From 6e78c6022c934aa9c6bdba6c2f969f3a1f59aa10 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Sun, 17 Dec 2023 19:34:41 +0100 Subject: [PATCH] Designate XDK (Recombinant lineage of XBB.1.16.11 (likely) and JN.1.1.1 (breakpoint between 5315 and 6182), France, from #2415 Resolves #2415 --- lineage_notes.txt | 2 + lineages.csv | 170 ++++++++++++++++++++++++++++++- pango_designation/alias_key.json | 3 +- 3 files changed, 172 insertions(+), 3 deletions(-) diff --git a/lineage_notes.txt b/lineage_notes.txt index a269498c..dfa0932d 100644 --- a/lineage_notes.txt +++ b/lineage_notes.txt @@ -2973,6 +2973,7 @@ HN.3.1 Alias of XBB.1.9.1.1.5.1.3.1, S:D253G, from sars-cov-2-variants/lineage-p HN.4 Alias of XBB.1.9.1.1.5.1.4, ORF1a:T403I HN.5 Alias of XBB.1.9.1.1.5.1.5, S:E554K, from sars-cov-2-variants/lineage-proposals#936 HN.6 Alias of XBB.1.9.1.1.5.1.6, ORF1a:D1933A +HN.7 Alias of XBB.1.9.1.1.5.1.7, C6388T, T20028C, C20115T, Europe FL.1.5.2 Alias of XBB.1.9.1.1.5.2, S:N481K, S:H681R, England/France/Denmark, from sars-cov-2-variants/lineage-proposals#614 KC.1 Alias of XBB.1.9.1.1.5.2.1, S:S490P, ORF1a:T4129I, ORF1a:S723F, Europe, from sars-cov-2-variants/lineage-proposals#614 KC.1.1 Alias of XBB.1.9.1.1.5.2.1.1, S:V1228L, England @@ -3711,6 +3712,7 @@ XDF Recombinant lineage of XBB* (with C335T) and EG.5.1.3 (breakpoint around 233 XDG Recombinant lineage of FL.37 and EG.5.2.4 (breakpoint at 6729-9693), from #2348 XDH Recombinant lineage of BN.1.2.8 and XBB.1.9.1 (or XBB.1.22) (breakpoint between 22630-22663), Lithuania/Belarus XDJ Recombinant lineage of XBB.1.16.6 and HK.3.1 (breakpoint between 14857 and 16877), France, from sars-cov-2-variants/lineage-proposals#997 +XDK Recombinant lineage of XBB.1.16.11 (likely) and JN.1.1.1 (breakpoint between 5315 and 6182), France, from #2415 *A.2.1 Withdrawn: Lineage with sequences predominantly from Panama *A.8 Withdrawn: Indian lineage merged with A.9 *A.10 Withdrawn: Spanish lineage reassigned to A.5 diff --git a/lineages.csv b/lineages.csv index 6fe575c6..8d32ba33 100644 --- a/lineages.csv +++ b/lineages.csv @@ -2500543,8 +2500543,6 @@ Sweden/M-SUS0022162/2023,JN.1.1.1 Sweden/M-SUS0022161/2023,JN.1.1.1 Sweden/M-SUS0022153/2023,JN.1.1.1 France/HDF-IPP22216/2023,JN.1.1.1 -France/HDF-IPP27487/2023,JN.1.1.1 -France/PDL-IPP27182/2023,JN.1.1.1 PuertoRico/PR-CVL-020313/2023,JN.1.2 USA/MIS-L370583849/2023,JN.1.2 USA/VIEW-L6997768932622/2023,JN.1.2 @@ -2506385,3 +2506383,171 @@ Greece/9698/2023,XBB.2.3.22 Greece/10303/2023,XBB.2.3.22 Greece/PHL_KEDY_12134/2023,XBB.2.3.22 Greece/11640/2023,XBB.2.3.22 +USA/NY-PRL-230818_82A09/2023,HN.7 +USA/NJ-PHEL-V23013993/2023,HN.7 +USA/NJ-PHEL-V23013992/2023,HN.7 +USA/NC-1085-9690/2023,HN.7 +DominicanRepublic/2157957-LNSPDD/2023,HN.7 +USA/NJ-PHEL-V23012898/2023,HN.7 +USA/NY-PRL-230630_81B08/2023,HN.7 +USA/OH-ODH-SC3032162/2023,HN.7 +USA/OH-ODH-SC3032352/2023,HN.7 +USA/OH-ODH-SC3032478/2023,HN.7 +USA/OH-ODH-SC3032001/2023,HN.7 +USA/OH-ODH-SC3032439/2023,HN.7 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+France/ARA-HCL023185647701/2023,XDK +France/HDF-IPP27487/2023,XDK +Belgium/ULG-301627/2023,XDK +France/PAC-HCL723001630801/2023,XDK +France/BRE-IPP28736/2023,XDK +France/PDL-IPP27182/2023,XDK +France/ARA-HCL023185798601/2023,XDK +France/ARA-HCL023186691701/2023,XDK +France/IDF-IPP29227/2023,XDK +France/IDF-IPP28259/2023,XDK diff --git a/pango_designation/alias_key.json b/pango_designation/alias_key.json index 72a3d83b..5b6b7de1 100644 --- a/pango_designation/alias_key.json +++ b/pango_designation/alias_key.json @@ -329,6 +329,7 @@ "XDF": ["XBB*","EG.5.1.3"], "XDG": ["FL.37","EG.5.2.4"], "XDH": ["BN.1.2.8","XBB.1.9.1"], - "XDJ": ["XBB.1.16.6","HK.3.1"] + "XDJ": ["XBB.1.16.6","HK.3.1"], + "XDK": ["XBB.1.16.11","JN.1.1.1"] }