Ebola/update bdbv 2026 09

data/nextstrain/ndv/class-1/AB524405/CHANGELOG.md

@@ -1,4 +1,4 @@
-## Unreleased
+## 2026-09-29T08:40:32Z
 
  - initial release of the draft NDV class 1 dataset
  - the class 2 reference NC_075404 is included in the reference tree as an outgroup, so that class 2 sequences attach to it and are reported as `class 2` instead of being placed inside the class 1 diversity

data/nextstrain/ndv/class-2/NC_075404/CHANGELOG.md

@@ -1,4 +1,4 @@
-## Unreleased
+## 2026-09-29T08:40:32Z
 
  - initial release of the draft NDV class 2 dataset
  - the class 1 reference AB524405 is included in the reference tree as an outgroup, so that class 1 sequences attach to it and are reported as `class 1` instead of being placed inside the class 2 diversity

data/nextstrain/orthoebolavirus/bdbv/CHANGELOG.md

@@ -1,3 +1,8 @@
+## Unreleased
+
+ - Update reference tree with more recent genomes
+ - Include putative ADAR edit-detection. Cluster of 3 or more T->C mutations will now be highlighed.
+
 ## 2026-07-03T09:35:04Z
 
  - Include open 2026 Outbreak sequences as examples;

data/nextstrain/orthoebolavirus/bdbv/pathogen.json

@@ -27,6 +27,27 @@
     "readme": "README.md",
     "reference": "reference.fasta"
   },
+  "mutationPatterns": {
+    "patterns": [
+      {
+        "id": "adar",
+        "name": "ADAR-like RNA editing",
+        "description": "ADAR-mediated A-to-I editing, observed as T>C in sequenced genomes",
+        "events": [
+          {
+            "type": "nucSubstitution",
+            "ref": ["T"],
+            "qry": ["C"],
+            "bothStrands": false
+          }
+        ],
+        "cluster": {
+          "windowSize": 50,
+          "cutoff": 2
+        }
+      }
+    ]
+  },
   "qc": {
     "frameShifts": {
       "enabled": true,

data_output/index.json

@@ -2416,6 +2416,13 @@
             ]
           },
           "versions": [
+            {
+              "tag": "unreleased",
+              "compatibility": {
+                "cli": "3.0.0-alpha.0",
+                "web": "3.0.0-alpha.0"
+              }
+            },
             {
               "updatedAt": "2026-07-03T09:35:04Z",
               "tag": "2026-07-03--09-35-04Z",
@@ -2450,8 +2457,7 @@
             }
           ],
           "version": {
-            "updatedAt": "2026-07-03T09:35:04Z",
-            "tag": "2026-07-03--09-35-04Z",
+            "tag": "unreleased",
             "compatibility": {
               "cli": "3.0.0-alpha.0",
               "web": "3.0.0-alpha.0"
@@ -7354,15 +7360,17 @@
           },
           "versions": [
             {
-              "tag": "unreleased",
+              "updatedAt": "2026-09-29T08:40:32Z",
+              "tag": "2026-09-29--08-40-32Z",
               "compatibility": {
                 "cli": "3.0.0-alpha.0",
                 "web": "3.0.0-alpha.0"
               }
             }
           ],
           "version": {
-            "tag": "unreleased",
+            "updatedAt": "2026-09-29T08:40:32Z",
+            "tag": "2026-09-29--08-40-32Z",
             "compatibility": {
               "cli": "3.0.0-alpha.0",
               "web": "3.0.0-alpha.0"
@@ -7402,15 +7410,17 @@
           },
           "versions": [
             {
-              "tag": "unreleased",
+              "updatedAt": "2026-09-29T08:40:32Z",
+              "tag": "2026-09-29--08-40-32Z",
               "compatibility": {
                 "cli": "3.0.0-alpha.0",
                 "web": "3.0.0-alpha.0"
               }
             }
           ],
           "version": {
-            "tag": "unreleased",
+            "updatedAt": "2026-09-29T08:40:32Z",
+            "tag": "2026-09-29--08-40-32Z",
             "compatibility": {
               "cli": "3.0.0-alpha.0",
               "web": "3.0.0-alpha.0"

data_output/nextstrain/ndv/class-1/AB524405/unreleased/CHANGELOG.md → data_output/nextstrain/ndv/class-1/AB524405/2026-09-29--08-40-32Z/CHANGELOG.md

