From 6637343d6226fd8dac057fdea05d39c1c51f419b Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Wed, 23 Oct 2024 00:57:09 +0200 Subject: [PATCH] Designate KP.1.1.6, NE.1, XEN Resolves #2649 Resolves #2791 --- lineage_notes.txt | 3 +++ lineages.csv | 38 ++++++++++++++++++++++++++++++++ pango_designation/alias_key.json | 4 +++- 3 files changed, 44 insertions(+), 1 deletion(-) diff --git a/lineage_notes.txt b/lineage_notes.txt index f592ec99..1fd66b83 100644 --- a/lineage_notes.txt +++ b/lineage_notes.txt @@ -1165,6 +1165,8 @@ LP.4 Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.4, S:T572I, ORF8:A65V 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 +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 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 @@ -4307,6 +4309,7 @@ XEJ Recombinant lineage of JN.1, LF.1.1.1 (breakpoint: 6574-16550), from #2786 XEK Recombinant lineage of KP.2.3, XEC (breakpoint: 9286-15402), from #2774 XEL Recombinant lineage of KS.1.1.2, JN.1 (breakpoint: 22929-24820), from #2751 XEM Recombinant lineage of KS.1, KP.3.3.1 (breakpoint: 22600-23038), from sars-cov-2-variants/lineage-proposals#2105 +XEN Recombinant lineage of KP.1.1.6, JN.1.11.1 (breakpoint: 22620-24818), from #2791 *A.2.1 Withdrawn: Lineage with sequences predominantly from Panama *A.8 Withdrawn: Indian lineage merged with A.9 *A.10 Withdrawn: Spanish lineage reassigned to A.5 diff --git a/lineages.csv b/lineages.csv index 44b762e7..5061c73c 100644 --- a/lineages.csv +++ b/lineages.csv @@ -2576801,3 +2576801,41 @@ USA/NY-CDC-LC1113708/2024,MC.14 USA/TX-HMH-M-142377/2024,MC.14 USA/IL-CDC-QDX24606247/2024,MC.14 USA/TX-HMH-MCoV-144699/2024,MC.14 +USA/NJ-CDC-LC1104056/2024,KP.1.1.6 +England/CLIMB-CM7YF16F/2024,KP.1.1.6 +Wales/CLIMB-CM7YRWMI/2024,KP.1.1.6 +USA/NY-GBW-GKPLAAAA10379/2024,KP.1.1.6 +Ireland/D-NVRL-GIRL00022068/2024,KP.1.1.6 +Singapore/R24MQ97/2024,KP.1.1.6 +CHN/HB-Huangshi-5470/2024,KP.1.1.6 +Hubei/HCDC-HS5470/2024,KP.1.1.6 +CHN/HB-Huangshi-5472/2024,KP.1.1.6 +Hubei/HCDC-HS5472/2024,KP.1.1.6 +Singapore/R25MQ51/2024,KP.1.1.6 +Singapore/R25MQ203/2024,KP.1.1.6 +Germany/BY-LGL-6316808/2024,KP.1.1.6 +USA/CA-GBW-GKPLAAAA34187/2024,KP.1.1.6 +India/OR-RMRC_B-ICMR-INSACOG-ILI-2568/2024,NE.1 +Australia/NSW-ICPMR-55181/2024,NE.1 +Japan/TKYnat17492/2024,NE.1 +USA/WA-GBW-GKPLAAAA28555/2024,NE.1 +USA/WA-GBW-GKISBBBD49128/2024,NE.1 +France/BFC-IPP11095/2024,NE.1 +Denmark/DCGC-688950/2024,NE.1 +Canada/SK-RRPL-738488/2024,XEN +USA/PA-CDC-LC1122248/2024,XEN +India/OR-RMRC_B-ICMR-INSACOG-ILI-2634/2024,XEN +India/OR-RMRC_B-ICMR-INSACOG-ILI-2561/2024,XEN +Singapore/R55MQ32/2024,XEN +Singapore/R55MQ46/2024,XEN +Singapore/R53MQ36/2024,XEN +Qatar/NIC-15-VI-0077063/2024,XEN +USA/HI-TAMC_3896/2024,XEN +Qatar/NIC-47-VI-0071938/2024,XEN +Qatar/NIC-47-VI-0070761/2024,XEN +Taiwan/CDC-W40269/2024,XEN +Singapore/R54MQ12/2024,XEN +USA/NJ-CDC-QDX24342667/2024,XEN +USA/UT-UPHL-241004732157/2024,XEN +USA/NY-GBW-GKPLAAAA16347/2024,XEN +Australia/VIC-VIDRL-00015101/2024,XEN diff --git a/pango_designation/alias_key.json b/pango_designation/alias_key.json index 13ee8329..b8b4a313 100644 --- a/pango_designation/alias_key.json +++ b/pango_designation/alias_key.json @@ -296,6 +296,7 @@ "NB": "XDV.1.5.1", "NC": "B.1.1.529.2.86.1.1.13.1.1.1.1", "ND": "B.1.1.529.2.86.1.1.16.1.8.1.1", + "NE": "B.1.1.529.2.86.1.1.11.1.1.1.6", "XA": ["B.1.1.7","B.1.177"], "XB": ["B.1.634","B.1.631"], "XC": ["AY.29","B.1.1.7"], @@ -422,6 +423,7 @@ "XEJ": ["JN.1", "LF.1.1.1"], "XEK": ["KP.2.3", "XEC"], "XEL": ["KS.1.1.2", "JN.1"], - "XEM": ["KS.1", "KP.3.3.1"] + "XEM": ["KS.1", "KP.3.3.1"], + "XEN": ["KP.1.1.6", "JN.1.11.1"] }