : Added 1993 sequences (2000 random minus dups) for BQ.1.1.20
202b91a - Angie Hinrichs, Fri Mar 17 15:06:56 2023 -0700 : Added 1381 sequences (1400 random minus dups) for BQ.1.18
d5f6a1e - Angie Hinrichs, Fri Mar 17 15:03:30 2023 -0700 : Correcting 30 designations from BQ.1.1.69 to BQ.1.18.
3247db2 - Angie Hinrichs, Fri Mar 17 14:33:22 2023 -0700 : Added 698 sequences (700 random minus dups) for BQ.1.1.13
9944ede - Angie Hinrichs, Fri Mar 17 14:31:22 2023 -0700 : Added 992 sequences (1000 random minus dups) for BQ.1.1.10
a4a64d4 - Angie Hinrichs, Fri Mar 17 14:29:51 2023 -0700 : Added 1491 sequences (1500 random minus dups) for XBB.2
347f2a2 - Angie Hinrichs, Fri Mar 17 14:27:35 2023 -0700 : Added 1490 sequences (1500 random minus dups) for BA.2.75.2
c8d2cf9 - Angie Hinrichs, Fri Mar 17 14:26:15 2023 -0700 : Added 296 sequences (300 random minus dups) for CM.8.1
6b40173 - Angie Hinrichs, Fri Mar 17 14:25:06 2023 -0700 : Added 4977 sequences (5000 random minus dups) for BQ.1.2
bcb4abb - Angie Hinrichs, Fri Mar 17 11:56:24 2023 -0700 : Added 352 sequences (400 random minus dups) for BF.7.7
2db361e - Angie Hinrichs, Fri Mar 17 11:51:50 2023 -0700 : Correcting some BE.1.4 designations that should be BF.7.7. History: commit b706220 added 111 BF.7.7 designations, but then 4cc824a wiped out all but one of them, redesignating them as BE.1.4 and adding some more sequences as BE.1.4 that should be BF.7.7.
be4348c - Angie Hinrichs, Fri Mar 17 10:52:51 2023 -0700 : Added 2981 sequences (3000 random minus dups) for BQ.1.3
454efa3 - Angie Hinrichs, Fri Mar 17 10:47:17 2023 -0700 : Added 994 sequences (1000 random minus dups) for BA.2.3.20
c3f7fac - Angie Hinrichs, Fri Mar 17 10:37:47 2023 -0700 : Added 997 sequences (1000 random minus dups) for XBB
55f29f7 - Angie Hinrichs, Fri Mar 17 10:35:41 2023 -0700 : Added 1489 sequences (1500 random minus dups) for BN.1
f2f47f1 - Angie Hinrichs, Fri Mar 17 10:32:26 2023 -0700 : Added 8948 sequences (9000 random minus dups) for BQ.1
53822b7 - Angie Hinrichs, Fri Mar 17 10:29:46 2023 -0700 : Added 5995 sequences (6000 random minus dups) for CH.1.1 which had only 6
475eba8 - Angie Hinrichs, Fri Mar 17 10:24:13 2023 -0700 : Added 9992 sequences (10000 random minus dups) for XBB.1.5 which had only 3
a09730f - Angie Hinrichs, Thu Mar 16 21:13:33 2023 -0700 : Add 9996 sequences (10000 random minus dups) for BQ.1.1 which had only 2
3f50157 - Cornelius Roemer, Mon Mar 20 18:22:19 2023 +0100 : Added lineage DV.5 (ORF1a:R24C, S:613H) from #1753
3812bd7 - Cornelius Roemer, Mon Mar 20 18:20:04 2023 +0100 : Added lineage CH.1.1.17 (M:S212G, on C21811T) from #1753
2fbaa60 - Cornelius Roemer, Mon Mar 20 18:18:08 2023 +0100 : Added lineage CH.1.1.16 (S:613H, ORF3a:S26L, on C193T branch) from #1753
9822bfb - Cornelius Roemer, Mon Mar 20 17:41:33 2023 +0100 : Added lineage XBB.1.26 (T10663C on 28297C branch)
