diff --git a/lineage_notes.txt b/lineage_notes.txt index 9403051b..bca1f91e 100644 --- a/lineage_notes.txt +++ b/lineage_notes.txt @@ -897,6 +897,7 @@ CH.1.1.23 Alias of B.1.1.529.2.75.3.4.1.1.1.1.23, found mainly in UK, from pango CH.1.1.24 Alias of B.1.1.529.2.75.3.4.1.1.1.1.24, T931C, T6676C CH.1.1.25 Alias of B.1.1.529.2.75.3.4.1.1.1.1.25, ORF1a:S330L, ORF1a:P4197S, US CH.1.1.26 Alias of B.1.1.529.2.75.3.4.1.1.1.1.26, C29296T, Japan +CH.1.1.27 Alias of B.1.1.529.2.75.3.4.1.1.1.1.27, ORF1a:S538L, New Zealand CH.2 Alias of B.1.1.529.2.75.3.4.1.1.2, defined by S:Q183H CH.3 Alias of B.1.1.529.2.75.3.4.1.1.3, defined by S:486P on ORF1b:Q2425R branch CH.3.1 Alias of B.1.1.529.2.75.3.4.1.1.3.1, S:S494P, Australia/Indonesia, from #1421 diff --git a/lineages.csv b/lineages.csv index 423c9159..da601d09 100644 --- a/lineages.csv +++ b/lineages.csv @@ -2254413,7 +2254413,6 @@ England/QEUH-326D9B1F/2023,CH.1.1 England/BRBR-32669F36/2022,CH.1.1 Denmark/DCGC-632254/2022,CH.1.1 Liechtenstein/FL-Risch-1117R14924/2022,CH.1.1 -Australia/NSW-NSWHP-41797/2023,CH.1.1 England/LSPA-32614617/2022,CH.1.1 Ireland/SO-NVRL-S23IRL00002502/2023,CH.1.1 Singapore/R6MR107/2023,CH.1.1 @@ -2254600,7 +2254599,6 @@ USA/PA-CDC-QDX44333935/2022,CH.1.1 USA/NC-CORVASEQ-UNC-9149/2023,CH.1.1 Australia/QLD0x0129D5/2022,CH.1.1 Denmark/DCGC-635462/2023,CH.1.1 -England/BRBR-326AC75D/2023,CH.1.1 Ireland/SO-Enfer-120123004_H8/2023,CH.1.1 Denmark/DCGC-640274/2023,CH.1.1 Canada/ON-PHL-23-04240/2023,CH.1.1 @@ -2254622,7 +2254620,6 @@ England/LSPA-3260AE85/2022,CH.1.1 England/LSPA-326953EA/2023,CH.1.1 Germany/BW-RKI-I-1108686/2023,CH.1.1 Germany/BY-MVP-000019214/2023,CH.1.1 -Australia/TAS004892/2023,CH.1.1 England/BRBR-3265A5AF/2022,CH.1.1 USA/CT-YNH-2410/2023,CH.1.1 USA/PA-CDC-STM-ECA5CP6A4/2023,CH.1.1 @@ -2254693,7 +2254690,6 @@ Scotland/LSPA-3263F85C/2022,CH.1.1 England/LSPA-32641EEC/2022,CH.1.1 Netherlands/FR-RIVM-123998/2023,CH.1.1 Netherlands/ZH-RIVM-123258/2022,CH.1.1 -Australia/NSW-ICPMR-42283/2023,CH.1.1 Scotland/SCOT-26152/2023,CH.1.1 Netherlands/NB-MVD-CWGS2300038/2023,CH.1.1 Netherlands/FR-RIVM-124390/2023,CH.1.1 @@ -2254732,7 +2254728,6 @@ Germany/BY-RKI-I-1105457/2023,CH.1.1 Netherlands/NH-AUMC-000175/2023,CH.1.1 Denmark/DCGC-638364/2023,CH.1.1 USA/NY-CDC-QDX46677709/2023,CH.1.1 -Germany/NW-RKI-I-1101932/2023,CH.1.1 USA/MD-CDC-QDX46136201/2023,CH.1.1 England/LSPA-325C2BFC/2022,CH.1.1 