From 622c0a2642a879a077fbea7ff0e382f84bdc1599 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Wed, 15 May 2024 21:42:30 +0200 Subject: [PATCH] Designate LE.1 (JN.1.4.7.1, S:R346T), KP.1.1.2 (S:P1162S, T2152C), JN.1.48.2 (S:R346T, ORF1a:A427V, A3829G, India) --- lineage_notes.txt | 3 + lineages.csv | 240 +++++++++++++++++++++---------- pango_designation/alias_key.json | 1 + 3 files changed, 170 insertions(+), 74 deletions(-) diff --git a/lineage_notes.txt b/lineage_notes.txt index 2ee01c06..66d64893 100644 --- a/lineage_notes.txt +++ b/lineage_notes.txt @@ -1077,6 +1077,7 @@ KV.1 Alias of B.1.1.529.2.86.1.1.4.5.1, S:S680F, after C28948T then A2356T KV.2 Alias of B.1.1.529.2.86.1.1.4.5.2, S:T572I, ORF1a:P971L, C11956T, USA, from sars-cov-2-variants/lineage-proposals#1097 JN.1.4.6 Alias of B.1.1.529.2.86.1.1.4.6, S:T572I, after T18453C, from sars-cov-2-variants/lineage-proposals#1097 JN.1.4.7 Alias of B.1.1.529.2.86.1.1.4.7, ORF3a:G18D +LE.1 Alias of B.1.1.529.2.86.1.1.4.7.1, S:R346T JN.1.5 Alias of B.1.1.529.2.86.1.1.5, ORF1b:V1271T, Singapore/Malaysia/Indonesia, from #2419 JN.1.6 Alias of B.1.1.529.2.86.1.1.6, G22627A JN.1.6.1 Alias of B.1.1.529.2.86.1.1.6.1, S:R346T, Sweden, from sars-cov-2-variants/lineage-proposals#1089 @@ -1101,6 +1102,7 @@ JN.1.11.1 Alias of B.1.1.529.2.86.1.1.11.1, S:F456L, after ORF1a:T2283I, India, KP.1 Alias of B.1.1.529.2.86.1.1.11.1.1, S:K1086R, from sars-cov-2-variants/lineage-proposals#1364 KP.1.1 Alias of B.1.1.529.2.86.1.1.11.1.1.1, S:R346T, from sars-cov-2-variants/lineage-proposals#1089 KP.1.1.1 Alias of B.1.1.529.2.86.1.1.11.1.1.1.1, S:K182N from #2510 +KP.1.1.2 Alias of B.1.1.529.2.86.1.1.11.1.1.1.2, S:P1162S, T2152C KP.1.2 Alias of B.1.1.529.2.86.1.1.11.1.1.2, S:T572I KP.2 Alias of B.1.1.529.2.86.1.1.11.1.2, S:R346T on JN.1.11.1 polytomy, from sars-cov-2-variants/lineage-proposals#1089 KP.2.1 Alias of B.1.1.529.2.86.1.1.11.1.2.1, S:Q1201K, from sars-cov-2-variants/lineage-proposals#1440 @@ -1183,6 +1185,7 @@ JN.1.47.2 Alias of B.1.1.529.2.86.1.1.47.2, S:T572I, S:R683Q, USA JN.1.48 Alias of B.1.1.529.2.86.1.1.48, G29134T, after T18471C, India JN.1.48.1 Alias of B.1.1.529.2.86.1.1.48.1, S:S60P, S:R346T, S:F456L, after ORF3a:A99V from #2547 LD.1 