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fix: update mpox dataset schema fields #436

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Merged
ivan-aksamentov merged 1 commit into from
Mar 6, 2026
Merged

fix: update mpox dataset schema fields #436

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6 changes: 5 additions & 1 deletion data/nextstrain/mpox/all-clades/CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -1,3 +1,7 @@
## Unreleased

- Align `pathogen.json` metadata with the current Nextclade schema layout.

## 2025-12-16T20:07:31Z

- Fix clade labeling of some clade Ia sequences wrongly reported as `unassigned` instead of `Ia`.
Expand All @@ -9,7 +13,7 @@

## 2025-12-10T14:52:38Z

- Breaking change: outbreak nomenclature now follows the system described in [Ruis et al. (2025)](https://www.nature.com/articles/s41591-025-03820-6). As a result, outbreak `hMPXV-1` is now called `sh2017`. In addition, the clade Ib outbreak is labeled as outbreak `sh2023`, and the clade Ia outbreak described in [Wawina-Bokalanga et al. (2025)](https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(25)00294-6) is labeled as outbreak `sh2024`.
- Breaking change: outbreak nomenclature now follows the system described in [Ruis et al. (2025)](https://www.nature.com/articles/s41591-025-03820-6). As a result, outbreak `hMPXV-1` is now called `sh2017`. In addition, the clade Ib outbreak is labeled as outbreak `sh2023`, and the clade Ia outbreak described in [Wawina-Bokalanga et al. (2025)](<https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(25)00294-6>) is labeled as outbreak `sh2024`.
- The clade Ib/IIb recombinant described in [Pullan et al. (2025)](https://virological.org/t/inter-clade-recombinant-mpox-virus-detected-in-england-in-a-traveller-recently-returned-from-asia/1015) is included in the reference tree with the ad-hoc clade and outbreak labels `Ib/IIb` and `recombinant`, respectively.

## 2025-09-09T12:13:13Z
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7 changes: 1 addition & 6 deletions data/nextstrain/mpox/all-clades/pathogen.json
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Original file line number Diff line number Diff line change
Expand Up @@ -17,9 +17,6 @@
"cli": "3.0.0-alpha.0",
"web": "3.0.0-alpha.0"
},
"deprecated": false,
"enabled": true,
"experimental": false,
"files": {
"changelog": "CHANGELOG.md",
"examples": "sequences.fasta",
Expand All @@ -29,7 +26,6 @@
"reference": "reference.fasta",
"treeJson": "tree.json"
},
"official": true,
"qc": {
"frameShifts": {
"enabled": true,
Expand Down Expand Up @@ -159,8 +155,7 @@
"missingData": {
"enabled": true,
"missingDataThreshold": 50000,
"scoreBias": 1000,
"scoreWeight": 50
"scoreBias": 1000
},
"mixedSites": {
"enabled": true,
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6 changes: 5 additions & 1 deletion data/nextstrain/mpox/clade-i/CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -1,6 +1,10 @@
## Unreleased

- Align `pathogen.json` metadata with the current Nextclade schema layout.

## 2025-12-10T14:52:38Z

- Breaking change: outbreak nomenclature now follows the system described in [Ruis et al. (2025)](https://www.nature.com/articles/s41591-025-03820-6). As a result, outbreak `hMPXV-1` is now called `sh2017`. In addition, the clade Ib outbreak is labeled as outbreak `sh2023`, and the clade Ia outbreak described in [Wawina-Bokalanga et al. (2025)](https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(25)00294-6) is labeled as outbreak `sh2024`.
- Breaking change: outbreak nomenclature now follows the system described in [Ruis et al. (2025)](https://www.nature.com/articles/s41591-025-03820-6). As a result, outbreak `hMPXV-1` is now called `sh2017`. In addition, the clade Ib outbreak is labeled as outbreak `sh2023`, and the clade Ia outbreak described in [Wawina-Bokalanga et al. (2025)](<https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(25)00294-6>) is labeled as outbreak `sh2024`.

## 2025-09-09T12:13:13Z

Expand Down
7 changes: 1 addition & 6 deletions data/nextstrain/mpox/clade-i/pathogen.json
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Original file line number Diff line number Diff line change
Expand Up @@ -17,9 +17,6 @@
"cli": "3.0.0-alpha.0",
"web": "3.0.0-alpha.0"
},
"deprecated": false,
"enabled": true,
"experimental": false,
"files": {
"changelog": "CHANGELOG.md",
"examples": "sequences.fasta",
Expand All @@ -29,7 +26,6 @@
"reference": "reference.fasta",
"treeJson": "tree.json"
},
"official": true,
"qc": {
"frameShifts": {
"enabled": true,
Expand All @@ -40,8 +36,7 @@
"missingData": {
"enabled": true,
"missingDataThreshold": 50000,
"scoreBias": 1000,
"scoreWeight": 50
"scoreBias": 1000
},
"mixedSites": {
"enabled": true,
Expand Down
4 changes: 4 additions & 0 deletions data/nextstrain/mpox/clade-iib/CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -1,3 +1,7 @@
## Unreleased

- Align `pathogen.json` metadata with the current Nextclade schema layout.

## 2025-12-10T14:52:38Z

- Breaking change: outbreak nomenclature now follows the system described in [Ruis et al. (2025)](https://www.nature.com/articles/s41591-025-03820-6). As a result, outbreak `hMPXV-1` is now called `sh2017`.
Expand Down
7 changes: 1 addition & 6 deletions data/nextstrain/mpox/clade-iib/pathogen.json
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Original file line number Diff line number Diff line change
Expand Up @@ -17,9 +17,6 @@
"cli": "3.0.0-alpha.0",
"web": "3.0.0-alpha.0"
},
"deprecated": false,
"enabled": true,
"experimental": false,
"files": {
"changelog": "CHANGELOG.md",
"examples": "sequences.fasta",
Expand All @@ -29,7 +26,6 @@
"reference": "reference.fasta",
"treeJson": "tree.json"
},
"official": true,
"qc": {
"frameShifts": {
"enabled": true,
Expand All @@ -47,8 +43,7 @@
"missingData": {
"enabled": true,
"missingDataThreshold": 50000,
"scoreBias": 1000,
"scoreWeight": 50
"scoreBias": 1000
},
"mixedSites": {
"enabled": true,
Expand Down
4 changes: 4 additions & 0 deletions data/nextstrain/mpox/lineage-b.1/CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -1,3 +1,7 @@
## Unreleased

- Align `pathogen.json` metadata with the current Nextclade schema layout.

## 2025-12-10T14:52:38Z

- Breaking change: outbreak nomenclature now follows the system described in [Ruis et al. (2025)](https://www.nature.com/articles/s41591-025-03820-6). As a result, outbreak `hMPXV-1` is now called `sh2017`.
Expand Down
7 changes: 1 addition & 6 deletions data/nextstrain/mpox/lineage-b.1/pathogen.json
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -17,9 +17,6 @@
"cli": "3.0.0-alpha.0",
"web": "3.0.0-alpha.0"
},
"deprecated": false,
"enabled": true,
"experimental": false,
"files": {
"changelog": "CHANGELOG.md",
"examples": "sequences.fasta",
Expand Down Expand Up @@ -100,7 +97,6 @@
"95034G": ["rev"]
}
},
"official": true,
"qc": {
"frameShifts": {
"enabled": true,
Expand All @@ -109,8 +105,7 @@
"missingData": {
"enabled": true,
"missingDataThreshold": 50000,
"scoreBias": 1000,
"scoreWeight": 50
"scoreBias": 1000
},
"mixedSites": {
"enabled": true,
Expand Down