From 74eed87670c3e6b6525d0dc5373cbfab29752fae Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Fri, 9 Jun 2023 21:14:25 +0200 Subject: [PATCH] Designate FE.1.1.1 (ORF1a:T999I, North America) with 180 seqs --- lineage_notes.txt | 1 + lineages.csv | 227 ++++++++++++++++++++++++++++++++++++---------- 2 files changed, 180 insertions(+), 48 deletions(-) diff --git a/lineage_notes.txt b/lineage_notes.txt index 55eab255..b546272e 100644 --- a/lineage_notes.txt +++ b/lineage_notes.txt @@ -2825,6 +2825,7 @@ XBB.1.18 Defined by A8001G, Brazil XBB.1.18.1 Defined by S:F486P, Brazil FE.1 Alias of XBB.1.18.1.1, S:F456L (T22928C), Brazil/Chile FE.1.1 Alias of XBB.1.18.1.1.1, ORF8:S67F, T4579A +FE.1.1.1 Alias of XBB.1.18.1.1.1.1, ORF1a:T999I, North America FE.1.2 Alias of XBB.1.18.1.1.2, A5488G XBB.1.19 Defined by S:486P, C541T, A10042G, T21363C, pre ORF8:8*, Pakistan, from #1680 XBB.1.19.1 Defined by S:E554K diff --git a/lineages.csv b/lineages.csv index 1f8a7cbb..fe8e8101 100644 --- a/lineages.csv +++ b/lineages.csv @@ -2376304,82 +2376304,42 @@ Spain/CT-HUGTiP-C2R135/2023,XBB.1.5.57 Spain/CT-HUGTiP-D1R135/2023,XBB.1.5.57 Spain/CT-HUGTiP-B8R133/2023,XBB.1.5.57 USA/FL-CDC-QDX47043293/2023,FE.1.1 -Canada/NS-NSH-613256/2023,FE.1.1 -Canada/NS-NSH-617507/2023,FE.1.1 Israel/ICH-741197040/2023,FE.1.1 Brazil/BA-LACEN-BA3670-292954602/2023,FE.1.1 USA/FL-CDC-QDX48956834/2023,FE.1.1 -USA/FL-CDC-QDX48956789/2023,FE.1.1 USA/WI-CDC-QDX49007165/2023,FE.1.1 USA/FL-CDC-QDX48733909/2023,FE.1.1 USA/FL-CDC-QDX48734057/2023,FE.1.1 -Canada/ON-PHL-23-21236-v2/2023,FE.1.1 -USA/IL-CDC-QDX49007143/2023,FE.1.1 -USA/FL-CDC-QDX48853910/2023,FE.1.1 -Ireland/WX-NVRL-SIRL00017537/2023,FE.1.1 Ireland/CO-CUH-S23C0201/2023,FE.1.1 Ireland/CO-CUH-S23C0205/2023,FE.1.1 USA/FL-CDC-QDX48854104/2023,FE.1.1 -Canada/ON-PHL-23-21424/2023,FE.1.1 -Canada/ON-PHL-23-21235-v2/2023,FE.1.1 -Canada/ON-PHL-23-21295-v2/2023,FE.1.1 Denmark/DCGC-646174/2023,FE.1.1 -Canada/ON-PHL-23-21943/2023,FE.1.1 -Canada/ON-PHL-23-21905/2023,FE.1.1 -Canada/ON-PHL-23-21278-v2/2023,FE.1.1 -Canada/ON-PHL-23-21232-v2/2023,FE.1.1 -Canada/ON-PHL-23-21233-v2/2023,FE.1.1 -Canada/ON-PHL-23-21234-v2/2023,FE.1.1 -Canada/ON-PHL-23-21274-v2/2023,FE.1.1 Austria/AGES-1135119/2023,FE.1.1 USA/FL-CDC-VSX-A063864/2023,FE.1.1 -Canada/QC-L00604347001/2023,FE.1.1 -Canada/QC-L00604360001/2023,FE.1.1 -Canada/QC-L00604319001/2023,FE.1.1 -Canada/QC-L00604515001/2023,FE.1.1 -Canada/QC-L00604624001/2023,FE.1.1 -Canada/QC-L00604839001/2023,FE.1.1 -Canada/QC-L00605905001/2023,FE.1.1 Japan/PG-471046/2023,FE.1.1 USA/IL-4222023055/2023,FE.1.1 South Korea/KDCA231041/2023,FE.1.1 Italy/VEN-ULSS3GEN-7002561523_VE/2023,FE.1.1 Italy/VEN-ULSS3GEN-7002565337_VE/2023,FE.1.1 -France/NAQ-HCL723000610701/2023,FE.1.1 South Korea/KDCA229842/2023,FE.1.1 USA/NJ-PHEL-V23009140/2023,FE.1.1 USA/TX-CDC-QDX49328225/2023,FE.1.1 -USA/TX-CDC-QDX49225964/2023,FE.1.1 -Canada/NS-NSH-620009/2023,FE.1.1 Brazil/SC-FIOCRUZ-2167/2023,FE.1.1 France/ARA-CHUCF-233001365401/2023,FE.1.1 