From 6fe574b411dee14802a7121619ff11be440ab82c Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Sat, 28 Jan 2023 20:51:26 +0100 Subject: [PATCH] Added lineage CH.1.1.6 (S:T732I) with 100 designations --- lineage_notes.txt | 1 + lineages.csv | 154 ++++++++++++++++++++++++++++++++++++---------- 2 files changed, 123 insertions(+), 32 deletions(-) diff --git a/lineage_notes.txt b/lineage_notes.txt index 8d9b1137..4cd09ec5 100644 --- a/lineage_notes.txt +++ b/lineage_notes.txt @@ -854,6 +854,7 @@ CH.1.1.2 Alias of B.1.1.529.2.75.3.4.1.1.1.1.2, defined by S:T883I, ORF1a:Y1846C CH.1.1.3 Alias of B.1.1.529.2.75.3.4.1.1.1.1.3, S:S255P, New Zealand/Australia/Hong Kong, from #1405 CH.1.1.4 Alias of B.1.1.529.2.75.3.4.1.1.1.1.4, S:H681R, Austria, from #1370 CH.1.1.5 Alias of B.1.1.529.2.75.3.4.1.1.1.1.5 found mainly in Denmark and UK, from pango-designation issue #1539 +CH.1.1.6 Alias of B.1.1.529.2.75.3.4.1.1.1.1.6 UK, dfeined by S:T732I 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 1a4c08af..3b712e96 100644 --- a/lineages.csv +++ b/lineages.csv @@ -2133182,10 +2133182,6 @@ England/LSPA-3262CC92/2022,BM.1.1.5 Belgium/UZB_548202210269/2022,BM.1.1.5 Belgium/UZA-UA-BB351A4YHW/2022,BM.1.1.5 Belgium/UZA-UA-BB351A4MGN/2022,BM.1.1.5 -OX396239.1,BM.1.1.5 -OX395506.1,BM.1.1.5 -OX395586.1,BM.1.1.5 -OX394694.1,BM.1.1.5 England/LSPA-3262C9C8/2022,BM.1.1.5 England/LSPA-3262C333/2022,BM.1.1.5 England/LSPA-3262D763/2022,BM.1.1.5 @@ -2133222,9 +2133218,7 @@ USA/VA-CDC-LC0953947/2022,BN.1.4.1 Ireland/LK-NVRL-S22IRL00471330/2022,BN.1.4.1 Germany/MV-RKI-I-1066971/2022,BN.1.4.1 USA/WA-UW-22112665758/2022,BN.1.4.1 -OX394965.1,BN.1.4.1 Germany/SH-RKI-I-1074447/2022,BN.1.4.1 -OX395774.1,BN.1.4.1 England/LSPA-32612190/2022,BN.1.4.1 France/GES-IPP59974/2022,BN.1.4.1 Scotland/LSPA-325F43F9/2022,BN.1.4.1 @@ -2133232,13 +2133226,9 @@ Australia/VIC76311/2022,BN.1.4.1 Scotland/SCOT-22344/2022,BN.1.4.1 Ireland/SO-NVRL-S22IRL00471328/2022,BN.1.4.1 Scotland/SCOT-22802/2022,BN.1.4.1 -OX395624.1,BN.1.4.1 Scotland/QEUH-325EF5FB/2022,BN.1.4.1 -OX400465.1,BN.1.4.1 Scotland/LSPA-32634E91/2022,BN.1.4.1 -OX400458.1,BN.1.4.1 Scotland/LSPA-3263FACF/2022,BN.1.4.1 -OX395001.1,BN.1.4.1 Scotland/LSPA-326172A7/2022,BN.1.4.1 Ireland/CE-NVRL-S22IRL00470196/2022,BN.1.4.1 