diff --git a/data/nextstrain/flu/h1n1pdm/ha/CY121680/CHANGELOG.md b/data/nextstrain/flu/h1n1pdm/ha/CY121680/CHANGELOG.md
index 076306db..89db5f98 100644
--- a/data/nextstrain/flu/h1n1pdm/ha/CY121680/CHANGELOG.md
+++ b/data/nextstrain/flu/h1n1pdm/ha/CY121680/CHANGELOG.md
@@ -1,8 +1,13 @@
+## Unreleased
+
+This release adds the subclade D.5 as specified in the (influenza-clade-nomenclature repository)[https://github.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/blob/main/CHANGELOG.md#2024-11-12].
+
 ## 2024-11-05T09:19:52Z
 
  - update reference trees
  - include subclade proposals
 
+
 ## 2024-07-03T08:29:55Z
 
  - add representative samples from early pandemic-era clades including 1, 2, 3, 4, 6C, 7, and 8 to improve clade label annotations for older sequences
diff --git a/data/nextstrain/flu/h1n1pdm/ha/CY121680/tree.json b/data/nextstrain/flu/h1n1pdm/ha/CY121680/tree.json
index 71066a2c..25dbd8ae 100644
--- a/data/nextstrain/flu/h1n1pdm/ha/CY121680/tree.json
+++ b/data/nextstrain/flu/h1n1pdm/ha/CY121680/tree.json
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/data/nextstrain/flu/h1n1pdm/ha/MW626062/CHANGELOG.md b/data/nextstrain/flu/h1n1pdm/ha/MW626062/CHANGELOG.md
index ef741a1b..da7157e2 100644
--- a/data/nextstrain/flu/h1n1pdm/ha/MW626062/CHANGELOG.md
+++ b/data/nextstrain/flu/h1n1pdm/ha/MW626062/CHANGELOG.md
@@ -1,9 +1,14 @@
+## Unreleased
+
+This release adds the subclade D.5 as specified in the (influenza-clade-nomenclature repository)[https://github.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/blob/main/CHANGELOG.md#2024-11-12].
+
 ## 2024-11-05T09:19:52Z
 
  - update reference trees
  - include subclade proposals
 
-## 2024-07-03T08:29:55Z
+
+ ## 2024-07-03T08:29:55Z
 
 Added configuration of current and recent vaccine strains as 'reference nodes' on the reference tree, against which query sequences can be compared. This feature is in addition to the new 'compare to clade founder' feature, allowing to compare each query sequence to the most ancestral node of a clade or lineage.
 
diff --git a/data/nextstrain/flu/h1n1pdm/ha/MW626062/tree.json b/data/nextstrain/flu/h1n1pdm/ha/MW626062/tree.json
index b416e21f..48a52ecd 100644
--- a/data/nextstrain/flu/h1n1pdm/ha/MW626062/tree.json
+++ b/data/nextstrain/flu/h1n1pdm/ha/MW626062/tree.json
@@ -1 +1 @@
-{"version": "v2", "meta": {"title": "Nextclade reference tree for Influenza type:h1n1pdm segment:ha with root MW626062 built on 2024-11-03", "updated": "2024-11-03", "build_url": "https://github.com/nextstrain/seasonal-flu", "data_provenance": [{"name": "GISAID"}], "maintainers": [{"name": "Nextstrain team", "url": "https://nextstrain.org"}], "display_defaults": {"color_by": "subclade", "distance_measure": "div", "branch_label": "subclade"}, "genome_annotations": {"HA1": {"end": 1052, "seqid": "dataset_config/h1n1pdm/ha/MW626062/annotation.gff", "start": 72, "strand": "+", "type": "gene"}, "HA2": {"end": 1718, "seqid": "dataset_config/h1n1pdm/ha/MW626062/annotation.gff", "start": 1053, "strand": "+", "type": "gene"}, "SigPep": {"end": 71, "seqid": "dataset_config/h1n1pdm/ha/MW626062/annotation.gff", "start": 21, "strand": "+", "type": "gene"}, "nuc": {"end": 1752, "start": 1, "strand": "+", "type": "source"}}, "colorings": [{"key": "clade_membership", "title": "Clade", "type": "categorical"}, {"key": "gt", "title": "Genotype", "type": "categorical"}, {"key": "subclade", "title": "Subclade", "type": "categorical"}, {"key": "proposedSubclade", "title": "Subclade proposals", "type": "categorical"}, {"key": "short-clade", "title": "short-clade", "type": "categorical"}, {"key": "strain", "title": "strain", "type": "categorical"}, {"key": "region", "title": "Region", "type": "categorical", "scale": [["China", "#4042C7"], ["Southeast Asia", "#4274CE"], ["South Asia", "#5199B7"], ["Japan Korea", "#69B091"], ["Oceania", "#88BB6C"], ["West Asia", "#ADBD51"], ["Africa", "#CEB541"], ["Europe", "#E39B39"], ["South America", "#E56C2F"], ["North America", "#DC2F24"]]}, {"key": "country", "title": "Country", "type": "categorical"}, {"key": "date", "title": "Sample Date", "type": "ordinal"}, {"key": "gisaid_epi_isl", "title": "gisaid_epi_isl", "type": "categorical"}, {"key": "accession_ha", "title": "accession_ha", "type": "categorical"}], "filters": ["region", "country", "clade_membership", "subclade"], "panels": ["tree", "entropy"], "extensions": {"nextclade": {"clade_node_attrs": [{"name": "short-clade", "displayName": "short-clade", "description": ""}, {"name": "subclade", "displayName": "Subclade", "description": "Experimental fine-grained subclade annotation."}, {"name": "proposedSubclade", "displayName": "Proposed subclade", "description": "Includes proposals of new subclades. These can change anytime.", "hideInWeb": true}]}}}, "tree": {"name": "NODE_0000656", "node_attrs": {"div": 0, "subclade": {"value": "unassigned"}, "proposedSubclade": {"value": "unassigned"}, "short-clade": {"value": "unassigned"}, "clade_membership": {"value": "2"}}, "branch_attrs": {"mutations": {"nuc": ["A42C", "G47A", "A57G", "G119A", "C161T", "A162G", "T164C", "G170A", "A188G", "A293C", "A322G", "A360G", "A416G", "T443C", "G456A", "T461A", "C485T", "C512T", "G515A", "G524A", "A539T", "A552C", "C558A", "A561T", "G599A", "C618T", "T625G", "G627A", "C701T", "C718T", "A776G", "T809A", "C820T", "A837G", "G849A", "G885A", "G918A", "T923G", "G954A", "G974A", "A977G", "G986A", "C1061T", "T1073C", "C1076T", "C1082T", "G1100A", "T1163C", "A1178G", "T1190C", "A1191G", "T1250A", "T1271G", "C1290T", "G1301A", "C1356T", "C1364T", "T1382C", "G1406A", "A1415G", "A1423G", "C1487T", "A1493G", "G1511A", "A1566G", "A1577G", "C1589A", "C1601T", "T1631C", "C1673T", "T1738G"], "HA1": ["N31D", "R74S", 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"short-clade": {"value": "5a.2a"}, "date": {"value": "2024-02-13"}, "region": {"value": "Europe"}}, "branch_attrs": {"mutations": {"nuc": ["A864G"], "HA1": ["I265V"]}, "labels": {"aa": "HA1: I265V"}}}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}}
\ No newline at end of file
diff --git a/data/nextstrain/flu/h3n2/ha/CY163680/CHANGELOG.md b/data/nextstrain/flu/h3n2/ha/CY163680/CHANGELOG.md
index d31d4875..89969ecd 100644
--- a/data/nextstrain/flu/h3n2/ha/CY163680/CHANGELOG.md
+++ b/data/nextstrain/flu/h3n2/ha/CY163680/CHANGELOG.md
@@ -1,5 +1,7 @@
-## 2024-11-05T09:19:52Z
+## Unreleased
+This release adds the subclades J.1.1, J.2.1, and J.2.2 as specified in the (influenza-clade-nomenclature repository)[https://github.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/blob/main/CHANGELOG.md#2024-11-12].
 
+## 2024-11-05T09:19:52Z
  - update reference trees
  - include subclade proposals
 
diff --git a/data/nextstrain/flu/h3n2/ha/CY163680/tree.json b/data/nextstrain/flu/h3n2/ha/CY163680/tree.json
index 2ccba6a8..cd5f27c4 100644
--- a/data/nextstrain/flu/h3n2/ha/CY163680/tree.json
+++ b/data/nextstrain/flu/h3n2/ha/CY163680/tree.json
@@ -1 +1 @@
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"EPI_ISL_18846030"}, "clade_membership": {"value": "3C.2a1b.2a.2a.3a.1"}, "short-clade": {"value": "2a.3a.1"}, "date": {"value": "2023-12-22"}, "subclade": {"value": "J.2"}, "region": {"value": "West Asia"}}, "branch_attrs": {"mutations": {"nuc": ["G688A", "A1170G"], "HA1": ["R208K"], "HA2": ["S40G"]}, "labels": {"aa": "HA1: R208K; HA2: S40G"}}}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}}
\ No newline at end of file
diff --git a/data/nextstrain/flu/h3n2/ha/EPI1857216/CHANGELOG.md b/data/nextstrain/flu/h3n2/ha/EPI1857216/CHANGELOG.md
index 25d41ee8..4afc72cb 100644
--- a/data/nextstrain/flu/h3n2/ha/EPI1857216/CHANGELOG.md
+++ b/data/nextstrain/flu/h3n2/ha/EPI1857216/CHANGELOG.md
@@ -1,8 +1,11 @@
-## 2024-11-05T09:19:52Z
+## Unreleased
+This release adds the subclades J.1.1, J.2.1, and J.2.2 as specified in the (influenza-clade-nomenclature repository)[https://github.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/blob/main/CHANGELOG.md#2024-11-12].
 
+## 2024-11-05T09:19:52Z
  - update reference trees
  - include subclade proposals
 
+
 ## 2024-08-08T05:08:21Z
 
 Fix numbering of RBD sites it the `pathogen.json`. The relevant positions were indexed 1-based, when they should have been indexed 0-based.
