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WIP: Describe the different views
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j23414 committed Feb 27, 2025
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Special thanks to individuals at the [Northwest Pathogen Genomics Center of Excellence](https://github.com/NW-PaGe) and [Grubaugh lab](https://grubaughlab.com/) for comments, code and suggestions.

We maintain four views of WNV evolution:

The first is [`wnv/global`](https://next.nextstrain.org/staging/WNV/global), which focuses on broader viral diversity for all WNV sequences submitted to GenBank which contain at least 75% of the genome length.

The second is [`wnv/wa`](https://next.nextstrain.org/staging/WNV/global), which focuses on Washington State WNV virus sequences with tiered subsampling from Washington, the surrounding states, and across the USA.

The third is [`wnv/lineage-1A`](https://next.nextstrain.org/staging/WNV/lineage-1A), which focuses on lineage 1A and uses X as the reference.

The third is [`wnv/lineage-2`](https://next.nextstrain.org/staging/WNV/lineage-2), which focuses on lineage 2 and uses X as the reference.

#### Underlying data

We curate sequence data and metadata from NCBI as starting point for our analyses. For global lineage designations, we query [pathoplexus](https://pathoplexus.org/) for lineage assignments and exclusively work with NCBI-sourced records at this time. Curated sequences and metadata are available as flat files at:

* [data.nextstrain.org/files/workflows/WNV/sequences.fasta.zst](https://data.nextstrain.org/files/workflows/WNV/sequences.fasta.zst)
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