Ireland/CE-NVRL-S22IRL00470503/2022,BN.1.4.1 @@ -2133254,7 +2133244,6 @@ Ireland/CE-NVRL-S22IRL00471368/2022,BN.1.4.1 Scotland/LSPA-325FBB27/2022,BN.1.4.1 Scotland/LSPA-325F4E25/2022,BN.1.4.1 England/LSPA-326105B4/2022,BN.1.4.1 -OX395515.1,BN.1.4.1 England/LSPA-32619384/2022,BN.1.4.1 Scotland/SCOT-21400/2022,BN.1.4.1 Scotland/SCOT-20925/2022,BN.1.4.1 @@ -2133281,7 +2133270,6 @@ England/LSPA-3261A602/2022,BN.1.4.1 Scotland/SCOT-21499/2022,BN.1.4.1 Scotland/SCOT-21401/2022,BN.1.4.1 Scotland/SCOT-21344/2022,BN.1.4.1 -OX400900.1,BN.1.4.1 Scotland/SCOT-22660/2022,BN.1.4.1 Scotland/QEUH-326131AE/2022,BN.1.4.1 Scotland/QEUH-3263B823/2022,BN.1.4.1 @@ -2133617,7 +2133605,6 @@ Germany/NW-RKI-I-1042158/2022,XBB.1.9 Indonesia/JB-NIHRD-34130/2022,XBB.1.9 Indonesia/JK-NIHRD-WGS-22-34099/2022,XBB.1.9 Sweden/9461429176/2022,XBB.1.9 -OX396075.1,XBB.1.9 England/QEUH-3261872F/2022,XBB.1.9 England/PHEP-YYGRKW9/2022,XBB.1.9 Singapore/15369/2022,XBB.1.9 @@ -2133810,14 +2133797,8 @@ Netherlands/NH-AUMC-034720/2022,XBB.1.9 Netherlands/NH-inBiome-212490/2022,XBB.1.9 Netherlands/NH-AUMC-034709/2022,XBB.1.9 England/LSPA-3261EC48/2022,XBB.1.9 -OX400442.1,XBB.1.9 England/LSPA-3264018A/2022,XBB.1.9 -OX396191.1,XBB.1.9 -OX396334.1,XBB.1.9 -OX395901.1,XBB.1.9 -OX396345.1,XBB.1.9 England/LSPA-3261EE9D/2022,XBB.1.9 -OX401202.1,XBB.1.9 England/LSPA-3261E9BA/2022,XBB.1.9 England/LSPA-3261EDCD/2022,XBB.1.9 England/LSPA-3261ED27/2022,XBB.1.9 @@ -2134382,10 +2134363,7 @@ USA/TN-CDC-QDX44483400/2022,BQ.1.1.35 USA/GA-CDC-QDX43795912/2022,BQ.1.1.35 England/LSPA-32624D3D/2022,BQ.1.1.35 England/BRBR-32631D97/2022,BQ.1.1.35 -OX394809.1,BQ.1.1.35 -OX395737.1,BQ.1.1.35 England/LSPA-3261FB59/2022,BQ.1.1.35 -OX400791.1,BQ.1.1.35 England/LSPA-326240F8/2022,BQ.1.1.35 Canada/QC-L00559274001/2022,BQ.1.1.35 Canada/QC-L00559210001/2022,BQ.1.1.35 @@ -2134460,7 +2134438,6 @@ England/LSPA-3260D72D/2022,BQ.1.1.35 England/LSPA-326028BC/2022,BQ.1.1.35 England/QEUH-3263E134/2022,BQ.1.1.35 England/QEUH-326407C4/2022,BQ.1.1.35 -OX400746.1,BQ.1.1.35 Wales/PHWC-PKJ9RD/2022,BQ.1.1.35 England/PHEC-YY81TEU/2022,BQ.1.1.35 England/PHEP-YYGF5ZG/2022,BQ.1.1.35 @@ -2134488,7 +2134465,6 @@ Canada/ON-PHL-22-58400/2022,BQ.1.1.35 Canada/ON-KHS-17050-v1/2022,BQ.1.1.35 