diff --git a/data/nextstrain/flu/h3n2/ha/EPI1857216/tree.json b/data/nextstrain/flu/h3n2/ha/EPI1857216/tree.json
index 7658bf51..a8a1e540 100644
--- a/data/nextstrain/flu/h3n2/ha/EPI1857216/tree.json
+++ b/data/nextstrain/flu/h3n2/ha/EPI1857216/tree.json
@@ -1 +1 @@
-{"version": "v2", "meta": {"title": "Nextclade reference tree for Influenza type:h3n2 segment:ha with root EPI1857216 built on 2024-11-03", "updated": "2024-11-03", "build_url": "https://github.com/nextstrain/seasonal-flu", "data_provenance": [{"name": "GISAID"}], "maintainers": [{"name": "Nextstrain team", "url": "https://nextstrain.org"}], "display_defaults": {"color_by": "subclade", "distance_measure": "div", "branch_label": "subclade"}, "genome_annotations": {"HA1": {"end": 1035, "seqid": "dataset_config/h3n2/ha/EPI1857216/annotation.gff", "start": 49, "strand": "+", "type": "gene"}, "HA2": {"end": 1698, "seqid": "dataset_config/h3n2/ha/EPI1857216/annotation.gff", "start": 1036, "strand": "+", "type": "gene"}, "SigPep": {"end": 48, "seqid": "dataset_config/h3n2/ha/EPI1857216/annotation.gff", "start": 1, "strand": "+", "type": "gene"}, "nuc": {"end": 1718, "start": 1, "strand": "+", "type": "source"}}, "colorings": [{"key": "clade_membership", "title": "Clade", "type": "categorical"}, {"key": "gt", "title": "Genotype", "type": "categorical"}, {"key": "subclade", "title": "Subclade", "type": "categorical"}, {"key": "proposedSubclade", "title": "Subclade proposals", "type": "categorical"}, {"key": "short-clade", "title": "short-clade", "type": "categorical"}, {"key": "strain", "title": "strain", "type": "categorical"}, {"key": "region", "title": "Region", "type": "categorical", "scale": [["China", "#4042C7"], ["Southeast Asia", "#4274CE"], ["South Asia", "#5199B7"], ["Japan Korea", "#69B091"], ["Oceania", "#88BB6C"], ["West Asia", "#ADBD51"], ["Africa", "#CEB541"], ["Europe", "#E39B39"], ["South America", "#E56C2F"], ["North America", "#DC2F24"]]}, {"key": "country", "title": "Country", "type": "categorical"}, {"key": "date", "title": "Sample Date", "type": "ordinal"}, {"key": "gisaid_epi_isl", "title": "gisaid_epi_isl", "type": "categorical"}, {"key": "accession_ha", "title": "accession_ha", "type": "categorical"}], "filters": ["region", "country", "clade_membership", "subclade"], "panels": ["tree", "entropy"], "extensions": {"nextclade": {"clade_node_attrs": [{"name": "subclade", "displayName": "Subclade", "description": "Experimental fine-grained subclade annotation."}, {"name": "short-clade", "displayName": "short-clade", "description": ""}, {"name": "proposedSubclade", "displayName": "Proposed subclade", "description": "Includes proposals of new subclades. These can change anytime.", "hideInWeb": true}]}}}, "tree": {"name": "NODE_0000837", "node_attrs": {"div": 0, "subclade": {"value": "unassigned"}, "clade_membership": {"value": "unassigned"}, "proposedSubclade": {"value": "unassigned"}, "short-clade": {"value": "unassigned"}}, "branch_attrs": {"mutations": {"nuc": ["A25T", "T39G", "A55C", "A57T", "T60C", "A70G", "T72C", "A138G", "G146A", "T172C", "A182G", "A186C", "T191C", "A197G", "G206A", "G233A", "G234A", "G264A", "C279T", "T285C", "G295A", "A316C", "A318C", "G323A", "A328T", "A411C", "A412G", "A440C", "A441T", "C447T", "T456C", "G460T", "G462T", "T467A", "G472A", "G479A", "G482A", "T483C", "T489C", "A501G", "A514C", "G515A", "C522A", "A523T", "A524T", "T527A", "T531C", "C538T", "A539T", "G561T", "C565A", "A605T", "G615T", "A616G", "C626T", "T632A", "T640G", "A660C", "G682A", "A693G", "G721A", "T729C", "T879C", "G882T", "G927A", "C930T", "C954T", "G983A", "C987T", "A1005G", "C1032T", "A1053C", "A1074T", "G1130T", "G1171A", "C1195A", "A1197G", "A1206G", "A1260G", "G1264A", "A1269G", "T1275C", "G1356A", "C1362T", "A1397G", "A1437C", "A1491C", "A1499G", "C1512T", "A1513G", "G1518A", "G1524A", "G1557A", "A1560C", "G1578A", "G1614A", "A1633G", "G1671A", "A1683G"], "HA1": ["I3L", "N8D", "R33Q", "N45S", "I48T", "E50G", "G53D", "G62E", "E83K", "R92K", "N94Y", "K121N", "N122D", "K131T", "A138S", "I140K", "G142R", "S144N", "S145N", "S156H", "N158K", "N159F", "I160K", "Q164L", "K171N", "Q173K", "D186V", "K189N", "N190D", "S193F", "F195Y", "S198A", "A212T", "D225N", "K278N", "S312N"], "HA2": ["R32I", "D46N", "V77I", "K121R", "E155G", "N160D", "M193I", "I200V"], "SigPep": ["N9Y"]}, "labels": {"aa": "HA1: I3L, N8D, R33Q, N45S, I48T, E50G, G53D, G62E, E83K, R92K, N94Y, K121N, N122D, K131T, A138S, I140K, G142R, S144N, S145N, S156H, N158K, N159F, I160K, Q164L, K171N, Q173K, D186V, K189N, N190D, S193F, F195Y, S198A, A212T, D225N, K278N, S312N; HA2: R32I, D46N, V77I, K121R, E155G, N160D, M193I, I200V; SigPep: N9Y"}}, "children": [{"name": "A/Wisconsin/67/2005", "node_attrs": {"div": 0.0, "gisaid_epi_isl": {"value": "EPI_ISL_154550"}, "country": {"value": "Usa"}, "accession_ha": {"value": "EPI367110"}, "strain": {"value": "A/Wisconsin/67/2005"}, "subclade": {"value": "unassigned"}, "region": {"value": "North America"}, "clade_membership": {"value": "unassigned"}, "date": {"value": "2005-XX-XX"}, "proposedSubclade": {"value": "unassigned"}, "short-clade": {"value": "unassigned"}}, "branch_attrs": {"mutations": {}}}, {"name": "NODE_0000648", "node_attrs": {"div": 0.00941, "subclade": {"value": "unassigned"}, "clade_membership": {"value": "unassigned"}, "proposedSubclade": {"value": "unassigned"}, "short-clade": {"value": "unassigned"}}, "branch_attrs": {"mutations": {"nuc": ["G70A", "G197A", "G412A", "T447C", "T460G", "A467T", "T605G", "A715G", "T930C", "T954C", "A1171G", "A1254C", "C1275T", "G1397A", "T1512C", "A1557G"], "HA1": ["D8N", "G50E", "D122N", "S138A", "K140I", "V186G", "I223V"], "HA2": ["N46D", 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{"div": 0.084, "strain": {"value": "A/HongKong/VB24163934/2024"}, "date": {"value": "2024-05-21"}, "accession_ha": {"value": "EPI3358179"}, "region": {"value": "China"}, "country": {"value": "Hong Kong"}, "clade_membership": {"value": "3C.2a1b.2a.2a.3a.1"}, "subclade": {"value": "J.2.1"}, "short-clade": {"value": "2a.3a.1"}, "proposedSubclade": {"value": "J.2.1"}, "gisaid_epi_isl": {"value": "EPI_ISL_19185733"}}, "branch_attrs": {"mutations": {"nuc": ["A117G", "C819T", "C950T", "G1087A", "A1176G", "G1356A"], "HA1": ["T301I"], "HA2": ["V18M"]}, "labels": {"aa": "HA1: T301I; HA2: V18M"}}}, {"name": "A/Guizhou-Bijiang/2123/2024", "node_attrs": {"div": 0.0828, "strain": {"value": "A/Guizhou-Bijiang/2123/2024"}, "date": {"value": "2024-03-11"}, "accession_ha": {"value": "EPI3466820"}, "region": {"value": "China"}, "country": {"value": "China"}, "clade_membership": {"value": "3C.2a1b.2a.2a.3a.1"}, "subclade": {"value": "J.2.1"}, "short-clade": {"value": "2a.3a.1"}, "proposedSubclade": {"value": "J.2.1"}, "gisaid_epi_isl": {"value": "EPI_ISL_19291123"}}, "branch_attrs": {"mutations": {"nuc": ["G615A", "T897C", "T911C", "C1593T"], "HA1": ["I288T"]}, "labels": {"aa": "HA1: I288T"}}}, {"name": "A/Guangdong-Yuancheng/1454/2024", "node_attrs": {"div": 0.0828, "strain": {"value": "A/Guangdong-Yuancheng/1454/2024"}, "date": {"value": "2024-07-01"}, "accession_ha": {"value": "EPI3528862"}, "region": {"value": "China"}, "country": {"value": "China"}, "clade_membership": {"value": "3C.2a1b.2a.2a.3a.1"}, "subclade": {"value": "J.2.1"}, "short-clade": {"value": "2a.3a.1"}, "proposedSubclade": {"value": "J.2.1"}, "gisaid_epi_isl": {"value": "EPI_ISL_19373959"}}, "branch_attrs": {"mutations": {"nuc": ["C387A", "C972T", "C1170A", "G1407A"]}}}, {"name": "NODE_0000117", "node_attrs": {"div": 0.081, "clade_membership": {"value": "3C.2a1b.2a.2a.3a.1"}, "subclade": {"value": "J.2.1"}, "short-clade": {"value": "2a.3a.1"}, "proposedSubclade": {"value": "J.2.1"}}, "branch_attrs": {"mutations": {"nuc": ["C77T"], "HA1": ["T10M"]}, "labels": {"aa": "HA1: T10M"}}, "children": [{"name": "A/Shanxi-Taiyuan/161/2024", "node_attrs": {"div": 0.0828, "strain": {"value": "A/Shanxi-Taiyuan/161/2024"}, "date": {"value": "2024-01-03"}, "accession_ha": {"value": "EPI3301760"}, "region": {"value": "China"}, "country": {"value": "China"}, "clade_membership": {"value": "3C.2a1b.2a.2a.3a.1"}, "subclade": {"value": "J.2.1"}, "short-clade": {"value": "2a.3a.1"}, "proposedSubclade": {"value": "J.2.1"}, "gisaid_epi_isl": {"value": "EPI_ISL_19150980"}}, "branch_attrs": {"mutations": {"nuc": ["G84A", "G983A", "C1203T"], "HA1": ["S312N"]}, "labels": {"aa": "HA1: S312N"}}}, {"name": "A/Kaluga/CRIE/472/2024", "node_attrs": {"div": 0.0828, "strain": {"value": "A/Kaluga/CRIE/472/2024"}, "date": {"value": "2024-01-23"}, "accession_ha": {"value": "EPI3006018"}, "region": {"value": "West Asia"}, "country": {"value": "Russia"}, "clade_membership": {"value": "3C.2a1b.2a.2a.3a.1"}, "subclade": {"value": "J.2.1"}, "short-clade": {"value": "2a.3a.1"}, "proposedSubclade": {"value": "J.2.1"}, "gisaid_epi_isl": {"value": "EPI_ISL_18873750"}}, "branch_attrs": {"mutations": {"nuc": ["C316A", "A611G", "C726T"], "HA1": ["D188G"]}, "labels": {"aa": "HA1: D188G"}}}, {"name": "NODE_0000118", "node_attrs": {"div": 0.0816, "clade_membership": {"value": "3C.2a1b.2a.2a.3a.1"}, "subclade": {"value": "J.2.1"}, "short-clade": {"value": "2a.3a.1"}, "proposedSubclade": {"value": "J.2.1"}}, "branch_attrs": {"mutations": {"nuc": ["C244T"]}}, "children": [{"name": "A/Victoria/817/2024", "node_attrs": {"div": 0.0834, "strain": {"value": "A/Victoria/817/2024"}, "date": {"value": "2024-05-31"}, "accession_ha": {"value": "EPI3439682"}, "region": {"value": "Oceania"}, "country": {"value": "Australia"}, "clade_membership": {"value": "3C.2a1b.2a.2a.3a.1"}, "subclade": {"value": "J.2.1"}, "short-clade": {"value": "2a.3a.1"}, "proposedSubclade": {"value": "J.2.1"}, "gisaid_epi_isl": {"value": "EPI_ISL_19267348"}}, "branch_attrs": {"mutations": {"nuc": ["G354A", "G945A", "A1254G"]}}}, {"name": "A/Liaoning-Tiexi/135/2024", "node_attrs": {"div": 0.0816, "strain": {"value": "A/Liaoning-Tiexi/135/2024"}, "date": {"value": "2024-02-06"}, "accession_ha": {"value": "EPI3466424"}, "region": {"value": "China"}, "country": {"value": "China"}, "clade_membership": {"value": "3C.2a1b.2a.2a.3a.1"}, "subclade": {"value": "J.2.1"}, "short-clade": {"value": "2a.3a.1"}, "proposedSubclade": {"value": "J.2.1"}, "gisaid_epi_isl": {"value": "EPI_ISL_19290991"}}, "branch_attrs": {"mutations": {}}}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}}
\ No newline at end of file
diff --git a/data_output/index.json b/data_output/index.json
index c0831cf9..9880cbb3 100644
--- a/data_output/index.json
+++ b/data_output/index.json
@@ -804,7 +804,7 @@
             "clades": 25,
             "customClades": {
               "short-clade": 16,
-              "subclade": 21,
+              "subclade": 22,
               "proposedSubclade": 22
             },
             "qc": [
@@ -818,6 +818,13 @@
             ]
           },
           "versions": [
+            {
+              "tag": "unreleased",
+              "compatibility": {
+                "cli": "3.0.0-alpha.0",
+                "web": "3.0.0-alpha.0"
+              }
+            },
             {
               "updatedAt": "2024-11-05T09:19:52Z",
               "tag": "2024-11-05--09-19-52Z",
@@ -852,8 +859,7 @@
             }
           ],
           "version": {
-            "updatedAt": "2024-11-05T09:19:52Z",
-            "tag": "2024-11-05--09-19-52Z",
+            "tag": "unreleased",
             "compatibility": {
               "cli": "3.0.0-alpha.0",
               "web": "3.0.0-alpha.0"
@@ -909,7 +915,7 @@
             "clades": 25,
             "customClades": {
               "short-clade": 16,
-              "subclade": 21,
+              "subclade": 22,
               "proposedSubclade": 22
             },
             "qc": [
@@ -923,6 +929,13 @@
             ]
           },
           "versions": [
+            {
+              "tag": "unreleased",
+              "compatibility": {
+                "cli": "3.0.0-alpha.0",
+                "web": "3.0.0-alpha.0"
+              }
+            },
             {
               "updatedAt": "2024-11-05T09:19:52Z",
               "tag": "2024-11-05--09-19-52Z",
@@ -957,8 +970,7 @@
             }
           ],
           "version": {
-            "updatedAt": "2024-11-05T09:19:52Z",
-            "tag": "2024-11-05--09-19-52Z",
+            "tag": "unreleased",
             "compatibility": {
               "cli": "3.0.0-alpha.0",
               "web": "3.0.0-alpha.0"
@@ -1113,7 +1125,7 @@
           "capabilities": {
             "clades": 37,
             "customClades": {
-              "subclade": 42,
+              "subclade": 45,
               "short-clade": 37,
               "proposedSubclade": 45
             },
@@ -1128,6 +1140,13 @@
             ]
           },
           "versions": [
+            {
+              "tag": "unreleased",
+              "compatibility": {
+                "cli": "3.0.0-alpha.0",
+                "web": "3.0.0-alpha.0"
+              }
+            },
             {
               "updatedAt": "2024-11-05T09:19:52Z",
               "tag": "2024-11-05--09-19-52Z",
@@ -1170,8 +1189,7 @@
             }
           ],
           "version": {
-            "updatedAt": "2024-11-05T09:19:52Z",
-            "tag": "2024-11-05--09-19-52Z",
+            "tag": "unreleased",
             "compatibility": {
               "cli": "3.0.0-alpha.0",
               "web": "3.0.0-alpha.0"
@@ -1226,7 +1244,7 @@
           "capabilities": {
             "clades": 34,
             "customClades": {
-              "subclade": 39,
+              "subclade": 42,
               "short-clade": 34,
               "proposedSubclade": 42
             },
@@ -1242,6 +1260,13 @@
             ]
           },
           "versions": [
+            {
+              "tag": "unreleased",
+              "compatibility": {
+                "cli": "3.0.0-alpha.0",
+                "web": "3.0.0-alpha.0"
+              }
+            },
             {
               "updatedAt": "2024-11-05T09:19:52Z",
               "tag": "2024-11-05--09-19-52Z",
@@ -1292,8 +1317,7 @@
             }
           ],
           "version": {
-            "updatedAt": "2024-11-05T09:19:52Z",
-            "tag": "2024-11-05--09-19-52Z",
+            "tag": "unreleased",
             "compatibility": {
               "cli": "3.0.0-alpha.0",
               "web": "3.0.0-alpha.0"
diff --git a/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/CHANGELOG.md b/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/CHANGELOG.md
new file mode 100644
index 00000000..89db5f98
--- /dev/null
+++ b/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/CHANGELOG.md
@@ -0,0 +1,31 @@
+## Unreleased
+
+This release adds the subclade D.5 as specified in the (influenza-clade-nomenclature repository)[https://github.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/blob/main/CHANGELOG.md#2024-11-12].
