We gratefully acknowledge the authors, originating and submitting laboratories of the genetic sequences and metadata for sharing their work.

Special thanks to Richard Daodu and Laura McMullan for comments, code and suggestions.

Please note that although data generators have generously shared data in an open fashion, that does not mean there should be free license to publish on this data. Data generators should be cited where possible and collaborations should be sought in some circumstances. Please try to avoid scooping someone else's work. Reach out if uncertain.

Much of the genomic data here comes from publications [Andersen et al 2015](https://doi.org/10.1016/j.cell.2015.07.020), [Siddle et al 2018](https://doi.org/10.1056/NEJMoa1804498
) and [Kafetzopoulou et al 2019](https://doi.org/10.1126/science.aau9343), but with more recent sequences from NCBI may not yet be published.

We maintain two views of Lassa virus evolution: one showing evolution of the [L segment](https://nextstrain.org/lassa/l) and the other showing evolution of the [S segment](https://nextstrain.org/lassa/s). A tangle tree showing [co-evolution of L and S](https://nextstrain.org/lassa/l:lassa/s) is also available.

### Lineage Calling - Nextclade

Nextclade datasets for lineage assignment are available at the following links:

| Focus | Reference | Reference Tree | URL to Lassa Nextclade Dataset |
| :-- | :-- | :-- | :-- |
| GPC gene | [NC_004296 (Josiah)](https://github.com/nextstrain/lassa/blob/HEAD/nextclade/defaults/gpc/reference.fasta) | [View Tree](https://next.nextstrain.org/fetch/raw.githubusercontent.com/nextstrain/lassa/HEAD/nextclade_data/gpc/tree.json?d=tree&p=full) | [Query GPC Nextclade dataset](https://clades.nextstrain.org/?dataset-url=https://github.com/nextstrain/lassa/tree/HEAD/nextclade_data/gpc/) |
| L segment | [NC_004297 (Josiah)](https://github.com/nextstrain/lassa/blob/HEAD/nextclade/defaults/l/reference.fasta) | [View Tree](https://next.nextstrain.org/fetch/raw.githubusercontent.com/nextstrain/lassa/HEAD/nextclade_data/l/tree.json?d=tree&p=full) | [Query L-segment Nextclade dataset](https://clades.nextstrain.org/?dataset-url=https://github.com/nextstrain/lassa/tree/HEAD/nextclade_data/l/) |
| S segment | [NC_004296 (Josiah)](https://github.com/nextstrain/lassa/blob/HEAD/nextclade/defaults/s/reference.fasta) | [View Tree](https://next.nextstrain.org/fetch/raw.githubusercontent.com/nextstrain/lassa/HEAD/nextclade_data/s/tree.json?d=tree&p=full) | [Query S-segment Nextclade dataset](https://clades.nextstrain.org/?dataset-url=https://github.com/nextstrain/lassa/tree/HEAD/nextclade_data/s/) |

### Underlying data

We curate sequence data and metadata from NCBI as the starting point for our analyses. Curated sequences and metadata are available as flat files at:

##### L segment
* [data.nextstrain.org/files/workflows/lassa/l/sequences.fasta.zst](https://data.nextstrain.org/files/workflows/lassa/l/sequences.fasta.zst)
* [data.nextstrain.org/files/workflows/lassa/l/metadata.tsv.zst](https://data.nextstrain.org/files/workflows/lassa/l/metadata.tsv.zst)

##### S segment
* [data.nextstrain.org/files/workflows/lassa/s/sequences.fasta.zst](https://data.nextstrain.org/files/workflows/lassa/s/sequences.fasta.zst)
* [data.nextstrain.org/files/workflows/lassa/s/metadata.tsv.zst](https://data.nextstrain.org/files/workflows/lassa/s/metadata.tsv.zst)

##### Both segments combined
* [data.nextstrain.org/files/workflows/lassa/all/sequences.fasta.zst](https://data.nextstrain.org/files/workflows/lassa/all/sequences.fasta.zst)
* [data.nextstrain.org/files/workflows/lassa/all/metadata.tsv.zst](https://data.nextstrain.org/files/workflows/lassa/all/metadata.tsv.zst)

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