USA/VA-VTVAS3-GSC42703/2023,FE.1.1 USA/CA-CDC-QDX49225968/2023,FE.1.1 USA/AZ-ASU101636/2023,FE.1.1 -USA/FL-CDC-QDX49125698/2023,FE.1.1 USA/FL-CDC-QDX49226269/2023,FE.1.1 Portugal/PT47494/2023,FE.1.1 -Canada/ON-PHL-23-22168/2023,FE.1.1 -Canada/ON-PHL-23-22167/2023,FE.1.1 -Canada/ON-PHL-23-22842/2023,FE.1.1 -USA/FL-CDC-QDX49125704/2023,FE.1.1 USA/FL-CDC-QDX49125729/2023,FE.1.1 -Canada/QC-L00596142001/2023,FE.1.1 -Canada/QC-L00596331001/2023,FE.1.1 USA/NJ-CDC-QDX48043347/2023,FE.1.1 USA/NJ-CDC-QDX47973737/2023,FE.1.1 Israel/ICH-741197031/2023,FE.1.1 USA/NY-CDC-QDX48094663/2023,FE.1.1 -Canada/ON-PHL-23-19603/2023,FE.1.1 Italy/PAB_SABES_7850021107/2023,FE.1.1 -USA/NJ-GBW-H20-314-1228/2023,FE.1.1 -Belgium/rega-47112/2023,FE.1.1 -France/OCC-HCL723000460501/2023,FE.1.1 USA/MN-CDC-QDX48043901/2023,FE.1.1 USA/MI-CDC-QDX48415431/2023,FE.1.1 -Canada/QC-L00599736001/2023,FE.1.1 USA/VA-CDC-LC1034213/2023,FE.1.1 -France/BFC-IPP08373/2023,FE.1.1 Denmark/DCGC-645713/2023,FE.1.1 USA/VA-GBW-H20-279-4238/2023,FE.1.1 USA/CA-GBW-H10-010-5244/2023,FE.1.1 @@ -2376389,7 +2376349,6 @@ Switzerland/VD-CHUV-GEN16473/2023,FE.1.1 Anhui/XCCDC-069/2023,FE.1.1 South Korea/KDCA229571/2023,FE.1.1 Anhui/XCCDC-076/2023,FE.1.1 -Canada/QC-L00604436001/2023,FE.1.1 USA/KS-KHEL-13367/2023,FE.1.1 Portugal/PT47194/2023,FE.1.1 USA/MI-CDC-QDX48551749/2023,FE.1.1 @@ -2376404,16 +2376363,11 @@ USA/NY-NYULH-P23-14126/2023,FE.1.1 USA/NY-CDC-QDX48316232/2023,FE.1.1 USA/NY-CDC-QDX48365416/2023,FE.1.1 USA/NJ-CDC-QDX48316185/2023,FE.1.1 -USA/NJ-GBW-H10-012-2488/2023,FE.1.1 -Belgium/rega-47172/2023,FE.1.1 -Belgium/rega-47120/2023,FE.1.1 Canada/BC-BCCDC-611116/2023,FE.1.1 Australia/VIC82460/2023,FE.1.1 Brazil/SP-IB_CEVC_2206278/2023,FE.1.1 Brazil/SP-IB_CEVC_2206264/2023,FE.1.1 USA/CA-CDC-QDX47595045/2023,FE.1.1 -Belgium/rega-47028/2023,FE.1.1 -Belgium/rega-47048/2023,FE.1.1 USA/FL-CDC-QDX47771693/2023,FE.1.1 USA/NC-MCPH-CLT-014384/2023,FE.1.1 Brazil/SP-IB_CEVC_2206061/2023,FE.1.2 @@ -2376641,10 +2376595,8 @@ Canada/ON-PHL-19954/2023,FE.1 Germany/MV-RKI-I-1129757/2023,FE.1 Germany/MV-RKI-I-1127571/2023,FE.1 Guadeloupe/IPP10473/2023,FE.1 -Chile/RM-15680/2023,FE.1 USA/NJ-GBW-H10-011-0301/2023,FE.1 USA/TN-CDC-LC1026619/2023,FE.1 -Chile/RM-ISPC-23017/2023,FE.1 France/HDF-IPP06124/2023,FE.1 USA/NJ-GBW-H20-297-8671/2023,FE.1 USA/CA-CDPH-500108158/2023,GA.1 @@ -2415786,3 +2415738,182 @@ France/PAC-HCL723000595901/2023,XCE France/NAQ-HCL723000688901/2023,XCE France/PAC-HCL723000595801/2023,XCE France/NAQ-HCL723000688801/2023,XCE +USA/IL-CDC-QDX49007143/2023,FE.1.1.1 +Italy/UMB-LAOP-116-2-38/2023,FE.1.1.1 +Brazil/RS-FIOCRUZ-4164/2023,FE.1.1.1 +France/GES-IPP14223/2023,FE.1.1.1 +USA/NY-NYULH-14838/2023,FE.1.1.1 +Italy/UMB-LAOP-119-2-17/2023,FE.1.1.1 +Peru/PUN-INS-45125/2023,FE.1.1.1 +Canada/BC-BCCDC-621173/2023,FE.1.1.1 +Italy/UMB-LAOP-116-2-51/2023,FE.1.1.1 +Italy/UMB-LAOP-116-2-50/2023,FE.1.1.1 +USA/SC-CDC-QDX80241752/2023,FE.1.1.1 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