+
+## 2024-11-05T09:19:52Z
+
+ - update reference trees
+ - include subclade proposals
+
+
+## 2024-07-03T08:29:55Z
+
+ - add representative samples from early pandemic-era clades including 1, 2, 3, 4, 6C, 7, and 8 to improve clade label annotations for older sequences
+
+ - added configuration of current and recent vaccine strains as 'reference nodes' on the reference tree, against which query sequences can be compared. This feature is in addition to the new 'compare to clade founder' feature, allowing to compare each query sequence to the most ancestral node of a clade or lineage. See Nextclade documentation for more details about 'relative mutations' functionality.
+
+## 2024-04-19T07:50:39Z
+
+ - aliasing of C.1.1.1 as D
+ - addition of subclades D.1 - D.4: [D.1](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/blob/main/subclades/D.1.yml), [D.2](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/blob/main/subclades/D.2.yml), [D.3](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/blob/main/subclades/D.3.yml), [D.4](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/blob/main/subclades/D.4.yml)
+ - addition of subclades [C.1.8](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/blob/main/subclades/C.1.8.yml) and [C.1.9](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/blob/main/subclades/C.1.9.yml)
+ - addition of subclades [C.1.7.1](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/blob/main/subclades/C.1.7.1.yml) and [C.1.7.2](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/blob/main/subclades/C.1.7.2.yml)
+
+
+## 2024-01-16T20:31:02Z
+
+Initial release for Nextclade v3!
+
+ - addition of subclade [C.1.7](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/blob/main/subclades/C.1.7.yml)
+
+Read more about Nextclade datasets in the documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html
diff --git a/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/README.md b/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/README.md
new file mode 100644
index 00000000..dff32cdf
--- /dev/null
+++ b/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/README.md
@@ -0,0 +1,40 @@
+# Influenza A(H1N1pdm) HA based on reference "A/California/07/2009"
+
+| Key                  | Value                |
+| -------------------- | -------------------- |
+| authors                | [Richard Neher](https://neherlab.org), [Nextstrain](https://nextstrain.org)                         |
+| name                 | Influenza A(H1N1pdm) HA                      |
+| reference            | A/California/07/2009                      |
+| dataset path         | flu/h1n1pdm/ha/CY121680                     |
+| reference accession  | CY121680   |
+| clade definitions  |  [github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/)  |
+
+
+## Scope of this dataset
+This dataset uses an older reference sequence (A/California/07/2009) and recent sequences will differ at a large number of positions from this reference.
+For the analysis of currently circulating viruses, the dataset using A/Wisconsin/588/2019 as reference might be more appropriate.
+
+## Features
+This dataset supports
+
+ * Assignment to clades and subclades based on the nomenclature defined in [github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/)
+ * Identification of glycosilation motifs
+ * Sequence QC
+ * Phylogenetic placement
+
+## Clades of seasonal influenza viruses
+
+The WHO Collaborating centers define "clades" as genetic groups of viruses with signature mutations to facilitate discussion of circulating diversity of the viruses.
+Clade demarcation do not always coincide with significantly different antigenic properties of the viruses.
+Clade names are structured as _Number-Letter_ binomials separated by periods as in `6B.1A.5a.2a.1`. These sometimes get shortened by omission of leading binomials like `5a.2a.1`.
+
+In addition to these clades, "subclades" are defined to break down diversity at higher resolution and allow following the spread of different viral groups.
+These follow a Pango-like nomenclature consisting of a letter followed by a numbers separated by periods as in `C.1.2`.
+The leading letter is an alias of a previous name.
+Details of the nomenclature system can be found at [github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/).
+
+
+
+## What is Nextclade dataset
+
+Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html
diff --git a/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/dataset.zip b/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/dataset.zip
new file mode 100644
index 00000000..3f530b08
Binary files /dev/null and b/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/dataset.zip differ
diff --git a/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/genome_annotation.gff3 b/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/genome_annotation.gff3
new file mode 100644
index 00000000..a3952a1f
--- /dev/null
+++ b/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/genome_annotation.gff3
@@ -0,0 +1,5 @@
+##gff-version 3
+##sequence-region CY121680.1 1 1752
+CY121680.1	feature	gene	21	71	.	+	.	gene_name="SigPep"
+CY121680.1	feature	gene	72	1052	.	+	.	gene_name="HA1"
+CY121680.1	feature	gene	1053	1718	.	+	.	gene_name="HA2"
diff --git a/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/pathogen.json b/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/pathogen.json
new file mode 100644
index 00000000..3063dca1
--- /dev/null
+++ b/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/pathogen.json
@@ -0,0 +1,126 @@
+{
+  "schemaVersion": "3.0.0",
+  "alignmentParams": {
+    "excessBandwidth": 9,
+    "terminalBandwidth": 100,
+    "allowedMismatches": 4,
+    "gapAlignmentSide": "right",
+    "minSeedCover": 0.1
+  },
+  "compatibility": {
+    "cli": "3.0.0-alpha.0",
+    "web": "3.0.0-alpha.0"
+  },
+  "defaultCds": "HA1",
+  "files": {
+    "changelog": "CHANGELOG.md",
+    "examples": "sequences.fasta",
+    "genomeAnnotation": "genome_annotation.gff3",
+    "pathogenJson": "pathogen.json",
+    "readme": "README.md",
+    "reference": "reference.fasta",
+    "treeJson": "tree.json"
+  },
+  "qc": {
+    "privateMutations": {
+      "enabled": true,
+      "typical": 5,
+      "cutoff": 15,
+      "weightLabeledSubstitutions": 2,
+      "weightReversionSubstitutions": 1,
+      "weightUnlabeledSubstitutions": 1
+    },
+    "missingData": {
+      "enabled": false,
+      "missingDataThreshold": 100,
+      "scoreBias": 10
+    },
+    "snpClusters": {
+      "enabled": false,
+      "windowSize": 100,
+      "clusterCutOff": 5,
+      "scoreWeight": 50
+    },
+    "mixedSites": {
+      "enabled": true,
+      "mixedSitesThreshold": 4
+    },
+    "frameShifts": {
+      "enabled": true
+    },
+    "stopCodons": {
+      "enabled": true,
+      "ignoredStopCodons": []
+    }
+  },
+  "cdsOrderPreference": [
+    "HA1",
+    "HA2"
+  ],
+  "maintenance": {
+    "website": [
+      "https://nextstrain.org",
+      "https://clades.nextstrain.org"
+    ],
+    "documentation": [
+      "https://github.com/nextstrain/seasonal-flu"
+    ],
+    "source code": [
+      "https://github.com/nextstrain/seasonal_flu"
+    ],
+    "issues": [
+      "https://github.com/nextstrain/seasonal_flu/issues"
+    ],
+    "organizations": [
+      "Nextstrain"
+    ],
+    "authors": [
+      "Nextstrain team <https://nextstrain.org>"
+    ]
+  },
+  "nucMutLabelMap": {},
+  "nucMutLabelMapReverse": {},
+  "shortcuts": [
+    "flu_h1n1pdm_ha_broad",
+    "nextstrain/flu/h1n1pdm/ha/california-7-2009"
+  ],
+  "aaMotifs": [
+    {
+      "name": "glycosylation",
+      "nameShort": "Glyc.",
+      "nameFriendly": "Glycosylation",
+      "description": "N-linked glycosylation motifs (N-X-S/T with X any amino acid other than P)",
+      "includeCdses": [
+        {
+          "cds": "HA1",
+          "ranges": []
+        },
+        {
+          "cds": "HA2",
+          "ranges": [
+            {
+              "begin": 0,
+              "end": 186
+            }
+          ]
+        }
+      ],
+      "motifs": [
+        "N[^P][ST]"
+      ]
+    }
+  ],
+  "attributes": {
+    "name": "Influenza A H1N1pdm HA",
+    "segment": "ha",
+    "reference accession": "CY121680",
+    "reference name": "A/California/7/2009-egg"
+  },
+  "version": {
+    "tag": "unreleased",
+    "compatibility": {
+      "cli": "3.0.0-alpha.0",
+      "web": "3.0.0-alpha.0"
+    }
+  }
+}
diff --git a/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/reference.fasta b/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/reference.fasta
new file mode 100644
index 00000000..a3b664be
--- /dev/null
+++ b/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/reference.fasta
@@ -0,0 +1,2 @@
+>CY121680.1 Influenza A virus (A/California/07/2009(H1N1)) hemagglutinin (HA) gene, complete cds
+GGAAAACAAAAGCAACAAAAATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACACATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAACAGTAACACACTCTGTTAACCTTCTAGAAGACAAGCATAACGGGAAACTATGCAAACTAAGAGGGGTAGCCCCATTGCATTTGGGTAAATGTAACATTGCTGGCTGGATCCTGGGAAATCCAGAGTGTGAATCACTCTCCACAGCAAGCTCATGGTCCTACATTGTGGAAACACCTAGTTCAGACAATGGAACGTGTTACCCAGGAGATTTCATCGATTATGAGGAGCTAAGAGAGCAATTGAGCTCAGTGTCATCATTTGAAAGGTTTGAGATATTCCCCAAGACAAGTTCATGGCCCAATCATGACTCGAACAAAGGTGTAACGGCAGCATGTCCTCATGCTGGAGCAAAAAGCTTCTACAAAAATTTAATATGGCTAGTTAAAAAAGGAAATTCATACCCAAAGCTCAGCAAATCCTACATTAATGATAAAGGGAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACTAGTGCTGACCAACAAAGTCTCTATCAGAATGCAGATGCATATGTTTTTGTGGGGTCATCAAGATACAGCAAGAAGTTCAAGCCGGAAATAGCAATAAGACCCAAAGTGAGGGATCGAGAAGGGAGAATGAACTATTACTGGACACTAGTAGAGCCGGGAGACAAAATAACATTCGAAGCAACTGGAAATCTAGTGGTACCGAGATATGCATTCGCAATGGAAAGAAATGCTGGATCTGGTATTATCATTTCAGATACACCAGTCCACGATTGCAATACAACTTGTCAAACACCCAAGGGTGCTATAAACACCAGCCTCCCATTTCAGAATATACATCCGATCACAATTGGAAAATGTCCAAAATATGTAAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATATCCCGTCTATTCAATCTAGAGGCCTATTTGGGGCCATTGCCGGTTTCATTGAAGGGGGGTGGACAGGGATGGTAGATGGATGGTACGGTTATCACCATCAAAATGAGCAGGGGTCAGGATATGCAGCCGACCTGAAGAGCACACAGAATGCCATTGACGAGATTACTAACAAAGTAAATTCTGTTATTGAAAAGATGAATACACAGTTCACAGCAGTAGGTAAAGAGTTCAACCACCTGGAAAAAAGAATAGAGAATTTAAATAAAAAAGTTGATGATGGTTTCCTGGACATTTGGACTTACAATGCCGAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTACCACGATTCAAATGTGAAGAACTTATATGAAAAGGTAAGAAGCCAGCTAAAAAACAATGCCAAGGAAATTGGAAACGGCTGCTTTGAATTTTACCACAAATGCGATAACACGTGCATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACAGAGAAGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGTCGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCAGTTTCTGGATGTGCTCTAATGGGTCTCTACAGTGTAGAATATGTATTTAACATTAGGATTTCAGAAGCATGAGAAAAACAC
diff --git a/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/sequences.fasta b/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/sequences.fasta
new file mode 100644