a69b4b2 - Cornelius Roemer, Mon Mar 20 17:38:14 2023 +0100 : Added lineage XBB.1.25 (C673T, G487T, on 28297C branch)
a48c0a4 - Cornelius Roemer, Mon Mar 20 17:35:34 2023 +0100 : fix: #1654 lineage from previous commit is XBB.1.24 not XBB.1.5.27
030b4fa - Cornelius Roemer, Sun Mar 19 23:48:48 2023 +0100 : Added lineage XBB.1.5.27 (S:F486P) from #1654 with 25 designations
1b038ea - Cornelius Roemer, Sun Mar 19 23:13:43 2023 +0100 : Added lineage XBB.2.7 (ORF1a:R3662H)
77ccad4 - Cornelius Roemer, Sun Mar 19 23:03:57 2023 +0100 : Added lineages XBJ.2 (C22006T), XBJ.3 (ORF1a:K2928N), XBJ.4 (S:G485D)
45761f6 - Cornelius Roemer, Sun Mar 19 22:59:12 2023 +0100 : Added XBJ.1 (A16011G) and XBJ.1.1 (S:G485D, N:R195K) from #1591
093c3c1 - Cornelius Roemer, Sun Mar 19 22:47:55 2023 +0100 : Added lineage XBB.1.23 (E:S68F)
04782b5 - Cornelius Roemer, Sun Mar 19 22:40:16 2023 +0100 : Added lineages XBB.1.9.4 (28603T) and XBB.1.9.5 (ORF1a:D629E)
d6e8d67 - Cornelius Roemer, Sun Mar 19 22:31:50 2023 +0100 : Added lineages XBB.1.22 (S:486P), XBB.1.22.1 (S:200C), XBB.1.22.2 from #1704
98038d6 - Cornelius Roemer, Sun Mar 19 22:08:34 2023 +0100 : Added lineage XBC.2.1 (S:K444T) from #1538 with 15 designations
efb56c9 - Cornelius Roemer, Sun Mar 19 21:48:27 2023 +0100 : Added lineage XBB.1.21 (S:F486A) with 30 designations from #1646
7df7196 - Cornelius Roemer, Sun Mar 19 21:34:11 2023 +0100 : Added lineage XBF.8.1 (S:P621S) with 30 designations from #1651
8501884 - Cornelius Roemer, Sun Mar 19 21:11:36 2023 +0100 : Added lineages XBB.1.5.26 (920T), EU.1 (S:521S), EU.1.1 (S:410V) from #1688
ed4a524 - Cornelius Roemer, Sun Mar 19 20:24:41 2023 +0100 : Added recombinant XBY (BR.2.1, XBF) from #1669 with 17 designations
ea09cdf - Cornelius Roemer, Sun Mar 19 19:39:26 2023 +0100 : Added recombinant XBW (XBB.1.5, BQ.1.14) with 19 designations from #1505
bbb71a0 - Cornelius Roemer, Sun Mar 19 19:04:48 2023 +0100 : Added lineage CP.8 (ORF1b:D1939G) with 600 designations
085e3fe - Cornelius Roemer, Sun Mar 19 18:47:04 2023 +0100 : Added lineage DV.1.1 (S:Q613H and N:T265I) with 300 designations from #1720
8c15ae7 - Cornelius Roemer, Sun Mar 19 18:28:53 2023 +0100 : Added recombinant XBV (CR.1, XBB.1) from #1460 with 25 designations
3e99cc6 - Cornelius Roemer, Sun Mar 19 17:40:15 2023 +0100 : Added lineage XBB.1.20 (ORF1a:P4312T, C541T, pre ORF8:8*) with 30 designations
403a93a - Cornelius Roemer, Sun Mar 19 17:37:49 2023 +0100 : Added lineage XBB.1.19.1 (S:E554K) with 60 designations
a4546ed - Cornelius Roemer, Sun Mar 19 17:32:32 2023 +0100 : Added lineage XBB.1.19 (S:486P, C541T, pre ORF8:8*) from #1680 with 80 designations
8e02db9 - Cornelius Roemer, Sun Mar 19 15:46:34 2023 +0100 : Added recombinant XBU (BA.2.75.3/BQ.1/BA.2.75.3) from #1425 with 30 designations
3f39aba - Cornelius Roemer, Sat Mar 18 22:55:27 2023 +0100 : Added lineage XBB.1.5.25 (S:97T) from #1643 with 150 designations
