From d39304704862930caed86d10b5785fa1131b2b17 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Fri, 25 Oct 2024 18:45:47 +0200 Subject: [PATCH] Designate NL.1 (LB.1.3.1.1), MU.2(.1), KP.2.3.11 --- lineage_notes.txt | 6 + lineages.csv | 961 ++++++++++++++++++++++++++++++- pango_designation/alias_key.json | 1 + 3 files changed, 950 insertions(+), 18 deletions(-) diff --git a/lineage_notes.txt b/lineage_notes.txt index bb1c07d1..95f1286c 100644 --- a/lineage_notes.txt +++ b/lineage_notes.txt @@ -1132,6 +1132,7 @@ LB.1.2.2 Alias of B.1.1.529.2.86.1.1.9.2.1.2.2, S:T572I, C22075T LB.1.2.3 Alias of B.1.1.529.2.86.1.1.9.2.1.2.3, S:F175L, ORF1a:I1568F LB.1.3 Alias of B.1.1.529.2.86.1.1.9.2.1.3, ORF1b:T1555I LB.1.3.1 Alias of B.1.1.529.2.86.1.1.9.2.1.3.1, S:445P, N:T379I, from sars-cov-2-variants/lineage-proposals#1620 +NL.1 Alias of B.1.1.529.2.86.1.1.9.2.1.3.1, S:R190S, S:C1243F LB.1.3.2 Alias of B.1.1.529.2.86.1.1.9.2.1.3.2, C25413T MH.1 Alias of B.1.1.529.2.86.1.1.9.2.1.3.2.1, S:T572I LB.1.3.3 Alias of B.1.1.529.2.86.1.1.9.2.1.3.3, S:K182R, from #2723 @@ -1168,6 +1169,8 @@ LP.7 Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.7, S:R190S KP.1.1.4 Alias of B.1.1.529.2.86.1.1.11.1.1.1.4, S:R214H, C11866T, C23929T,from sars-cov-2-variants/lineage-proposals#1593 KP.1.1.5 Alias of B.1.1.529.2.86.1.1.11.1.1.1.5, S:F59S MU.1 Alias of B.1.1.529.2.86.1.1.11.1.1.1.5.1, S:T572I, ORF1a:P4339T, ORF1b:T1902I +MU.2 Alias of B.1.1.529.2.86.1.1.11.1.1.1.5.2, ORF1a:A2785V, ORF1a:A4357V +MU.2.1 Alias of B.1.1.529.2.86.1.1.11.1.1.1.5.2.1, S:S680Y KP.1.1.6 Alias of B.1.1.529.2.86.1.1.11.1.1.1.6, S:S31F, after ORF1b:L2213F, from #2649 NE.1 Alias of B.1.1.529.2.86.1.1.11.1.1.1.6.1, S:K478T, S:F32S KP.1.2 Alias of B.1.1.529.2.86.1.1.11.1.1.2, S:T572I, from sars-cov-2-variants/lineage-proposals#1097 @@ -1193,6 +1196,7 @@ KP.2.3.9 Alias of B.1.1.529.2.86.1.1.11.1.2.3.9, S:Q173R NG.1 Alias of B.1.1.529.2.86.1.1.11.1.2.3.9.1, S:T22N, ORF1a:I1215M, Brazil KP.2.3.10 Alias of B.1.1.529.2.86.1.1.11.1.2.3.10, S:K478T (rev), India NK.1 Alias of B.1.1.529.2.86.1.1.11.1.2.3.10.1, S:R190S, ORF8:S67F, India +KP.2.3.11 Alias of B.1.1.529.2.86.1.1.11.1.2.3.11, ORF1a:R1973S, A29647G KP.2.4 Alias of B.1.1.529.2.86.1.1.11.1.2.4, S:T250N, from sars-cov-2-variants/lineage-proposals#1524 KP.2.5 Alias of B.1.1.529.2.86.1.1.11.1.2.5, S:N185D, from sars-cov-2-variants/lineage-proposals#1527 KP.2.6 Alias of B.1.1.529.2.86.1.1.11.1.2.6, S:W64R, S:F32del @@ -1262,6 +1266,7 @@ KP.3.1.7 Alias of B.1.1.529.2.86.1.1.11.1.3.1.7, S:L84I, from #2709 KP.3.1.8 Alias of B.1.1.529.2.86.1.1.11.1.3.1.8, S:F59S, A9235G, Georgia MY.1 Alias of B.1.1.529.2.86.1.1.11.1.3.1.8.1, S:P174S, ORF3a:T64I, Georgia KP.3.1.9 Alias of B.1.1.529.2.86.1.1.11.1.3.1.9, S:N148S, S:P174S +KP.3.1.10 Alias of B.1.1.529.2.86.1.1.11.1.3.1.10, S:N185D, ORF1a:V3917I KP.3.2 Alias of B.1.1.529.2.86.1.1.11.1.3.2, A2611C, C22858T KP.3.2.1 Alias of B.1.1.529.2.86.1.1.11.1.3.2.1, S:A263V, Australia/Singapore, from sars-cov-2-variants/lineage-proposals#1556 KP.3.2.2 Alias of B.1.1.529.2.86.1.1.11.1.3.2.2, S:W258R @@ -1442,6 +1447,7 @@ JN.1.47.2 Alias of