Israel/ICH-741194588/2022,CH.1.1 @@ -2254784,7 +2254779,6 @@ England/BRBR-3265792E/2022,CH.1.1 Sweden/SUS0020784/2023,CH.1.1 England/BRBR-326B0BA5/2023,CH.1.1 Germany/NW-RKI-I-1035418/2022,CH.1.1 -USA/CA-CDC-STM-ZJFAQW5JV/2022,CH.1.1 USA/TX-HMH-M-125072/2023,CH.1.1 Austria/LB-R00108-S190/2022,CH.1.1 England/QEUH-326DBEBA/2023,CH.1.1 @@ -2255628,7 +2255622,6 @@ Thailand/NIC_STI_546/2023,CH.1.1 England/PHEC-YY8THBA/2022,CH.1.1 England/PHEC-YY8ETZJ/2022,CH.1.1 England/PHEC-YYER8QP/2023,CH.1.1 -Australia/NSW-ICPMR-42193/2023,CH.1.1 Japan/TKYkbm73429/2022,CH.1.1 England/PHEC-YY81MPX/2022,CH.1.1 Netherlands/LI-RIVM-126146/2023,CH.1.1 @@ -2255730,7 +2255723,6 @@ England/PHEC-YY87Q1M/2023,CH.1.1 Germany/NW-RKI-I-1086342/2023,CH.1.1 Thailand/NIC_SKW_25607/2022,CH.1.1 England/QEUH-326D9159/2023,CH.1.1 -Ireland/CN-NVRL-S23IRL00003450/2023,CH.1.1 Germany/BY-RKI-I-1084732/2022,CH.1.1 Canada/AB-ABPHL-89834/2022,CH.1.1 England/QEUH-3261CF32/2022,CH.1.1 @@ -2255841,7 +2255833,6 @@ England/PHEC-YY8AQ5D/2022,CH.1.1 USA/CA-CDC-LC0998393/2023,CH.1.1 Germany/NW-RKI-I-1097979/2023,CH.1.1 Japan/TKYmbc32160/2023,CH.1.1 -England/BRBR-326AC8A5/2023,CH.1.1 England/PHEP-YYGJBQM/2023,CH.1.1 England/QEUH-32686883/2023,CH.1.1 Sweden/SUS0020805/2023,CH.1.1 @@ -2256286,7 +2256277,6 @@ Germany/HH-RKI-I-1102919/2023,CH.1.1 USA/NC-CDC-LC0975527/2022,CH.1.1 Scotland/LSPA-3268A281/2023,CH.1.1 England/LSPA-326260F6/2022,CH.1.1 -Australia/QLD0x0124DB/2022,CH.1.1 England/QEUH-32605F87/2022,CH.1.1 Canada/ON-PHL-23-07541/2023,CH.1.1 Germany/BY-RKI-I-1108880/2023,CH.1.1 @@ -2256392,7 +2256382,6 @@ Japan/PG-421863/2022,CH.1.1 Austria/LB-R00122-S040/2023,CH.1.1 Denmark/DCGC-633217/2022,CH.1.1 Ireland/TA-Enfer-030123003_E3/2023,CH.1.1 -England/BRBR-326AC711/2023,CH.1.1 Thailand/NIC_PTE_25039/2022,CH.1.1 Australia/NSW-ICPMR-42340/2023,CH.1.1 USA/CA-CDC-STM-ZJ7SS85U4/2023,CH.1.1 @@ -2256837,7 +2256826,6 @@ England/QEUH-3264306C/2022,CH.1.1 England/PHEC-YY8OZHE/2022,CH.1.1 England/QEUH-326E7765/2023,CH.1.1 England/BRBR-326F52BE/2023,CH.1.1 -Germany/BW-RKI-I-1085250/2023,CH.1.1 Belgium/Jessa_11-2310-000082/2023,CH.1.1 Japan/TKYmbc19559/2022,CH.1.1 Sweden/SUS0020743/2023,CH.1.1 @@ -2257133,7 +2257121,6 @@ England/QEUH-32645CFD/2022,CH.1.1 Germany/SH-RKI-I-1114080/2023,CH.1.1 Japan/TKYkbm82174/2023,CH.1.1 Japan/TKYkbm87375/2023,CH.1.1 -Australia/VIC81161/2023,CH.1.1 