From 3177a360166e1e78e668733bc86bcd690a7d221c Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Fri, 20 Dec 2024 18:36:32 +0100 Subject: [PATCH] Designate NV.1 (KP.3.2.9.1) and XET Resolves sars-cov-2-variants/lineage-proposals#2302 --- lineage_notes.txt | 2 + lineages.csv | 135 +++++++++++++++++++++++-------- pango_designation/alias_key.json | 4 +- 3 files changed, 107 insertions(+), 34 deletions(-) diff --git a/lineage_notes.txt b/lineage_notes.txt index 53c21c5e..1e20f612 100644 --- a/lineage_notes.txt +++ b/lineage_notes.txt @@ -1345,6 +1345,7 @@ KP.3.2.6 Alias of B.1.1.529.2.86.1.1.11.1.3.2.6, S:S31P, G11761A, G25617A, Asia, KP.3.2.7 Alias of B.1.1.529.2.86.1.1.11.1.3.2.7, S:S31-, ORF1a:I1005L, from sars-cov-2-variants/lineage-proposals#2180 KP.3.2.8 Alias of B.1.1.529.2.86.1.1.11.1.3.2.8, S:S31-, C14790T, C21590T, C18981T, from sars-cov-2-variants/lineage-proposals#2081 KP.3.2.9 Alias of B.1.1.529.2.86.1.1.11.1.3.2.9, ORF1b:K2557R +NV.1 Alias of B.1.1.529.2.86.1.1.11.1.3.2.9.1, S:S31-, with C7267T KP.3.3 Alias of B.1.1.529.2.86.1.1.11.1.3.3, N:R204P, from sars-cov-2-variants/lineage-proposals#1531 KP.3.3.1 Alias of B.1.1.529.2.86.1.1.11.1.3.3.1, S:T547K, ORF3a:F87S, from sars-cov-2-variants/lineage-proposals#1651 NQ.1 Alias of B.1.1.529.2.86.1.1.11.1.3.3.1.1, S:S680P, S:A435S, ORF1b:Q1441H, South Korea/Japan @@ -4468,6 +4469,7 @@ XEP Recombinant lineage of KP.3.1.1, NP.2 (breakpoint: 21656-22864), from sars-c XEQ Recombinant lineage of KS.1.1.2, KP.3 (breakpoint: 22600-23038), from #2817 XER Recombinant lineage of KS.2, LF.7 (breakpoint: 18349-21626), from sars-cov-2-variants/lineage-proposals#2259 XES Recombinant lineage of KP.2.3.15, KP.3.3 (breakpoint: 22001-22598), from #2783 +XET Recombinant lineage of KP.1.1.1., KP.3.1.1 (breakpoint: 20105-21652), from sars-cov-2-variants/lineage-proposals#2302 *A.2.1 Withdrawn: Lineage with sequences predominantly from Panama *A.8 Withdrawn: Indian lineage merged with A.9 *A.10 Withdrawn: Spanish lineage reassigned to A.5 diff --git a/lineages.csv b/lineages.csv index 106c5ee0..c2575a03 100644 --- a/lineages.csv +++ b/lineages.csv @@ -2579291,42 +2579291,9 @@ Scotland/CLIMB-CM7YKRY6/2024,KP.3.2.9 Scotland/CLIMB-CM7YJ4PC/2024,KP.3.2.9 Scotland/CLIMB-CM7YJAKJ/2024,KP.3.2.9 Scotland/CLIMB-CM7Y8198/2024,KP.3.2.9 -Sweden/M-SUS0023703/2024,KP.3.2.9 -USA/NY-CDC-LC1119854/2024,KP.3.2.9 -Spain/PV-HUD-97036472/2024,KP.3.2.9 -France/GES-IPP07949/2024,KP.3.2.9 -Wales/CLIMB-CM7YJI9A/2024,KP.3.2.9 -USA/NY-PRL-241022_83C01/2024,KP.3.2.9 -Denmark/DCGC-687131/2024,KP.3.2.9 -Sweden/AB-01_SE100_24CS501870/2024,KP.3.2.9 Sweden/1260995099R4/2024,KP.3.2.9 -Spain/MD-HGUGM-65710778/2024,KP.3.2.9 -France/ARA-HCL024124709401/2024,KP.3.2.9 -USA/VA-CDC-LC1114535/2024,KP.3.2.9 -USA/CA-GBW-GKPLAAAA46820/2024,KP.3.2.9 -USA/CA-GBW-GKISBBBE42336/2024,KP.3.2.9 -USA/OH-PLMI-4W2-27506/2024,KP.3.2.9 -USA/FL-CDC-QDX24407965/2024,KP.3.2.9 USA/2474216/2024,KP.3.2.9 USA/2471535/2024,KP.3.2.9 -USA/NY-PRL-241022_83C12/2024,KP.3.2.9 -Canada/ON-PHL-202417538/2024,KP.3.2.9 -Canada/ON-PHL-202417555/2024,KP.3.2.9 -Canada/ON-PHL-202417536/2024,KP.3.2.9 -Canada/ON-PHL-202417522/2024,KP.3.2.9 -Canada/ON-PHL-202417569/2024,KP.3.2.9 -Canada/ON-PHL-202417532/2024,KP.3.2.9 -Canada/ON-PHL-202417511/2024,KP.3.2.9 -Canada/ON-PHL-202417571/2024,KP.3.2.9 -Canada/ON-PHL-202418440/2024,KP.3.2.9 -Canada/ON-PHL-202418106/2024,KP.3.2.9 -Canada/ON-PHL-202417817/2024,KP.3.2.9 -Canada/ON-PHL-202418874/2024,KP.3.2.9 -Canada/ON-PHL-202418437/2024,KP.3.2.9 -Canada/ON-PHL-202418125/2024,KP.3.2.9 -Canada/ON-PHL-202417596/2024,KP.3.2.9 -Canada/ON-PHL-202417508/2024,KP.3.2.9 -Canada/ON-PHL-202418436/2024,KP.3.2.9 Canada/QC-L00791254001/2024,XEC.3 Ireland/D-BH-02342282/2024,XEC.3 Canada/NB-CHUDGLD-18J-MM00036R/2024,XEC.3 @@ -2591376,3 +2591343,105 @@ Chile/RM-87521/2024,KP.3.3.5 Denmark/DCGC-690804/2024,KP.3.3.5 USA/CO-CDPHE-42481723/2024,KP.3.3.5 USA/CO-CDPHE-42481572/2024,KP.3.3.5 +Spain/PV-HUD-97036472/2024,NV.1 +France/GES-IPP07949/2024,NV.1 +France/ARA-HCL024124709401/2024,NV.1 +Spain/MD-HGUGM-65710778/2024,NV.1 +Sweden/AB-01_SE100_24CS501870/2024,NV.1 +USA/NY-PRL-241022_83C01/2024,NV.1 +Wales/CLIMB-CM7YJI9A/2024,NV.1 +Denmark/DCGC-687131/2024,NV.1 +Spain/CB-HUMV-256797/2024,NV.1 +Greece/PHLnetwork_5243/2024,NV.1 +Canada/BC-BCCDC-747489/2024,NV.1 +Japan/FR302-1496/2024,NV.1 +USA/MN-MDH-44400/2024,NV.1 +USA/VA-CDC-LC1114535/2024,NV.1 +USA/CA-GBW-GKISBBBE42336/2024,NV.1 +USA/CA-GBW-GKPLAAAA46820/2024,NV.1 +Canada/AB-ABPHL-128230/2024,NV.1 +Canada/AB-ABPHL-125725/2024,NV.1 +Canada/AB-ABPHL-125655/2024,NV.1 +Sweden/M-SUS0023703/2024,NV.1 +USA/NY-CDC-LC1119854/2024,NV.1 +USA/IA-SHL-2474216/2024,NV.1 +USA/IA-SHL-2471535/2024,NV.1 +USA/FL-CDC-QDX24407965/2024,NV.1 +USA/OH-PLMI-WJ5-28610/2024,NV.1 +USA/OH-PLMI-4W2-27506/2024,NV.1 +USA/NY-CDC-LC1124655/2024,NV.1 +USA/NY-SUNYQB-XL2974/2024,NV.1 +USA/NY-SUNYQB-XL2980/2024,NV.1 +USA/NY-SUNYQB-XL2955/2024,NV.1 +USA/NY-SUNYQB-XL2977/2024,NV.1 +USA/NY-SUNYQB-XL2975/2024,NV.1 +USA/NY-SUNYQB-X939059/2024,NV.1 +USA/NY-SUNYQB-X289660/2024,NV.1 +USA/NY-SUNYQB-X11747/2024,NV.1 +USA/NY-SUNYQB-X194301/2024,NV.1 +USA/NY-SUNYQB-XL2952/2024,NV.1 +USA/NY-SUNYQB-X4168017/2024,NV.1 +USA/NY-SUNYQB-X730304/2024,NV.1 +USA/NY-SUNYQB-X4166690/2024,NV.1 +USA/NY-SUNYQB-XL2995/2024,NV.1 +USA/DE-DHSS-579/2024,NV.1 +Italy/LAZ-UCBM-2024-21/2024,NV.1 +USA/NY-PRL-241022_83C12/2024,NV.1 +Canada/ON-PHL-202419522/2024,NV.1 +Canada/ON-PHL-202419518/2024,NV.1 +Canada/ON-PHL-202419515/2024,NV.1 +Canada/ON-PHL-202419514/2024,NV.1 +Canada/ON-PHL-202419512/2024,NV.1 +Canada/ON-PHL-202418440/2024,NV.1 +Canada/ON-PHL-202419523/2024,NV.1 +Canada/ON-PHL-202418125/2024,NV.1 +Canada/ON-PHL-202418106/2024,NV.1 +Canada/ON-PHL-202417817/2024,NV.1 +Canada/ON-PHL-202417596/2024,NV.1 +Canada/ON-PHL-202417571/2024,NV.1 +Canada/ON-PHL-202417569/2024,NV.1 +Canada/ON-PHL-202417555/2024,NV.1 +Canada/ON-PHL-202417538/2024,NV.1 +Canada/ON-PHL-202417536/2024,NV.1 +Canada/ON-PHL-202417532/2024,NV.1 +Canada/ON-PHL-202417522/2024,NV.1 +Canada/ON-PHL-202417511/2024,NV.1 +Canada/ON-PHL-202417508/2024,NV.1 +Canada/ON-PHL-202420397/2024,NV.1 +Canada/ON-PHL-202420145/2024,NV.1 +Canada/ON-PHL-202419990/2024,NV.1 +Canada/ON-PHL-202419683/2024,NV.1 +Canada/ON-PHL-202419678/2024,NV.1 +Canada/ON-PHL-202419664/2024,NV.1 +Canada/ON-PHL-202419461/2024,NV.1 +Canada/ON-PHL-202419434/2024,NV.1 +Canada/ON-PHL-202419061/2024,NV.1 +Canada/ON-PHL-202418874/2024,NV.1 +Canada/ON-PHL-202418437/2024,NV.1 +Canada/ON-PHL-202418436/2024,NV.1 +USA/CA-SCPHL-24WGS00789/2024,XET +Canada/BC-BCCDC-733139/2024,XET +Canada/BC-BCCDC-732935/2024,XET +Canada/BC-BCCDC-733134/2024,XET +Canada/BC-BCCDC-740680/2024,XET +USA/NY-URMC-O8S1Q565-1/2024,XET +Canada/BC-BCCDC-740545/2024,XET +Canada/BC-BCCDC-737118/2024,XET +Canada/BC-BCCDC-735115/2024,XET +USA/OH-PLMI-3C5-26878/2024,XET +USA/OH-PLMI-5HB-25728/2024,XET +USA/NY-CDC-QDX24189046/2024,XET +USA/NY-CDC-QDX24124912/2024,XET +Canada/BC-BCCDC-740362/2024,XET +Canada/BC-BCCDC-736977/2024,XET +PuertoRico/CVL025784/2024,XET +PuertoRico/CVL025783/2024,XET +USA/MN-MDH-43116/2024,XET +USA/MN-MDH-42971/2024,XET +USA/MN-MDH-43599/2024,XET +USA/MN-MDH-43834/2024,XET +USA/MN-MDH-43816/2024,XET +USA/WI-WSLH-2403078/2024,XET +USA/MN-MDH-44042/2024,XET +USA/MN-MDH-44081/2024,XET +USA/MN-MDH-44463/2024,XET diff --git a/pango_designation/alias_key.json b/pango_designation/alias_key.json index 7bf2106b..e3592cd1 100644 --- a/pango_designation/alias_key.json +++ b/pango_designation/alias_key.json @@ -311,6 +311,7 @@ "NS": "B.1.1.529.2.86.1.1.16.3", "NT": "B.1.1.529.2.86.1.1.16.1.7.1.2", "NU": "B.1.1.529.2.86.1.1.55.2", + "NV": "B.1.1.529.2.86.1.1.11.1.3.2.9", "XA": ["B.1.1.7","B.1.177"], "XB": ["B.1.634","B.1.631"], "XC": ["AY.29","B.1.1.7"], @@ -442,6 +443,7 @@ "XEP": ["KP.3.1.1","NP.2"], "XEQ": ["KS.1.1.2","KP.3"], "XER": ["KS.2","LF.7"], - "XES": ["KP.2.3","KP.3.3"] + "XES": ["KP.2.3","KP.3.3"], + "XET": ["KP.1.1.1","KP.3.1.1"] }