B.1.1.529.2.86.1.1.47.2, S:T572I, S:R683Q, USA, from sars-cov 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 (T22928C), after ORF3a:A99V, on T3913A, C8092T branch from #2547 LD.1 Alias of B.1.1.529.2.86.1.1.48.1.1, S:T572I from #2547 +LD.2 Alias of B.1.1.529.2.86.1.1.48.1.2, S:N185D, ORF1a:E637K, ORF1b:T2099I, N:T166I JN.1.48.2 Alias of B.1.1.529.2.86.1.1.48.2, S:R346T, ORF1a:A427V, A3829G, India, from sars-cov-2-variants/lineage-proposals#1089 JN.1.48.3 Alias of B.1.1.529.2.86.1.1.48.3, S:60P, S:R346T, S:F456L, ORF3a:S60F, ORF1a:T1761I, on T3913A, C8092T branch, South Africa JN.1.49 Alias of B.1.1.529.2.86.1.1.49, ORF3a:T89I, India diff --git a/lineages.csv b/lineages.csv index 63f8aee7..e922699d 100644 --- a/lineages.csv +++ b/lineages.csv @@ -2537879,8 +2537879,6 @@ USA/CA-GBW-GKISBBBB33553/2024,KP.2.3 USA/NJ-GBW-GKISBBBB35844/2024,KP.2.3 Canada/BC-BCCDC-706766/2024,KP.2.3 Australia/WA15963/2024,KP.2.3 -USA/CA-GBW-H20-362-1799/2024,KP.2.3 -USA/CA-GBW-H10-020-6643/2024,KP.2.3 USA/WA-GBW-H10-019-5824/2024,KP.2.3 USA/WA-GBW-H20-351-0455/2024,KP.2.3 USA/IL-CDC-QDX87530389/2023,JN.1.47 @@ -2544027,8 +2544025,6 @@ England/CLIMB-CM7YMAWS/2024,KP.3.1 England/CLIMB-CM7YFX1T/2024,KP.3.1 USA/UT-UPHL-240417372124/2024,KP.3.1 USA/UT-UPHL-240405461970/2024,KP.3.1 -USA/NC-CDC-LC1103951/2024,KP.3.1 -USA/IL-CDC-LC1103176/2024,KP.3.1 Australia/SA1389983/2024,KP.3.1 Australia/SA1384726/2024,KP.3.1 France/ARA-HCL024069962301/2024,KP.3.1 @@ -2559075,20 +2559071,6 @@ France/CVL-ChuTo-292851/2024,KP.1.1.5 France/IDF-RELAB-IPP05044/2024,KP.1.1.5 France/IDF-RELAB-IPP05600/2024,KP.1.1.5 Ireland/LK-UHL-684768/2024,KP.1.1.5 -England/CLIMB-CM7Y8E6R/2024,KP.1.1.5 -USA/NY-NYULH-19653/2024,KP.1.1.5 -USA/CO-CDPHE-41915535/2024,KP.1.1.5 -USA/NY-GBW-GKPLAAAA26238/2024,KP.1.1.5 -USA/VA-GBW-GKISBBBB69633/2024,KP.1.1.5 -USA/VA-GBW-GKPLAAAA21074/2024,KP.1.1.5 -England/CLIMB-CM7YMMHJ/2024,KP.1.1.5 -England/CLIMB-CM7YJT7C/2024,KP.1.1.5 -England/CLIMB-CM7YJE1W/2024,KP.1.1.5 -England/CLIMB-CM7YJD1B/2024,KP.1.1.5 -England/CLIMB-CM7Y84SC/2024,KP.1.1.5 -England/CLIMB-CM7YJSNH/2024,KP.1.1.5 -England/CLIMB-CM7YFSMJ/2024,KP.1.1.5 -England/CLIMB-CM7YGKOM/2024,KP.1.1.5 France/IDF-IPP06650/2024,XDD.3 USA/CA-GBW-GKPLAAAA22680/2024,XDD.3 USA/CA-GBW-GKISBBBC04593/2024,XDD.3 @@ -2577380,3 +2577362,946 @@ USA/IL-RIPHL_14687_G/2024,LP.7 USA/IL-RIPHL_123294_G/2024,LP.7 USA/IL-RIPHL_123288_G/2024,LP.7 USA/MN-MDH-42042/2024,LP.7 +USA/NY-CDC-LC1104189/2024,KP.2.3.11 +Singapore/R22MQ60/2024,KP.2.3.11 +Israel/ICH-741201591/2024,KP.2.3.11 +Germany/BW-RKI-I-1144307/2024,KP.2.3.11 +Germany/NW-RKI-I-1144382/2024,KP.2.3.11 +Australia/NSW-ICPMR-55018/2024,KP.2.3.11 +Denmark/DCGC-670909/2024,KP.2.3.11 +Ireland/WD-SVUH-FAZ98986-034/2024,KP.2.3.11 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a/pango_designation/alias_key.json +++ b/pango_designation/alias_key.json @@ -302,6 +302,7 @@ "NH": "B.1.1.529.2.86.1.1.11.1.2.2.1", "NJ": "B.1.1.529.2.86.1.1.11.2", "NK": "B.1.1.529.2.86.1.1.11.1.2.3.10", + "NL": "B.1.1.529.2.86.1.1.9.2.1.3.1", "XA": ["B.1.1.7","B.1.177"], "XB": ["B.1.634","B.1.631"], "XC": ["AY.29","B.1.1.7"],