feat: add example ebolavirus mutation pattern configs

data/nextstrain/mpox/all-clades/CHANGELOG.md

@@ -1,3 +1,7 @@
+## Unreleased
+
+- Add an example mutation pattern for APOBEC3-like cytosine deamination (C>T in TCW context on both strands). It has no clustering, because these mutations are scattered across the genome
+
 ## 2026-07-07T14:07:11Z
 
 - Breaking change: Clade Ib outbreak sh2023 now has lineages defined. Those lineages follow the same scheme as the existing clade IIb outbreak sh2017 lineage system. The root lineage is A, B might become an alias for another lineage than in IIb/sh2017. Hence, to unambiguously refer to a lineage, the outbreak must be included as well. To faciliate this, a new outbreakLineage field has been added that concatenates outbreak and lineage separated by a slash, e.g. `sh2017/B.1`. Existing `clade`, `outbreak`, and `lineage` fields remain unchanged - except that `lineage` `A` is now assigned to both clade Ib/sh2023 lineage `A` and clade IIb/sh2017 lineage `A`. The new `outbreakLineage` field is the way to unambiguously refer to a lineage.

data/nextstrain/mpox/all-clades/pathogen.json

@@ -26,6 +26,31 @@
     "reference": "reference.fasta",
     "treeJson": "tree.json"
   },
+  "mutationPatterns": {
+    "patterns": [
+      {
+        "id": "apobec",
+        "name": "APOBEC3-like cytosine deamination",
+        "description": "APOBEC3-like cytosine deamination, observed as C>T in TCW context, and as G>A in WGA context on the opposite strand",
+        "events": [
+          {
+            "type": "nucSubstitution",
+            "ref": [
+              "C"
+            ],
+            "qry": [
+              "T"
+            ],
+            "motifs": [
+              "T(C)W"
+            ],
+            "bothStrands": true
+          }
+        ],
+        "cluster": false
+      }
+    ]
+  },
   "qc": {
     "frameShifts": {
       "enabled": true,

data/nextstrain/mpox/clade-i/CHANGELOG.md

@@ -1,3 +1,7 @@
+## Unreleased
+
+- Add an example mutation pattern for APOBEC3-like cytosine deamination (C>T in TCW context on both strands). It has no clustering, because these mutations are scattered across the genome
+
 ## 2026-07-07T14:07:11Z
 
 - Breaking change: Clade Ib outbreak sh2023 now has lineages defined. Those lineages follow the same scheme as the existing clade IIb outbreak sh2017 lineage system. The root lineage is A, and B might become an alias for another lineage than in IIb/sh2017. Hence, to unambiguously refer to a lineage, the outbreak must be included as well. To facilitate this, a new `outbreakLineage` field has been added that concatenates outbreak and lineage separated by a slash, e.g. `sh2023/A.1`. Existing `clade`, `outbreak`, and `lineage` fields remain unchanged - except that `lineage` `A` is now assigned to both clade Ib/sh2023 lineage `A` and (in datasets that contain it) clade IIb/sh2017 lineage `A`. The new `outbreakLineage` field is the way to unambiguously refer to a lineage.

data/nextstrain/mpox/clade-i/pathogen.json

@@ -26,6 +26,31 @@
     "reference": "reference.fasta",
     "treeJson": "tree.json"
   },
+  "mutationPatterns": {
+    "patterns": [
+      {
+        "id": "apobec",
+        "name": "APOBEC3-like cytosine deamination",
+        "description": "APOBEC3-like cytosine deamination, observed as C>T in TCW context, and as G>A in WGA context on the opposite strand",
+        "events": [
+          {
+            "type": "nucSubstitution",
+            "ref": [
+              "C"
+            ],
+            "qry": [
+              "T"
+            ],
+            "motifs": [
+              "T(C)W"
+            ],
+            "bothStrands": true
+          }
+        ],
+        "cluster": false
+      }
+    ]
+  },
   "qc": {
     "frameShifts": {
       "enabled": true,

data/nextstrain/mpox/clade-iib/CHANGELOG.md

@@ -1,3 +1,7 @@
+## Unreleased
+
+- Add an example mutation pattern for APOBEC3-like cytosine deamination (C>T in TCW context on both strands). It has no clustering, because these mutations are scattered across the genome
+
 ## 2026-07-07T14:07:11Z
 
 - A new `outbreakLineage` field has been added that concatenates outbreak and lineage separated by a slash, e.g. `sh2017/B.1`. It unambiguously identifies a lineage across outbreaks: clade Ib outbreak sh2023 now also has a lineage system that reuses the same lineage names (e.g. root lineage `A`) as clade IIb outbreak sh2017. Existing `clade`, `outbreak`, and `lineage` fields remain unchanged. Clade Ib sequences are not part of this clade IIb dataset; use `nextstrain/mpox/all-clades` or `nextstrain/mpox/clade-i` for those.

data/nextstrain/mpox/clade-iib/pathogen.json

@@ -26,6 +26,31 @@
     "reference": "reference.fasta",
     "treeJson": "tree.json"
   },
+  "mutationPatterns": {
+    "patterns": [
+      {
+        "id": "apobec",
+        "name": "APOBEC3-like cytosine deamination",
+        "description": "APOBEC3-like cytosine deamination, observed as C>T in TCW context, and as G>A in WGA context on the opposite strand",
+        "events": [
+          {
+            "type": "nucSubstitution",
+            "ref": [
+              "C"
+            ],
+            "qry": [
+              "T"
+            ],
+            "motifs": [
+              "T(C)W"
+            ],
+            "bothStrands": true
+          }
+        ],
+        "cluster": false
+      }
+    ]
+  },
   "qc": {
     "frameShifts": {
       "enabled": true,

data/nextstrain/orthoebolavirus/bdbv/CHANGELOG.md

@@ -1,3 +1,7 @@
+## Unreleased
+
+- Add example mutation patterns for ADAR-like RNA editing (A>G on both strands) and APOBEC3-like cytosine deamination (C>T in TCW context on both strands), with simulated example sequences
+
 ## 2026-07-03T09:35:04Z
 
  - Include open 2026 Outbreak sequences as examples;