nextstrain · xonq · Aug 6, 2025 · Aug 6, 2025 · Aug 6, 2025 · Aug 6, 2025
diff --git a/data/community/collection.json b/data/community/collection.json
@@ -29,6 +29,7 @@
     "community/v-gen-lab/dengue/denv2",
     "community/v-gen-lab/dengue/denv3",
     "community/v-gen-lab/dengue/denv4",
-    "community/genspectrum/marburg/HK1980/all-lineages"
+    "community/genspectrum/marburg/HK1980/all-lineages",
+    "community/theiagen/rabies/all-clades"
   ]
 }
diff --git a/data/community/theiagen/rabies/all-clades/CHANGELOG.md b/data/community/theiagen/rabies/all-clades/CHANGELOG.md
@@ -0,0 +1,3 @@
+## Unreleased
+
+Initial release of *Lyssavirus rabies* Nextclade dataset.
diff --git a/data/community/theiagen/rabies/all-clades/README.md b/data/community/theiagen/rabies/all-clades/README.md
@@ -0,0 +1,124 @@
+# Example dataset for Rabies virus
+
+This is a minimal example dataset for *Lyssavirus rabies*. 
+
+# Overview
+
+The phylogenetic tree was generated from all complete *Lyssavirus rabies* genomes obtained from [NCBI Nucleotide](https://ftp.ncbi.nlm.nih.gov/genomes/Viruses/AllNuclMetadata/) (accessed 2025/05/01) with > 95% unambiguous nucleotides and < 15,000 bp. Clade, subclade, and other associated metadata were acquired referencing the original rabies Nextstrain build and [RABV-GLUE's metadata](https://github.com/giffordlabcvr/RABV-GLUE/blob/master/tabular/reference-set-data.tsv). Clade- and subclade-specific mutations [were extracted for all monophyletic major and minor lineages](https://github.com/theiagen/utilities/pull/21), and disregarded for previously assigned clades that were not monophyletic in the phylogeny. Complete genome assemblies were aligned with `mafft v7.525` using default parameters and the phylogeny was reconstructed using `iqtree v2.4.0` with 1000 ultrafast bootstrap iterations and GTR+F+I+R7 selected as the evolutionary model by the *ModelFinder* module. A root node internal to the *L. rabies* phylogeny was selected by reconstructing an additional phylogeny using the same methodology with *L. australis* (NC_003243.1) and *L. gannoruwa* (KU244266.2) included as known outgroups ([Baynard & Fooks, 2021](https://doi.org/10.1016/B978-0-12-809633-8.20936-9)).
+
+# Metadata acquisition
+
+Clade classification metadata was acquired from [RABV-GLUE's metadata](https://github.com/giffordlabcvr/RABV-GLUE/blob/master/tabular/reference-set-data.tsv) (referenced [2025/06/01](https://github.com/giffordlabcvr/RABV-GLUE/blob/357613e78c397e10499e77bbd6f2b5aeeb9d10e6/tabular/reference-set-data.tsv#L4)). Sample, submitter, location, and host metadata was acquired from NCBI using the following `datasets` command:
+
+```bash
+datasets summary virus genome accession \
+  --inputfile <ACCESIONS> \
+  --as-json-lines | \
+dataformat tsv virus-genome \
+  --fields accession,geo-region,host-common-name,submitter-names,isolate-collection-date
+```
+
+# Included clades
+
+We conservatively assigned clades as all accessions that descend from a most-recent common ancestor (MRCA) of classified accessions within the metadata. Subclades that were not monophyletic or did not contain uniquely defining mutations were removed. Clade-defining mutations were extracted using a [script](https://github.com/theiagen/utilities/blob/4c5a1126aa20d4a767fa709842242c156014daa7/scripts/extract_nextclades.py). The following are the accounted clades, except where exclusion criteria are noted:
+
+| Clade | Subclade | Exclusion Criteria |
+|-------|----------|-------------------|