England/QEUH-325FD660/2022,BQ.1.1.35 England/QEUH-3263E42C/2022,BQ.1.1.35 -OX400735.1,BQ.1.1.35 England/PHEC-YY8ZARK/2022,BQ.1.1.35 Netherlands/ZH-MVD-C2204124/2022,BQ.1.1.35 Wales/PHWC-PKKARE/2023,BQ.1.1.35 @@ -2134555,7 +2134531,6 @@ Belgium/rega-46514/2022,BQ.1.1.35 France/HDF-cerba-22S0653811/2022,BQ.1.1.35 France/HDF-IPP60304/2022,BQ.1.1.35 England/LSPA-3263E7BA/2022,BQ.1.1.35 -OX401078.1,BQ.1.1.35 England/QEUH-3266CF33/2022,BQ.1.1.35 England/LSPA-3262BCC0/2022,BQ.1.1.35 England/QEUH-3265312A/2022,BQ.1.1.35 @@ -2134718,9 +2134693,6 @@ Wales/PHWC-PKJ6OM/2022,BQ.1.1.36 Brazil/BA-LACEN-BA2257-292737002/2022,BQ.1.1.36 Denmark/DCGC-633147/2023,BQ.1.1.36 Denmark/DCGC-633481/2023,BQ.1.1.36 -OX402962.1,BQ.1.1.36 -OX403027.1,BQ.1.1.36 -OX403525.1,BQ.1.1.36 USA/UT-UPHL-221219541458/2022,BQ.1.1.36 Brazil/BA-FIOCRUZ-PVM104037/2022,BQ.1.1.36 France/NAQ-HCL722004263101/2022,BQ.1.1.36 @@ -2134807,7 +2134779,6 @@ Brazil/SE-FIOCRUZ-25808/2022,BQ.1.1.36 Brazil/BA-FIOCRUZ-PVM103642/2022,BQ.1.1.36 England/LSPA-326204A5/2022,BQ.1.1.36 England/LSPA-32621644/2022,BQ.1.1.36 -OX395886.1,BQ.1.1.36 England/LSPA-3261FFB7/2022,BQ.1.1.36 France/PAC-cerba-22S0504649/2022,BQ.1.1.36 France/OCC-cerba-22S0584910/2022,BQ.1.1.36 @@ -2134903,9 +2134874,6 @@ Brazil/BA-LACEN-BA-2238-292704121/2022,BQ.1.1.36 Brazil/BA-LACEN-BA2262-292704463/2022,BQ.1.1.36 England/BRBR-32666203/2022,BQ.1.1.36 England/BRBR-32666652/2022,BQ.1.1.36 -OX403283.1,BQ.1.1.36 -OX403201.1,BQ.1.1.36 -OX403465.1,BQ.1.1.36 England/BRBR-3266617F/2022,BQ.1.1.36 England/PHEC-YY8ZEJO/2022,BQ.1.1.36 England/QEUH-3266F49B/2022,BQ.1.1.36 @@ -2136368,4 +2136336,126 @@ England/LSPA-32659ED2/2022,DV.3 England/LSPA-326590EB/2022,DV.3 England/LSPA-3265AF56/2022,DV.3 England/LSPA-326595EC/2022,DV.3 +England/PHEC-YY8AKDA/2023,CH.1.1.6 +England/PHEP-YYGBDSE/2022,CH.1.1.6 +England/PHEC-YY87HFA/2023,CH.1.1.6 +England/LSPA-326405E8/2022,CH.1.1.6 +Ireland/MO-Enfer-030123002_C4/2023,CH.1.1.6 +England/QEUH-3269DE5A/2023,CH.1.1.6 +England/LSPA-3269DE3C/2023,CH.1.1.6 +England/PHEC-YY87RJE/2023,CH.1.1.6 +Wales/PHWC-PKMRMC/2023,CH.1.1.6 +England/QEUH-326A0030/2023,CH.1.1.6 +England/DHSC-CYRTMPE/2023,CH.1.1.6 +England/DHSC-CYF3KH3/2022,CH.1.1.6 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