7d4a398 - Cornelius Roemer, Sat Mar 18 22:32:16 2023 +0100 : Added lineage XBB.1.5.24 (C2710T, pre T17124C) with 700 designations
3b74521 - Cornelius Roemer, Sat Mar 18 22:16:14 2023 +0100 : Added lineages XBB.1.18 (A8001G) and XBB.1.18.1 (S:S486P)
d08a99c - Cornelius Roemer, Sat Mar 18 21:52:44 2023 +0100 : Added lineage XBB.1.5.23 (ORF1a:P4220L, pre 17124C) with 170 designations
93241c1 - Cornelius Roemer, Sat Mar 18 21:44:47 2023 +0100 : Added lineage XBB.1.5.22 (ORF1a:E1498A, pre T17124C) with 150 designations
a7f228a - Cornelius Roemer, Sat Mar 18 20:54:21 2023 +0100 : Added lineages XBB.1.17 (T27995C,ORF1a:L469F), XBB.1.17.1 (S:215H, S:486P), XBB.1.17.2 from issue #1712
b2a317e - InfrPopGen, Thu Mar 16 19:48:09 2023 +0000 : Merge pull request #1767 from InfrPopGen/master
682898d - InfrPopGen, Thu Mar 16 19:46:27 2023 +0000 : Added new lineage XBC.1.6 from #1755 with 29 new sequence designations, and 0 updated
e958443 - Angie Hinrichs, Thu Mar 16 09:36:27 2023 -0700 : Fixing inconsistency of lineage_notes.txt vs. alias_key.json and #1058, flagged by @janko-js in #1762.
065b11e - InfrPopGen, Thu Mar 16 11:19:28 2023 +0000 : Merge pull request #1766 from InfrPopGen/master
7fc4433 - InfrPopGen, Thu Mar 16 11:17:48 2023 +0000 : Added new lineage ET.1 from #1732 with 152 new sequence designations, and 32 updated from BQ.1.1.35
63184eb - Angie Hinrichs, Wed Mar 15 11:54:32 2023 -0700 : Merge pull request #1756 from ciscorucinski/master
4a58d66 - ciscorucinski, Tue Mar 14 23:53:49 2023 +0900 : fixed phrasing irregularity
0bd3991 - InfrPopGen, Sat Mar 11 12:11:13 2023 +0000 : Merge pull request #1750 from InfrPopGen/master
a6a3943 - InfrPopGen, Sat Mar 11 12:10:10 2023 +0000 : Added new lineage BQ.1.32 from #1731 with 39 new sequence designations, and 0 updated
6acebab - Cornelius Roemer, Fri Mar 10 12:12:42 2023 +0100 : Added lineage BF.7.4.3 (S:F157L, N:A90S) from #1743
fb067af - InfrPopGen, Thu Mar 9 16:34:06 2023 +0000 : Merge pull request #1744 from InfrPopGen/master
4e7d507 - InfrPopGen, Thu Mar 9 16:32:46 2023 +0000 : Added new lineage CH.1.1.15 from #1726 with 159 new sequence designations, and 0 updated
7328e53 - InfrPopGen, Thu Mar 9 11:03:45 2023 +0000 : Merge pull request #1742 from InfrPopGen/master
39ad5fa - InfrPopGen, Thu Mar 9 11:02:06 2023 +0000 : Added new lineage ES.1 from #1722 with 62 new sequence designations, and 44 updated from BQ.1.1.65
e1c3f87 - InfrPopGen, Tue Mar 7 15:55:32 2023 +0000 : Merge pull request #1737 from InfrPopGen/master
6e17e79 - InfrPopGen, Tue Mar 7 15:54:03 2023 +0000 : Added new lineage ER.1.1 from #1715 with 0 new sequence designations, and 69 updated from ER.1
2331efb - Cornelius Roemer, Tue Mar 7 13:17:12 2023 +0100 : Add extra XBB.1.16 designations for more robust inference
7f20135 - InfrPopGen, Sun Mar 5 16:36:25 2023 +0000 : Merge pull request #1730 from InfrPopGen/master