index 00000000..6c731514
--- /dev/null
+++ b/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/sequences.fasta
@@ -0,0 +1,1549 @@
+>A/Connecticut/39/2022
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diff --git a/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/tree.json b/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/tree.json
new file mode 100644
index 00000000..25dbd8ae
--- /dev/null
+++ b/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/tree.json
@@ -0,0 +1 @@
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"short-clade": {"value": "5a.2a"}}, "branch_attrs": {"mutations": {}}}, {"name": "A/EspiritoSanto/8329/2024", "node_attrs": {"div": 0.0616, "gisaid_epi_isl": {"value": "EPI_ISL_19290365"}, "accession_ha": {"value": "EPI3463121"}, "clade_membership": {"value": "6B.1A.5a.2a"}, "subclade": {"value": "C.1.9"}, "region": {"value": "South America"}, "proposedSubclade": {"value": "C.1.9"}, "country": {"value": "Brazil"}, "date": {"value": "2024-05-13"}, "strain": {"value": "A/EspiritoSanto/8329/2024"}, "short-clade": {"value": "5a.2a"}}, "branch_attrs": {"mutations": {"nuc": ["T527C", "A683G", "T923C", "C938T", "A1430G"]}}}]}, {"name": "NODE_0000666", "node_attrs": {"div": 0.0603, "clade_membership": {"value": "6B.1A.5a.2a"}, "subclade": {"value": "C.1.9"}, "proposedSubclade": {"value": "C.1.9"}, "short-clade": {"value": "5a.2a"}}, "branch_attrs": {"mutations": {"nuc": ["T1600C", "T1610C", "T1611C", "T1688C"], "HA2": ["I183T"]}, "labels": {"aa": "HA2: I183T"}}, "children": [{"name": "A/Victoria/349/2024", "node_attrs": {"div": 0.0615, "gisaid_epi_isl": {"value": "EPI_ISL_19194636"}, "accession_ha": {"value": "EPI3364613"}, "clade_membership": {"value": "6B.1A.5a.2a"}, "subclade": {"value": "C.1.9"}, "region": {"value": "Oceania"}, "proposedSubclade": {"value": "C.1.9"}, "country": {"value": "Australia"}, "date": {"value": "2024-04-24"}, "strain": {"value": "A/Victoria/349/2024"}, "short-clade": {"value": "5a.2a"}}, "branch_attrs": {"mutations": {"nuc": ["T866C", "C1364T"]}}}, {"name": "A/Victoria/59/2024", "node_attrs": {"div": 0.0615, "gisaid_epi_isl": {"value": "EPI_ISL_18955339"}, "accession_ha": {"value": "EPI3092573"}, "clade_membership": {"value": "6B.1A.5a.2a"}, "subclade": {"value": "C.1.9"}, "region": {"value": "Oceania"}, "proposedSubclade": {"value": "C.1.9"}, "country": {"value": "Australia"}, "date": {"value": "2024-02-06"}, "strain": {"value": "A/Victoria/59/2024"}, "short-clade": {"value": "5a.2a"}}, "branch_attrs": {"mutations": {"nuc": ["A188G", "A1491G"], "HA2": ["T147A"]}, "labels": {"aa": "HA2: T147A"}}}, {"name": "A/Canberra/158/2024", "node_attrs": {"div": 0.0615, "gisaid_epi_isl": {"value": "EPI_ISL_19234700"}, "accession_ha": {"value": "EPI3415473"}, "clade_membership": {"value": "6B.1A.5a.2a"}, "subclade": {"value": "C.1.9"}, "region": {"value": "Oceania"}, "proposedSubclade": {"value": "C.1.9"}, "country": {"value": "Australia"}, "date": {"value": "2024-05-22"}, "strain": {"value": "A/Canberra/158/2024"}, "short-clade": {"value": "5a.2a"}}, "branch_attrs": {"mutations": {"nuc": ["G1286A", "A1668G"], "HA2": ["I206V"]}, "labels": {"aa": "HA2: I206V"}}}, {"name": "NODE_0000667", "node_attrs": {"div": 0.0609, "clade_membership": {"value": "6B.1A.5a.2a"}, "subclade": {"value": "C.1.9"}, "proposedSubclade": {"value": "C.1.9"}, "short-clade": {"value": "5a.2a"}}, "branch_attrs": {"mutations": {"nuc": ["A1058G"]}}, "children": [{"name": "A/India/883/2024", "node_attrs": {"div": 0.0615, "gisaid_epi_isl": {"value": "EPI_ISL_19355178"}, "accession_ha": {"value": "EPI3518924"}, "clade_membership": {"value": "6B.1A.5a.2a"}, "subclade": {"value": "C.1.9"}, "region": {"value": "South Asia"}, "proposedSubclade": {"value": "C.1.9"}, "country": {"value": "India"}, "date": {"value": "2024-02-06"}, "strain": {"value": "A/India/883/2024"}, "short-clade": {"value": "5a.2a"}}, "branch_attrs": {"mutations": {"nuc": ["A839C"]}}}, {"name": "A/Manitoba/RV03655/2024", "node_attrs": {"div": 0.0643, "gisaid_epi_isl": {"value": "EPI_ISL_19254984"}, "accession_ha": {"value": "EPI3426913"}, "clade_membership": {"value": "6B.1A.5a.2a"}, "subclade": {"value": "C.1.9"}, "region": {"value": "North America"}, "proposedSubclade": {"value": "C.1.9"}, "country": {"value": "Canada"}, "date": {"value": "2024-05-28"}, "strain": {"value": "A/Manitoba/RV03655/2024"}, "short-clade": {"value": "5a.2a"}}, "branch_attrs": {"mutations": {"nuc": ["G515A", "G771A", "G843A", "C1316T", "C1673T", "A1739C"], "HA1": ["V234I", "E258K"]}, "labels": {"aa": "HA1: V234I, E258K"}}}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}}
\ No newline at end of file
diff --git a/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/CHANGELOG.md b/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/CHANGELOG.md
new file mode 100644
index 00000000..da7157e2
--- /dev/null
+++ b/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/CHANGELOG.md
@@ -0,0 +1,33 @@
+## Unreleased
+
+This release adds the subclade D.5 as specified in the (influenza-clade-nomenclature repository)[https://github.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/blob/main/CHANGELOG.md#2024-11-12].
+
+## 2024-11-05T09:19:52Z
+
+ - update reference trees
+ - include subclade proposals
+
+
+ ## 2024-07-03T08:29:55Z
+
+Added configuration of current and recent vaccine strains as 'reference nodes' on the reference tree, against which query sequences can be compared. This feature is in addition to the new 'compare to clade founder' feature, allowing to compare each query sequence to the most ancestral node of a clade or lineage.
+
+The datasets themselves remain unchanged.
+
+See Nextclade documentation for more details about 'relative mutations' functionality.
+
+## 2024-04-19T07:50:39Z
+
+ - aliasing of C.1.1.1 as D
+ - addition of subclades D.1 - D.4: [D.1](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/blob/main/subclades/D.1.yml), [D.2](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/blob/main/subclades/D.2.yml), [D.3](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/blob/main/subclades/D.3.yml), [D.4](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/blob/main/subclades/D.4.yml)
+ - addition of subclades [C.1.8](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/blob/main/subclades/C.1.8.yml) and [C.1.9](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/blob/main/subclades/C.1.9.yml)
+ - addition of subclades [C.1.7.1](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/blob/main/subclades/C.1.7.1.yml) and [C.1.7.2](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/blob/main/subclades/C.1.7.2.yml)
+
+
+## 2024-01-16T20:31:02Z
+
+Initial release for Nextclade v3!
+
+ - addition of subclade [C.1.7](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/blob/main/subclades/C.1.7.yml)
+
+Read more about Nextclade datasets in the documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html
diff --git a/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/README.md b/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/README.md
new file mode 100644
index 00000000..9c589a21
--- /dev/null
+++ b/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/README.md
@@ -0,0 +1,37 @@
+# Influenza A(H1N1pdm) HA based on reference "A/Wisconsin/588/2019"
+
+| Key                  | Value                |
+| -------------------- | -------------------- |
+| authors                | [Richard Neher](https://neherlab.org), [Nextstrain](https://nextstrain.org)                         |
+| name                 | Influenza A(H1N1pdm) HA                      |
+| reference            | A/Wisconsin/588/2019                      |
+| dataset path         | flu/h1n1pdm/ha/MW626062                     |
+| reference accession  | MW626062   |
+| clade definitions  |  [github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/)  |
+
+# Scope of this dataset
+This dataset uses a recent reference sequence (A/Wisconsin/588/2019) and is suitable for the analysis of currently circulating viruses.
+
+
+## Features
+This dataset supports
+
+ * Assignment to clades and subclades based on the nomenclature defined in [github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/)
+ * Identification of glycosilation motifs
+ * Sequence QC
+ * Phylogenetic placement
+
+## Clades of seasonal influenza viruses
+
+The WHO Collaborating centers define "clades" as genetic groups of viruses with signature mutations to facilitate discussion of circulating diversity of the viruses.
+Clade demarcation do not always coincide with significantly different antigenic properties of the viruses.
+Clade names are structured as _Number-Letter_ binomials separated by periods as in `6B.1A.5a.2a.1`. These sometimes get shortened by omission of leading binomials like `5a.2a.1`.
+
+In addition to these clades, "subclades" are defined to break down diversity at higher resolution and allow following the spread of different viral groups.
+These follow a Pango-like nomenclature consisting of a letter followed by a numbers separated by periods as in `C.1.2`.
+The leading letter is an alias of a previous name.
+Details of the nomenclature system can be found at [github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/).
+
+## What is Nextclade dataset
+
+Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html
diff --git a/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/dataset.zip b/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/dataset.zip
new file mode 100644
index 00000000..2808b6bd
Binary files /dev/null and b/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/dataset.zip differ
diff --git a/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/genome_annotation.gff3 b/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/genome_annotation.gff3
new file mode 100644
index 00000000..825fe437
--- /dev/null
+++ b/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/genome_annotation.gff3
@@ -0,0 +1,5 @@
+##gff-version 3
+##sequence-region MW626062.1 1 1752
+MW626062.1	feature	gene	21	71	.	+	.	gene_name="SigPep"
+MW626062.1	feature	gene	72	1052	.	+	.	gene_name="HA1"
+MW626062.1	feature	gene	1053	1718	.	+	.	gene_name="HA2"
diff --git a/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/pathogen.json b/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/pathogen.json
new file mode 100644
index 00000000..b8379077
--- /dev/null
+++ b/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/pathogen.json
@@ -0,0 +1,128 @@
+{
+  "schemaVersion": "3.0.0",
+  "alignmentParams": {
+    "excessBandwidth": 9,
+    "terminalBandwidth": 100,
+    "allowedMismatches": 4,
+    "gapAlignmentSide": "right",
+    "minSeedCover": 0.1
+  },
+  "compatibility": {
+    "cli": "3.0.0-alpha.0",
+    "web": "3.0.0-alpha.0"
+  },
+  "defaultCds": "HA1",
+  "files": {
+    "changelog": "CHANGELOG.md",
