adding R.1, R.2 and B.1.1.318

cov-lineages · Feb 21, 2021 · d484393 · d484393
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diff --git a/lineage_notes.txt b/lineage_notes.txt
@@ -341,6 +341,7 @@ B.1.1.314	Brazilian lineage, previously part of B.1.1.33
 B.1.1.315	Previously D.1, UK/ UAE lineage
 B.1.1.316	International lineage with E484K mutation
 B.1.1.317	Russian lineage
+B.1.1.318	Lineage circulating in multiple countries with a number of variants of concern (Spike D614G, Spike D796H, Spike E484K, Spike P681H, Spike T95I, Spike Y144del). pango-designation issue #15
 B.1.2	USA lineage
 B.1.3	USA lineage 
 *B.1.3.1	South Korean lineage
@@ -1022,3 +1023,5 @@ N.3	Alias of B.1.1.33.3, Argentinian lineage
 N.4	Alias of B.1.1.33.4, Chilean lineage
 P.1	Alias of B.1.1.28.1, Brazilian lineage with a number of spike mutaions with likely functional significance E484K, K417T, and N501Y. Described in https://virological.org/t/genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-manaus-preliminary-findings/586.
 P.2	Alias of B.1.1.28.2, Brazilian lineage
+R.1	Alias of B.1.1.316.1. Sublineage of B.1.1.316 with 3 additional spike mutations, circulating in a number of countries. pango-designation issue #17
+R.2	Alias of B.1.1.316.2. Sublineage of B.1.1.316 with E484K. pango-designation issue #18
diff --git a/lineages.csv b/lineages.csv
@@ -174166,18 +174166,6 @@ USA/HI-H200048/2020,B.1.1
 USA/HI-H200106/2020,B.1.1
 USA/WV-CDC-7935/2020,B.1.1
 USA/VA-DCLS-1043/2020,B.1.1
-USA/MD-HP01030/2020,B.1.1.316
-USA/NMDOH-2021015923/2021,B.1.1.316
-USA/NY-NYCPHL-002453/2021,B.1.1.316
-USA/MD-HP01225/2021,B.1.1.316
-USA/NY-NYCPHL-002418/2021,B.1.1.316
-USA/MD-HP12155/2020,B.1.1.316
-USA/MD-HP01154/2021,B.1.1.316
-England/ALDP-B82A0D/2020,B.1.1.316
-USA/MD-MDH-0664/2021,B.1.1.316
-USA/DE-CDC-STM-A100307/2021,B.1.1.316
-USA/IA-GMF-46406/2021,B.1.1.316
-United_Arab_Emirates/4275/2020,B.1.1.316
 Luxembourg/LNS7866283/2020,B.1.1
 Russia/KDA-RII-MH4836S/2020,B.1.1
 Russia/STA-RII-MH3407S/2020,B.1.1
@@ -175787,3 +175775,124 @@ French_Guiana/IPP01936/2021,P.2
 England/ALDP-1195BDE/2021,P.2
 England/OXON-F49822/2021,P.2
 Scotland/EDB14636/2021,P.2
+USA/WI-UW-2750/2021,R.1
+Aruba/AW-RIVM-12814/2021,R.1
+USA/CA-CDC-LC00000823/2020,R.1
+USA/MA-MASPHL-01294/2020,R.1
+USA/TX-DSHS-2348/2021,R.1
+USA/MI-UM-10037814075/2021,R.1
+USA/CA-CDC-LC00001122/2020,R.1
+USA/NJ-CDC-LC00001339/2020,R.1
+USA/NY-NYCPHL-002418/2021,R.1
+USA/CA-UCSF-UC1096/2021,R.1
+USA/WI-UW-2646/2020,R.1
+USA/WI-UW-2664/2020,R.1
+Belgium/rega-1637/2021,R.1
+England/ALDP-1196593/2021,R.1
+Ghana/NMIMR-TRA-182/2021,R.1
+Ghana/WACCBIP-GS149/2021,R.1
+England/MILK-11A5634/2021,R.1
+England/MILK-11A568F/2021,R.1
+England/ALDP-120176F/2021,R.1
+France/PAC-IHU-3302-1/2021,R.1
+Belgium/Jessa_11-2103-004837/2021,R.1
+Belgium/Jessa_11-2103-004725/2021,R.1
+Belgium/Jessa_11-2103-004826/2021,R.1
+Finland/HEL-8-35_S354/2021,R.1
+Canada/ON-PHL-21-00510/2020,R.1
+Canada/ON-PHL-21-00690/2021,R.1
