adding updated strains and clade annotations

nextstrain · Nov 17, 2024 · da8a4f9 · da8a4f9
1 parent f4a55e8
commit da8a4f9
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Showing 8 changed files with 2,231 additions and 5 deletions.
diff --git a/clade-labeling/h5n1-clades.tsv b/clade-labeling/h5n1-clades.tsv
diff --git a/clade-labeling/h5nx-clades.tsv b/clade-labeling/h5nx-clades.tsv
diff --git a/config/h5n1/dropped_strains_h5n1.txt b/config/h5n1/dropped_strains_h5n1.txt
@@ -14,6 +14,9 @@ A/chicken/Poland/003/2020
 A/chicken/Scotland/128320/2023
 A/Tuftedduck/Netherlands/1/2023
 A/teal/Nuble/2335162/2023
+A/pheasant/England/121396/2023
+A/DomesticDuck/England/137313/2023
+
 
 
 # Duplicated entries in GISAID

diff --git a/config/h5n1/include_strains_h5n1_2y.txt b/config/h5n1/include_strains_h5n1_2y.txt
@@ -14,7 +14,29 @@ A/domesticcat/Poland/H252/2023
 A/domesticcat/Poland/H249/2023
 A/domesticcat/Poland/H253/2023
 A/domesticcat/Poland/H248/2023
-A/domesticcat/Poland/H247/2023
+A/domesticcat/Poland/H247/2023
+A/Washington/240/2024
+A/Washington/239/2024
+A/Washington/247/2024
+A/California/150/2024
+A/CacklingGoose/BritishColumbia/AIVPHL2533/2024
+A/CacklingGoose/BritishColumbia/AIVPHL2534/2024
+A/CacklingGoose/BritishColumbia/AIVPHL2535/2024
+A/CacklingGoose/BritishColumbia/AIVPHL2540/2024
+A/CacklingGoose/BritishColumbia/AIVPHL2541/2024
+A/SnowGoose/BritishColumbia/AIVPHL2538/2024
+A/CanadaGoose/BritishColumbia/AIVPHL2531/2024
+A/CanadaGoose/BritishColumbia/AIVPHL2530/2024
+A/CanadaGoose/BritishColumbia/AIVPHL2528/2024
+A/GreenWingedTeal/BritishColumbia/AIVPHL2526/2024
+A/CanadaGoose/BritishColumbia/AIVPHL2524/2024
+A/RedTailedHawk/BritishColumbia/AIVPHL2513/2024
+A/British_Columbia/PHL-2032/2024
+A/Chicken/BC/FAV-0285-1/2024
+A/Chicken/BC/FAV-0268-1/2024
+A/Chicken/BC/FAV-0266-1/2024
+A/Turkey/BC/FAV-0267-1/2024
+
 
 # US dairy cattle outbreak
 # Cattle sequences
@@ -303,7 +325,6 @@ A/pigeon/Texas/24008765001/2024
 A/raccoon/NewMexico/24009496002/2024
 A/skunk/Montana/24007939001/2024
 A/skunk/NewMexico/24006483001/2024
-A/skunk/Utah/24008032004/2024
 A/skunk/Washington/24005959001/2024
 A/skunk/Washington/24005959002/2024
 A/skunk/Washington/24005959003/2024

diff --git a/config/h5n1/include_strains_h5n1_all-time.txt b/config/h5n1/include_strains_h5n1_all-time.txt
@@ -37,4 +37,25 @@ A/feline/USA/24008764002original/2024
 A/feline/USA/23037332001original/2023
 A/feline/USA/24008850002original/2024
 A/feline/USA/24009311004original/2024
-A/Missouri/121/2024
+A/Missouri/121/2024
+A/Washington/240/2024
+A/Washington/239/2024
+A/Washington/247/2024
+A/California/150/2024
+A/CacklingGoose/BritishColumbia/AIVPHL2533/2024
+A/CacklingGoose/BritishColumbia/AIVPHL2534/2024
+A/CacklingGoose/BritishColumbia/AIVPHL2535/2024
+A/CacklingGoose/BritishColumbia/AIVPHL2540/2024
+A/CacklingGoose/BritishColumbia/AIVPHL2541/2024
+A/SnowGoose/BritishColumbia/AIVPHL2538/2024
+A/CanadaGoose/BritishColumbia/AIVPHL2531/2024
+A/CanadaGoose/BritishColumbia/AIVPHL2530/2024
+A/CanadaGoose/BritishColumbia/AIVPHL2528/2024
+A/GreenWingedTeal/BritishColumbia/AIVPHL2526/2024
+A/CanadaGoose/BritishColumbia/AIVPHL2524/2024
+A/RedTailedHawk/BritishColumbia/AIVPHL2513/2024
+A/British_Columbia/PHL-2032/2024
+A/Chicken/BC/FAV-0285-1/2024
+A/Chicken/BC/FAV-0268-1/2024
+A/Chicken/BC/FAV-0266-1/2024
+A/Turkey/BC/FAV-0267-1/2024
diff --git a/config/h5nx/dropped_strains_h5nx.txt b/config/h5nx/dropped_strains_h5nx.txt
@@ -29,6 +29,8 @@ A/chicken/Poland/003/2020
 A/chicken/Scotland/128320/2023
 A/Tuftedduck/Netherlands/1/2023
 A/teal/Nuble/2335162/2023
+A/pheasant/England/121396/2023
+A/DomesticDuck/England/137313/2023
 