+    "examples": "sequences.fasta",
+    "genomeAnnotation": "genome_annotation.gff3",
+    "pathogenJson": "pathogen.json",
+    "readme": "README.md",
+    "reference": "reference.fasta",
+    "treeJson": "tree.json"
+  },
+  "qc": {
+    "privateMutations": {
+      "enabled": true,
+      "typical": 5,
+      "cutoff": 15,
+      "weightLabeledSubstitutions": 2,
+      "weightReversionSubstitutions": 1,
+      "weightUnlabeledSubstitutions": 1
+    },
+    "missingData": {
+      "enabled": false,
+      "missingDataThreshold": 100,
+      "scoreBias": 10
+    },
+    "snpClusters": {
+      "enabled": false,
+      "windowSize": 100,
+      "clusterCutOff": 5,
+      "scoreWeight": 50
+    },
+    "mixedSites": {
+      "enabled": true,
+      "mixedSitesThreshold": 4
+    },
+    "frameShifts": {
+      "enabled": true
+    },
+    "stopCodons": {
+      "enabled": true,
+      "ignoredStopCodons": []
+    }
+  },
+  "cdsOrderPreference": [
+    "HA1",
+    "HA2"
+  ],
+  "maintenance": {
+    "website": [
+      "https://nextstrain.org",
+      "https://clades.nextstrain.org"
+    ],
+    "documentation": [
+      "https://github.com/nextstrain/seasonal-flu"
+    ],
+    "source code": [
+      "https://github.com/nextstrain/seasonal_flu"
+    ],
+    "issues": [
+      "https://github.com/nextstrain/seasonal_flu/issues"
+    ],
+    "organizations": [
+      "Nextstrain"
+    ],
+    "authors": [
+      "Nextstrain team <https://nextstrain.org>"
+    ]
+  },
+  "nucMutLabelMap": {},
+  "nucMutLabelMapReverse": {},
+  "shortcuts": [
+    "flu_h1n1pdm_ha",
+    "nextstrain/flu/h1n1pdm",
+    "nextstrain/flu/h1n1pdm/ha",
+    "nextstrain/flu/h1n1pdm/ha/wisconsin-588-2019"
+  ],
+  "aaMotifs": [
+    {
+      "name": "glycosylation",
+      "nameShort": "Glyc.",
+      "nameFriendly": "Glycosylation",
+      "description": "N-linked glycosylation motifs (N-X-S/T with X any amino acid other than P)",
+      "includeCdses": [
+        {
+          "cds": "HA1",
+          "ranges": []
+        },
+        {
+          "cds": "HA2",
+          "ranges": [
+            {
+              "begin": 0,
+              "end": 186
+            }
+          ]
+        }
+      ],
+      "motifs": [
+        "N[^P][ST]"
+      ]
+    }
+  ],
+  "attributes": {
+    "name": "Influenza A H1N1pdm HA",
+    "segment": "ha",
+    "reference accession": "MW626062",
+    "reference name": "A/Wisconsin/588/2019"
+  },
+  "version": {
+    "tag": "unreleased",
+    "compatibility": {
+      "cli": "3.0.0-alpha.0",
+      "web": "3.0.0-alpha.0"
+    }
+  }
+}
diff --git a/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/reference.fasta b/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/reference.fasta
new file mode 100644
index 00000000..546126e1
--- /dev/null
+++ b/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/reference.fasta
@@ -0,0 +1,27 @@
+>MW626062.1 Influenza A virus (A/Wisconsin/588/2019(H1N1)) segment 4 hemagglutinin (HA) gene, complete cds
+GGAAAACAAAAGCAACAAAAATGAAGGCAATACTAGTAGTTATGCTGTATACATTTACAACCGCAAATGC
+AGACACATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTGGACACAGTACTAGAAAAGAAT
+GTAACAGTAACACACTCTGTCAATCTTCTGGAAGACAAGCATAACGGAAAACTATGCAAACTAAGAGGGG
+TAGCCCCATTGCATTTGGGTAAATGTAACATTGCTGGCTGGATCCTGGGAAATCCAGAGTGTGAATCACT
+CTCCACAGCAAGATCATGGTCCTACATTGTGGAAACATCTAATTCAGACAATGGAACGTGTTACCCAGGA
+GATTTCATCAATTATGAGGAGCTAAGAGAGCAATTGAGCTCAGTGTCATCATTTGAAAGGTTTGAAATAT
+TCCCCAAGACAAGTTCATGGCCTAATCATGACTCGGACAATGGTGTAACGGCAGCATGTCCTCACGCTGG
+AGCAAAAAGCTTCTACAAAAACTTGATATGGCTGGTTAAAAAAGGAAAATCATACCCAAAGATCAACCAA
+ACCTACATTAATGATAAAGGGAAAGAAGTCCTCGTGCTGTGGGGCATTCACCATCCACCTACTATTGCTG
+ACCAACAAAGTCTCTATCAGAATGCAGATGCATATGTTTTTGTGGGGACATCAAGATACAGCAAGAAGTT
+CAAGCCGGAAATAGCAACAAGACCCAAAGTGAGGGATCAAGAAGGGAGAATGAACTATTACTGGACACTA
+GTAGAACCGGGAGACAAAATAACATTCGAAGCAACTGGTAATCTAGTGGCACCGAGATATGCATTCACAA
+TGGAAAGAGATGCTGGATCTGGTATTATCATTTCAGATACACCAGTCCACGATTGCAATACAACTTGTCA
+GACACCCGAGGGTGCTATAAACACCAGCCTCCCATTTCAGAATGTACATCCGATCACAATTGGGAAATGT
+CCAAAGTATGTAAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATGTCCCGTCTATTCAATCTA
+GAGGCCTATTCGGGGCCATTGCTGGCTTCATCGAAGGGGGGTGGACAGGGATGGTAGATGGATGGTACGG
+TTATCACCATCAAAATGAGCAGGGGTCAGGATATGCAGCCGATCTGAAGAGCACACAAAATGCCATTGAT
+AAGATTACTAACAAAGTAAATTCTGTTATTGAAAAGATGAATACACAGTTCACAGCAGTTGGTAAAGAGT
+TCAACCACCTTGAAAAAAGAATAGAGAATCTAAATAAAAAGGTTGATGATGGTTTCCTGGACATTTGGAC
+TTACAATGCCGAACTGTTGGTTCTACTGGAAAACGAAAGAACTTTGGACTATCACGATTCAAATGTGAAG
+AACTTGTATGAAAAAGTAAGAAACCAGTTAAAAAACAATGCCAAGGAAATTGGAAACGGCTGCTTTGAAT
+TTTACCACAAATGCGACAACACATGCATGGAAAGTGTCAAGAATGGGACTTATGACTACCCAAAATACTC
+AGAGGAAGCAAAATTAAACAGAGAAAAAATAGATGGAGTAAAGCTGGACTCAACAAGGATCTACCAGATT
+TTGGCGATCTATTCAACTGTTGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCAGCTTCTGGA
+TGTGCTCTAATGGGTCTCTACAGTGTAGAATATGTATTTAACATTAGGATTTCAGAATCATGAGAAAAAC
+AC
diff --git a/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/sequences.fasta b/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/sequences.fasta
new file mode 100644
index 00000000..2050072c
--- /dev/null
+++ b/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/sequences.fasta
@@ -0,0 +1,1550 @@
+>A/Wisconsin/14/2021
+ggaaaacaaaagcaacaaaaatgaaggcaatactagtagttctgctgtatacatttacaa
+ccgcaaatgcagacacattatgtataggttatcatgcgaacaattcaacagacactgtag
+acacagtactagaaaagaatgtaacagtaacacactctgtcaatcttctggaagacaagc
+ataacggaaaactatgcaaactaagaggggtagccccattgcatttgggtaaatgtaaca
+ttgctggctggatcctgggaaatccagagtgtgaatcactctccacagcaagatcatggt
+cctacattgtggaaacatctaattcagacaatggaacgtgttacccaggagatttcatca
+attatgaggagctaagagagcaattgagttcagtgtcatcatttgaaaagtttgaaatat
+tccccaagacaagttcatggcctaatcatgactcggacaaaggtgtaacggcagcatgtc
+ctcacgctggagcaaaaagcttctacaaaaacttgatatggctggttaaaaaaggaaatt
+catacccaaagctcaaccaaacctacattaatgataaagggaaagaagtcctcgtgctgt
+ggggcattcaccatccacctactattgctgcccaagaaagtctctatcagaatgcagatg
+catatgtttttgtggggacatcaagatacagcaagaagttcaagccggaaatagcaacaa
+gacccaaagtgagggatcaagaagggagaatgaactattactggacactagtagaaccgg
+gagacaaaataacattcgaagcaactggaaatctagtggtaccgagatatgcattcacaa
+tggaaagagatgctggatctggtattatcatttcagatacaccagtccacgattgcaata
+caacttgtcagacacccgagggtgctataaacaccagccttccatttcagaatgtacatc
+cgattacaattgggaaatgtccaaagtatgtaaaaagcacaaagttgagactggccacag
+gattgaggaatgtcccgtctattcaatctagaggcctattcggggccattgctggcttca
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diff --git a/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/tree.json b/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/tree.json
new file mode 100644
index 00000000..48a52ecd
--- /dev/null
+++ b/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/tree.json
@@ -0,0 +1 @@
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"Tunisia"}, "proposedSubclade": {"value": "C.1.9"}, "accession_ha": {"value": "EPI3426474"}, "strain": {"value": "A/Tunisia/3493/2024"}, "clade_membership": {"value": "6B.1A.5a.2a"}, "subclade": {"value": "C.1.9"}, "gisaid_epi_isl": {"value": "EPI_ISL_19252739"}, "short-clade": {"value": "5a.2a"}, "date": {"value": "2024-03-18"}, "region": {"value": "Africa"}}, "branch_attrs": {"mutations": {"nuc": ["T575C", "T626C"]}}}, {"name": "A/Netherlands/10070/2024", "node_attrs": {"div": 0.0576, "country": {"value": "Netherlands"}, "proposedSubclade": {"value": "C.1.9"}, "accession_ha": {"value": "EPI2968891"}, "strain": {"value": "A/Netherlands/10070/2024"}, "clade_membership": {"value": "6B.1A.5a.2a"}, "subclade": {"value": "C.1.9"}, "gisaid_epi_isl": {"value": "EPI_ISL_18842188"}, "short-clade": {"value": "5a.2a"}, "date": {"value": "2024-01-10"}, "region": {"value": "Europe"}}, "branch_attrs": {"mutations": {"nuc": ["A1399G"], "HA2": ["K116R"]}, "labels": {"aa": "HA2: K116R"}}}, {"name": "A/Victoria/100/2024", "node_attrs": {"div": 0.0581, "country": {"value": "Australia"}, "proposedSubclade": {"value": "C.1.9"}, "accession_ha": {"value": "EPI3236159"}, "strain": {"value": "A/Victoria/100/2024"}, "clade_membership": {"value": "6B.1A.5a.2a"}, "subclade": {"value": "C.1.9"}, "gisaid_epi_isl": {"value": "EPI_ISL_19074210"}, "short-clade": {"value": "5a.2a"}, "date": {"value": "2024-02-23"}, "region": {"value": "Oceania"}}, "branch_attrs": {"mutations": {"nuc": ["C836T", "C1160T"]}}}, {"name": "A/Ukraine/2558/2024", "node_attrs": {"div": 0.0576, "country": {"value": "Ukraine"}, "proposedSubclade": {"value": "C.1.9"}, "accession_ha": {"value": "EPI3412822"}, "strain": {"value": "A/Ukraine/2558/2024"}, "clade_membership": {"value": "6B.1A.5a.2a"}, "subclade": {"value": "C.1.9"}, "gisaid_epi_isl": {"value": "EPI_ISL_19229313"}, "short-clade": {"value": "5a.2a"}, "date": {"value": "2024-02-14"}, "region": {"value": "Europe"}}, "branch_attrs": {"mutations": {"nuc": ["A753G"], "HA1": ["N228D"]}, "labels": {"aa": "HA1: N228D"}}}, {"name": "A/Para/5535-IEC/2024", "node_attrs": {"div": 0.0576, "country": {"value": "Brazil"}, "proposedSubclade": {"value": "C.1.9"}, "accession_ha": {"value": "EPI3144854"}, "strain": {"value": "A/Para/5535-IEC/2024"}, "clade_membership": {"value": "6B.1A.5a.2a"}, "subclade": {"value": "C.1.9"}, "gisaid_epi_isl": {"value": "EPI_ISL_19008210"}, "short-clade": {"value": "5a.2a"}, "date": {"value": "2024-02-13"}, "region": {"value": "South America"}}, "branch_attrs": {"mutations": {"nuc": ["A1391G"]}}}, {"name": "A/Luxembourg/LNS5499751/2024", "node_attrs": {"div": 0.0581, "country": {"value": "Luxembourg"}, "proposedSubclade": {"value": "C.1.9"}, "accession_ha": {"value": "EPI3446499"}, "strain": {"value": "A/Luxembourg/LNS5499751/2024"}, "clade_membership": {"value": "6B.1A.5a.2a"}, "subclade": {"value": "C.1.9"}, "gisaid_epi_isl": {"value": "EPI_ISL_19272084"}, "short-clade": {"value": "5a.2a"}, "date": {"value": "2024-02-19"}, "region": {"value": "Europe"}}, "branch_attrs": {"mutations": {"nuc": ["T22A", "T242C"], "SigPep": ["M1K"]}, "labels": {"aa": "SigPep: M1K"}}}, {"name": "A/France/ARA-HCL023193207701/2023", "node_attrs": {"div": 0.0575, "country": {"value": "France"}, "proposedSubclade": {"value": "C.1.9"}, "accession_ha": {"value": "EPI2938182"}, "strain": {"value": "A/France/ARA-HCL023193207701/2023"}, "clade_membership": {"value": "6B.1A.5a.2a"}, "subclade": {"value": "C.1.9"}, "gisaid_epi_isl": {"value": "EPI_ISL_18795120"}, "short-clade": {"value": "5a.2a"}, "date": {"value": "2023-12-07"}, "region": {"value": "Europe"}}, "branch_attrs": {"mutations": {"nuc": ["C1000A"], "HA1": ["T310K"]}, "labels": {"aa": "HA1: T310K"}}}, {"name": "NODE_0000651", "node_attrs": {"div": 0.0576, "proposedSubclade": {"value": "C.1.9"}, "clade_membership": {"value": "6B.1A.5a.2a"}, "subclade": {"value": "C.1.9"}, "short-clade": {"value": "5a.2a"}}, "branch_attrs": {"mutations": {"nuc": ["C500T"]}}, "children": [{"name": "A/Kenya/NIRL24-679/2024", "node_attrs": {"div": 