@@ -1,4 +1,4 @@
-## Unreleased
+## 2026-09-29T08:40:32Z
 
  - initial release of the draft NDV class 1 dataset
  - the class 2 reference NC_075404 is included in the reference tree as an outgroup, so that class 2 sequences attach to it and are reported as `class 2` instead of being placed inside the class 1 diversity

data_output/nextstrain/ndv/class-1/AB524405/unreleased/pathogen.json → data_output/nextstrain/ndv/class-1/AB524405/2026-09-29--08-40-32Z/pathogen.json

@@ -95,7 +95,8 @@
     "L"
   ],
   "version": {
-    "tag": "unreleased",
+    "updatedAt": "2026-09-29T08:40:32Z",
+    "tag": "2026-09-29--08-40-32Z",
     "compatibility": {
       "cli": "3.0.0-alpha.0",
       "web": "3.0.0-alpha.0"

data_output/nextstrain/ndv/class-2/NC_075404/unreleased/CHANGELOG.md → data_output/nextstrain/ndv/class-2/NC_075404/2026-09-29--08-40-32Z/CHANGELOG.md

@@ -1,4 +1,4 @@
-## Unreleased
+## 2026-09-29T08:40:32Z
 
  - initial release of the draft NDV class 2 dataset
  - the class 1 reference AB524405 is included in the reference tree as an outgroup, so that class 1 sequences attach to it and are reported as `class 1` instead of being placed inside the class 2 diversity

data_output/nextstrain/ndv/class-2/NC_075404/unreleased/pathogen.json → data_output/nextstrain/ndv/class-2/NC_075404/2026-09-29--08-40-32Z/pathogen.json

@@ -163,7 +163,8 @@
     "L"
   ],
   "version": {
-    "tag": "unreleased",
+    "updatedAt": "2026-09-29T08:40:32Z",
+    "tag": "2026-09-29--08-40-32Z",
     "compatibility": {
       "cli": "3.0.0-alpha.0",
       "web": "3.0.0-alpha.0"

data_output/nextstrain/orthoebolavirus/bdbv/unreleased/CHANGELOG.md

@@ -0,0 +1,28 @@
+## Unreleased
+
+ - Update reference tree with more recent genomes
+ - Include putative ADAR edit-detection. Cluster of 3 or more T->C mutations will now be highlighed.
+
+## 2026-07-03T09:35:04Z
+
+ - Include open 2026 Outbreak sequences as examples;
+ - squash zero length branches
+ - change display defaults to show mutations relative to reference tree
+
+
+## 2026-05-22T16:04:17Z
+
+- adjust QC param settings to reduce private mutation threshold (outbreak genomes should be very similar)
+- add SNP cluster QC rule to trigger on stretches of high private mutation density
+- update tree
+
+## 2026-05-18T20:09:34Z
+
+- Add outbreak annotation
+- add GP_003:367 to known stop codons
+- Include 2026 genomes
+
+
+## 2026-05-15T16:16:45Z
+
+Initial release of this dataset.

data_output/nextstrain/orthoebolavirus/bdbv/unreleased/README.md

@@ -0,0 +1,15 @@
+# Nextclade dataset for Bundibugyo virus (Orthoebolavirus bundibugyoense)
+
+| Key                    | Value                                                                           |
+| ---------------------- | ------------------------------------------------------------------------------- |
+| authors                | [Richard Neher](https://neherlab.org) |
+| data source            | Genbank                                             |
+| nextclade dataset path | nextstrain/orthoebolavirus/bdbv                     |
+| annotation             | [NC_014373.1](https://www.ncbi.nlm.nih.gov/nuccore/NC_014373.1)                   |
+
+This Nextclade dataset for Bundibugyo virus [(Orthoebolavirus bundibugyoense)](https://ictv.global/report/chapter/filoviridae/filoviridae/orthoebolavirus) aligns to the reference sequence [NC_014373.1](https://www.ncbi.nlm.nih.gov/nuccore/NC_014373) and translates major CDS. It scores the sequence with respect to unexpected frameshifts or stop codons, missing sequence (in form of `NNN`s) and mixed bases.
+
+Data from the 2026 outbreak were generously shared by the groups of Prof. Placide Mbala-Kingebeni (INRB, DRC) and Dr Isaac Ssewanyana (CPHL, Uganda) to facilitate the public health response and containment of the virus. These data are described in a post on [Virological.org](https://virological.org/t/initial-genomes-from-may-2026-bundibugyo-virus-disease-outbreak-in-the-democratic-republic-of-the-congo-and-uganda/1032) and were deposited in Pathoplexus under [Restricted Data-Use terms](https://pathoplexus.org/about/terms-of-use/restricted-data). Please consult the authors and the [data-use terms](https://pathoplexus.org/about/terms-of-use/restricted-data) before using these sequences.
+
+
+