USA/MD-CDC-QDX45592813/2023,CH.1.1 USA/NM-UNM-2023005496/2023,CH.1.1 Netherlands/UT-RIVM-125655/2023,CH.1.1 @@ -2257376,7 +2257363,6 @@ France/ARA-HCL722004521401/2022,CH.1.1 USA/MD-CDC-LC0991554/2023,CH.1.1 England/BRBR-326B5E10/2023,CH.1.1 Austria/AGES-6052899/2022,CH.1.1 -England/QEUH-326D5339/2023,CH.1.1 England/LSPA-3269B144/2023,CH.1.1 England/LSPA-3269EC6E/2023,CH.1.1 Scotland/SCOT-24383/2023,CH.1.1 @@ -2257557,7 +2257543,6 @@ Germany/BY-RKI-I-1111975/2023,CH.1.1 France/NOR-CHURouen-77040181/2022,CH.1.1 Germany/BY-RKI-I-1093610/2023,CH.1.1 Israel/SMC-7109656/2022,CH.1.1 -England/BRBR-326AC8F0/2023,CH.1.1 England/PHEP-YYG8F9E/2023,CH.1.1 Austria/AGES-1166677/2022,CH.1.1 Germany/BE-ChVir-LB-230310-48160/2023,CH.1.1 @@ -2257575,7 +2257560,6 @@ England/PHEC-YY8WDGB/2022,CH.1.1 England/QEUH-32674E86/2022,CH.1.1 France/ARA-HCL723000159201/2023,CH.1.1 Ireland/KY-NVRL-S23IRL00002539/2023,CH.1.1 -Australia/NSW-ICPMR-42272/2023,CH.1.1 Germany/NW-RKI-I-1110370/2023,CH.1.1 Canada/ON-PHL-23-15535/2023,CH.1.1 USA/FL-CDC-QDX45530286/2023,CH.1.1 @@ -2257725,7 +2257709,6 @@ France/CVL-IPP59414/2022,CH.1.1 Australia/VIC78999/2022,CH.1.1 Netherlands/LI-RIVM-125996/2023,CH.1.1 Thailand/NIC_NPT_25175/2022,CH.1.1 -Australia/WA11482/2023,CH.1.1 Germany/BW-RKI-I-1099142/2023,CH.1.1 Austria/AGES-1158456/2022,CH.1.1 USA/MO-CDC-QDX44940205/2022,CH.1.1 @@ -2257769,7 +2257752,6 @@ Thailand/DMSc-15035/2022,CH.1.1 Denmark/DCGC-607887/2022,CH.1.1 USA/CA-CDC-STM-T3H9GDRHA/2023,CH.1.1 Japan/PG-408873/2022,CH.1.1 -England/PHEC-YY87SCO/2022,CH.1.1 Germany/BW-RKI-I-1092060/2023,CH.1.1 Sweden/9467156763/2023,CH.1.1 Reunion/ChuReu-723011467901/2023,CH.1.1 @@ -2257789,7 +2257771,6 @@ England/LSPA-3267E5B4/2023,CH.1.1 Denmark/DCGC-642637/2023,CH.1.1 England/LSPA-3264AF77/2022,CH.1.1 Canada/ON-PHL-23-15026/2023,CH.1.1 -Australia/WA11839/2023,CH.1.1 Thailand/NIC_STI_27583/2022,CH.1.1 USA/DE-CDC-LC0958237/2022,CH.1.1 England/QEUH-326D8FC9/2023,CH.1.1 @@ -2257801,7 +2257782,6 @@ England/PLYM-325D21E8/2022,CH.1.1 USA/CA-CDC-STM-ME7ZA56T9/2022,CH.1.1 Sweden/14_SE300_DC23-001855/2023,CH.1.1 England/BRBR-3265A0CC/2022,CH.1.1 -England/BRBR-326AC9A2/2023,CH.1.1 England/PHEC-YY8HDFU/2023,CH.1.1 USA/CA-CDPH-FS27890764/2022,CH.1.1 Germany/BW-RKI-I-1115599/2023,CH.1.1 @@ -2257940,7 +2257920,6 @@ Sweden/1599895964/2022,CH.1.1 India/MH_BJCOG_INSACOG_illumina_Run_8_4901/2022,CH.1.1 