0.0599, "country": {"value": "Kenya"}, "proposedSubclade": {"value": "C.1.9"}, "accession_ha": {"value": "EPI3242952"}, "strain": {"value": "A/Kenya/NIRL24-679/2024"}, "clade_membership": {"value": "6B.1A.5a.2a"}, "subclade": {"value": "C.1.9"}, "gisaid_epi_isl": {"value": "EPI_ISL_19078558"}, "short-clade": {"value": "5a.2a"}, "date": {"value": "2024-02-09"}, "region": {"value": "Africa"}}, "branch_attrs": {"mutations": {"nuc": ["G174A", "G429A", "C904T", "G974A"], "HA1": ["D35N", "A120T", "T278I"]}, "labels": {"aa": "HA1: D35N, A120T, T278I"}}}, {"name": "A/Netherlands/10145/2024", "node_attrs": {"div": 0.0576, "country": {"value": "Netherlands"}, "proposedSubclade": {"value": "C.1.9"}, "accession_ha": {"value": "EPI3008482"}, "strain": {"value": "A/Netherlands/10145/2024"}, "clade_membership": {"value": "6B.1A.5a.2a"}, "subclade": {"value": "C.1.9"}, "gisaid_epi_isl": {"value": "EPI_ISL_18877869"}, "short-clade": {"value": "5a.2a"}, "date": {"value": "2024-01-16"}, "region": {"value": "Europe"}}, "branch_attrs": {"mutations": {}}}]}, {"name": "NODE_0000652", "node_attrs": {"div": 0.057, "proposedSubclade": {"value": "C.1.9"}, "clade_membership": {"value": "6B.1A.5a.2a"}, "subclade": {"value": "C.1.9"}, "short-clade": {"value": "5a.2a"}}, "branch_attrs": {"mutations": {}}, "children": [{"name": "A/Berlin/6/2024", "node_attrs": {"div": 0.057, "country": {"value": "Germany"}, "proposedSubclade": {"value": "C.1.9"}, "accession_ha": {"value": "EPI3195249"}, "strain": {"value": "A/Berlin/6/2024"}, "clade_membership": {"value": "6B.1A.5a.2a"}, "subclade": {"value": "C.1.9"}, "gisaid_epi_isl": {"value": "EPI_ISL_19047010"}, "short-clade": {"value": "5a.2a"}, "date": {"value": "2024-01-11"}, "region": {"value": "Europe"}}, "branch_attrs": {"mutations": {}}}, {"name": "A/Badajoz/18616394/2024", "node_attrs": {"div": 0.057, "country": {"value": "Spain"}, "proposedSubclade": {"value": "C.1.9"}, "accession_ha": {"value": "EPI3050058"}, "strain": {"value": "A/Badajoz/18616394/2024"}, "clade_membership": {"value": "6B.1A.5a.2a"}, "subclade": {"value": "C.1.9"}, "gisaid_epi_isl": {"value": "EPI_ISL_18912985"}, "short-clade": {"value": "5a.2a"}, "date": {"value": "2024-01-10"}, "region": {"value": "Europe"}}, "branch_attrs": {"mutations": {}}}]}, {"name": "NODE_0000653", "node_attrs": {"div": 0.0575, "proposedSubclade": {"value": "C.1.9"}, "clade_membership": {"value": "6B.1A.5a.2a"}, "subclade": {"value": "C.1.9"}, "short-clade": {"value": "5a.2a"}}, "branch_attrs": {"mutations": {"nuc": ["G409A"], "HA1": ["R113K"]}, "labels": {"aa": "HA1: R113K"}}, "children": [{"name": "A/France/ARA-HCL023203677001/2023", "node_attrs": {"div": 0.0575, "country": {"value": "France"}, "proposedSubclade": {"value": "C.1.9"}, "accession_ha": {"value": "EPI2940753"}, "strain": {"value": "A/France/ARA-HCL023203677001/2023"}, "clade_membership": {"value": "6B.1A.5a.2a"}, "subclade": {"value": "C.1.9"}, 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"branch_attrs": {"mutations": {"nuc": ["G1727T"]}}, "children": [{"name": "A/SaoPaulo/357530127-IAL/2024", "node_attrs": {"div": 0.0581, "country": {"value": "Brazil"}, "proposedSubclade": {"value": "C.1.9"}, "accession_ha": {"value": "EPI3265764"}, "strain": {"value": "A/SaoPaulo/357530127-IAL/2024"}, "clade_membership": {"value": "6B.1A.5a.2a"}, "subclade": {"value": "C.1.9"}, "gisaid_epi_isl": {"value": "EPI_ISL_19109212"}, "short-clade": {"value": "5a.2a"}, "date": {"value": "2024-02-27"}, "region": {"value": "South America"}}, "branch_attrs": {"mutations": {"nuc": ["C1529T"]}}}, {"name": "A/Luxembourg/LNS6779666/2024", "node_attrs": {"div": 0.0599, "country": {"value": "Luxembourg"}, "proposedSubclade": {"value": "C.1.9"}, "accession_ha": {"value": "EPI3445969"}, "strain": {"value": "A/Luxembourg/LNS6779666/2024"}, "clade_membership": {"value": "6B.1A.5a.2a"}, "subclade": {"value": "C.1.9"}, "gisaid_epi_isl": {"value": "EPI_ISL_19272016"}, "short-clade": {"value": "5a.2a"}, "date": {"value": "2024-01-31"}, "region": {"value": "Europe"}}, "branch_attrs": {"mutations": {"nuc": ["T22A", "G674A", "C957A", "C1457T"], "HA1": ["H296N"], "SigPep": ["M1K"]}, "labels": {"aa": "HA1: H296N; SigPep: M1K"}}}, {"name": "A/Bahia/293561523/2024", "node_attrs": {"div": 0.0581, "country": {"value": "Brazil"}, "proposedSubclade": {"value": "C.1.9"}, "accession_ha": {"value": "EPI3504783"}, "strain": {"value": "A/Bahia/293561523/2024"}, "clade_membership": {"value": "6B.1A.5a.2a"}, "subclade": {"value": "C.1.9"}, "gisaid_epi_isl": {"value": "EPI_ISL_19333491"}, "short-clade": {"value": "5a.2a"}, "date": {"value": "2024-03-19"}, "region": {"value": "South America"}}, "branch_attrs": {"mutations": {"nuc": ["G1510A"], "HA2": ["R153K"]}, "labels": {"aa": "HA2: R153K"}}}, {"name": "NODE_0000655", "node_attrs": {"div": 0.0581, "proposedSubclade": {"value": "C.1.9"}, "clade_membership": {"value": "6B.1A.5a.2a"}, "subclade": {"value": "C.1.9"}, "short-clade": {"value": "5a.2a"}}, "branch_attrs": {"mutations": {"nuc": ["A775G"], "HA1": ["E235G"]}, "labels": {"aa": "HA1: E235G"}}, "children": [{"name": "A/England/235040286/2023", "node_attrs": {"div": 0.0581, "country": {"value": "United Kingdom"}, "proposedSubclade": {"value": "C.1.9"}, "accession_ha": {"value": "EPI2934626"}, "strain": {"value": "A/England/235040286/2023"}, "clade_membership": {"value": "6B.1A.5a.2a"}, "subclade": {"value": "C.1.9"}, "gisaid_epi_isl": {"value": "EPI_ISL_18794424"}, "short-clade": {"value": "5a.2a"}, "date": {"value": "2023-12-13"}, "region": {"value": "Europe"}}, "branch_attrs": {"mutations": {}}}, {"name": "A/France/ARA-RELAB-HCL024031548001/2024", "node_attrs": {"div": 0.0587, "country": {"value": "France"}, "proposedSubclade": {"value": "C.1.9"}, "accession_ha": {"value": "EPI3151635"}, "strain": {"value": "A/France/ARA-RELAB-HCL024031548001/2024"}, "clade_membership": {"value": "6B.1A.5a.2a"}, "subclade": {"value": "C.1.9"}, "gisaid_epi_isl": {"value": "EPI_ISL_19011300"}, "short-clade": {"value": "5a.2a"}, "date": {"value": "2024-02-13"}, "region": {"value": "Europe"}}, "branch_attrs": {"mutations": {"nuc": ["A864G"], "HA1": ["I265V"]}, "labels": {"aa": "HA1: I265V"}}}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}}
\ No newline at end of file
diff --git a/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/CHANGELOG.md b/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/CHANGELOG.md
new file mode 100644
index 00000000..89969ecd
--- /dev/null
+++ b/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/CHANGELOG.md
@@ -0,0 +1,40 @@
+## Unreleased
+This release adds the subclades J.1.1, J.2.1, and J.2.2 as specified in the (influenza-clade-nomenclature repository)[https://github.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/blob/main/CHANGELOG.md#2024-11-12].
+
+## 2024-11-05T09:19:52Z
+ - update reference trees
+ - include subclade proposals
+
+## 2024-07-03T08:29:55Z
+
+Added configuration of current and recent vaccine strains as 'reference nodes' on the reference tree, against which query sequences can be compared. This feature is in addition to the new 'compare to clade founder' feature, allowing to compare each query sequence to the most ancestral node of a clade or lineage.
+
+The datasets themselves remain unchanged.
+
+See Nextclade documentation for more details about 'relative mutations' functionality.
+
+## 2024-04-19T07:50:39Z
+
+Update of the datasets with more recent data. No new clades were added on this occasion.
+
+## 2024-02-22T16:12:03Z
+
+After discussion with various members of the seasonal influenza virus surveillance community, it was decided that subclade names starting with `H` have the potential to be confused with major influenza hemagglutinin subtypes. These subclades where therefore renamed to start with the alias `J`.
+
+ - `H` --> `J`
+ - `H.1` --> `J.1`
+ - `H.2` --> `J.2`
+ - `H.3` --> `J.3`
+ - `H.4` --> `J.4`
+
+The subclades `H` and `H.*` were revoked, and a comment was added to explain the reason. No subclade definitions were changed.
+
+
+## 2024-01-16T20:31:02Z
+
+Initial release for Nextclade v3!
+
+ - Addition of subclade H.1, H.2, H.3, and H.4
+ - Aliasing of G.1.3.1.1 as subclade H
+
+Read more about Nextclade datasets in the documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html
diff --git a/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/README.md b/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/README.md
new file mode 100644
index 00000000..59c9a903
--- /dev/null
+++ b/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/README.md
@@ -0,0 +1,37 @@
+# Influenza A(H3N2) HA dataset based on reference "A/Wisconsin/67/2005"
+
+| Key                  | Value                |
+| -------------------- | -------------------- |
+| authors                | [Richard Neher](https://neherlab.org), [Nextstrain](https://nextstrain.org)                         |
+| name                 | Influenza A(H3N2) HA                      |
+| reference            | A/Wisconsin/67/2005                      |
+| dataset path         | flu/h3n2/ha/CY163680                     |
+| reference accession  | CY163680   |
+| clade definitions  |  [github.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/](https://github.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/)  |
+
+## Scope of this dataset
+This dataset uses an older reference sequence (A/Wisconsin/67/2005) and recent sequences will differ at a large number of positions from this reference.
+For the analysis of currently circulating viruses, the dataset using A/Darwin/6/2021 as reference might be more appropriate.
+
+## Features
+This dataset supports
+
+ * Assignment to clades and subclades based on the nomenclature defined in [github.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/](https://github.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/)
+ * Identification of glycosilation motifs
+ * Sequence QC
+ * Phylogenetic placement
+
+## Clades of seasonal influenza viruses
+
+The WHO Collaborating centers define "clades" as genetic groups of viruses with signature mutations to facilitate discussion of circulating diversity of the viruses.
+Clade demarcation do not always coincide with significantly different antigenic properties of the viruses.
+Clade names are structured as _Number-Letter_ binomials (with exceptions) separated by periods as in `3C.2a1b.2a.2a.1a`. These sometimes get shortened by omission of leading binomials like `2a.1`.
+
+In addition to these clades, "subclades" are defined to break down diversity at higher resolution and allow following the spread of different viral groups.
+These follow a Pango-like nomenclature consisting of a letter followed by a numbers separated by periods as in `G.1.3.1`.
+The leading letter is an alias of a previous name.
+Details of the nomenclature system can be found at [github.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/](https://github.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/).
