From 764d273ccfac460fe94555ceb840be338a2a8182 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Tue, 21 Mar 2023 23:50:56 +0100 Subject: [PATCH] Added lineage EY.1 (EF.1.1.1 with S:Q613H) with 150 designations --- lineage_notes.txt | 1 + lineages.csv | 199 ++++++++++++++++++++++++------- pango_designation/alias_key.json | 1 + 3 files changed, 158 insertions(+), 43 deletions(-) diff --git a/lineage_notes.txt b/lineage_notes.txt index eb0a2776..dc75d6c9 100644 --- a/lineage_notes.txt +++ b/lineage_notes.txt @@ -1298,6 +1298,7 @@ BQ.1.1.13 Alias of B.1.1.529.5.3.1.1.1.1.1.1.13, Denmark/Israel/Switzerland/Fran EF.1 Alias of B.1.1.529.5.3.1.1.1.1.1.1.13.1, C6040T EF.1.1 Alias of B.1.1.529.5.3.1.1.1.1.1.1.13.1.1, C23086T,T7783C EF.1.1.1 Alias of B.1.1.529.5.3.1.1.1.1.1.1.13.1.1.1, Brazil, S:F157L +EY.1 Alias of B.1.1.529.5.3.1.1.1.1.1.1.13.1.1.1.1, Brazil/USA, S:Q613H EF.1.2 Alias of B.1.1.529.5.3.1.1.1.1.1.1.13.1.2, Spain, T15492C EF.1.3 Alias of B.1.1.529.5.3.1.1.1.1.1.1.13.1.3, N:T166I EF.2 Alias of B.1.1.529.5.3.1.1.1.1.1.1.13.2, UK, ORF1b:V119I diff --git a/lineages.csv b/lineages.csv index a6051e51..c153da68 100644 --- a/lineages.csv +++ b/lineages.csv @@ -2202767,48 +2202767,6 @@ Brazil/RJ-FIOCRUZ-28010/2022,EF.1.1.1 Brazil/ES-LACENES-321335267/2022,EF.1.1.1 Brazil/RJ-NVBS28584GENOV852331645227/2022,EF.1.1.1 Sweden/SUS0018703/2022,EF.1.1.1 -Brazil/MG-FUNED-311357443/2022,EF.1.1.1 -Germany/NW-RKI-I-1097336/2023,EF.1.1.1 -Brazil/MG-FUNED-311357481/2022,EF.1.1.1 -Brazil/MG-FUNED-311357496/2022,EF.1.1.1 -Brazil/MG-FUNED-311357546/2022,EF.1.1.1 -Brazil/MG-FIOCRUZ-4072/2022,EF.1.1.1 -Brazil/MG-FIOCRUZ-4071/2022,EF.1.1.1 -USA/WA-CDC-UW23011824994/2023,EF.1.1.1 -Brazil/MG-FIOCRUZ-4320/2022,EF.1.1.1 -USA/TX-TAMGHRC-SHS_88934/2023,EF.1.1.1 -Brazil/ES-LACENES-321346355/2023,EF.1.1.1 -Chile/BI-7262/2023,EF.1.1.1 -Brazil/SC-NVBS28213GENOV044928028449/2022,EF.1.1.1 -USA/WA-CDC-UW23013003012/2023,EF.1.1.1 -USA/TX-CDC-QDX45529215/2023,EF.1.1.1 -USA/CA-HLX-STM-CKNBSP8HB/2023,EF.1.1.1 -Brazil/MG-NVBS26478GENOV101228032601/2022,EF.1.1.1 -USA/TX-CDC-QDX45182269/2023,EF.1.1.1 -Singapore/R4MR108/2023,EF.1.1.1 -Brazil/MG-NVBS26581GENOV101227889701/2022,EF.1.1.1 -USA/CA-HLX-STM-2T7QRWYJP/2023,EF.1.1.1 -Brazil/MG-FIOCRUZ-4134/2022,EF.1.1.1 -Brazil/MG-FIOCRUZ-4142/2022,EF.1.1.1 -Brazil/MG-FIOCRUZ-4326/2022,EF.1.1.1 -Brazil/MG-FIOCRUZ-4278/2022,EF.1.1.1 -Brazil/MG-FIOCRUZ-3725/2022,EF.1.1.1 -Brazil/MG-FIOCRUZ-4328/2022,EF.1.1.1 -Italy/LAZ-IFO-2212140106/2022,EF.1.1.1 -Brazil/SP-IB_CEVC_2205526/2023,EF.1.1.1 -USA/FL-ASC-210965631/2023,EF.1.1.1 -Brazil/MG-FIOCRUZ-4132/2022,EF.1.1.1 -Brazil/MG-FIOCRUZ-4319/2022,EF.1.1.1 -Brazil/MG-FIOCRUZ-4322/2022,EF.1.1.1 -Brazil/MG-FUNED-311357503/2022,EF.1.1.1 -USA/WA-CDC-LC0975061/2022,EF.1.1.1 -Brazil/MG-FIOCRUZ-3632/2022,EF.1.1.1 -Brazil/ES-LACENES-321343610/2023,EF.1.1.1 -Brazil/ES-LACENES-321347560/2023,EF.1.1.1 -USA/NC-CDC-LC1002937/2023,EF.1.1.1 -USA/FL-CDC-LC1001444/2023,EF.1.1.1 -USA/FL-CDC-QDX45740573/2023,EF.1.1.1 -USA/FL-CDC-LC0968331/2022,EF.1.1.1 Austria/AGES-1154627/2022,EF.1.2 Spain/CU-81492/2022,EF.1.2 France/ARA-HCL723000079201/2023,EF.1.2 @@ -2351081,7 +2351039,6 @@ England/PHEC-YYER6I8/2023,EV.1 England/QEUH-326D8257/2023,EV.1 OX449498.1,EV.1 England/BRBR-326EDC15/2023,EV.1 -strain,EW.1 SouthAfrica/NICD-N52178/2023,EW.1 SouthAfrica/NICD-N51685/2023,EW.1 USA/TX-HMH-MCoV-123549/2023,EW.1 @@ -2351458,3 +2351415,159 @@ USA/NY-GBW-H10-011-4369/2023,EW.3 SouthAfrica/NICD-N51527/2023,EW.3 SouthAfrica/NICD-N53747/2023,EW.3 SouthAfrica/NICD-N51690/2023,EW.3 +strain,EY.1 +USA/CA-CDC-LC1022690/2023,EY.1 +Netherlands/NH-AUMC-000816/2023,EY.1 +USA/CO-CDC-QDX46612059/2023,EY.1 +Brazil/MG-FIOCRUZ-4593/2023,EY.1 +Brazil/MG-FIOCRUZ-4598/2023,EY.1 +Brazil/DF-FIOCRUZ-28644/2022,EY.1 +Brazil/MG-FIOCRUZ-4626/2023,EY.1 +Brazil/TO-FIOCRUZ-28207/2022,EY.1 +Brazil/MG-FIOCRUZ-4600/2023,EY.1 +USA/WA-GBW-H10-010-9384/2023,EY.1 +USA/WA-UW-23020256489/2023,EY.1 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+Brazil/MG-FIOCRUZ-4557/2023,EY.1 +Brazil/MG-FIOCRUZ-4387/2023,EY.1 +Brazil/GO-FIOCRUZ-667/2023,EY.1 +Brazil/ES-LACENES-321346355/2023,EY.1 +Brazil/MG-FIOCRUZ-4326/2022,EY.1 +Brazil/MG-FIOCRUZ-4278/2022,EY.1 +USA/CA-HLX-STM-CJN8RX8WK/2023,EY.1 +USA/CA-HLX-STM-HKU9M8R5U/2023,EY.1 +USA/CA-HLX-STM-5YGHCF6US/2023,EY.1 +USA/CA-LACPHL-AF19585/2023,EY.1 +USA/CA-LACPHL-AF19583/2023,EY.1 +USA/CA-HLX-STM-2T7QRWYJP/2023,EY.1 +USA/CA-CDC-QDX46552204/2023,EY.1 +USA/CA-CDC-QDX46724917/2023,EY.1 +USA/CA-CDC-LC1010448/2023,EY.1 +USA/CA-HLX-STM-WP3TJMHF6/2023,EY.1 +USA/CA-HLX-STM-WW87HHPF2/2023,EY.1 +Brazil/MG-FIOCRUZ-4560/2023,EY.1 +Brazil/MG-FIOCRUZ-4134/2022,EY.1 +Brazil/ES-LACENES-321350354/2023,EY.1 +Brazil/ES-LACENES-321349456/2023,EY.1 +Brazil/MG-FIOCRUZ-4190/2022,EY.1 +Brazil/MG-FIOCRUZ-4142/2022,EY.1 +USA/NY-CDC-QDX46677899/2023,EY.1 +USA/FL-CDC-QDX46501536/2023,EY.1 +USA/VA-VTVAS3-GSC41838/2023,EY.1 +USA/FL-CDC-LC1011872/2023,EY.1 +Brazil/MG-FUNED-311393343/2023,EY.1 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+USA/CA-HLX-STM-85CE3U4CE/2023,EY.1 +USA/CA-HLX-STM-ZQ8BED8XS/2023,EY.1 diff --git a/pango_designation/alias_key.json b/pango_designation/alias_key.json index 4286b19d..ee62f655 100644 --- a/pango_designation/alias_key.json +++ b/pango_designation/alias_key.json @@ -129,6 +129,7 @@ "EU": "XBB.1.5.26", "EV": "B.1.1.529.5.3.1.1.1.1.1.1.71", "EW": "B.1.1.529.5.3.1.1.1.1.1.1.38", + "EY": "B.1.1.529.5.3.1.1.1.1.1.1.13.1.1.1", "XA": ["B.1.1.7","B.1.177"], "XB": ["B.1.634","B.1.631"], "XC": ["AY.29","B.1.1.7"],