3a9eb42 - InfrPopGen, Sun Mar 5 16:33:57 2023 +0000 : Added new lineage ER.1 from #1429 with 225 new sequence designations, and 10 updated from BQ.1.1.22
d6dd885 - InfrPopGen, Sun Mar 5 12:29:15 2023 +0000 : Merge pull request #1728 from InfrPopGen/master
dfe6991 - InfrPopGen, Sun Mar 5 12:28:01 2023 +0000 : Added new lineage XBB.1.16 from #1723 with 3 new sequence designations, and 0 updated
81bffd6 - InfrPopGen, Fri Mar 3 16:29:40 2023 +0000 : Merge pull request #1721 from InfrPopGen/master
91827c9 - InfrPopGen, Fri Mar 3 16:28:34 2023 +0000 : Added new lineage BQ.1.1.71 from #1713 with 26 new sequence designations, and 0 updated
ffea223 - InfrPopGen, Thu Mar 2 15:41:03 2023 +0000 : Merge pull request #1716 from InfrPopGen/master
15b9804 - InfrPopGen, Thu Mar 2 15:39:50 2023 +0000 : Added new lineage CP.7 from #1473 with 206 new sequence designations, and 0 updated
7e5d357 - InfrPopGen, Tue Feb 28 16:18:55 2023 +0000 : Merge pull request #1707 from InfrPopGen/master
d052e83 - InfrPopGen, Tue Feb 28 16:17:43 2023 +0000 : Added new lineage CY.2 from #1474 with 259 new sequence designations, and 0 updated
302d70a - InfrPopGen, Tue Feb 28 15:44:22 2023 +0000 : Merge pull request #1706 from InfrPopGen/master
9530ac7 - InfrPopGen, Tue Feb 28 15:42:52 2023 +0000 : Added new lineage EQ.1 from #1522 with 8 new sequence designations, and 213 updated from BA.5.1.33
c57183b - Cornelius Roemer, Sun Feb 26 14:04:31 2023 +0100 : Add #1479 to DY.1 lineage notes
5692c5c - Cornelius Roemer, Sun Feb 26 08:02:58 2023 +0100 : Added lineage XBC.1.5 (ORF1a:T708I) from #1671
4a49d94 - Cornelius Roemer, Sun Feb 26 07:56:13 2023 +0100 : Added lineages EP.1 (BM.1.1.4 with S:L452R) from #1676 and EP.2 (S:S1147L, N:G212S)
97474fd - Cornelius Roemer, Sun Feb 26 07:33:17 2023 +0100 : Added lineage EN.1 (BQ.1.1.46 with S:V1264L) from #1696
d863b3d - Cornelius Roemer, Sun Feb 26 07:25:35 2023 +0100 : Added lineage XBB.1.5.21 (ORF1a:K322R) with 400 designations
06fb9df - Cornelius Roemer, Sun Feb 26 07:23:06 2023 +0100 : Added lineage XBB.1.5.20 (C9532T) with 590 designations
7527580 - Cornelius Roemer, Sun Feb 26 07:21:28 2023 +0100 : Added lineage XBB.1.5.19 (ORF1b:R172C) with 500 designations
fb38540 - Cornelius Roemer, Sun Feb 26 07:19:31 2023 +0100 : Added lineage XBB.1.5.18 (ORF1a:T2300I) with 500 designations
20ec43c - Cornelius Roemer, Sun Feb 26 07:15:02 2023 +0100 : Added lineage XBB.1.5.17 (C23635T) with 800 designations
eacc937 - Cornelius Roemer, Sun Feb 26 07:13:01 2023 +0100 : Added lineage XBB.1.5.16 (T14766C) with 500 designations
1c9afe9 - Cornelius Roemer, Sun Feb 26 07:09:13 2023 +0100 : Added EK.2 (XBB.1.5.13 with S:T259I) with 80 designations
145737c - Cornelius Roemer, Sun Feb 26 07:06:48 2023 +0100 : Added lineage XBB.1.5.15 (G15957T) with 1000 designations
246161b - Cornelius Roemer, Sun Feb 26 07:04:28 2023 +0100 : Added lineage EM.1 (XBB.1.5.7.1, S:R214L) with 200 designations