+Canada/ON-PHL-21-00487/2020,R.1
+USA/NY-Wadsworth-21009443-01/2021,R.1
+USA/NY-PRL-2020_1229_00F02/2020,R.1
+USA/NMDOH-2021015923/2021,R.1
+USA/NM-DOH-2021020859/2021,R.1
+USA/NY-NYCPHL-002453/2021,R.1
+USA/NY-PRL-2020_1229_01A01/2020,R.1
+USA/NY-QDX-4256/2021,R.1
+USA/NY-Wadsworth-21008556-01/2021,R.1
+USA/NY-Wadsworth-21008581-01/2021,R.1
+USA/NY-UB-00422/2020,R.1
+USA/NY-Wadsworth-21007975-01/2021,R.1
+USA/NY-UB-00453/2020,R.1
+England/OXON-F58A2A/2021,R.1
+USA/MD-HP01225/2021,R.1
+USA/MD-CDC-LC0003984/2021,R.1
+USA/DE-CDC-STM-A100307/2021,R.1
+USA/MD-HP02259/2021,R.1
+USA/MD-HP02265/2021,R.1
+USA/NY-PRL-2021_0205_00G03/2021,R.1
+USA/NY-PRL-2021_0210_06A10/2021,R.1
+USA/NY-PRL-2021_0203_01H02/2021,R.1
+USA/HI-H210992/2021,R.1
+England/ALDP-B82A0D/2020,R.1
+USA/MD-HP01385/2021,R.1
+USA/MD-HP02146/2021,R.1
+Ghana/WACCBIP-GS118/2021,R.1
+USA/NY-PRL-2021_0125_00H11/2021,R.1
+USA/NY-PRL-2020_1229_01F04/2020,R.1
+Nigeria/CV633/2020,R.1
+USA/MA-MASPHL-01784/2021,R.1
+USA/MA-MASPHL-01782/2021,R.1
+Ghana/NMIMR-TRA-137/2021,R.1
+USA/MD-HP02230/2021,R.1
+USA/OR-OHSU-9225/2021,R.1
+USA/OR-OHSU-9366/2021,R.1
+USA/IA-GMF-46406/2021,R.1
+USA/IA-GMF-47250/2021,R.1
+USA/WI-GMF-47936/2021,R.1
+Ghana/NMIMR-TRA-188/2021,R.1
+Netherlands/NH-RIVM-11236/2021,R.1
+Netherlands/NH-RIVM-12660/2021,R.1
+Netherlands/NH-RIVM-10435/2021,R.1
+Switzerland/GE-33067062/2021,R.1
+Ghana/NMIMR-NTRA-15381/2020,R.1
+Belgium/ULG-11636/2021,R.1
+Belgium/ULG-11632/2021,R.1
+Belgium/ULG-11727/2021,R.1
+Belgium/ULG-11767/2021,R.1
+Belgium/ULG-11927/2021,R.1
+Belgium/ULG-11749/2021,R.1
+Japan/IC-0386/2020,R.1
+USA/MD-HP01030/2020,R.1
+USA/MD-CDC-LC00000458/2020,R.1
+USA/MD-HP12155/2020,R.1
+USA/MD-HP02219/2021,R.1
+Japan/PG-13348/2020,R.1
+Japan/PG-13349/2020,R.1
+United_Arab_Emirates/4275/2020,R.1
+Ghana/WACCBIP-GS78/2021,R.1
+USA/MD-MDH-0664/2021,R.1
+USA/MD-HP02226/2021,R.1
+USA/MD-HP02377/2021,R.1
+USA/MD-HP02387/2021,R.1
+USA/PA-CDC-LC0004419/2021,R.1
+Australia/NSW1502/2021,R.1
+Australia/NSW-R0054/2021,R.1
+USA/MD-HP01154/2021,R.1
+USA/TX-DSHS-2403/2021,R.1
+USA/TX-DSHS-2402/2021,R.1
+USA/NY-NYCPHL-002765/2021,R.2
+USA/RI-Broad_RIDOH-00153/2021,R.2
+USA/RI-Broad_RIDOH-00166/2021,R.2
+USA/MA-Broad_CRSP-00367/2021,R.2
+USA/RI-Broad_RIDOH-00171/2021,R.2
+USA/RI-Broad_RIDOH-00154/2021,R.2
+USA/RI-Broad_RIDOH-00142/2021,R.2
+USA/MA-CDC-STM-000002438/2021,R.2
+Switzerland/ZH-ETHZ-471146/2021,B.1.1.318
+Nigeria/CV648/2021,B.1.1.318
+USA/NY-PRL-2021_0205_00G06/2021,B.1.1.318
+Nigeria/CV702/2021,B.1.1.318
+Nigeria/CV705/2021,B.1.1.318
+Nigeria/CV681/2021,B.1.1.318
+Nigeria/BCVL-18562/2021,B.1.1.318
+Nigeria/BCVL-18757/2021,B.1.1.318
+Nigeria/BCVL-18579/2021,B.1.1.318
+USA/NY-NYCPHL-003028/2021,B.1.1.318
+England/MILK-1150CEB/2021,B.1.1.318
+England/CAMC-1234C82/2021,B.1.1.318
+England/MILK-1169960/2021,B.1.1.318
+England/CAMC-1263130/2021,B.1.1.318
+England/ALDP-1184695/2021,B.1.1.318
+England/ALDP-115DB1E/2021,B.1.1.318
+England/ALDP-114DEBE/2021,B.1.1.318