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feat(datasets): add example ebolavirus mutation pattern configs
Placeholder mutationPatterns configuration for BDBV, EBOV, and SUDV to demonstrate the feature; parameters are not scientifically validated. - BDBV: ADAR (A>G, T>C) and APOBEC (G>A in YGH context), window 50, cutoff 3, with synthetic example sequences - EBOV: ADAR (A>G, T>C) and APOBEC-like CpG deamination (C>T in HCG context), window 100, cutoff 5 - SUDV: ADAR (A>G, T>C), window 80, cutoff 4
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‎data/nextstrain/orthoebolavirus/bdbv/CHANGELOG.md‎

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## Unreleased
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- Add mutationPatterns config for ADAR-mediated A-to-I editing detection (A>G and T>C substitution type filtering)
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## 2026-05-22T16:04:17Z
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- adjust QC param settings to reudce private mutation threshold (outbreak genomes should be very similar)
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- add GP_003:367 to known stop codons
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- Include 2026 genomes
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## 2026-05-15T16:16:45Z
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Initial release of this dataset.

‎data/nextstrain/orthoebolavirus/bdbv/examples.fasta‎

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‎data/nextstrain/orthoebolavirus/bdbv/pathogen.json‎

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"reference": "reference.fasta"
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},
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"defaultCds": "GP",
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"mutationPatterns": {
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"patterns": [
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{
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"id": "adar",
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"name": "ADAR-like RNA editing",
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"description": "ADAR-mediated A-to-I editing (observed as A>G and complementary T>C)",
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"events": [
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{
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"type": "nucSubstitution",
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"ref": ["A"],
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"qry": ["G"]
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},
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{
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"type": "nucSubstitution",
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"ref": ["T"],
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"qry": ["C"]
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}
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],
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"cluster": {
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"windowSize": 50,
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"cutoff": 3
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}
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},
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{
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"id": "apobec",
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"name": "APOBEC-like cytosine deamination",
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"description": "APOBEC-like cytosine deamination (observed as G>A)",
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"events": [
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{
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"type": "nucSubstitution",
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"ref": ["G"],
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"qry": ["A"],
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"motifs": ["[CT]G[ACT]"]
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}
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],
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"cluster": {
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"windowSize": 50,
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"cutoff": 3
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}
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}
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]
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},
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"qc": {
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"frameShifts": {
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"enabled": true,
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},
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"stopCodons": {
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"enabled": true,
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"ignoredStopCodons": [{"cdsName": "GP_003", "codon": 366}],
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"ignoredStopCodons": [
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{
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"cdsName": "GP_003",
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"codon": 366
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}
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],
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"scoreWeight": 20
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}
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},

‎data/nextstrain/orthoebolavirus/ebov/CHANGELOG.md‎

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## Unreleased
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- Add mutationPatterns config for ADAR editing and APOBEC-like CpG deamination detection
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## 2026-04-14T11:55:23Z
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- Align `pathogen.json` metadata with the current Nextclade schema layout.

‎data/nextstrain/orthoebolavirus/ebov/pathogen.json‎

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"readme": "README.md",
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"reference": "reference.fasta"
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},
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"mutationPatterns": {
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"patterns": [
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{
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"id": "rna_editing",
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"name": "RNA editing signatures",
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"description": "ADAR editing (A>G, T>C) and APOBEC-like deamination (C>T in CpG context)",
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"events": [
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{
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"type": "nucSubstitution",
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"ref": ["A"],
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"qry": ["G"]
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},
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{
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"type": "nucSubstitution",
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"ref": ["T"],
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"qry": ["C"]
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},
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{
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"type": "nucSubstitution",
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"ref": ["C"],
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"qry": ["T"],
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"motifs": ["[ACGT]CG"]
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}
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],
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"cluster": {
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"windowSize": 100,
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"cutoff": 5
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}
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}
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]
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},
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"qc": {
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"frameShifts": {
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"enabled": true,
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"ignoredFrameShifts": [
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],
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"ignoredFrameShifts": [],
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"scoreWeight": 50
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},
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"missingData": {
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},
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"stopCodons": {
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"enabled": true,
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"ignoredStopCodons": [
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],
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"ignoredStopCodons": [],
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"scoreWeight": 50
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}
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},

‎data/nextstrain/orthoebolavirus/sudv/CHANGELOG.md‎

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## Unreleased
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- Add mutationPatterns config for ADAR editing detection
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## 2026-04-14T11:55:23Z
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- Align `pathogen.json` metadata with the current Nextclade schema layout.

