Merge pull request #192 from nextstrain/mpox-2024-04

Update mpox datasets to include new lineages B.1.21, B.1.22, and C.1.1
nextstrain · Apr 17, 2024 · 83de556 · 83de556
2 parents fb4a856 + 6016124
commit 83de556
Show file tree

Hide file tree

Showing 31 changed files with 2,015 additions and 9 deletions.
diff --git a/data/nextstrain/mpox/all-clades/CHANGELOG.md b/data/nextstrain/mpox/all-clades/CHANGELOG.md
@@ -1,3 +1,8 @@
+## Unreleased
+
+- New hMPXV-1 lineages B.1.21, B.1.22, and C.1.1 are now included in the dataset. For more information on these lineages, see the [hMPXV-1 lineage definitions PR](https://github.com/mpxv-lineages/lineage-designation/pull/37)
+- The sequences used in the reference trees have been updated to include the latest sequences available in Genbank as of 2024-04-16
+
 ## 2024-01-16T20:31:02Z
 
 Initial release of this dataset. This dataset is similar to the v2 dataset [`MPXV/ancestral`](https://github.com/nextstrain/nextclade_data/tree/2023-08-17--15-51-24--UTC/data/datasets/MPXV/references/ancestral/versions/2023-08-01T12%3A00%3A00Z/files) with some differences.

diff --git a/data/nextstrain/mpox/all-clades/tree.json b/data/nextstrain/mpox/all-clades/tree.json
diff --git a/data/nextstrain/mpox/clade-iib/CHANGELOG.md b/data/nextstrain/mpox/clade-iib/CHANGELOG.md
@@ -1,3 +1,8 @@
+## Unreleased
+
+- New hMPXV-1 lineages B.1.21, B.1.22, and C.1.1 are now included in the dataset. For more information on these lineages, see the [hMPXV-1 lineage definitions PR](https://github.com/mpxv-lineages/lineage-designation/pull/37)
+- The sequences used in the reference trees have been updated to include the latest sequences available in Genbank as of 2024-04-16
+
 ## 2024-01-16T20:31:02Z
 
 Initial release of this dataset. This dataset is similar to the v2 dataset [`hMPXV/NC_063383.1`](https://github.com/nextstrain/nextclade_data/tree/2023-08-17--15-51-24--UTC/data/datasets/hMPXV/references/NC_063383.1/versions/2023-08-01T12%3A00%3A00Z/files) with some differences.

diff --git a/data/nextstrain/mpox/clade-iib/tree.json b/data/nextstrain/mpox/clade-iib/tree.json
diff --git a/data/nextstrain/mpox/lineage-b.1/CHANGELOG.md b/data/nextstrain/mpox/lineage-b.1/CHANGELOG.md
@@ -1,3 +1,8 @@
+## Unreleased
+
+- New hMPXV-1 lineages B.1.21, B.1.22, and C.1.1 are now included in the dataset. For more information on these lineages, see the [hMPXV-1 lineage definitions PR](https://github.com/mpxv-lineages/lineage-designation/pull/37)
+- The sequences used in the reference trees have been updated to include the latest sequences available in Genbank as of 2024-04-16
+
 ## 2024-01-16T20:31:02Z
 
 Initial release of this dataset. This dataset is similar to the v2 dataset [`hMPXV_B.1/pseudo_ON563414`](https://github.com/nextstrain/nextclade_data/tree/2023-08-17--15-51-24--UTC/data/datasets/hMPXV_B.1/references/pseudo_ON563414/versions/2023-08-01T12%3A00%3A00Z/files) with some differences.

