From 325315cebd6f5b8a6f49ea0e79d0cb057603b6ef Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Sun, 15 Oct 2023 21:01:10 +0200 Subject: [PATCH] Designate JG.3.1 (EG.5.1.3.3.1, S:T307I) with 170 seqs --- lineage_notes.txt | 1 + lineages.csv | 160 ++++++++++++++++++++++++++++++++++++++++++---- 2 files changed, 147 insertions(+), 14 deletions(-) diff --git a/lineage_notes.txt b/lineage_notes.txt index c813bf4e..9bd8c08d 100644 --- a/lineage_notes.txt +++ b/lineage_notes.txt @@ -3078,6 +3078,7 @@ EG.5.1.3 Alias of XBB.1.9.2.5.1.3, ORF1a:R542C, C22570T from https://github.com/ JG.1 Alias of XBB.1.9.2.5.1.3.1, S:T732I, France, from #2218 JG.2 Alias of XBB.1.9.2.5.1.3.2, S:G75V, Europe, from #2249 JG.3 Alias of XBB.1.9.2.5.1.3.3, S:L455F, S:S704L, Europe, from #2231 +JG.3.1 Alias of XBB.1.9.2.5.1.3.3.1, S:T307I JG.4 Alias of XBB.1.9.2.5.1.3.4, C1684T, Europe EG.5.1.4 Alias of XBB.1.9.2.5.1.4, ORF1b:K2557R, from #2117 JJ.1 Alias of XBB.1.9.2.5.1.4.1, S:L455F, ORF3a:I47V, China/Japan, from #2208 diff --git a/lineages.csv b/lineages.csv index 056062ac..e7e889da 100644 --- a/lineages.csv +++ b/lineages.csv @@ -2463843,20 +2463843,6 @@ Spain/CT-HUGTiP-E6R153/2023,JG.3 Spain/CT-HUGTiP-E1R037/2023,JG.3 Spain/CT-HUGTiP-C6R153/2023,JG.3 Denmark/DCGC-658859/2023,JG.3 -England/CLIMB-CM7YKHDN/2023,JG.3 -Denmark/DCGC-659117/2023,JG.3 -Denmark/DCGC-659153/2023,JG.3 -Denmark/DCGC-659019/2023,JG.3 -England/CLIMB-CM7YK4S6/2023,JG.3 -England/CLIMB-CM7YFQIM/2023,JG.3 -England/CLIMB-CM7YEDAS/2023,JG.3 -Germany/BY-LGL-5989806/2023,JG.3 -England/CLIMB-CM7YR7ND/2023,JG.3 -England/CLIMB-CM7YGZB4/2023,JG.3 -England/CLIMB-CM7YEDCI/2023,JG.3 -USA/NY-PRL-230901_82C09/2023,JG.3 -Germany/SH-RKI-I-1137367/2023,JG.3 -Wales/CLIMB-CM7Y8G8Q/2023,JG.3 Guatemala/1365-DLNS/2023,XBB.1.5.106 Guatemala/1305-LNS/2023,XBB.1.5.106 Guatemala/1311-LNS/2023,XBB.1.5.106 @@ -2476316,3 +2476302,149 @@ Germany/NW-RKI-I-1138227/2023,JY.1.1 England/CLIMB-CM7YR8PM/2023,JY.1.1 England/CLIMB-CM7Y84OM/2023,JY.1.1 England/CLIMB-CM7Y81CD/2023,JY.1.1 +Denmark/DCGC-659153/2023,JG.3.1 +Denmark/DCGC-659247/2023,JG.3.1 +Romania/NIID_3547/2023,JG.3.1 +Germany/BE-ChVir43742/2023,JG.3.1 +Denmark/DCGC-659368/2023,JG.3.1 +Denmark/DCGC-659505/2023,JG.3.1 +Denmark/DCGC-659391/2023,JG.3.1 +Sweden/G-23-571655/2023,JG.3.1 +Norway/Ahus-5025/2023,JG.3.1 +Denmark/DCGC-661026/2023,JG.3.1 +Canada/BC-BCCDC-652793/2023,JG.3.1 +Denmark/DCGC-659301/2023,JG.3.1 +Denmark/DCGC-659019/2023,JG.3.1 +Denmark/DCGC-659285/2023,JG.3.1 +Denmark/DCGC-659300/2023,JG.3.1 +Austria/AGES-1141089/2023,JG.3.1 +Sweden/G-23-700759/2023,JG.3.1 +Germany/BY-LGL-6005447/2023,JG.3.1 +Iceland/L-4574/2023,JG.3.1 +Denmark/DCGC-659117/2023,JG.3.1 +Wales/CLIMB-CM7YEIZN/2023,JG.3.1 +Denmark/DCGC-661031/2023,JG.3.1 +Italy/VEN-ULSS3GEN-7002632107_VE/2023,JG.3.1 +Israel/ICH-741199338/2023,JG.3.1 +Iceland/L-4644/2023,JG.3.1 +Iceland/L-4572/2023,JG.3.1 +Denmark/DCGC-661124/2023,JG.3.1 +Denmark/DCGC-661029/2023,JG.3.1 +Denmark/DCGC-659771/2023,JG.3.1 +Denmark/DCGC-659452/2023,JG.3.1 +England/CLIMB-CM7YERC7/2023,JG.3.1 +Denmark/DCGC-659677/2023,JG.3.1 +Denmark/DCGC-659697/2023,JG.3.1 +Denmark/DCGC-659765/2023,JG.3.1 +Denmark/DCGC-659763/2023,JG.3.1 +Denmark/DCGC-659579/2023,JG.3.1 +Denmark/DCGC-659498/2023,JG.3.1 +USA/CA-HLX-STM-6HR9XRYNB/2023,JG.3.1 +England/CLIMB-CM7YGN1O/2023,JG.3.1 +Austria/AGES-1141403/2023,JG.3.1 +Austria/AGES-1141146/2023,JG.3.1 +Austria/AGES-1141070/2023,JG.3.1 +Germany/SH-RKI-I-1138087/2023,JG.3.1 +Germany/SH-RKI-I-1138084/2023,JG.3.1 +Germany/SH-ChVir43851_V143/2023,JG.3.1 +Greece/NPHO-ILI_3950/2023,JG.3.1 +Germany/BE-RKI-I-1138388/2023,JG.3.1 +Sweden/C-03_SE600_000200626464N2/2023,JG.3.1 +Germany/BB-RKI-I-1138124/2023,JG.3.1 +Germany/BB-RKI-I-1137921/2023,JG.3.1 +Denmark/DCGC-659568/2023,JG.3.1 +Denmark/DCGC-659455/2023,JG.3.1 +Denmark/DCGC-660910/2023,JG.3.1 +Denmark/DCGC-659526/2023,JG.3.1 +Denmark/DCGC-660881/2023,JG.3.1 +Denmark/DCGC-661120/2023,JG.3.1 +Denmark/DCGC-660961/2023,JG.3.1 +Canada/ON-KHS-23-06501-v1/2023,JG.3.1 +Canada/ON-KHS-23-06516-v1/2023,JG.3.1 +England/CLIMB-CM7YFU81/2023,JG.3.1 +Iceland/L-4626/2023,JG.3.1 +Germany/NI-RKI-I-1138246/2023,JG.3.1 +Italy/LOM_ASSTMonza_6000291605_20230921112000/2023,JG.3.1 +Canada/ON-PHL-23-31107/2023,JG.3.1 +USA/WA-GBW-H20-335-6250/2023,JG.3.1 +USA/WA-GBW-H20-335-7044/2023,JG.3.1 +USA/WA-GBW-H10-016-8968/2023,JG.3.1 +England/CLIMB-CM7YMUQQ/2023,JG.3.1 +England/CLIMB-CM7Y8KF3/2023,JG.3.1 +England/CLIMB-CM7YRAD9/2023,JG.3.1 +England/CLIMB-CM7YRQDE/2023,JG.3.1 +England/CLIMB-CM7YKHDN/2023,JG.3.1 +England/CLIMB-CM7YJXMT/2023,JG.3.1 +England/CLIMB-CM7Y8FKE/2023,JG.3.1 +England/CLIMB-CM7Y8M1Q/2023,JG.3.1 +England/CLIMB-CM7YEH36/2023,JG.3.1 +England/CLIMB-CM7YRHQ7/2023,JG.3.1 +Germany/SH-RKI-I-1137367/2023,JG.3.1 +England/CLIMB-CM7YFGXB/2023,JG.3.1 +Iceland/L-4515/2023,JG.3.1 +Finland/THL-06984/2023,JG.3.1 +Denmark/DCGC-660975/2023,JG.3.1 +Canada/AB-ABPHL-103751/2023,JG.3.1 +Canada/AB-ABPHL-103087/2023,JG.3.1 +France/ARA-HCL-023154589001/2023,JG.3.1 +Italy/LOM_45089211BAC/2023,JG.3.1 +Netherlands/OV-RIVM-131748/2023,JG.3.1 +France/NAQ-HCL-723001311301/2023,JG.3.1 +Norway/Ahus-5039/2023,JG.3.1 +USA/MN-MDH-36274/2023,JG.3.1 +USA/UT-UPHL-230913252369/2023,JG.3.1 +France/ARA-HCL723001241801/2023,JG.3.1 +Germany/BY-LGL-5989806/2023,JG.3.1 +England/CLIMB-CM7YK4S6/2023,JG.3.1 +USA/CA-CDC-LC1056731/2023,JG.3.1 +England/CLIMB-CM7YFQIM/2023,JG.3.1 +England/CLIMB-CM7YEDAS/2023,JG.3.1 +Germany/BE-RKI-I-1137943/2023,JG.3.1 +England/CLIMB-CM7Y8FSN/2023,JG.3.1 +England/CLIMB-CM7YGZB4/2023,JG.3.1 +England/CLIMB-CM7YMPQZ/2023,JG.3.1 +England/CLIMB-CM7YR7ND/2023,JG.3.1 +England/CLIMB-CM7YRR7H/2023,JG.3.1 +England/CLIMB-CM7YG9Y6/2023,JG.3.1 +England/CLIMB-CM7YJESI/2023,JG.3.1 +England/CLIMB-CM7YGNIB/2023,JG.3.1 +England/CLIMB-CM7YG9MU/2023,JG.3.1 +England/CLIMB-CM7YG5WG/2023,JG.3.1 +England/CLIMB-CM7YMSUX/2023,JG.3.1 +Scotland/CLIMB-CM7Y8GPT/2023,JG.3.1 +England/CLIMB-CM7YJ48J/2023,JG.3.1 +England/CLIMB-CM7YEDCI/2023,JG.3.1 +Wales/CLIMB-CM7Y8G8Q/2023,JG.3.1 +Sweden/AB-01_SE100_23CS502424/2023,JG.3.1 +USA/VA-CDC-LC1058520/2023,JG.3.1 +France/GES-IPP22374/2023,JG.3.1 +Denmark/DCGC-659472/2023,JG.3.1 +England/CLIMB-CM7YFD7R/2023,JG.3.1 +Norway/9719/2023,JG.3.1 +Sweden/O-14_SE300_DC23-005649/2023,JG.3.1 +Northern_Ireland/CLIMB-CM7YFFO6/2023,JG.3.1 +Canada/ON-PHL-23-34223/2023,JG.3.1 +Italy/EMR_AUSLRomagna_C041-23-11/2023,JG.3.1 +Italy/EMR_AUSLRomagna_C041-23-13/2023,JG.3.1 +Italy/EMR_AUSLRomagna_C041-23-12/2023,JG.3.1 +Italy/EMR_AUSLRomagna_C042-23-13/2023,JG.3.1 +Italy/EMR_AUSLRomagna_C041-23-10/2023,JG.3.1 +Italy/EMR_AUSLRomagna_C042-23-14/2023,JG.3.1 +Italy/EMR_AUSLRomagna_C042-23-11/2023,JG.3.1 +Italy/EMR_AUSLRomagna_C042-23-12/2023,JG.3.1 +Austria/AGES-1140979/2023,JG.3.1 +USA/CA-HLX-STM-GQEGZEFMQ/2023,JG.3.1 +England/CLIMB-CM7YMCCO/2023,JG.3.1 +USA/NY-PRL-230901_82C09/2023,JG.3.1 +Sweden/U-R031087/2023,JG.3.1 +England/CLIMB-CM7YGIDB/2023,JG.3.1 +England/CLIMB-CM7YJR7Y/2023,JG.3.1 +England/CLIMB-CM7YGFKJ/2023,JG.3.1 +USA/UT-UPHL-231003421332/2023,JG.3.1 +France/ARA-HCL-723001276301/2023,JG.3.1 +USA/UT-UPHL-230926686889/2023,JG.3.1 +USA/NC-1085-10214/2023,JG.3.1 +USA/CA-HLX-STM-8GR5HPCKB/2023,JG.3.1 +USA/UT-UPHL-231003921249/2023,JG.3.1 +USA/UT-UPHL-231003307566/2023,JG.3.1 +Italy/LOM_Unimi-2989-23/2023,JG.3.1