Update mpox datasets to support newly designated clade Ib outbreak sh2023 lineages

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

@@ -1,3 +1,8 @@
+## Unreleased
+
+- 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.
+- New sequences that have become available on Pathoplexus between December 2025 and June 2026 are now included in the dataset.
+
 ## 2026-04-14T11:55:23Z
 
 - Align `pathogen.json` metadata with the current Nextclade schema layout.

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

@@ -12,7 +12,11 @@
 
 ## Scope of this dataset
 
-This dataset is for Mpox viruses of all clades (Ia, Ib, IIa and IIb). For a focused analysis of sequences from clade IIb, you may want to use the more specific dataset: "Clade IIb" (`nextstrain/mpox/clade-iib`). For an even more focused analysis of 2022-2023 outbreak sequences (lineage B.1 and sublineages), you may want to use the even more specific dataset: "Lineage B.1" (`nextstrain/mpox/lineage-b.1`). For clade I sequences, you may want to use the dataset "Clade I" (`nextstrain/mpox/clade-i`).
+This dataset is for Mpox viruses of all clades (Ia, Ib, IIa and IIb). For a focused analysis of sequences from clade IIb, you may want to use the more specific dataset: "Clade IIb" (`nextstrain/mpox/clade-iib`). For an even more focused analysis of clade IIb outbreak sh2017 lineage B.1 sequences (lineage B.1 and sublineages), you may want to use the even more specific dataset: "Lineage B.1" (`nextstrain/mpox/lineage-b.1`). For clade I sequences, you may want to use the dataset "Clade I" (`nextstrain/mpox/clade-i`).
+
+## Clade, outbreak and lineage nomenclature
+
+The clade, outbreak and lineage nomenclature used in this dataset is described in [Ruis et al. (2025)](https://www.nature.com/articles/s41591-025-03820-6). Clades comprise Ia, Ib, IIa, and IIb. Outbreaks are labeled as `sh2017` (clade IIb), `sh2023` (clade Ib), and `sh2024` (clade Ia). Some outbreaks have lineage systems that follow [Happi et al. (2022)](https://doi.org/10.1371/journal.pbio.3001769). To unambiguously refer to a lineage, include the outbreak, e.g. `sh2017/B.1` for clade IIb outbreak sh2017 lineage B.1. Up to date outbreak and lineage definitions, including aliases, defining mutations and reference sequences are available at [github.com/mpxv-lineages/lineage-designation](https://github.com/mpxv-lineages/lineage-designation).
 
 ## Reference sequence and reference tree
 
@@ -22,6 +26,4 @@ Sequences for the reference tree come from NCBI/Genbank and are downsampled to a
 
 ## Further reading
 
-The lineage system used is described in [Happi et al. (2022)](https://doi.org/10.1371/journal.pbio.3001769). The sustained outbreak system is described in [Ruis et al. (2025)](https://www.nature.com/articles/s41591-025-03820-6). Lineage definitions are available at [github.com/mpxv-lineages/lineage-designation](https://github.com/nextstrain/mpox/nextclade).
-
 Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

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

@@ -1,3 +1,9 @@
+## Unreleased
+
+- 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.
+- New sequences that have become available on Pathoplexus between December 2025 and June 2026 are now included in the dataset.
+- The range 185990-186092 is no longer masked for placement. It is informative, reliable and relevant for assignment `sh2023/A.1`.
+
 ## 2026-04-14T11:55:23Z
 
 - Align `pathogen.json` metadata with the current Nextclade schema layout.

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

@@ -23,8 +23,10 @@ This is in contrast to the reference used in the other Nextclade mpox datasets,
 
 The reference tree consists of all good quality clade I sequences available within Genbank at the time of dataset creation (with identical sequences deduplicated to 1), as well as 3 outgroup genomes (a reconstructed ancestor of all clades, and one sequence for each of clade IIa and clade IIb).
 
-## Further reading
+## Clade, outbreak and lineage nomenclature
+
+The clade, outbreak and lineage nomenclature used in this dataset is described in [Ruis et al. (2025)](https://www.nature.com/articles/s41591-025-03820-6). Clade I comprises clades Ia and Ib. The clade Ib outbreak is labeled `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 `sh2024`. Clade Ib outbreak sh2023 now has a lineage system that follows [Happi et al. (2022)](https://doi.org/10.1371/journal.pbio.3001769), reusing the same lineage names as clade IIb outbreak sh2017. To unambiguously refer to a lineage, include the outbreak, e.g. `sh2023/A.1` for clade Ib outbreak sh2023 lineage A.1. Up to date outbreak and lineage definitions, including aliases, defining mutations and reference sequences are available at [github.com/mpxv-lineages/lineage-designation](https://github.com/mpxv-lineages/lineage-designation).
 