 
 # Duplicated entries in GISAID

diff --git a/config/h5nx/include_strains_h5nx_2y.txt b/config/h5nx/include_strains_h5nx_2y.txt
@@ -16,6 +16,28 @@ A/domesticcat/Poland/H253/2023
 A/domesticcat/Poland/H248/2023
 A/domesticcat/Poland/H247/2023
 A/StateofMexico/INERINF645/2024
+A/Washington/240/2024
+A/Washington/239/2024
+A/Washington/247/2024
+A/CacklingGoose/BritishColumbia/AIVPHL2533/2024
+A/CacklingGoose/BritishColumbia/AIVPHL2534/2024
+A/CacklingGoose/BritishColumbia/AIVPHL2535/2024
+A/CacklingGoose/BritishColumbia/AIVPHL2540/2024
+A/CacklingGoose/BritishColumbia/AIVPHL2541/2024
+A/California/150/2024
+A/SnowGoose/BritishColumbia/AIVPHL2538/2024
+A/CanadaGoose/BritishColumbia/AIVPHL2531/2024
+A/CanadaGoose/BritishColumbia/AIVPHL2530/2024
+A/CanadaGoose/BritishColumbia/AIVPHL2528/2024
+A/GreenWingedTeal/BritishColumbia/AIVPHL2526/2024
+A/CanadaGoose/BritishColumbia/AIVPHL2524/2024
+A/RedTailedHawk/BritishColumbia/AIVPHL2513/2024
+A/British_Columbia/PHL-2032/2024
+A/Chicken/BC/FAV-0285-1/2024
+A/Chicken/BC/FAV-0268-1/2024
+A/Chicken/BC/FAV-0266-1/2024
+A/Turkey/BC/FAV-0267-1/2024
+
 
 # US dairy cattle outbreak
 # Cattle sequences
@@ -304,7 +326,6 @@ A/pigeon/Texas/24008765001/2024
 A/raccoon/NewMexico/24009496002/2024
 A/skunk/Montana/24007939001/2024
 A/skunk/NewMexico/24006483001/2024
-A/skunk/Utah/24008032004/2024
 A/skunk/Washington/24005959001/2024
 A/skunk/Washington/24005959002/2024
 A/skunk/Washington/24005959003/2024

diff --git a/config/h5nx/include_strains_h5nx_all-time.txt b/config/h5nx/include_strains_h5nx_all-time.txt
@@ -27,4 +27,26 @@ A/goat/Minnesota/24007234009original/2024
 A/goat/Minnesota/24007234003original/2024
 A/Texas/37/2024
 A/StateofMexico/INERINF645/2024
-A/Missouri/121/2024
+A/Missouri/121/2024
+A/Washington/240/2024
+A/Washington/239/2024
+A/Washington/247/2024
+A/California/150/2024
+A/CacklingGoose/BritishColumbia/AIVPHL2533/2024
+A/CacklingGoose/BritishColumbia/AIVPHL2534/2024
+A/CacklingGoose/BritishColumbia/AIVPHL2535/2024
+A/CacklingGoose/BritishColumbia/AIVPHL2540/2024
+A/CacklingGoose/BritishColumbia/AIVPHL2541/2024
+A/SnowGoose/BritishColumbia/AIVPHL2538/2024
+A/CanadaGoose/BritishColumbia/AIVPHL2531/2024
+A/CanadaGoose/BritishColumbia/AIVPHL2530/2024
+A/CanadaGoose/BritishColumbia/AIVPHL2528/2024
+A/GreenWingedTeal/BritishColumbia/AIVPHL2526/2024
+A/CanadaGoose/BritishColumbia/AIVPHL2524/2024
+A/RedTailedHawk/BritishColumbia/AIVPHL2513/2024
+A/British_Columbia/PHL-2032/2024
+A/Chicken/BC/FAV-0285-1/2024
+A/Chicken/BC/FAV-0268-1/2024
+A/Chicken/BC/FAV-0266-1/2024
+A/Turkey/BC/FAV-0267-1/2024
+