‎data/nextstrain/orthoebolavirus/sudv/pathogen.json‎

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"readme": "README.md",
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"reference": "reference.fasta"
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},
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"mutationPatterns": {
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"patterns": [
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{
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"id": "adar",
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"name": "ADAR-like RNA editing",
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"description": "ADAR-mediated A-to-I editing",
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"events": [
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{
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"type": "nucSubstitution",
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"ref": ["A"],
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"qry": ["G"]
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},
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{
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"type": "nucSubstitution",
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"ref": ["T"],
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"qry": ["C"]
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}
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],
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"cluster": {
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"windowSize": 80,
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"cutoff": 4
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}
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}
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]
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},
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"qc": {
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"frameShifts": {
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"enabled": true,
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"ignoredFrameShifts": [
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],
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"ignoredFrameShifts": [],
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"scoreWeight": 20
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},
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"missingData": {
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},
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"stopCodons": {
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"enabled": true,
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"ignoredStopCodons": [
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],
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"ignoredStopCodons": [],
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"scoreWeight": 20
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}
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},

‎data_output/index.json‎

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]
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},
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"versions": [
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{
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"tag": "unreleased",
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"compatibility": {
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"cli": "3.0.0-alpha.0",
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"web": "3.0.0-alpha.0"
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}
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},
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{
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"updatedAt": "2026-04-14T11:55:23Z",
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"tag": "2026-04-14--11-55-23Z",
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}
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],
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"version": {
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"tag": "unreleased",
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"compatibility": {
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"cli": "3.0.0-alpha.0",
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"web": "3.0.0-alpha.0"
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]
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"versions": [
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"tag": "unreleased",
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"compatibility": {
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"cli": "3.0.0-alpha.0",
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"web": "3.0.0-alpha.0"
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}
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},
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"updatedAt": "2026-04-14T11:55:23Z",
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}
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],
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"version": {
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"updatedAt": "2026-04-14T11:55:23Z",
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"tag": "2026-04-14--11-55-23Z",
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"tag": "unreleased",
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"compatibility": {
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"cli": "3.0.0-alpha.0",
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"web": "3.0.0-alpha.0"
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]
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},
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"versions": [
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"tag": "unreleased",
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"compatibility": {
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"cli": "3.0.0-alpha.0",
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"web": "3.0.0-alpha.0"
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}
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},
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"updatedAt": "2026-05-22T16:04:17Z",
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"tag": "2026-05-22--16-04-17Z",
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}
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"version": {
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"tag": "2026-05-22--16-04-17Z",
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"tag": "unreleased",
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"compatibility": {
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"cli": "3.0.0-alpha.0",
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"web": "3.0.0-alpha.0"

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

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## Unreleased
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- Add mutationPatterns config for ADAR-mediated A-to-I editing detection (A>G and T>C substitution type filtering)
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## 2026-05-22T16:04:17Z
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- adjust QC param settings to reudce private mutation threshold (outbreak genomes should be very similar)
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- add SNP cluster QC rule to trigger on stretches of high private mutation density
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- update tree
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## 2026-05-18T20:09:34Z
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- Add outbreak annotation
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- add GP_003:367 to known stop codons
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- Include 2026 genomes
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## 2026-05-15T16:16:45Z
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Initial release of this dataset.

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

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# Nextclade dataset for Bundibugyo virus (Orthoebolavirus bundibugyoense)
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| Key | Value |
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| ---------------------- | ------------------------------------------------------------------------------- |
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| authors | [Richard Neher](https://neherlab.org) |
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| data source | Genbank |
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| nextclade dataset path | nextstrain/orthoebolavirus/bdbv |
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| annotation | [NC_014373.1](https://www.ncbi.nlm.nih.gov/nuccore/NC_014373.1) |
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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.
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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.
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