2cfb89f - Cornelius Roemer, Sun Feb 26 07:00:35 2023 +0100 : Added lineage XBB.8 (T14574C) with 300 designations
e0f696f - Cornelius Roemer, Sun Feb 26 06:47:12 2023 +0100 : Added lineage XBB.2.6 (C5144T, T5731A) with 2000 designations
71480a8 - InfrPopGen, Fri Feb 24 16:59:34 2023 +0000 : Merge pull request #1691 from InfrPopGen/master
12f0e95 - InfrPopGen, Fri Feb 24 16:58:18 2023 +0000 : Added new lineage BF.7.14.7 from #1672 with 6 new sequence designations, and 1 updated from BF.7.14
7d015c1 - InfrPopGen, Fri Feb 24 15:05:46 2023 +0000 : Merge pull request #1690 from InfrPopGen/master
8fc0ca1 - InfrPopGen, Fri Feb 24 15:04:11 2023 +0000 : Added new lineage DV.3.1 from #1626 with 24 new sequence designations, and 25 updated from DV.3
7e0ab33 - InfrPopGen, Thu Feb 23 16:41:46 2023 +0000 : Merge pull request #1686 from InfrPopGen/master
778f076 - InfrPopGen, Thu Feb 23 16:40:29 2023 +0000 : Added new lineage DB.3 from #1613 with 10 new sequence designations, and 0 updated
cd3f3c9 - InfrPopGen, Thu Feb 23 10:48:56 2023 +0000 : Merge pull request #1685 from InfrPopGen/master
37f1772 - InfrPopGen, Thu Feb 23 10:47:30 2023 +0000 : Withdrawn lineage BA.5.2.64 from #1640, redesignated BA.5.12
e8dc78d - InfrPopGen, Wed Feb 22 17:10:59 2023 +0000 : Merge pull request #1683 from InfrPopGen/master
645f51a - InfrPopGen, Wed Feb 22 17:09:35 2023 +0000 : Added new lineage BA.5.2.64 from #1640 with 206 new sequence designations, and 0 updated
f25a2e4 - Cornelius Roemer, Tue Feb 21 17:45:42 2023 +0100 : Add issue #1631 to EL.1
f961da0 - Cornelius Roemer, Tue Feb 21 17:42:09 2023 +0100 : Make XAY/XBA alias_key.json more precise, thanks @ciscorucinski
62738a9 - Christopher Rucinski, Wed Feb 22 01:38:29 2023 +0900 : Added EL alias key (#1678)
aca49a0 - Cornelius Roemer, Tue Feb 21 00:34:54 2023 +0100 : Added lineages XBB.1.5.14 (C2695T) and EL.1 (XBB.1.5.14.1, S:Q675H)
b0b6a4d - Cornelius Roemer, Mon Feb 20 15:24:18 2023 +0100 : Add #1622 to XBC.1.4
018ed31 - Cornelius Roemer, Mon Feb 20 00:59:09 2023 +0100 : Reference #1664 in lineage notes for EG.1
74e8720 - Cornelius Roemer, Mon Feb 20 00:57:56 2023 +0100 : Add issue number to DY.3 lineage notes
4ec5aa1 - Cornelius Roemer, Sun Feb 19 23:19:23 2023 +0100 : Added lineage DV.4 (S:I714V) from #1617
b10c61c - Cornelius Roemer, Sun Feb 19 23:14:44 2023 +0100 : Added lineage EK.1 (XBB.1.5.13 with S:K417S) from #1638
2a44139 - Cornelius Roemer, Sun Feb 19 23:01:34 2023 +0100 : Added lineages XBB.1.5.11 (ORF1a:G401S), XBB.1.5.12 (S:T323I), XBB.1.5.13 (T21880C,G28079T)
8baca36 - Cornelius Roemer, Sun Feb 19 22:47:22 2023 +0100 : Added lineage DS.3 (ORF3a:G254V)
4940b75 - Cornelius Roemer, Sun Feb 19 22:44:59 2023 +0100 : Added lineages BN.1.4.2 (S:Q1113K), BN.1.4.3 (ORF1a:P1096T), BN.1.4.4 (ORF1b:V1149L, ORF1b:V1723M), BN.1.4.5 (ORF1a:T3287I), BN.1.5.2 (S:N481K)