+
+## What is Nextclade dataset
+
+Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html
diff --git a/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/dataset.zip b/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/dataset.zip
new file mode 100644
index 00000000..94f59e10
Binary files /dev/null and b/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/dataset.zip differ
diff --git a/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/genome_annotation.gff3 b/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/genome_annotation.gff3
new file mode 100644
index 00000000..579ff7ff
--- /dev/null
+++ b/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/genome_annotation.gff3
@@ -0,0 +1,5 @@
+##gff-version 3
+##sequence-region CY163680.1 1 1737
+CY163680.1	feature	gene	18	65	.	+	.	gene_name="SigPep"
+CY163680.1	feature	gene	66	1052	.	+	.	gene_name="HA1"
+CY163680.1	feature	gene	1053	1715	.	+	.	gene_name="HA2"
diff --git a/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/pathogen.json b/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/pathogen.json
new file mode 100644
index 00000000..a55f3330
--- /dev/null
+++ b/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/pathogen.json
@@ -0,0 +1,126 @@
+{
+  "schemaVersion": "3.0.0",
+  "alignmentParams": {
+    "excessBandwidth": 9,
+    "terminalBandwidth": 100,
+    "allowedMismatches": 4,
+    "gapAlignmentSide": "right",
+    "minSeedCover": 0.1
+  },
+  "compatibility": {
+    "cli": "3.0.0-alpha.0",
+    "web": "3.0.0-alpha.0"
+  },
+  "defaultCds": "HA1",
+  "files": {
+    "changelog": "CHANGELOG.md",
+    "examples": "sequences.fasta",
+    "genomeAnnotation": "genome_annotation.gff3",
+    "pathogenJson": "pathogen.json",
+    "readme": "README.md",
+    "reference": "reference.fasta",
+    "treeJson": "tree.json"
+  },
+  "qc": {
+    "privateMutations": {
+      "enabled": true,
+      "typical": 5,
+      "cutoff": 15,
+      "weightLabeledSubstitutions": 2,
+      "weightReversionSubstitutions": 1,
+      "weightUnlabeledSubstitutions": 1
+    },
+    "missingData": {
+      "enabled": false,
+      "missingDataThreshold": 100,
+      "scoreBias": 10
+    },
+    "snpClusters": {
+      "enabled": false,
+      "windowSize": 100,
+      "clusterCutOff": 5,
+      "scoreWeight": 50
+    },
+    "mixedSites": {
+      "enabled": true,
+      "mixedSitesThreshold": 4
+    },
+    "frameShifts": {
+      "enabled": true
+    },
+    "stopCodons": {
+      "enabled": true,
+      "ignoredStopCodons": []
+    }
+  },
+  "cdsOrderPreference": [
+    "HA1",
+    "HA2"
+  ],
+  "maintenance": {
+    "website": [
+      "https://nextstrain.org",
+      "https://clades.nextstrain.org"
+    ],
+    "documentation": [
+      "https://github.com/nextstrain/seasonal-flu"
+    ],
+    "source code": [
+      "https://github.com/nextstrain/seasonal_flu"
+    ],
+    "issues": [
+      "https://github.com/nextstrain/seasonal_flu/issues"
+    ],
+    "organizations": [
+      "Nextstrain"
+    ],
+    "authors": [
+      "Nextstrain team <https://nextstrain.org>"
+    ]
+  },
+  "nucMutLabelMap": {},
+  "nucMutLabelMapReverse": {},
+  "shortcuts": [
+    "flu_h3n2_ha_broad",
+    "nextstrain/flu/h3n2/ha/wisconsin-67-2005"
+  ],
+  "aaMotifs": [
+    {
+      "name": "glycosylation",
+      "nameShort": "Glyc.",
+      "nameFriendly": "Glycosylation",
+      "description": "N-linked glycosylation motifs (N-X-S/T with X any amino acid other than P)",
+      "includeCdses": [
+        {
+          "cds": "HA1",
+          "ranges": []
+        },
+        {
+          "cds": "HA2",
+          "ranges": [
+            {
+              "begin": 0,
+              "end": 186
+            }
+          ]
+        }
+      ],
+      "motifs": [
+        "N[^P][ST]"
+      ]
+    }
+  ],
+  "attributes": {
+    "name": "Influenza A H3N2 HA",
+    "segment": "ha",
+    "reference accession": "CY163680",
+    "reference name": "A/Wisconsin/67/2005-egg"
+  },
+  "version": {
+    "tag": "unreleased",
+    "compatibility": {
+      "cli": "3.0.0-alpha.0",
+      "web": "3.0.0-alpha.0"
+    }
+  }
+}
diff --git a/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/reference.fasta b/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/reference.fasta
new file mode 100644
index 00000000..a4df05fb
--- /dev/null
+++ b/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/reference.fasta
@@ -0,0 +1,26 @@
+>CY163680.1 Influenza A virus (A/Wisconsin/67/2005(H3N2)) hemagglutinin (HA) gene, complete cds
+GGATAATTCTATTAACCATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAA
+ACTTCCCGGAAATGACAACAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATA
+GTGAAAACAATCACGAATGACCAAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAGTTCCTCAACAG
+GTGGAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGG
+AGACCCTCAGTGTGATGGCTTCCAAAATAAGAAATGGGACCTTTTTGTTGAACGCAGCAAAGCCTACAGC
+AACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGG
+AGTTTAACGATGAAAGCTTCAATTGGACTGGAGTCACTCAAAATGGAACAAGCTCTTCTTGCAAAAGGAG
+ATCTAATAACAGTTTCTTTAGTAGATTGAATTGGTTGACCCACTTAAAATTCAAATACCCAGCATTGAAC
+GTGACTATGCCAAACAATGAAAAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGTTACGGACA
+ATGACCAAATCTTCCTGTATGCTCAAGCATCAGGAAGAATCACAGTCTCTACCAAAAGAAGCCAACAAAC
+TGTAATCCCGAATATCGGATCTAGACCCAGAATAAGGAATATCCCCAGCAGAATAAGCATCTATTGGACA
+ATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCA
+AAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAAATGCAATTCTGAATGCAT
+CACTCCAAATGGAAGCATTCCCAATGACAAACCATTTCAAAATGTAAACAGGATCACATATGGGGCCTGT
+CCCAGATATGTTAAGCAAAACACTCTGAAATTGGCAACAGGGATGCGAAATGTACCAGAGAAACAAACTA
+GAGGCATATTTGGCGCAATCGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGTGGATGGTTGGTACGG
+TTTCAGGCATCAAAATTCTGAGGGAATAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCAAT
+CAAATCAATGGGAAGCTGAATAGGTTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAAT
+TCTCAGAAGTAGAAGGGAGAATTCAGGACCTCGAGAAATATGTTGAGGACACTAAAATAGATCTCTGGTC
+ATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAAC
+AAACTGTTTGAAAGAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAA
+TATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCATGATGTATACAG
+AGATGAAGCATTAAACAACCGGTTCCAGATCAAAGGCGTTGAGCTGAAGTCAGGATACAAAGATTGGATC
+CTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCT
+GCCAAAAAGGCAACATTAGGTGCAACATTTGCATTTGAGTGCATTAATTAAAAACAC
diff --git a/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/sequences.fasta b/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/sequences.fasta
new file mode 100644
index 00000000..07993bc5
--- /dev/null
+++ b/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/sequences.fasta
@@ -0,0 +1,1500 @@
+>A/Iowa/3/2020
+ggataattctattaaccatgaagactatcattgctttgagctacattctatgtctggttt
+tcactcaaaaaattcctggaaatgacaatagcacggcaacgctgtgccttgggcaccatg
+cagtaccaaacggaacgatagtgaaaacaatcacaaatgaccgaattgaagttactaatg
+ctactgagttggttcagaattcctcaataggtaaaatatgcgacagtcctcatcagatcc
+ttgatggagggaactgcacactaatagatgctctattgggggaccctcagtgtgacggct
+ttcaaaataagaaatgggacctttttgttgaacgaagcagagcctacagcaactgttacc
+cttatgatgtgccggattatgcctcccttaggtcactagttgcctcatccggcacactgg
+agtttaaaaatgaaagcttcaattgggctggagtcactcaaaacggaaaaagtttttctt
+gcataaggggatctaatagtagtttctttagtagattaaattggttgacccatttaaact
+acacatatccagcactgaacgtgactatgccaaacaaggaacaatttgacaaattgtaca
+tttggggggttcaccacccgggtacggacaaggaccaaatctccctgtatgctcaatcat
+caggaagaatcacagtatctaccaaaagaagccaacaggctgtaatcccaaatatcggat
+ctagacccagaataagggatatccctagcagaataagcatctattggacaatagtaaaac
+cgggagacatacttttgattaacagcacagggaatctaattgctcctaggggttacttca
+aaatacgaagtgggaaaagctcgataatgagatcagatgcacccattggcaaatgcaagt
+ctgaatgcatcactccaaatggaagcattcccaatgacaaaccattccaaaatgtgaaca
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+cctttgccatatcatgttttttgctttgtgttgctttgttggggttcatcatgtgggcct
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+>A/Washington/3/2024
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+>A/Texas/11/2022
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+>A/Iowa/17/2020
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diff --git a/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/tree.json b/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/tree.json
new file mode 100644
index 00000000..cd5f27c4
--- /dev/null
+++ b/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/tree.json
@@ -0,0 +1 @@
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{"aa": "HA1: E83G"}}}, {"name": "NODE_0000799", "node_attrs": {"div": 0.0779, "proposedSubclade": {"value": "J.2"}, "clade_membership": {"value": "3C.2a1b.2a.2a.3a.1"}, "short-clade": {"value": "2a.3a.1"}, "subclade": {"value": "J.2"}}, "branch_attrs": {"mutations": {"nuc": ["G496A", "A893C", "A963G", "T1442C"], "HA1": ["S144N", "E276D", "I300V"]}, "labels": {"aa": "HA1: S144N, E276D, I300V"}}, "children": [{"name": "A/Irkutsk/RII-MH169085S/2024", "node_attrs": {"div": 0.0779, "accession_ha": {"value": "EPI3221388"}, "country": {"value": "Russia"}, "strain": {"value": "A/Irkutsk/RII-MH169085S/2024"}, "proposedSubclade": {"value": "J.2"}, "gisaid_epi_isl": {"value": "EPI_ISL_19061041"}, "clade_membership": {"value": "3C.2a1b.2a.2a.3a.1"}, "short-clade": {"value": "2a.3a.1"}, "date": {"value": "2024-01-18"}, "subclade": {"value": "J.2"}, "region": {"value": "West Asia"}}, "branch_attrs": {"mutations": {}}}, {"name": "A/Irkutsk/RII-MH169086S/2024", "node_attrs": {"div": 0.0785, "accession_ha": {"value": "EPI3221396"}, "country": {"value": "Russia"}, "strain": {"value": "A/Irkutsk/RII-MH169086S/2024"}, "proposedSubclade": {"value": "J.2"}, "gisaid_epi_isl": {"value": "EPI_ISL_19061042"}, "clade_membership": {"value": "3C.2a1b.2a.2a.3a.1"}, "short-clade": {"value": "2a.3a.1"}, "date": {"value": "2024-01-22"}, "subclade": {"value": "J.2"}, "region": {"value": "West Asia"}}, "branch_attrs": {"mutations": {"nuc": ["A564G"], "HA1": ["T167A"]}, "labels": {"aa": "HA1: T167A"}}}]}, {"name": "NODE_0000800", "node_attrs": {"div": 0.0762, "proposedSubclade": {"value": "J.2"}, "clade_membership": {"value": "3C.2a1b.2a.2a.3a.1"}, "short-clade": {"value": "2a.3a.1"}, "subclade": {"value": "J.2"}}, "branch_attrs": {"mutations": {"nuc": ["T1656C"]}}, "children": [{"name": "A/Cheboksary/CRIE/146/2023", "node_attrs": {"div": 0.0762, "accession_ha": {"value": "EPI2816729"}, "country": {"value": "Russia"}, "strain": {"value": "A/Cheboksary/CRIE/146/2023"}, "proposedSubclade": {"value": "J.2"}, "gisaid_epi_isl": {"value": "EPI_ISL_18598566"}, "clade_membership": {"value": "3C.2a1b.2a.2a.3a.1"}, "short-clade": {"value": "2a.3a.1"}, "date": {"value": "2023-11-24"}, "subclade": {"value": "J.2"}, "region": {"value": "West Asia"}}, "branch_attrs": {"mutations": {}}}, {"name": "A/StPetersburg/RII-313/2023", "node_attrs": {"div": 0.0762, "accession_ha": {"value": "EPI3095297"}, "country": {"value": "Russia"}, "strain": {"value": "A/StPetersburg/RII-313/2023"}, "proposedSubclade": {"value": "J.2"}, "gisaid_epi_isl": {"value": "EPI_ISL_18957854"}, "clade_membership": {"value": "3C.2a1b.2a.2a.3a.1"}, "short-clade": {"value": "2a.3a.1"}, "date": {"value": "2023-12-21"}, "subclade": {"value": "J.2"}, "region": {"value": "West Asia"}}, "branch_attrs": {"mutations": {}}}, {"name": "NODE_0000801", "node_attrs": {"div": 0.0773, "proposedSubclade": {"value": "J.2"}, "clade_membership": {"value": "3C.2a1b.2a.2a.3a.1"}, "short-clade": {"value": "2a.3a.1"}, "subclade": {"value": "J.2"}}, "branch_attrs": {"mutations": {"nuc": ["T602C", "G1247A"]}}, "children": [{"name": "A/StPetersburg/RII-MH151514S/2023", "node_attrs": {"div": 0.0779, "accession_ha": {"value": "EPI2867784"}, "country": {"value": "Russia"}, "strain": {"value": "A/StPetersburg/RII-MH151514S/2023"}, "proposedSubclade": {"value": "J.2"}, "gisaid_epi_isl": {"value": "EPI_ISL_18685279"}, "clade_membership": {"value": "3C.2a1b.2a.2a.3a.1"}, "short-clade": {"value": "2a.3a.1"}, "date": {"value": "2023-11-17"}, "subclade": {"value": "J.2"}, "region": {"value": "West Asia"}}, "branch_attrs": {"mutations": {"nuc": ["T617C"]}}}, {"name": "A/StPetersburg/RII-6787S/2023", "node_attrs": {"div": 0.0773, "accession_ha": {"value": "EPI2870837"}, "country": {"value": "Russia"}, "strain": {"value": "A/StPetersburg/RII-6787S/2023"}, "proposedSubclade": {"value": "J.2"}, "gisaid_epi_isl": {"value": "EPI_ISL_18698244"}, "clade_membership": {"value": "3C.2a1b.2a.2a.3a.1"}, "short-clade": {"value": "2a.3a.1"}, "date": {"value": "2023-12-09"}, "subclade": {"value": "J.2"}, "region": {"value": "West Asia"}}, "branch_attrs": {"mutations": {}}}, {"name": "A/Victoria/53/2024", "node_attrs": {"div": 0.0791, "accession_ha": {"value": "EPI3006736"}, "country": {"value": "Australia"}, "strain": {"value": "A/Victoria/53/2024"}, "proposedSubclade": {"value": "J.2"}, "gisaid_epi_isl": {"value": "EPI_ISL_18876507"}, "clade_membership": {"value": "3C.2a1b.2a.2a.3a.1"}, "short-clade": {"value": "2a.3a.1"}, "date": {"value": "2024-01-20"}, "subclade": {"value": "J.2"}, "region": {"value": "Oceania"}}, "branch_attrs": {"mutations": {"nuc": ["G163A", "C259A", "C1220T"], "HA1": ["R33Q", "T65K"]}, "labels": {"aa": "HA1: R33Q, T65K"}}}, {"name": "A/Saratov/RII-10/2023", "node_attrs": {"div": 0.0785, "accession_ha": {"value": "EPI2970695"}, "country": {"value": "Russia"}, "strain": {"value": "A/Saratov/RII-10/2023"}, "proposedSubclade": {"value": "J.2"}, "gisaid_epi_isl": {"value": "EPI_ISL_18846030"}, "clade_membership": {"value": "3C.2a1b.2a.2a.3a.1"}, "short-clade": {"value": "2a.3a.1"}, "date": {"value": "2023-12-22"}, "subclade": {"value": "J.2"}, "region": {"value": "West Asia"}}, "branch_attrs": {"mutations": {"nuc": ["G688A", "A1170G"], "HA1": ["R208K"], "HA2": ["S40G"]}, "labels": {"aa": "HA1: R208K; HA2: S40G"}}}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}}
\ No newline at end of file
diff --git a/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/CHANGELOG.md b/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/CHANGELOG.md
new file mode 100644
index 00000000..4afc72cb
--- /dev/null
+++ b/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/CHANGELOG.md
@@ -0,0 +1,45 @@
+## Unreleased
+This release adds the subclades J.1.1, J.2.1, and J.2.2 as specified in the (influenza-clade-nomenclature repository)[https://github.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/blob/main/CHANGELOG.md#2024-11-12].