diff --git a/data/nextstrain/mpox/lineage-b.1/tree.json b/data/nextstrain/mpox/lineage-b.1/tree.json
diff --git a/data_output/index.json b/data_output/index.json
@@ -1357,6 +1357,13 @@
             ]
           },
           "versions": [
+            {
+              "tag": "unreleased",
+              "compatibility": {
+                "cli": "3.0.0-alpha.0",
+                "web": "3.0.0-alpha.0"
+              }
+            },
             {
               "updatedAt": "2024-01-16T20:31:02Z",
               "tag": "2024-01-16--20-31-02Z",
@@ -1367,8 +1374,7 @@
             }
           ],
           "version": {
-            "updatedAt": "2024-01-16T20:31:02Z",
-            "tag": "2024-01-16--20-31-02Z",
+            "tag": "unreleased",
             "compatibility": {
               "cli": "3.0.0-alpha.0",
               "web": "3.0.0-alpha.0"
@@ -1406,6 +1412,13 @@
             ]
           },
           "versions": [
+            {
+              "tag": "unreleased",
+              "compatibility": {
+                "cli": "3.0.0-alpha.0",
+                "web": "3.0.0-alpha.0"
+              }
+            },
             {
               "updatedAt": "2024-01-16T20:31:02Z",
               "tag": "2024-01-16--20-31-02Z",
@@ -1416,8 +1429,7 @@
             }
           ],
           "version": {
-            "updatedAt": "2024-01-16T20:31:02Z",
-            "tag": "2024-01-16--20-31-02Z",
+            "tag": "unreleased",
             "compatibility": {
               "cli": "3.0.0-alpha.0",
               "web": "3.0.0-alpha.0"
@@ -1458,6 +1470,13 @@
             ]
           },
           "versions": [
+            {
+              "tag": "unreleased",
+              "compatibility": {
+                "cli": "3.0.0-alpha.0",
+                "web": "3.0.0-alpha.0"
+              }
+            },
             {
               "updatedAt": "2024-01-16T20:31:02Z",
               "tag": "2024-01-16--20-31-02Z",
@@ -1468,8 +1487,7 @@
             }
           ],
           "version": {
-            "updatedAt": "2024-01-16T20:31:02Z",
-            "tag": "2024-01-16--20-31-02Z",
+            "tag": "unreleased",
             "compatibility": {
               "cli": "3.0.0-alpha.0",
               "web": "3.0.0-alpha.0"

diff --git a/data_output/nextstrain/mpox/all-clades/unreleased/CHANGELOG.md b/data_output/nextstrain/mpox/all-clades/unreleased/CHANGELOG.md
@@ -0,0 +1,18 @@
+## Unreleased
+
+- New hMPXV-1 lineages B.1.21, B.1.22, and C.1.1 are now included in the dataset. For more information on these lineages, see the [hMPXV-1 lineage definitions PR](https://github.com/mpxv-lineages/lineage-designation/pull/37)
+- The sequences used in the reference trees have been updated to include the latest sequences available in Genbank as of 2024-04-16
+
+## 2024-01-16T20:31:02Z
+
+Initial release of this dataset. This dataset is similar to the v2 dataset [`MPXV/ancestral`](https://github.com/nextstrain/nextclade_data/tree/2023-08-17--15-51-24--UTC/data/datasets/MPXV/references/ancestral/versions/2023-08-01T12%3A00%3A00Z/files) with some differences.
+
+### New and changed gene names
+
+Some genes have been renamed and one has been added. The new annotation is based on NCBI refseq annotations that were released in November 2022. The v2 dataset predates this refseq:
+
+- The 4 genes in the inverted terminal repeat segment (ITR) on both ends of the genome (OPG001, OPG002, OPG003,OPG015) are now all included. The genes on the 3' end (~positions 190000-197000) now have an `_dup` appended to distinguish them.
+- The gene previously named `NBT03_gp052` is now called `OPG073`
+- The gene previously named `NBT03_gp174` is now called `OPG016`
+- The gene previously named `NBT03_gp175` is now called `OPG015_dup`
+- Gene `OPG166` has been added
diff --git a/data_output/nextstrain/mpox/all-clades/unreleased/README.md b/data_output/nextstrain/mpox/all-clades/unreleased/README.md
@@ -0,0 +1,27 @@
+# Nextclade dataset for "Mpox virus (All Clades)"
+
+| Key                    | Value                                                                                                                 |
+| ---------------------- | --------------------------------------------------------------------------------------------------------------------- |
+| authors                | [Cornelius Roemer](https://neherlab.org), [Richard Neher](https://neherlab.org), [Nextstrain](https://nextstrain.org) |
+| data source            | Genbank                                                                                                               |
+| workflow               | [github.com/nextstrain/mpox/nextclade](https://github.com/nextstrain/mpox/nextclade)                                  |
+| nextclade dataset path | nextstrain/mpox/all-clades                                                                                            |
+| annotation             | [NC_063383.1](https://www.ncbi.nlm.nih.gov/nuccore/NC_063383)                                                         |
+| clade definitions      | [github.com/mpxv-lineages/lineage-designation](https://github.com/mpxv-lineages/lineage-designation)                  |
+| related datasets       | Mpox virus (Clade IIb): `nextstrain/mpox/clade-iib`<br> Mpox virus (Lineage B.1) `nextstrain/mpox/lineage-b.1`        |
+
+## Scope of this dataset
+
+This dataset is for Mpox viruses of all clades (I, 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`).
+
+## 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`).
+
+Sequences for the reference tree come from NCBI/Genbank and are downsampled to around 500 sequences from the diversity of clades, lineages, countries and collection dates.
+
+## Further reading
+
+The lineage system used is described 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).
+
+Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html
diff --git a/data_output/nextstrain/mpox/all-clades/unreleased/dataset.zip b/data_output/nextstrain/mpox/all-clades/unreleased/dataset.zip