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chore: rebuild [skip ci]
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‎data_output/index.json‎

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"missingData",
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"mixedSites",
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"privateMutations",
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"snpClusters",
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"stopCodons"
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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": "2026-05-18T20:09:34Z",
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"tag": "2026-05-18--20-09-34Z",
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}
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],
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"version": {
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"updatedAt": "2026-05-18T20:09:34Z",
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"tag": "2026-05-18--20-09-34Z",
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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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- 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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‎data_output/nextstrain/orthoebolavirus/bdbv/unreleased/dataset.zip‎

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‎data_output/nextstrain/orthoebolavirus/bdbv/unreleased/examples.fasta‎

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‎data_output/nextstrain/orthoebolavirus/bdbv/unreleased/genome_annotation.gff3‎

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##gff-version 3
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#!gff-spec-version 1.21
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#!processor NCBI annotwriter
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##sequence-region NC_014373.1 1 18940
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##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=565995
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NC_014373.1 RefSeq region 1 18940 . + . ID=NC_014373.1:1..18940;Dbxref=taxon:565995;collection-date=Nov-2007;country=Uganda;gbkey=Src;genome=genomic;isolate=Bundibugyo virus/H.sapiens-tc/UGA/2007/Butalya-811250;isolation-source=blood;mol_type=viral cRNA;nat-host=Homo sapiens;old-name=Bundibugyo ebolavirus
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NC_014373.1 RefSeq CDS 458 2677 . + 0 Name=NP;gene=NP;gbkey=CDS;locus_tag=BDBVp1;product=nucleoprotein;protein_id=YP_003815432.1;ID=cds-YP_003815432.1;Note=encapsidation of genomic RNA;Dbxref=GenBank:YP_003815432.1,GeneID:9487269
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NC_014373.1 RefSeq CDS 3108 4133 . + 0 Name=VP35;gbkey=CDS;gene=VP35;locus_tag=BDBVp2;protein_id=YP_003815433.1;ID=cds-YP_003815433.1;product=polymerase complex protein;Note=putative type-1 IFN antagonist;Dbxref=GenBank:YP_003815433.1,GeneID:9487263
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NC_014373.1 RefSeq CDS 4461 5441 . + 0 Name=VP40;gbkey=CDS;gene=VP40;locus_tag=BDBVp3;product=matrix protein;protein_id=YP_003815434.1;ID=cds-YP_003815434.1;Dbxref=GenBank:YP_003815434.1,GeneID:9487264
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NC_014373.1 RefSeq CDS 6021 6905 . + 0 Name=GP;gene=GP;gbkey=CDS;locus_tag=BDBVp4;exception=RNA editing;protein_id=YP_003815435.1;ID=cds-YP_003815435.1;product=spike glycoprotein;Dbxref=GenBank:YP_003815435.1,GeneID:9487265;Note=GP1%2C2%3B structural glycoprotein%3B cleaved by furin into subunits GP1 and GP2 to yield a heterodimer linked by a disulfide bond
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NC_014373.1 RefSeq CDS 6905 8050 . + 0 Name=GP;gene=GP;gbkey=CDS;locus_tag=BDBVp4;exception=RNA editing;protein_id=YP_003815435.1;ID=cds-YP_003815435.1;product=spike glycoprotein;Dbxref=GenBank:YP_003815435.1,GeneID:9487265;Note=GP1%2C2%3B structural glycoprotein%3B cleaved by furin into subunits GP1 and GP2 to yield a heterodimer linked by a disulfide bond
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NC_014373.1 RefSeq CDS 6021 7142 . + 0 Name=GP_003;gene=GP;gbkey=CDS;locus_tag=BDBVp4;protein_id=YP_003815436.1;ID=cds-YP_003815436.1;product=small secreted glycoprotein;Dbxref=GenBank:YP_003815436.1,GeneID:9487265;Note=solulbe secreted glycoprotein%3B small non-structural secreted glycoprotein%3B sGP
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NC_014373.1 RefSeq CDS 8496 9365 . + 0 Name=VP30;gbkey=CDS;gene=VP30;locus_tag=BDBVp5;protein_id=YP_003815438.1;ID=cds-YP_003815438.1;product=minor nucleoprotein;Note=polymerase complex protein;Dbxref=GenBank:YP_003815438.1,GeneID:9487266
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NC_014373.1 RefSeq CDS 10335 11090 . + 0 Name=VP24;gbkey=CDS;gene=VP24;locus_tag=BDBVp6;protein_id=YP_003815439.1;ID=cds-YP_003815439.1;product=membrane-associated protein;Dbxref=GenBank:YP_003815439.1,GeneID:9487267
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NC_014373.1 RefSeq CDS 11567 18199 . + 0 Name=L;gene=L;gbkey=CDS;locus_tag=BDBVp7;protein_id=YP_003815440.1;ID=cds-YP_003815440.1;product=RNA-dependent RNA polymerase;Dbxref=GenBank:YP_003815440.1,GeneID:9487268;Note=synthesis of viral RNAs%3B transcriptional RNA editing

‎data_output/nextstrain/orthoebolavirus/bdbv/unreleased/pathogen.json‎

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{
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"$schema": "https://raw.githubusercontent.com/nextstrain/nextclade/refs/heads/release/packages/nextclade-schemas/input-pathogen-json.schema.json",
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"alignmentParams": {
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"excessBandwidth": 100,
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"terminalBandwidth": 300,
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"allowedMismatches": 10,
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"windowSize": 40,
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"minSeedCover": 0.03,
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"gapAlignmentSide": "left",
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"retryReverseComplement": true
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},
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"attributes": {
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"name": "Bundibugyo ebolavirus",
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"reference accession": "NC_014373.1",
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"reference name": "UGA/2007/Butalya-811250",
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"experimental": true
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},
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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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"files": {
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"treeJson": "tree.json",
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"changelog": "CHANGELOG.md",
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"examples": "examples.fasta",
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"genomeAnnotation": "genome_annotation.gff3",
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"pathogenJson": "pathogen.json",
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"readme": "README.md",
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"reference": "reference.fasta"
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},
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"defaultCds": "GP",
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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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"scoreWeight": 50
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},
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"missingData": {
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"enabled": true,
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"missingDataThreshold": 3000,
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"scoreBias": 500
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},
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"mixedSites": {
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"enabled": true,
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"mixedSitesThreshold": 20
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},
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"privateMutations": {
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"cutoff": 10,
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"enabled": true,
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"typical": 3,
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"weightLabeledSubstitutions": 3,
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"weightReversionSubstitutions": 3,
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"weightUnlabeledSubstitutions": 1
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},
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"snpClusters": {
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"clusterCutOff": 3,
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"enabled": true,
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"scoreWeight": 50,
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"windowSize": 50
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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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"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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},
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"schemaVersion": "3.0.0",
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"shortcuts": [
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"nextstrain/ebola/bdbv"
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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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}
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}

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