Japan/TKYmbc22456/2022,CH.1.1 Germany/NW-RKI-I-1102145/2023,CH.1.1 -USA/WA-CDC-LC1005477/2023,CH.1.1 Denmark/DCGC-633370/2022,CH.1.1 Austria/AGES-1110981/2023,CH.1.1 Germany/SN-RKI-I-1078016/2022,CH.1.1 @@ -2257984,7 +2257963,6 @@ England/BRBR-32658583/2022,CH.1.1 England/BRBR-326E406D/2023,CH.1.1 Germany/BW-RKI-I-1109966/2023,CH.1.1 England/QEUH-3269EA82/2023,CH.1.1 -Germany/BW-RKI-I-1085266/2023,CH.1.1 England/LSPA-326685CC/2022,CH.1.1 Austria/MUIV-0640/2022,CH.1.1 England/PLYM-326C832A/2023,CH.1.1 @@ -2258212,7 +2258190,6 @@ Germany/SN-RKI-I-1109284/2023,CH.1.1 England/PLYM-326D69CD/2023,CH.1.1 Germany/BW-RKI-I-1105937/2023,CH.1.1 Denmark/DCGC-631043/2022,CH.1.1 -Australia/NSW-ICPMR-40648/2023,CH.1.1 Canada/NL-PHML-597300/2023,CH.1.1 England/BRBR-326BDABA/2023,CH.1.1 France/NAQ-HCL723000249601/2023,CH.1.1 @@ -2258369,7 +2258346,6 @@ Austria/AGES-1116259/2023,CH.1.1 England/BRBR-326AD6B9/2023,CH.1.1 England/LSPA-32680661/2023,CH.1.1 Luxembourg/LNS4080162/2023,CH.1.1 -England/QEUH-3263853E/2022,CH.1.1 Australia/QLD0x012B0D/2022,CH.1.1 Netherlands/NB-RIVM-121699/2022,CH.1.1 England/PHEC-YY8AXP9/2022,CH.1.1 @@ -2258467,7 +2258443,6 @@ Japan/RB23-001-53-P0/2022,CH.1.1 Austria/LB-R00124-S010/2023,CH.1.1 England/QEUH-325DE313/2022,CH.1.1 Japan/PG-457015/2023,CH.1.1 -Australia/ACT10745/2023,CH.1.1 England/PHEC-YY8WA3F/2022,CH.1.1 Germany/BW-RKI-I-1081139/2022,CH.1.1 Germany/BY-RKI-I-1109073/2023,CH.1.1 @@ -2258527,7 +2258502,6 @@ England/QEUH-3269205F/2023,CH.1.1 Austria/AGES-1114542/2023,CH.1.1 Netherlands/LI-RIVM-126178/2023,CH.1.1 Austria/MUIV-0891/2022,CH.1.1 -England/BRBR-326ABFFC/2023,CH.1.1 England/LSPA-326645A2/2022,CH.1.1 England/LSPA-32623897/2022,CH.1.1 USA/TX-HMH-M-124479/2023,CH.1.1 @@ -2258568,7 +2258542,6 @@ Sweden/01_SE100_23CS500544/2023,CH.1.1 England/PHEC-YY8HNJC/2022,CH.1.1 Singapore/R4MR124/2023,CH.1.1 England/QEUH-326C61AA/2023,CH.1.1 -England/BRBR-326AC966/2023,CH.1.1 Netherlands/ZE-MVD-C2300193/2023,CH.1.1 England/PHEP-YYGF6TX/2022,CH.1.1 England/LSPA-326152A9/2022,CH.1.1 @@ -2258628,7 +2258601,6 @@ Japan/TKYmbc29307/2022,CH.1.1 Denmark/DCGC-640148/2023,CH.1.1 England/BRBR-3267B58A/2022,CH.1.1 England/LSPA-3268F4C2/2023,CH.1.1 -England/BRBR-326AC070/2023,CH.1.1 Ireland/LH-NVRL-SIRL00007026/2023,CH.1.1 Canada/ON-PHL-10518-v2/2023,CH.1.1 USA/IL-CDC-QDX44067895/2022,CH.1.1 @@ -2258782,7 +2258754,6 @@ Germany/NW-RKI-I-1101126/2023,CH.1.1 