From 4d852e2fd33babea2102e6cc8f569697e8081e39 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Sat, 22 Apr 2023 22:47:06 +0200 Subject: [PATCH] Added lineage FU.1 (XBB.1.16.1 with T3802C) with 150 designations --- lineage_notes.txt | 1 + lineages.csv | 140 ++++++++++++++++++++++++++++--- pango_designation/alias_key.json | 1 + 3 files changed, 132 insertions(+), 10 deletions(-) diff --git a/lineage_notes.txt b/lineage_notes.txt index 820cfb4b..1b7f7913 100644 --- a/lineage_notes.txt +++ b/lineage_notes.txt @@ -2686,6 +2686,7 @@ XBB.1.14 S:G75V, S:E554K XBB.1.15 Defined by ORF1a:A540V on ORF8:G8* polytomy, found in USA, Guatemala, and Mexico. Automatically inferred by https://github.com/jmcbroome/autolin. XBB.1.16 Defined by S:E180V, S:478R, found in India, USA, Singapore, and Europe, from pango-designation issue #1723 XBB.1.16.1 Defined by S:T547I +FU.1 Alias of XBB.1.16.1.1, T3802C XBB.1.16.2 Defined by ORF3a:V13L, ORF1a:P926H, India XBB.1.16.3 Defined by A2893C, India XBB.1.17 Defined by T27995C and ORF1a:L469F, from issue #1712 diff --git a/lineages.csv b/lineages.csv index 9589b67e..a381660f 100644 --- a/lineages.csv +++ b/lineages.csv @@ -2349231,17 +2349231,7 @@ India/GJ-GBRC10317/2023,XBB.1.16.1 India/GJ-GBRC10340/2023,XBB.1.16.1 India/GJ-GBRC10327/2023,XBB.1.16.1 India/GJ-GBRC10338/2023,XBB.1.16.1 -USA/CA-GBW-H20-306-0197/2023,XBB.1.16.1 -India/KA-20708_S1_R1_001/2023,XBB.1.16.1 -USA/VA-GBW-H20-295-4939/2023,XBB.1.16.1 -USA/WA-GBW-H20-276-2723/2023,XBB.1.16.1 -USA/WA-GBW-H10-011-5635/2023,XBB.1.16.1 -USA/CA-GBW-H20-294-0352/2023,XBB.1.16.1 -USA/CA-GBW-H10-010-4703/2023,XBB.1.16.1 -India/PY-20729_S1_R1_001/2023,XBB.1.16.1 -India/PY-20728_S1_R1_001/2023,XBB.1.16.1 India/MH-ICMR-NIV-G-13114/2023,XBB.1.16.1 -India/MH_BJCOG5109/2023,XBB.1.16.1 USA/AZ-ASU98776/2023,XBB.1.5.27 USA/AZ-ASU99023/2023,XBB.1.5.27 USA/AZ-ASU98824/2023,XBB.1.5.27 @@ -2370918,3 +2370908,133 @@ India/GJ-GBRC11799/2023,XBB.1.16.3 Japan/PG-464783/2023,XBB.1.16.3 Japan/PG-464822/2023,XBB.1.16.3 Japan/PG-464784/2023,XBB.1.16.3 +USA/WA-GBW-H20-303-9814/2023,FU.1 +Singapore/R23MR287/2023,FU.1 +Australia/NSW-ICPMR-44698/2023,FU.1 +Canada/ON-PHL-23-20952/2023,FU.1 +SouthKorea/KDCA227370/2023,FU.1 +India/DL-ILBS-8098/2023,FU.1 +India/PY-20864_S1_R1_001/2023,FU.1 +India/DL-ILBS-8545/2023,FU.1 +India/DL-ILBS-8556/2023,FU.1 +India/DL-ILBS-7901/2023,FU.1 +Australia/SA530244/2023,FU.1 +Singapore/NPHL-R23MR65/2023,FU.1 +India/GJ-GBRC11477/2023,FU.1 +Singapore/NPHL-R22MR317/2023,FU.1 +Singapore/NPHL-R22MR432/2023,FU.1 +Australia/NSW-ICPMR-44448/2023,FU.1 +USA/WA-CDC-UW23032466470/2023,FU.1 +Australia/NSW-ICPMR-44099/2023,FU.1 +USA/OH-CDC-QDX47973871/2023,FU.1 +IND/2922/2023,FU.1 +USA/CA-GBW-H20-306-0197/2023,FU.1 +USA/VA-GBW-H20-295-4939/2023,FU.1 +India/PY-20833_S1_R1_001/2023,FU.1 +Singapore/NPHL-R22MR391/2023,FU.1 +Singapore/NPHL-R22MR351/2023,FU.1 +Singapore/NPHL-R23MR46/2023,FU.1 +Singapore/NPHL-R22MR301/2023,FU.1 +USA/PA-CDC-LC1027064/2023,FU.1 +India/KA-20764_S1_R1_001/2023,FU.1 +Singapore/R21MR457/2023,FU.1 +Singapore/R22MR150/2023,FU.1 +India/DL-ILBS-7660/2023,FU.1 +India/KA-20708_S1_R1_001/2023,FU.1 +USA/WA-GBW-H10-011-3211/2023,FU.1 +Singapore/R20MR444/2023,FU.1 +Singapore/R21MR166/2023,FU.1 +Australia/NSW-ICPMR-44148/2023,FU.1 +Canada/QC-L00597327001/2023,FU.1 +USA/WA-GBW-H20-282-4000/2023,FU.1 +Singapore/R21MR409/2023,FU.1 +Singapore/R21MR465/2023,FU.1 +Australia/NSW-ICPMR-45059/2023,FU.1 +England/PHEP-YYG1ZEQ/2023,FU.1 +Singapore/R23MR400/2023,FU.1 +Singapore/R23MR289/2023,FU.1 +Singapore/NPHL-R23MR61/2023,FU.1 +India/GJ-INSACOG-GBRC11676/2023,FU.1 +Singapore/R23MR466/2023,FU.1 +Singapore/R23MR410/2023,FU.1 +Australia/NSW-ICPMR-44699/2023,FU.1 +SouthKorea/KDCA226166/2023,FU.1 +SouthKorea/KDCA222470/2023,FU.1 +USA/RI-CDC-LC1036205/2023,FU.1 +Singapore/NPHL-R22MR478/2023,FU.1 +Singapore/R21MR296/2023,FU.1 +USA/WA-GBW-H20-276-2723/2023,FU.1 +USA/WA-GBW-H10-011-5635/2023,FU.1 +Japan/IC-16452/2023,FU.1 +India/PY-20844_S1_R1_001/2023,FU.1 +Singapore/R23MR211/2023,FU.1 +USA/VA-GBW-H20-297-7729/2023,FU.1 +USA/VA-GBW-H10-013-1803/2023,FU.1 +Japan/5GA-243/2023,FU.1 +Japan/PG-466762/2023,FU.1 +USA/IL-4142023084/2023,FU.1 +India/PY-20846_S1_R1_001/2023,FU.1 +India/GJ-GBRC11070/2023,FU.1 +India/MH-CSIR-NEERI2851/2023,FU.1 +India/TN-SPHL-2919/2023,FU.1 +Singapore/R21MR214/2023,FU.1 +USA/CA-GBW-H20-281-2301/2023,FU.1 +USA/CA-CDC-QDX48637276/2023,FU.1 +USA/CA-GBW-H10-012-2862/2023,FU.1 +India/PY-20817_S1_R1_001/2023,FU.1 +India/PY-20729_S1_R1_001/2023,FU.1 +India/PY-20728_S1_R1_001/2023,FU.1 +India/GJ-INSACOG-GBRC11785/2023,FU.1 +India/GJ-GBRC10988/2023,FU.1 +Austria/AGES-1134324/2023,FU.1 +Austria/AGES-1134339/2023,FU.1 +SouthKorea/KDCA227263/2023,FU.1 +Austria/AGES-1132816/2023,FU.1 +USA/CA-GBW-H10-013-2280/2023,FU.1 +USA/CA-GBW-H20-316-9411/2023,FU.1 +USA/NJ-GBW-H20-264-7264/2023,FU.1 +USA/CA-GBW-H20-305-8829/2023,FU.1 +USA/FL-TGH-4992/2023,FU.1 +USA/NC-CORVASEQ-1086-4446/2023,FU.1 +HongKong/VB23023166/2023,FU.1 +USA/NJ-GBW-H20-299-2353/2023,FU.1 +South_Korea/KDCA229570/2023,FU.1 +SouthKorea/KDCA229570/2023,FU.1 +USA/MO-CDC-QDX47771568/2023,FU.1 +USA/PA-CDC-QDX48587130/2023,FU.1 +USA/FL-CDC-QDX48587493/2023,FU.1 +USA/IL-CDC-QDX48685611/2023,FU.1 +SouthKorea/KDCA0009/2023,FU.1 +USA/GA-GBW-H10-012-5062/2023,FU.1 +USA/GA-GBW-H20-318-0676/2023,FU.1 +USA/CA-GBW-H20-294-0352/2023,FU.1 +SouthKorea/KDCA225284/2023,FU.1 +USA/CA-GBW-H10-010-4703/2023,FU.1 +Shanghai/SCDC-SH-XG04-2050/2023,FU.1 +CHN/SH-XG2304-2050/2023,FU.1 +Japan/TKYkbm88875/2023,FU.1 +USA/HI-H2321017/2023,FU.1 +Japan/5GA-265/2023,FU.1 +Israel/ICH-741196922/2023,FU.1 +Israel/ICH-741196888/2023,FU.1 +Japan/5GA-264/2023,FU.1 +USA/WA-GBW-H10-011-3863/2023,FU.1 +India/GJ-INSACOG-GBRC10570/2023,FU.1 +Singapore/R21MR439/2023,FU.1 +India/MH-ICMR-NIV-232024/2023,FU.1 +India/DL-ILBS-8497/2023,FU.1 +USA/WA-GBW-H10-011-3834/2023,FU.1 +India/DL-AIIMS148014/2023,FU.1 +USA/WA-GBW-H20-282-1700/2023,FU.1 +USA/NJ-GBW-H20-299-3468/2023,FU.1 +USA/WA-GBW-H20-283-1971/2023,FU.1 +USA/MN-CDC-QDX48551717/2023,FU.1 +India/MH-ICMR-NIV-G-13694/2023,FU.1 +India/MH_BJCOG5109/2023,FU.1 +India/MH-RFIP17779/2023,FU.1 +India/MH-RFIP17780/2023,FU.1 +Israel/ICH-741197560/2023,FU.1 +Scotland/SCOT-29102/2023,FU.1 +India/MH-RFIP17830/2023,FU.1 +India/MH-RFIP17826/2023,FU.1 +India/MH-ICMR-NIV-G-13340/2023,FU.1 diff --git a/pango_designation/alias_key.json b/pango_designation/alias_key.json index da93bc3b..b3ad42e1 100644 --- a/pango_designation/alias_key.json +++ b/pango_designation/alias_key.json @@ -149,6 +149,7 @@ "FR": "B.1.1.529.2.75.5.1.2.3", "FS": "B.1.1.529.2.75.3.4.1.1.1.1.12", "FT": "XBB.1.5.39", + "FU": "XBB.1.16.1", "XA": ["B.1.1.7","B.1.177"], "XB": ["B.1.634","B.1.631"], "XC": ["AY.29","B.1.1.7"],