From 8e6f6dd8c103cfed1bd388a733055d805f252440 Mon Sep 17 00:00:00 2001 From: InfrPopGen Date: Fri, 21 Apr 2023 14:12:44 +0100 Subject: [PATCH] Added new lineage FR.1 from #1814 with 244 new sequence designations, and 4 updated from BN.1.2.3 --- lineage_notes.txt | 1 + lineages.csv | 253 ++++++++++++++++++++++++++++++- pango_designation/alias_key.json | 1 + 3 files changed, 250 insertions(+), 5 deletions(-) diff --git a/lineage_notes.txt b/lineage_notes.txt index 9a8620e6..493b54ae 100644 --- a/lineage_notes.txt +++ b/lineage_notes.txt @@ -912,6 +912,7 @@ BN.1.2 Alias of B.1.1.529.2.75.5.1.2, Singapore/England, E:D72G BN.1.2.1 Alias of B.1.1.529.2.75.5.1.2.1, England/Portugal, S:T470N BN.1.2.2 Alias of B.1.1.529.2.75.5.1.2.2, C29546T BN.1.2.3 Alias of B.1.1.529.2.75.5.1.2.3, C1471T +FR.1 Alias of B.1.1.529.2.75.5.1.2.3.1, found mainly in Japan, Taiwan and USA, from pango-designation issue #1814 BN.1.2.4 Alias of B.1.1.529.2.75.5.1.2.4, ORF1b:D1746H BN.1.3 Alias of B.1.1.529.2.75.5.1.3, India, ORF3a:T229I BN.1.3.1 Alias of B.1.1.529.2.75.5.1.3.1, found mainly in Israel, England and Denmark, from pango-designation issue #1257 diff --git a/lineages.csv b/lineages.csv index be08f6af..f75cdc7c 100644 --- a/lineages.csv +++ b/lineages.csv @@ -2216498,11 +2216498,10 @@ Thailand/NIC_SNI_27760/2022,BN.1.2.3 Thailand/NIC_KBI_27675/2022,BN.1.2.3 Thailand/NIC_BKK_24769/2022,BN.1.2.3 Thailand/NIC_NBI_24714/2022,BN.1.2.3 -Singapore/R9MR9/2023,BN.1.2.3 -Singapore/R2NP46/2023,BN.1.2.3 -Taiwan/F78295/2023,BN.1.2.3 -Singapore/R8MR21/2023,BN.1.2.3 -SouthKorea/KDCA205226/2023,BN.1.2.3 +Singapore/R9MR9/2023,FR.1 +Singapore/R2NP46/2023,FR.1 +Taiwan/F78295/2023,FR.1 +Singapore/R8MR21/2023,FR.1 France/BRE-IPP56765/2022,BN.1.2.3 Singapore/14645/2022,BN.1.2.3 USA/CA-CDPH-FS48079521/2022,BN.1.2.3 @@ -2366383,3 +2366382,247 @@ England/PHEC-YYEXJYT/2023,XBB.1.34 Israel/SMC-7112051/2023,XBB.1.34 England/QEUH-326D4C20/2023,XBB.1.34 France/IDF-IPP07447/2023,XBB.1.34 +Australia/NSW-ICPMR-42686/2023,FR.1 +Japan/PG-459138/2023,FR.1 +Anhui/HSCDC-27/2023,FR.1 +Singapore/R21MR44/2023,FR.1 +Taiwan/CDC-F78637/2023,FR.1 +Japan/TKYmbc36493/2023,FR.1 +Japan/PG-465545/2023,FR.1 +Japan/TKYkbm88950/2023,FR.1 +Japan/TKYkbm88618/2023,FR.1 +Japan/TKYmbc31295/2022,FR.1 +Japan/PG-460353/2023,FR.1 +Taiwan/CDC-F79061/2023,FR.1 +Japan/TKYnat12679/2023,FR.1 +Japan/PG-466630/2023,FR.1 +Singapore/R21MR408/2023,FR.1 +Japan/PG-458305/2023,FR.1 +Japan/TKYmbc36803/2023,FR.1 +Japan/TKYmbc35953/2023,FR.1 +Taiwan/F77506/2022,FR.1 +Japan/TKYkbm83705/2023,FR.1 +Taiwan/NCKUH-061023000511/2023,FR.1 +Japan/PG-463633/2023,FR.1 +Japan/PG-454235/2023,FR.1 +Japan/TKYnat12861/2023,FR.1 +Malaysia/IMR_CV05432/2023,FR.1 +Japan/PG-458376/2023,FR.1 +Japan/PG-464030/2023,FR.1 +Japan/PG-464741/2023,FR.1 +USA/NY-CDC-LC1020222/2023,FR.1 +Japan/PG-466158/2023,FR.1 +Canada/ON-PHL-12398/2023,FR.1 +Thailand/NIC_CBI_792/2023,FR.1 +Japan/TKYmbc36640/2023,FR.1 +Japan/PG-464699/2023,FR.1 +USA/NJ-PHEL-V008129/2023,FR.1 +USA/WA-CDC-UW23012444092/2023,FR.1 +Japan/PG-464706/2023,FR.1 +Japan/PG-466157/2023,FR.1 +Japan/PG-452884/2023,FR.1 +Taiwan/CDC-F78669/2023,FR.1 +USA/WA-CDC-UW23011087527/2023,FR.1 +Australia/QLD0x012D67/2023,FR.1 +Japan/PG-458707/2023,FR.1 +Japan/PG-449069/2023,FR.1 +Japan/PG-465136/2023,FR.1 +Taiwan/CDC-F78677/2023,FR.1 +USA/CA-TCPHL022823-94/2023,FR.1 +Japan/PG-457445/2023,FR.1 +USA/WA-CDC-UW23012447727/2023,FR.1 +Taiwan/NCKUH-061023000840/2023,FR.1 +Japan/PG-456912/2023,FR.1 +Canada/ON-PHL-12386/2023,FR.1 +Japan/PG-453196/2023,FR.1 +Japan/TKYnat12641/2023,FR.1 +Taiwan/NCKUH-061023000709/2023,FR.1 +France/IDF-IPP07653/2023,FR.1 +Japan/PG-448575/2023,FR.1 +Japan/PG-463089/2023,FR.1 +Japan/PG-465842/2023,FR.1 +Japan/PG-467378/2023,FR.1 +Singapore/R6MR101/2023,FR.1 +Japan/PG-464936/2023,FR.1 +Japan/TKYkbm88646/2023,FR.1 +Myanmar/DMR-22114/2023,FR.1 +USA/CA-GBW-H20-290-3202/2023,FR.1 +Japan/TKYnat12864/2023,FR.1 +Japan/PG-468382/2023,FR.1 +Japan/PG-456842/2023,FR.1 +Japan/PG-455068/2023,FR.1 +USA/WA-CDC-UW23031322114/2023,FR.1 +Malaysia/IMR_CV05427/2023,FR.1 +Japan/PG-464873/2023,FR.1 +Japan/PG-468320/2023,FR.1 +Taiwan/F78385/2023,FR.1 +France/GES-IPP-03512/2023,FR.1 +Japan/TKYnat12198/2023,FR.1 +USA/CA-CDPH-500106936/2023,FR.1 +Japan/PG-465042/2023,FR.1 +Japan/PG-448108/2023,FR.1 +Japan/PG-461405/2023,FR.1 +Taiwan/CDC-F78689/2023,FR.1 +Japan/PG-463667/2023,FR.1 +Japan/PG-457460/2023,FR.1 +Taiwan/NCKUH-061023000691/2023,FR.1 +Singapore/R22MR349/2023,FR.1 +Singapore/R15MR8/2023,FR.1 +Japan/TKYkbm85603/2023,FR.1 +Japan/PG-463732/2023,FR.1 +Norway/Ahus-4949/2023,FR.1 +Japan/PG-458949/2023,FR.1 +Japan/IC-16416/2023,FR.1 +Japan/PG-463046/2023,FR.1 +Japan/TKYkbm87811/2023,FR.1 +Japan/TKYnat12813/2023,FR.1 +Japan/TKYmbc36755/2023,FR.1 +Australia/VIC81301/2023,FR.1 +Japan/PG-464951/2023,FR.1 +Jiangsu/YCCDC-093/2023,FR.1 +Taiwan/NCKUH-061023000510/2023,FR.1 +Japan/PG-461414/2023,FR.1 +Japan/PG-442906/2023,FR.1 +Taiwan/F78360/2023,FR.1 +Japan/PG-463765/2023,FR.1 +Japan/PG-465583/2023,FR.1 +Japan/PG-459151/2023,FR.1 +England/PHEC-YYEROYY/2023,FR.1 +Japan/PG-466667/2023,FR.1 +Japan/PG-466788/2023,FR.1 +Japan/TKYkbm88566/2023,FR.1 +Japan/TKYkbm88783/2023,FR.1 +Taiwan/CDC-F78688/2023,FR.1 +Japan/PG-467328/2023,FR.1 +Japan/PG-465550/2023,FR.1 +Japan/PG-468439/2023,FR.1 +Japan/TKYnat13035/2023,FR.1 +USA/CA-GBW-H20-299-0965/2023,FR.1 +USA/WA-CDC-UW23012610154/2023,FR.1 +Australia/QLD0x012D75/2023,FR.1 +Japan/TKYnat12842/2023,FR.1 +Japan/PG-456813/2023,FR.1 +Japan/TKYkbm87805/2023,FR.1 +Singapore/R21MR56/2023,FR.1 +Japan/TKYkbm84941/2023,FR.1 +Taiwan/CDC-F78701/2023,FR.1 +Japan/TKYkbm88492/2023,FR.1 +Japan/PG-465588/2023,FR.1 +USA/CA-GBW-H10-010-7289/2023,FR.1 +Japan/PG-452769/2023,FR.1 +Japan/PG-460521/2023,FR.1 +Taiwan/NCKUH-061023000694/2023,FR.1 +USA/CA-CDPH-A3000000314980/2023,FR.1 +Japan/TKYnat12989/2023,FR.1 +Singapore/R9MR44/2023,FR.1 +Australia/QLD0x013096/2023,FR.1 +Australia/QLD0x012D87/2023,FR.1 +Japan/PG-460488/2023,FR.1 +Japan/PG-466633/2023,FR.1 +Japan/PG-466775/2023,FR.1 +England/PHEC-YYE8GRH/2023,FR.1 +Taiwan/CDC-F78638/2023,FR.1 +Singapore/16560/2022,FR.1 +Japan/TKYmbc36766/2023,FR.1 +Singapore/R22MR517/2023,FR.1 +Taiwan/F78384/2023,FR.1 +Guam/GU-H2319364/2023,FR.1 +Japan/TKYmbc36509/2023,FR.1 +Japan/PG-458708/2023,FR.1 +Japan/TKYkbm88730/2023,FR.1 +Japan/TKYmbc36795/2023,FR.1 +Japan/PG-465546/2023,FR.1 +USA/CA-CDC-LC1004299/2023,FR.1 +Japan/PG-465587/2023,FR.1 +Japan/TKYnat12697/2023,FR.1 +Japan/PG-453590/2023,FR.1 +Japan/PG-466680/2023,FR.1 +Japan/PG-457449/2023,FR.1 +Japan/TKYnat12107/2023,FR.1 +Japan/PG-463039/2023,FR.1 +Japan/PG-467062/2023,FR.1 +Singapore/R20MR308/2023,FR.1 +Japan/PG-464871/2023,FR.1 +Japan/PG-460229/2023,FR.1 +Malaysia/USM_M234_21391/2023,FR.1 +USA/CA-GBW-H10-010-5422/2023,FR.1 +Japan/PG-443355/2023,FR.1 +France/ARA-HCL023013920201/2023,FR.1 +Japan/TKYkbm88915/2023,FR.1 +Japan/PG-444380/2023,FR.1 +Japan/PG-465514/2023,FR.1 +Japan/TKYnat12755/2023,FR.1 +Japan/PG-466924/2023,FR.1 +Australia/VIC82170/2023,FR.1 +Japan/TKYmbc36804/2023,FR.1 +Taiwan/CDC-F78671/2023,FR.1 +Japan/TKYkbm88540/2023,FR.1 +Canada/ON-PHL-11090/2023,FR.1 +Israel/ICH-741195736/2023,FR.1 +Japan/PG-465887/2023,FR.1 +Singapore/R21MR80/2023,FR.1 +USA/CA-ASC-210968069/2023,FR.1 +Japan/PG-438848/2023,FR.1 +Japan/PG-467329/2023,FR.1 +Brunei/7123022862/2023,FR.1 +Canada/ON-PHL-23-16319/2023,FR.1 +Japan/PG-466695/2023,FR.1 +Japan/PG-466696/2023,FR.1 +Taiwan/CDC-F78619/2023,FR.1 +Japan/TKYmbc36643/2023,FR.1 +Japan/PG-467386/2023,FR.1 +Japan/PG-468177/2023,FR.1 +Singapore/R18MR144/2023,FR.1 +USA/CA-HLX-STM-XJCPS69Y4/2023,FR.1 +Japan/PG-456786/2023,FR.1 +Singapore/R20MR119/2023,FR.1 +USA/CA-CDC-QDX46500627/2023,FR.1 +Japan/PG-468258/2023,FR.1 +Japan/PG-464886/2023,FR.1 +Japan/PG-461413/2023,FR.1 +USA/CA-CDPH-A3000000314633/2023,FR.1 +Taiwan/CDC-F78621/2023,FR.1 +Japan/PG-468350/2023,FR.1 +Japan/PG-453234/2023,FR.1 +Singapore/R5MR80/2023,FR.1 +Singapore/R8MR43/2023,FR.1 +Japan/PG-462785/2023,FR.1 +Japan/TKYkbm87951/2023,FR.1 +USA/CA-HLX-STM-P49ZFSSKK/2023,FR.1 +Japan/PG-468424/2023,FR.1 +Japan/TKYmbc36700/2023,FR.1 +Japan/PG-444024/2023,FR.1 +Japan/PG-445133/2023,FR.1 +Japan/TKYkbm88304/2023,FR.1 +Australia/QLD0x012DC0/2023,FR.1 +Japan/TKYnat12877/2023,FR.1 +Taiwan/CDC-F79091/2023,FR.1 +Japan/TKYkbm88445/2023,FR.1 +Japan/TKYmbc36697/2023,FR.1 +Japan/TKYnat12255/2023,FR.1 +Japan/PG-452883/2023,FR.1 +Japan/TKYnat12590/2023,FR.1 +Japan/PG-441247/2023,FR.1 +Indonesia/JK-NIHRD-W00768/2023,FR.1 +Japan/PG-456599/2023,FR.1 +Taiwan/CDC-F78686/2023,FR.1 +USA/CA-CDC-QDX46826687/2023,FR.1 +USA/CA-HLX-STM-KZHTN97M5/2023,FR.1 +Japan/PG-458372/2023,FR.1 +Japan/PG-466862/2023,FR.1 +Japan/TKYnat12728/2023,FR.1 +Japan/TKYkbm88315/2023,FR.1 +Japan/PG-461422/2023,FR.1 +Japan/PG-458373/2023,FR.1 +Japan/TKYkbm88698/2023,FR.1 +Taiwan/CDC-F79107/2023,FR.1 +USA/WA-CDC-UW23011043545/2023,FR.1 +Japan/PG-465597/2023,FR.1 +Canada/ON-PHL-23-14857/2023,FR.1 +France/HDF-IPP07652/2023,FR.1 +Japan/TKYnat12894/2023,FR.1 +Japan/PG-427906/2022,FR.1 +Canada/ON-PHL-23-12767/2023,FR.1 +Japan/PG-463169/2023,FR.1 +Japan/PG-466752/2023,FR.1 +Taiwan/NCKUH-061023000646/2023,FR.1 diff --git a/pango_designation/alias_key.json b/pango_designation/alias_key.json index 3441e326..eddf9a45 100644 --- a/pango_designation/alias_key.json +++ b/pango_designation/alias_key.json @@ -146,6 +146,7 @@ "FN": "B.1.1.529.5.3.1.1.1.1.1.1.74", "FP": "XBB.1.11.1", "FQ": "B.1.1.529.5.3.1.1.1.1.1.1.39", + "FR": "B.1.1.529.2.75.5.1.2.3", "XA": ["B.1.1.7","B.1.177"], "XB": ["B.1.634","B.1.631"], "XC": ["AY.29","B.1.1.7"],