+
+## 2024-11-05T09:19:52Z
+ - update reference trees
+ - include subclade proposals
+
+
+## 2024-08-08T05:08:21Z
+
+Fix numbering of RBD sites it the `pathogen.json`. The relevant positions were indexed 1-based, when they should have been indexed 0-based.
+
+## 2024-07-03T08:29:55Z
+
+Added configuration of current and recent vaccine strains as 'reference nodes' on the reference tree, against which query sequences can be compared. This feature is in addition to the new 'compare to clade founder' feature, allowing to compare each query sequence to the most ancestral node of a clade or lineage.
+
+The datasets themselves remain unchanged.
+
+See Nextclade documentation for more details about 'relative mutations' functionality.
+
+## 2024-04-19T07:50:39Z
+
+Update of the datasets with more recent data. No new clades were added on this occasion.
+
+## 2024-02-22T16:12:03Z
+
+After discussion with various members of the seasonal influenza virus surveillance community, it was decided that subclade names starting with `H` have the potential to be confused with major influenza hemagglutinin subtypes. These subclades where therefore renamed to start with the alias `J`.
+
+ - `H` --> `J`
+ - `H.1` --> `J.1`
+ - `H.2` --> `J.2`
+ - `H.3` --> `J.3`
+ - `H.4` --> `J.4`
+
+The subclades `H` and `H.*` were revoked, and a comment was added to explain the reason. No subclade definitions were changed.
+
+
+## 2024-01-16T20:31:02Z
+
+Initial release for Nextclade v3!
+
+ - Addition of subclade H.1, H.2, H.3, and H.4
+ - Aliasing of G.1.3.1.1 as subclade H
+
+Read more about Nextclade datasets in the documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html
diff --git a/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/README.md b/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/README.md
new file mode 100644
index 00000000..af06f06f
--- /dev/null
+++ b/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/README.md
@@ -0,0 +1,37 @@
+# Influenza A(H3N2) HA dataset based on reference "A/Darwin/6/2021"
+
+| Key                  | Value                |
+| -------------------- | -------------------- |
+| authors                | [Richard Neher](https://neherlab.org), [Nextstrain](https://nextstrain.org)                         |
+| name                 | Influenza A H3N2 HA                      |
+| reference            | A/Darwin/6/2021                     |
+| dataset path         | flu/h3n2/ha/EPI1857216                     |
+| reference accession  | EPI1857216   |
+| clade definitions  |  [github.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/](https://github.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/)  |
+
+## Scope of this dataset
+This dataset uses a recent reference sequence (A/Darwin/6/2021) and is suitable for the analysis of circulating viruses.
+
+## Features
+This dataset supports
+
+ * Assignment to clades and subclades based on the nomenclature defined in [github.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/](https://github.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/)
+ * Identification of glycosilation motifs
+ * Counting of mutations in the RBD
+ * Sequence QC
+ * Phylogenetic placement
+
+## Clades of seasonal influenza viruses
+
+The WHO Collaborating centers define "clades" as genetic groups of viruses with signature mutations to facilitate discussion of circulating diversity of the viruses.
+Clade demarcation do not always coincide with significantly different antigenic properties of the viruses.
+Clade names are structured as _Number-Letter_ binomials (with exceptions) separated by periods as in `3C.2a1b.2a.2a.1a`. These sometimes get shortened by omission of leading binomials like `2a.1`.
+
+In addition to these clades, "subclades" are defined to break down diversity at higher resolution and allow following the spread of different viral groups.
+These follow a Pango-like nomenclature consisting of a letter followed by a numbers separated by periods as in `G.1.3.1`.
+The leading letter is an alias of a previous name.
+Details of the nomenclature system can be found at [github.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/](https://github.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/).
+
+## What is Nextclade dataset
+
+Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html
diff --git a/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/dataset.zip b/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/dataset.zip
new file mode 100644
index 00000000..681e8635
Binary files /dev/null and b/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/dataset.zip differ
diff --git a/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/genome_annotation.gff3 b/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/genome_annotation.gff3
new file mode 100644
index 00000000..f33ff5bc
--- /dev/null
+++ b/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/genome_annotation.gff3
@@ -0,0 +1,5 @@
+##gff-version 3
+##sequence-region EPI1857216 1 1718
+EPI1857216	feature	gene	1	48	.	+	.	gene_name="SigPep"
+EPI1857216	feature	gene	49	1035	.	+	.	gene_name="HA1"
+EPI1857216	feature	gene	1036	1698	.	+	.	gene_name="HA2"
diff --git a/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/pathogen.json b/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/pathogen.json
new file mode 100644
index 00000000..6a442760
--- /dev/null
+++ b/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/pathogen.json
@@ -0,0 +1,174 @@
+{
+  "schemaVersion": "3.0.0",
+  "alignmentParams": {
+    "excessBandwidth": 9,
+    "terminalBandwidth": 100,
+    "allowedMismatches": 4,
+    "gapAlignmentSide": "right",
+    "minSeedCover": 0.1
+  },
+  "compatibility": {
+    "cli": "3.0.0-alpha.0",
+    "web": "3.0.0-alpha.0"
+  },
+  "defaultCds": "HA1",
+  "files": {
+    "changelog": "CHANGELOG.md",
+    "examples": "sequences.fasta",
+    "genomeAnnotation": "genome_annotation.gff3",
+    "pathogenJson": "pathogen.json",
+    "readme": "README.md",
+    "reference": "reference.fasta",
+    "treeJson": "tree.json"
+  },
+  "qc": {
+    "privateMutations": {
+      "enabled": true,
+      "typical": 5,
+      "cutoff": 15,
+      "weightLabeledSubstitutions": 2,
+      "weightReversionSubstitutions": 1,
+      "weightUnlabeledSubstitutions": 1
+    },
+    "missingData": {
+      "enabled": false,
+      "missingDataThreshold": 100,
+      "scoreBias": 10
+    },
+    "snpClusters": {
+      "enabled": false,
+      "windowSize": 100,
+      "clusterCutOff": 5,
+      "scoreWeight": 50
+    },
+    "mixedSites": {
+      "enabled": true,
+      "mixedSitesThreshold": 4
+    },
+    "frameShifts": {
+      "enabled": true
+    },
+    "stopCodons": {
+      "enabled": true,
+      "ignoredStopCodons": []
+    }
+  },
+  "cdsOrderPreference": [
+    "HA1",
+    "HA2"
+  ],
+  "maintenance": {
+    "website": [
+      "https://nextstrain.org",
+      "https://clades.nextstrain.org"
+    ],
+    "documentation": [
+      "https://github.com/nextstrain/seasonal-flu"
+    ],
+    "source code": [
+      "https://github.com/nextstrain/seasonal_flu"
+    ],
+    "issues": [
+      "https://github.com/nextstrain/seasonal_flu/issues"
+    ],
+    "organizations": [
+      "Nextstrain"
+    ],
+    "authors": [
+      "Nextstrain team <https://nextstrain.org>"
+    ]
+  },
+  "nucMutLabelMap": {},
+  "nucMutLabelMapReverse": {},
+  "shortcuts": [
+    "flu_h3n2_ha",
+    "nextstrain/flu/h3n2",
+    "nextstrain/flu/h3n2/ha",
+    "nextstrain/flu/h3n2/ha/darwin-6-2021"
+  ],
+  "phenotypeData": [
+    {
+      "name": "RBD",
+      "nameFriendly": "RBD mutations",
+      "description": "This column displays the number of differences between the sequence and the reference at positions identified by Koel et al. (145, 155, 156, 158, 159, 189, and 193 in HA1)",
+      "cds": "HA1",
+      "aaRange": {
+        "begin": 100,
+        "end": 200
+      },
+      "ignore": {
+        "clades": [
+          "outgroup"
+        ]
+      },
+      "data": [
+        {
+          "name": "differences",
+          "weight": 1,
+          "locations": {
+            "144": {
+              "default": 1
+            },
+            "154": {
+              "default": 1
+            },
+            "155": {
+              "default": 1
+            },
+            "157": {
+              "default": 1
+            },
+            "158": {
+              "default": 1
+            },
+            "188": {
+              "default": 1
+            },
+            "192": {
+              "default": 1
+            }
+          }
+        }
+      ]
+    }
+  ],
+  "aaMotifs": [
+    {
+      "name": "glycosylation",
+      "nameShort": "Glyc.",
+      "nameFriendly": "Glycosylation",
+      "description": "N-linked glycosylation motifs (N-X-S/T with X any amino acid other than P)",
+      "includeCdses": [
+        {
+          "cds": "HA1",
+          "ranges": []
+        },
+        {
+          "cds": "HA2",
+          "ranges": [
+            {
+              "begin": 0,
+              "end": 186
+            }
+          ]
+        }
+      ],
+      "motifs": [
+        "N[^P][ST]"
+      ]
+    }
+  ],
+  "attributes": {
+    "name": "Influenza A H3N2 HA",
+    "segment": "ha",
+    "reference accession": "EPI1857216",
+    "reference name": "A/Darwin/6/2021"
+  },
+  "version": {
+    "tag": "unreleased",
+    "compatibility": {
+      "cli": "3.0.0-alpha.0",
+      "web": "3.0.0-alpha.0"
+    }
+  }
+}
diff --git a/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/reference.fasta b/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/reference.fasta
new file mode 100644
index 00000000..427694bc
--- /dev/null
+++ b/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/reference.fasta
@@ -0,0 +1,23 @@
+>EPI_ISL_1563628 | A/Darwin/6/2021 | A / H3N2 |  | 2021-03-16
+ATGAAGACTATCATTGCTTTGAGCAACATTCTATGTCTTGTTTTCGCTCAAAAAATACCTGGAAATGACAATAGCACGGC
+AACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACAAATGACCGAATTGAAGTTACTA
+ATGCTACTGAGTTGGTTCAGAATTCATCAATAGGTGAAATATGCGGCAGTCCTCATCAGATCCTTGATGGAGGGAACTGC
+ACACTAATAGATGCTCTATTGGGGGACCCTCAGTGTGACGGCTTTCAAAATAAGGAATGGGACCTTTTTGTTGAAAGAAG
+CAGAGCCAACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACAC
+TGGAGTTTAAAAATGAAAGCTTCAATTGGACTGGAGTCAAACAAAACGGAACAAGTTCTGCGTGCATAAGGGGATCTAGT
+AGTAGTTTTTTTAGTAGATTAAATTGGTTGACCAGCTTAAACAACATATATCCAGCACAGAACGTGACTATGCCAAACAA
+GGAACAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGATACGGACAAGAACCAAATCTCCCTGTTTGCTCAAT
+CATCAGGAAGAATCACAGTATCTACCAAAAGAAGCCAACAAGCTGTAATCCCAAATATCGGATCTAGACCCAGAATAAGG
+GATATCCCTAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCT
+AATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAAATGTA
+AGTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCGTTCCAAAATGTAAACAGGATCACATACGGGGCC
+TGTCCCAGATATGTTAAGCAAAGCACCCTGAAATTGGCAACAGGAATGCGAAATGTACCAGAGAAACAAACCAGAGGCAT
+ATTTGGCGCAATAGCGGGTTTCATAGAAAATGGATGGGAGGGAATGGTGGATGGTTGGTACGGTTTCAGGCATCAAAATT
+CTGAGGGAAGAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGATCAAATCAATGGGAAGCTGAATCGATTG
+ATCGGAAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTAGAAGGAAGAGTTCAAGACCTTGAGAA
+ATATGTTGAGGACACTAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACGATTG
+ACCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGAAAT
+GGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATAAGAAATGAAACTTATGACCACAATGTGTA
+CAGGGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGAGTTGAGCTGAAGTCAGGGTACAAAGATTGGATCCTATGGA
+TTTCCTTTGCCATGTCATGTTTTTTGCTTTGTATTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAGGGCAACATT
+AGATGCAACATTTGCATTTGAGTGCATTAATTAAAAAC
diff --git a/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/sequences.fasta b/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/sequences.fasta
new file mode 100644
index 00000000..9b3e770a
--- /dev/null
+++ b/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/sequences.fasta
@@ -0,0 +1,1500 @@
+>A/Wisconsin/21/2021
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diff --git a/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/tree.json b/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/tree.json
new file mode 100644
index 00000000..a8a1e540
--- /dev/null
+++ b/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/tree.json
@@ -0,0 +1 @@
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