# LASV dataset

| Key  | Value  |
| :-- | :-- |
| name  | Lassa GPC Tree |
| authors | [Nextstrain](https://nextstrain.org) |
| reference | NC_004296 |
| workflow  | https://github.com/nextstrain/lassa/tree/main/nextclade  |
| path  | `nextstrain/lassa` |


## Scope of this dataset

This Nextclade dataset places query sequences on a GPC scaffold tree for Lassa lineage assignments.

## References


| reference | paper | note |
| --- | --- | --- |
| 2019Ehichioya | Ehichioya, D.U., Dellicour, S., Pahlmann, M., Rieger, T., Oestereich, L., Becker-Ziaja, B., Cadar, D., Ighodalo, Y., Olokor, T., Omomoh, E. and Oyakhilome, J., 2019. [Phylogeography of Lassa virus in Nigeria](https://doi.org/10.1128/jvi.00929-19). _Journal of virology_, _93_(21), pp.10-1128. | lineage VI* (cluster c) |
| 2025Daodu | Daodu, Richard Olumide, Ebenezer Awotoro, Jens-Uwe Ulrich, and Denise Kühnert. [CLASV: Rapid Lassa virus lineage assignment with random forest](https://doi.org/10.1371/journal.pntd.0013512). _PLOS Neglected Tropical Diseases_ 19, no. 9 (2025): e0013512. | https://github.com/JoiRichi/CLASV/<br>https://github.com/JoiRichi/LASV_ML_manuscript_data |
| RefSeq | | Based on RefSeq annotation |
| GenBank | | Based on GenBank annotation |
| manuallAnnotationDaodu | | Based on manual annotation with link to commit |
| 2015Andersen | Andersen, K.G., Shapiro, B.J., Matranga, C.B., Sealfon, R.S., Lin, A.E., et al., 2015. [Clinical Sequencing Uncovers Origins and Evolution of Lassa Virus](https://doi.org/10.1016/j.cell.2015.07.020). _Cell_, _162_(4): 738–750. | origins and evolution — Lineages I–IV |
| 2015Manning | Manning, J.T., Forrester, N., & Paessler, S., 2015. [Lassa virus isolates from Mali and the Ivory Coast represent an emerging fifth lineage](https://doi.org/10.3389/fmicb.2015.01037). _Frontiers in Microbiology_, _6_: 1037. | lineage V |
| 2016Olayemi | Olayemi, A., Cadar, D., Magassouba, N., Obadare, A., Kourouma, F., et al., 2016. [New Hosts of The Lassa Virus](https://doi.org/10.1038/srep25280). _Scientific Reports_, _6_: 25280. | new hosts — lineage VI |
| 2018Whitmer | Whitmer, S.L.M., Strecker, T., Cadar, D., Dienes, H.-P., Faber, K., et al., 2018. [New Lineage of Lassa Virus, Togo, 2016](https://doi.org/10.3201/eid2403.171905). _Emerging Infectious Diseases_, _24_(3): 599–602. | lineage VII (combination of lineages IV and V) |

## Features

This dataset supports:

- Assignment of lineages
- Phylogenetic placement
- Sequence quality control (QC)

## What are Nextclade datasets

Read more about Nextclade datasets in the Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html