England/PHEC-YY87QOX/2023,CH.1.1 Denmark/DCGC-636824/2023,CH.1.1 Sweden/DA10534364/2022,CH.1.1 -USA/CA-CDC-STM-K42W69H56/2023,CH.1.1 Israel/SMC-7111924/2023,CH.1.1 England/PHEP-YYGJ4DE/2023,CH.1.1 England/QEUH-3260601A/2022,CH.1.1 @@ -2258792,7 +2258763,6 @@ Switzerland/AG-Risch-1026R14335/2022,CH.1.1 Singapore/R2MR22/2023,CH.1.1 France/OCC-HCL-723000286801/2023,CH.1.1 Japan/TKYkbm85590/2023,CH.1.1 -Australia/QLD0x012CF3/2023,CH.1.1 Israel/ICH-741193828/2022,CH.1.1 Japan/PG-451067/2023,CH.1.1 Japan/TKYkbm71810/2022,CH.1.1 @@ -2258996,7 +2258966,6 @@ USA/TX-CDC-QDX46327359/2023,CH.1.1 Japan/PG-415449/2022,CH.1.1 England/PLYM-326AB0BD/2023,CH.1.1 Netherlands/GE-RIVM-125275/2023,CH.1.1 -Germany/BW-RKI-I-1088525/2023,CH.1.1 England/LSPA-32614D8B/2022,CH.1.1 USA/PA-DHSS-B1261474/2023,CH.1.1 Sweden/723368/2023,CH.1.1 @@ -2259094,7 +2259063,6 @@ England/PHEP-YYGE7OC/2023,CH.1.1 England/LSPA-3269F368/2023,CH.1.1 Canada/BC-BCCDC-566871/2022,CH.1.1 Belgium/Jessa_11-2307-006046/2023,CH.1.1 -England/BRBR-326AC83C/2023,CH.1.1 England/LSPA-326385C5/2022,CH.1.1 England/LSPA-325F1FCB/2022,CH.1.1 Netherlands/UT-RIVM-125352/2023,CH.1.1 @@ -2385704,3 +2385672,380 @@ England/PHEC-YYEMOGG/2023,DV.6 England/PHEC-YYEMOY1/2023,DV.6 England/PHEC-YYEMO8R/2023,DV.6 England/PHEC-YY87NUI/2023,DV.6 +NewZealand/23YA0789/2023,CH.1.1.27 +NewZealand/23XA0332/2023,CH.1.1.27 +NewZealand/23YA0371/2023,CH.1.1.27 +NewZealand/23XA0783/2023,CH.1.1.27 +NewZealand/23XA0874/2023,CH.1.1.27 +NewZealand/23XA0591/2023,CH.1.1.27 +Australia/NSW-NSWHP-42078/2023,CH.1.1.27 +NewZealand/22YA4981/2022,CH.1.1.27 +NewZealand/22XA6834/2022,CH.1.1.27 +Australia/QLD0x0125F2/2022,CH.1.1.27 +NewZealand/22YA5580/2022,CH.1.1.27 +NewZealand/22XA6166/2022,CH.1.1.27 +NewZealand/22YA5178/2022,CH.1.1.27 +NewZealand/22YA4983/2022,CH.1.1.27 +NewZealand/22XA6860/2022,CH.1.1.27 +NewZealand/22YA4644/2022,CH.1.1.27 +NewZealand/22XA5377/2022,CH.1.1.27 +NewZealand/22YA4125/2022,CH.1.1.27 +NewZealand/22YA4356/2022,CH.1.1.27 +NewZealand/22XA4936/2022,CH.1.1.27 +NewZealand/22YA4942/2022,CH.1.1.27 +NewZealand/22YA4171/2022,CH.1.1.27 +NewZealand/22YA4186/2022,CH.1.1.27 +NewZealand/22YA4393/2022,CH.1.1.27 +NewZealand/22YA4394/2022,CH.1.1.27 +NewZealand/22XA4666/2022,CH.1.1.27 +NewZealand/22XA5034/2022,CH.1.1.27 +NewZealand/22YA4301/2022,CH.1.1.27 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