-The sustained outbreak system is described in [Ruis et al. (2025)](https://www.nature.com/articles/s41591-025-03820-6). Outbreak definitions are available at [github.com/mpxv-lineages/lineage-designation](https://github.com/nextstrain/mpox/nextclade).
+## Further reading
 
 Read more about Nextclade datasets in the Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

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

@@ -1,3 +1,8 @@
+## Unreleased
+
+- 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.
+- New sequences that have become available on Pathoplexus between December 2025 and June 2026 are now included in the dataset.
+
 ## 2026-04-14T11:55:23Z
 
 - Align `pathogen.json` metadata with the current Nextclade schema layout.

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

@@ -20,8 +20,10 @@ The reference used in this dataset is the clade IIb NCBI refseq `NC_063383.1` (I
 
 The reference tree consists of around 500 sequences with representatives from all clade IIb lineages.
 
-## Further reading
+## Clade, outbreak and lineage nomenclature
+
+The clade, outbreak and lineage nomenclature used in this dataset is described in [Ruis et al. (2025)](https://www.nature.com/articles/s41591-025-03820-6). Clade IIb sequences belong to outbreak `sh2017`, which has a lineage system that follows [Happi et al. (2022)](https://doi.org/10.1371/journal.pbio.3001769). To unambiguously refer to a lineage, include the outbreak, e.g. `sh2017/B.1` for clade IIb outbreak sh2017 lineage B.1. This matters because other outbreaks (e.g. clade Ib outbreak sh2023) reuse the same lineage names. Up to date outbreak and lineage definitions, including aliases, defining mutations and reference sequences are available at [github.com/mpxv-lineages/lineage-designation](https://github.com/mpxv-lineages/lineage-designation).
 
-The lineage system used is defined in [Happi et al. (2022)](https://doi.org/10.1371/journal.pbio.3001769). Lineage definitions are available at [github.com/mpxv-lineages/lineage-designation](https://github.com/nextstrain/mpox/nextclade).
+## Further reading
 
 Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

data/nextstrain/mpox/lineage-b.1/CHANGELOG.md

@@ -1,3 +1,8 @@
+## Unreleased
+
+- 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.
+- New sequences that have become available on Pathoplexus between December 2025 and June 2026 are now included in the dataset.
+
 ## 2026-04-14T11:55:23Z
 
 - Align `pathogen.json` metadata with the current Nextclade schema layout.

data/nextstrain/mpox/lineage-b.1/README.md

@@ -12,16 +12,18 @@
 
 ## Scope of this dataset
 
-This dataset is for Mpox viruses of the 2022-2023 outbreak lineage B.1. Two broader datasets for clade IIb and all clades are available as well: `nextstrain/mpox/clade-iib` for Clade IIb and `nextstrain/mpox/all-clades` for all clades (I, IIa and IIb).
+This dataset is for Mpox viruses of clade IIb outbreak sh2017 lineage B.1 (the 2022 global outbreak lineage). Two broader datasets for clade IIb and all clades are available as well: `nextstrain/mpox/clade-iib` for Clade IIb and `nextstrain/mpox/all-clades` for all clades (I, IIa and IIb).
 
 ## Reference sequence and reference tree
 
 The reference used in this dataset is the clade IIb NCBI refseq `NC_063383.1` (Isolate `MPXV-M5312_HM12_Rivers`) with all B.1 defining SNPs added to make the mutation view less cluttered.
 
 The reference tree consists of around 1000 sequences with representatives from all B.1 sublineages.
 
-## Further reading
+## Clade, outbreak and lineage nomenclature
+
+The clade, outbreak and lineage nomenclature used in this dataset is described in [Ruis et al. (2025)](https://www.nature.com/articles/s41591-025-03820-6). Lineage B.1 belongs to clade IIb outbreak `sh2017`, which has a lineage system that follows [Happi et al. (2022)](https://doi.org/10.1371/journal.pbio.3001769). To unambiguously refer to a lineage, include the outbreak, e.g. `sh2017/B.1` for clade IIb outbreak sh2017 lineage B.1. This matters because other outbreaks (e.g. clade Ib outbreak sh2023) reuse the same lineage names. Up to date outbreak and lineage definitions, including aliases, defining mutations and reference sequences are available at [github.com/mpxv-lineages/lineage-designation](https://github.com/mpxv-lineages/lineage-designation).
 