+| Africa-2 | - | - |
+| Africa-3 | - | - |
+| Arctic | - | - |
+| Arctic | A | - |
+| Arctic | AL1a | - |
+| Arctic | AL1b | - |
+| Arctic | AL2 | - |
+| Arctic | <s>AL3</s> | Mutations are not unique |
+| Asian | - | - |
+| Asian | SEA1a | - |
+| Asian | SEA1b | - |
+| Asian | SEA2a | - |
+| Asian | SEA2b | - |
+| Asian | SEA3 | - |
+| Asian | SEA4 | - |
+| Asian | SEA5 | - |
+| Bats | - | - |
+| Bats | <s>AP</s> | Mutations are not unique |
+| Bats | DR | - |
+| Bats | <s>EF-E1</s> | Mutations are not unique |
+| Bats | <s>EF-E2</s> | Mutations are not unique |
+| Bats | EF-W1 | - |
+| Bats | EF-W2 | - |
+| Bats | <s>LB1</s> | Mutations are not unique |
+| Bats | <s>LB2</s> | Mutations are not unique |
+| Bats | <s>LC</s> | Mutations are not unique |
+| Bats | LI | - |
+| Bats | <s>LN</s> | Mutations are not unique |
+| Bats | <s>LS</s> | Mutations are not unique |
+| Bats | <s>LX</s> | Mutations are not unique |
+| Bats | MYsp | - |
+| Bats | <s>MYu</s> | Mutations are not unique |
+| Bats | <s>PH</s> | Not monophyletic |
+| Bats | PS | - |
+| Bats | TB1 | - |
+| Bats | TB2 | - |
+| Cosmopolitan | - | - |
+| Cosmopolitan | AF1a | - |
+| Cosmopolitan | AF1b | - |
+| Cosmopolitan | AF1c | - |
+| Cosmopolitan | AF4 | - |
+| Cosmopolitan | AM1 | - |
+| Cosmopolitan | AM2a | - |
+| Cosmopolitan | AM2b | - |
+| Cosmopolitan | AM3a | - |
+| Cosmopolitan | AM3b | - |
+| Cosmopolitan | AM4 | - |
+| Cosmopolitan | CA1 | - |
+| Cosmopolitan | CA2 | - |
+| Cosmopolitan | CA3 | - |
+| Cosmopolitan | CE | - |
+| Cosmopolitan | EE | - |
+| Cosmopolitan | ME1a | - |
+| Cosmopolitan | ME1b | - |
+| Cosmopolitan | ME2 | - |
+| Cosmopolitan | NEE | - |
+| Cosmopolitan | Vac | - |
+| Cosmopolitan | <s>Vac2</s> | Mutations are not unique |
+| Cosmopolitan | WE | - |
+| Cosmopolitan | <s>YUGCOW</s> | Mutations are not unique |
+| Cosmopolitan | <s>YUGFOX</s> | Mutations are not unique |
+| Indian-Sub | - | - |
+| RAC-SK | - | - |
+
+
+# Phylogenetic tree reconstruction
+
+The tree was generated using the following commands:
+
+Align relative to the reference sequence
+```bash
+augur align -s rabv.fna --nthreads 8 --output rabv.mafft.fna --reference-name NC_001542.1 --debug
+```
+
+Build the tree with 1000 ultrafast bootstrap iterations
+```bash
+iqtree -s rabv.mafft.fna -B 1000 -m GTR+F+I+R7
+```
+
+Root the tree with the MRCA of the identified outgroup sequences
+```python
+from ete3 import Tree
+
+t = Tree('rabv.mafft.fna.contree')
+mrca = t.get_common_ancestor(['OU524413.1', 'JQ685954.1'])
+t.set_outgroup(mrca)
+
+with open('rabv.rooted.newick', 'w') as out:
+    out.write(t.write())
+```
+
+# References
+
+- Troupin C, Dacheux L, Tanguy M, Sabeta C, Blanc H, Bouchier C, Vignuzzi M, Duchene S, Holmes E C, Bourhy H. Large-Scale Phylogenomic Analysis Reveals the Complex Evolutionary History of Rabies Virus in Multiple Carnivore Hosts. PLoS Pathog 2016 Dec, 15;12(12):e1006041. doi:10.1371/journal.ppat.1006041.
+
+- Campbell F, Blank L, Cantrell A, Baxter S, Blackmore C, Dixon J, Goyder E. Factors that influence mental health of university and college students in the UK: a systematic review. BMC Public Health. 2022 Sep 20;22(1):1778. doi: 10.1186/s12889-022-13943-x.
+
+- Baynard A, Fooks A. Rabies and Other Lyssaviruses (Rhabdoviridae). Encyclopedia of Virology 2021 Mar, 1;4(1):738. doi:doi.org/10.1016/B978-0-12-809633-8.20936-9.
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		## Unreleased

		Initial release of Lyssavirus rabies Nextclade dataset.