Alias of B.1.1.529.2.86.1.1.48.1.1, S:T572I +JN.1.48.2 Alias of B.1.1.529.2.86.1.1.48.2, S:R346T, ORF1a:A427V, A3829G, India JN.2 Alias of B.1.1.529.2.86.1.2, ORF1a:Y621C, Europe/North America, from #2284 JN.2.1 Alias of B.1.1.529.2.86.1.2.1, S:S31F, Sweden/Australia JN.2.2 Alias of B.1.1.529.2.86.1.2.2, S:T572I, N:G25C, ORF1a:L3644F, Netherlands, from #2433 diff --git a/lineages.csv b/lineages.csv index f1f6f0de..ee56f580 100644 --- a/lineages.csv +++ b/lineages.csv @@ -2537534,62 +2537534,6 @@ NewZealand/24ZA0992/2024,JN.1.4.7 NewZealand/24YA0913/2024,JN.1.4.7 NewZealand/24YA1245/2024,JN.1.4.7 NewZealand/24ZA0744/2024,JN.1.4.7 -Spain/CL-COV46291/2024,JN.1.4.7 -Netherlands/NB-RIVM-137636/2024,JN.1.4.7 -Kenya/RVR-961/2024,JN.1.4.7 -USA/CA-CDPH-500133508/2024,JN.1.4.7 -Switzerland/VD-CHUV-GEN19381/2024,JN.1.4.7 -Spain/CL-COV46231/2024,JN.1.4.7 -Nigeria/NCDC-NRL-GL-00073/2024,JN.1.4.7 -USA/VA-GBW-H10-018-9580/2024,JN.1.4.7 -France/OCC-ChuMtp-99240182387/2024,JN.1.4.7 -France/ARA-HCL023196506901/2023,JN.1.4.7 -USA/NY-CDC-QDX91770491/2024,JN.1.4.7 -Spain/CL-COV46166/2024,JN.1.4.7 -USA/VA-GBW-H20-353-1346/2024,JN.1.4.7 -USA/NY-CDC-QDX92153008/2024,JN.1.4.7 -Slovakia/ruvzbb_24_01_00000010/2023,JN.1.4.7 -France/ARA-HCL024001190501/2024,JN.1.4.7 -France/ARA-HCL023205276801/2023,JN.1.4.7 -France/ARA-HCL024007602001/2024,JN.1.4.7 -Canada/ON-PHL-202405874/2024,JN.1.4.7 -Canada/ON-PHL-202405941/2024,JN.1.4.7 -Canada/ON-PHL-202405796/2024,JN.1.4.7 -Sweden/C-03_SE600_000200671328N2/2024,JN.1.4.7 -Sweden/W-49805841LX/2024,JN.1.4.7 -Sweden/AB-01_SE100_24CS500084/2024,JN.1.4.7 -Germany/ST-RKI-I-1142811/2024,JN.1.4.7 -Kenya/HF232108/2023,JN.1.4.7 -England/CLIMB-CM7YGDTJ/2024,JN.1.4.7 -Canada/ON-PHL-202404995/2024,JN.1.4.7 -SouthAfrica/NICD-N57627/2024,JN.1.4.7 -Canada/ON-PHL-202404766/2024,JN.1.4.7 -USA/CA-HLX-STM-5Z4PN63GZ/2024,JN.1.4.7 -Canada/ON-KHS-01553-v1/2024,JN.1.4.7 -Canada/ON-KHS-01415-v1/2024,JN.1.4.7 -USA/PA-CDC-LC1101197/2024,JN.1.4.7 -England/CLIMB-CM7Y8J9D/2024,JN.1.4.7 -England/CLIMB-CM7YKEHJ/2024,JN.1.4.7 -USA/VA-CDC-QDX93409204/2024,JN.1.4.7 -England/CLIMB-CM7YEZZD/2024,JN.1.4.7 -USA/NY-GBW-H20-348-4432/2024,JN.1.4.7 -USA/NY-GBW-H20-348-4430/2024,JN.1.4.7 -USA/MN-MDH-40979/2024,JN.1.4.7 -USA/TX-HMH-M-137327/2024,JN.1.4.7 -USA/NY-URMC-O2S1L895-1/2024,JN.1.4.7 -USA/NY-SUNYQB-X8672/2024,JN.1.4.7 -USA/NY-URMC-O1S1L391-1/2024,JN.1.4.7 -USA/NY-URMC-O2S1L648-1/2024,JN.1.4.7 -USA/NY-URMC-03S1M254-1/2024,JN.1.4.7 -USA/NY-URMC-O2S1L966-1/2024,JN.1.4.7 -Scotland/CLIMB-CM7Y8E55/2024,JN.1.4.7 -Scotland/CLIMB-CM7YRKNT/2024,JN.1.4.7 -Scotland/CLIMB-CM7YF69N/2024,JN.1.4.7 -Scotland/CLIMB-CM7YKPGG/2024,JN.1.4.7 -Scotland/CLIMB-CM7YGOC8/2024,JN.1.4.7 -Scotland/CLIMB-CM7YK6Q7/2024,JN.1.4.7 -Scotland/CLIMB-CM7YMBO7/2024,JN.1.4.7 -Scotland/CLIMB-CM7Y8EWR/2024,JN.1.4.7 USA/TX-HMH-M-139990/2024,KV.2 Mexico/TAM_CIAD_01001340/2024,KV.2 USA/TX-TAMGHRC-SHS-104942/2024,KV.2 @@ -2539441,23 +2539385,6 @@ Canada/ON-PHL-202405802/2024,JN.1.48 Canada/ON-PHL-202405057/2024,JN.1.48 USA/RI-RISHL2400775/2024,JN.1.48 USA/RISHL24COV00775/2024,JN.1.48 -India/MH_BJCOG_INSACOG_6352/2024,JN.1.48 -USA/HI-H2327653/2024,JN.1.48 -Spain/GA-CHUAC-12131/2024,JN.1.48 -India/MH_BJCOG_6457/2024,JN.1.48 -India/MH_BJCOG_INSACOG_6589/2024,JN.1.48 -India/MH_BJCOG_6496/2024,JN.1.48 -India/MH_BJCOG_INSACOG_6561/2024,JN.1.48 -India/MH_BJCOG_6428/2024,JN.1.48 -India/MH_BJCOG_INSACOG_6542/2024,JN.1.48 -India/MH_BJCOG_6433/2024,JN.1.48 -India/MH_BJCOG_INSACOG_6375/2024,JN.1.48 -India/MH_BJCOG_INSACOG_6324/2024,JN.1.48 -India/MH_BJCOG_6513/2024,JN.1.48 -India/MH_BJCOG_6491/2024,JN.1.48 -India/MH_BJCOG_INSACOG_6269/2024,JN.1.48 -India/MH_BJCOG_INSACOG_6248/2024,JN.1.48 -India/MH_BJCOG_INSACOG_6246/2024,JN.1.48 India/MH_BJCOG_INSACOG_6345/2024,JN.1.48 India/KA-RFNB-21220/2024,JN.1.48 India/KA-RFNB-21187/2024,JN.1.48 @@ -2543247,7 +2543174,6 @@ Japan/PG-599135/2024,JN.1 Indonesia/JK-BIOKES-W00269/2024,JN.1 Scotland/CLIMB-CM7YJRN8/2024,JN.1 USA/CA-CDPH-500131417/2023,JN.1 -Slovakia/RNA/2023,JN.1 France/PAC-HCL723001748301/2023,JN.1 France/PAC-HCL723001748401/2023,JN.1 Slovakia/BA_26_00010292/2023,JN.1 @@ -2543835,3 +2543761,169 @@ Canada/ON-PHL-202407376/2024,LD.1 Wales/CLIMB-CM7YMCMM/2024,LD.1 USA/PR-CVL-023286/2024,LD.1 USA/NY-URMC-O4S1N310-1/2024,LD.1 +India/MH_BJCOG_INSACOG_6324/2024,JN.1.48.2 +India/MH_BJCOG_INSACOG_6375/2024,JN.1.48.2 +India/MH_BJCOG_6433/2024,JN.1.48.2 +India/MH_BJCOG_INSACOG_6542/2024,JN.1.48.2 +India/MH_BJCOG_6428/2024,JN.1.48.2 +India/MH_BJCOG_INSACOG_6561/2024,JN.1.48.2 +India/MH_BJCOG_6496/2024,JN.1.48.2 +India/MH_BJCOG_INSACOG_6589/2024,JN.1.48.2 +Australia/QLD0x014277/2024,JN.1.48.2 +India/MH_BJCOG_INSACOG_6677/2024,JN.1.48.2 +India/MH_BJCOG_INSACOG_6647/2024,JN.1.48.2 +USA/CA-Stanford-182_S15/2024,JN.1.48.2 +USA/HI-H2327653/2024,JN.1.48.2 +India/MH_BJCOG_INSACOG_6352/2024,JN.1.48.2 +Spain/GA-CHUAC-12131/2024,JN.1.48.2 +India/MH_BJCOG_INSACOG_6667/2024,JN.1.48.2 +India/MH_BJCOG_INSACOG_6650/2024,JN.1.48.2 +India/MH_BJCOG_6457/2024,JN.1.48.2 +India/MH_BJCOG_INSACOG_6687/2024,JN.1.48.2 +India/MH_BJCOG_6513/2024,JN.1.48.2 +India/MH_BJCOG_6491/2024,JN.1.48.2 +India/MH_BJCOG_INSACOG_6269/2024,JN.1.48.2 +India/MH_BJCOG_INSACOG_6248/2024,JN.1.48.2 +India/MH_BJCOG_INSACOG_6246/2024,JN.1.48.2 +USA/2024CV0747/2024,JN.1.48.2 +USA/AZ-ASPHL-0747/2024,JN.1.48.2 +USA/MN-MDH-41424/2024,JN.1.48.2 +USA/MN-MDH-41460/2024,JN.1.48.2 +USA/MN-MDH-41446/2024,JN.1.48.2 +England/CLIMB-CM7YMAEN/2024,KP.1.1.2 +Canada/ON-PHL-202407022/2024,KP.1.1.2 +Australia/NSW-ICPMR-53375/2024,KP.1.1.2 +England/CLIMB-CM7YRAX9/2024,KP.1.1.2 +Singapore/R16MQ1/2024,KP.1.1.2 +Shanghai/SCDC-HG-634/2024,KP.1.1.2 +CHN/SH-HG20240304-634/2024,KP.1.1.2 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+USA/NJ-CDC-QDX96017855/2024,LE.1 +Denmark/DCGC-684522/2024,LE.1 +USA/CA-KP002295/2024,LE.1 +USA/VA-CDC-QDX93409204/2024,LE.1 +Netherlands/NB-RIVM-138359/2024,LE.1 +Netherlands/NB-RIVM-138360/2024,LE.1 +Scotland/CLIMB-CM7YGY3E/2024,LE.1 +NewZealand/24YA3471/2024,LE.1 +England/CLIMB-CM7YEZZD/2024,LE.1 +USA/CA-GBW-GKPLAAAA19518/2024,LE.1 +USA/CA-GBW-GKPLAAAA19514/2024,LE.1 +USA/CA-GBW-GKISBBBB97628/2024,LE.1 +USA/DE-DHSS-B1333373/2024,LE.1 +USA/NY-GBW-H20-348-4432/2024,LE.1 +USA/NY-GBW-H20-348-4430/2024,LE.1 diff --git a/pango_designation/alias_key.json b/pango_designation/alias_key.json index ecea42b5..661ab061 100644 --- a/pango_designation/alias_key.json +++ b/pango_designation/alias_key.json @@ -250,6 +250,7 @@ "LB": "B.1.1.529.2.86.1.1.9.2", "LC": "B.1.1.529.2.86.1.1.1.7", "LD": "B.1.1.529.2.86.1.1.48.1", + "LE": "B.1.1.529.2.86.1.1.4.7", "XA": ["B.1.1.7","B.1.177"], "XB": ["B.1.634","B.1.631"], "XC": ["AY.29","B.1.1.7"],