-The lineage system used is defined in [Happi et al. (2022)](https://doi.org/10.1371/journal.pbio.3001769). The sustained outbreak system is described in [Ruis et al. (2025)](https://www.nature.com/articles/s41591-025-03820-6). Lineage definitions are available at [github.com/mpxv-lineages/lineage-designation](https://github.com/nextstrain/mpox/nextclade).
+## Further reading
 
 Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

data_output/index.json

@@ -1804,7 +1804,8 @@
             "clades": 8,
             "customClades": {
               "outbreak": 4,
-              "lineage": 59
+              "lineage": 62,
+              "outbreakLineage": 66
             },
             "qc": [
               "frameShifts",
@@ -1816,6 +1817,13 @@
             ]
           },
           "versions": [
+            {
+              "tag": "unreleased",
+              "compatibility": {
+                "cli": "3.0.0-alpha.0",
+                "web": "3.0.0-alpha.0"
+              }
+            },
             {
               "updatedAt": "2026-04-14T11:55:23Z",
               "tag": "2026-04-14--11-55-23Z",
@@ -1898,8 +1906,7 @@
             }
           ],
           "version": {
-            "updatedAt": "2026-04-14T11:55:23Z",
-            "tag": "2026-04-14--11-55-23Z",
+            "tag": "unreleased",
             "compatibility": {
               "cli": "3.0.0-alpha.0",
               "web": "3.0.0-alpha.0"
@@ -1925,7 +1932,9 @@
           "capabilities": {
             "clades": 4,
             "customClades": {
-              "outbreak": 2
+              "outbreak": 2,
+              "lineage": 7,
+              "outbreakLineage": 7
             },
             "qc": [
               "frameShifts",
@@ -1937,6 +1946,13 @@
             ]
           },
           "versions": [
+            {
+              "tag": "unreleased",
+              "compatibility": {
+                "cli": "3.0.0-alpha.0",
+                "web": "3.0.0-alpha.0"
+              }
+            },
             {
               "updatedAt": "2026-04-14T11:55:23Z",
               "tag": "2026-04-14--11-55-23Z",
@@ -1995,8 +2011,7 @@
             }
           ],
           "version": {
-            "updatedAt": "2026-04-14T11:55:23Z",
-            "tag": "2026-04-14--11-55-23Z",
+            "tag": "unreleased",
             "compatibility": {
               "cli": "3.0.0-alpha.0",
               "web": "3.0.0-alpha.0"
@@ -2026,7 +2041,8 @@
             "clades": 2,
             "customClades": {
               "outbreak": 1,
-              "lineage": 59
+              "lineage": 59,
+              "outbreakLineage": 59
             },
             "qc": [
               "frameShifts",
@@ -2038,6 +2054,13 @@
             ]
           },
           "versions": [
+            {
+              "tag": "unreleased",
+              "compatibility": {
+                "cli": "3.0.0-alpha.0",
+                "web": "3.0.0-alpha.0"
+              }
+            },
             {
               "updatedAt": "2026-04-14T11:55:23Z",
               "tag": "2026-04-14--11-55-23Z",
@@ -2096,8 +2119,7 @@
             }
           ],
           "version": {
-            "updatedAt": "2026-04-14T11:55:23Z",
-            "tag": "2026-04-14--11-55-23Z",
+            "tag": "unreleased",
             "compatibility": {
               "cli": "3.0.0-alpha.0",
               "web": "3.0.0-alpha.0"
@@ -2127,7 +2149,8 @@
             "clades": 2,
             "customClades": {
               "outbreak": 1,
-              "lineage": 46
+              "lineage": 46,
+              "outbreakLineage": 46
             },
             "qc": [
               "frameShifts",
@@ -2142,6 +2165,13 @@
             ]
           },
           "versions": [
+            {
+              "tag": "unreleased",
+              "compatibility": {
+                "cli": "3.0.0-alpha.0",
+                "web": "3.0.0-alpha.0"
+              }
+            },
             {
               "updatedAt": "2026-04-14T11:55:23Z",
               "tag": "2026-04-14--11-55-23Z",
@@ -2200,8 +2230,7 @@
             }
           ],
           "version": {
-            "updatedAt": "2026-04-14T11:55:23Z",
-            "tag": "2026-04-14--11-55-23Z",
+            "tag": "unreleased",
             "compatibility": {
               "cli": "3.0.0-alpha.0",
               "web": "3.0.0-alpha.0"