e08a85d - Cornelius Roemer, Sun Feb 19 22:32:19 2023 +0100 : Added lineages BN.1.2.2 (C29546T), BN.1.2.3 (C1471T), BN.1.2.4 (ORF1b:D1746H)
1444034 - Cornelius Roemer, Sun Feb 19 22:22:15 2023 +0100 : Added lineages BN.1.3.6 (M:R174Q), BN.1.3.7 (ORF1a:T1429I), BN.1.3.8 (S:D1139H), EJ.1 (BN.1.3.8 with S:I1225V), EJ.2 (ORF1a:T4355I)
cb95a05 - Cornelius Roemer, Sun Feb 19 22:01:27 2023 +0100 : Added lineages CH.1.1.10 (ORF1a:G442S), CH.1.1.11 (ORF1a:A1176T), CH.1.1.12 (S:L858I), CH.1.1.13 (ORF3a:S171L) and CH.1.1.14 (N:T362I)
64a2e7f - Cornelius Roemer, Sun Feb 19 20:55:39 2023 +0100 : Added lineage BF.7.27 (C8752T)
9788743 - Cornelius Roemer, Sun Feb 19 20:48:09 2023 +0100 : Added lineages BF.7.14.4 (ORF1a:T1844I), BF.7.14.5 (C20703T), BF.7.14.6 (C1973T)
ab4f6cf - Cornelius Roemer, Sun Feb 19 20:31:12 2023 +0100 : Added lineage DY.4 (ORF1b:T2432I) and extra BA.5.2.48 designations
e7b3e70 - Cornelius Roemer, Sun Feb 19 20:24:18 2023 +0100 : Added lineage DY.3 (ORF1a:T1788M)
dffaa34 - Cornelius Roemer, Sun Feb 19 20:22:02 2023 +0100 : Added DY.2 (N:Q241K) from #1478
00d8629 - Cornelius Roemer, Sun Feb 19 20:08:05 2023 +0100 : Add extra XBF designations
a3cf13e - Cornelius Roemer, Sun Feb 19 20:07:40 2023 +0100 : Add deduplicate_keeping_first.py script to add extra designations without touching sublineages
2140218 - Cornelius Roemer, Sun Feb 19 20:00:14 2023 +0100 : Added lineage XBF.8 (T9931C, C12970T)
8561c09 - Cornelius Roemer, Sun Feb 19 19:56:44 2023 +0100 : Added lineage XBF.7.1 (S:T323I) with 30 designations
5dce2b9 - Cornelius Roemer, Sun Feb 19 19:54:04 2023 +0100 : Added lineages XBF.5 (C2455T), XBF.6 (ORF1a:V3986A) and XBF.7 (N:T379I)
625b0d0 - Cornelius Roemer, Sun Feb 19 19:04:15 2023 +0100 : Added lineage EH.1 (S:S247N, S:Y248S) from #1648
d39071c - Cornelius Roemer, Sun Feb 19 18:50:45 2023 +0100 : Added recombinant XBT (BA.5.2.34, BA.2.75, BA.5.2.34) from #1576
5ba0df0 - Cornelius Roemer, Sun Feb 19 18:21:04 2023 +0100 : Added recombinant XBS (BA.2.75* and BQ.1 (with S:R346T)) from #1567
ac001e2 - Cornelius Roemer, Sun Feb 19 18:12:59 2023 +0100 : Added recombinant XBR (BA.2.75* and BQ.1 (with S:R346T)) from #1637
23d8aed - Cornelius Roemer, Sun Feb 19 17:33:10 2023 +0100 : Added lineage XBK.1 (S:P1162S) from #1551
4753bfa - Cornelius Roemer, Sun Feb 19 17:31:06 2023 +0100 : Added lineage XBF.4 (ORF1a:H417Y)
2d744cd - Cornelius Roemer, Sun Feb 19 17:28:53 2023 +0100 : Added lineage XBB.2.5 (S:Q613H)
12f6d0b - Cornelius Roemer, Sun Feb 19 17:27:06 2023 +0100 : Added lineage XBB.1.9.3 (ORF1b:G2005S, ORF1b:G1568C)
18da557 - Cornelius Roemer, Sun Feb 19 17:24:09 2023 +0100 : Added lineage EG.1 (XBB.1.9.2 with S:Q613H) with 100 designations
a0c1961 - Cornelius Roemer, Sun Feb 19 17:17:33 2023 +0100 : Added lineage XBB.1.15 (ORF1ab:A540V) with 800 designations
31f1cc5 - Cornelius Roemer, Sun Feb 19 17:12:11 2023 +0100 : Added recombinant XBQ (BA.5.2 and CJ.1) with 80 designations from #1440 and autolin