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About

This repository analyzes West Nile Viral (WNV) genomes using Nextstrain to understand the circulation and transmission of WNV within the United States. This repository was developed based on the WNV repository used for the Twenty years of West Nile Virus in the Americas Nextstrain Narrative

Data

This build pulls WNV genomes that are publicly available from NCBI.

Installation

Follow the standard installation instructions for Nextstrain's suite of software tools.

Clone this repository

git clone https://github.com/nextstrain/WNV.git
cd WNV

Try running Augur and Auspice

augur -help
auspice -help

Run the build

This build can process and output global or Washington state focused WNV information. The build can also be run by workflows which is helpful when troubleshoting or all at once.

To run the build by workflows first run the ingest workflow

nextstrain build ingest

Inside the ingest folder there should be two output files: metadata_all.tsv and sequences_all.tsv

Run the phylogenetic workflow Execute the global build

nextstrain build phylogenetic

Or execute the Washington focused build

nextstrain build phylogenetic --configfile build-configs/washington-state/config.yaml

Inside the phylogenetic folder there should be at least one output file: WNV-nextstrain_NA.json

Run the build all at once. This option defaults to the global build.

nextstrain build phylogenetic

File Structure

This Nextstrain build follows the structure detailed in the Pathogen Repo Guide

Decision Points

The following are critical decisions that were made during the development of the WNV build that should be kept in mind when analyzing the data.

Global and Washington Focused Outputs

This build can process and output global or Washington state focused WNV information. To accomplish this, a washington-state.yaml file was added to the build-configs which specifies Washington subsampling preferences. This file can be adopted and mofidied to accomodate other sampling references appropiate to other regions or states.

Root Selection

The Global and the Washington focused WNV builds use different roots.

The Global WNV build uses the sequence AF260968 which is the first WNV L1 (cluster 1) strain recovered in Egypt from 1951. Mencattelli, G., Ndione, M.H.D., Silverj, A. et al. Spatial and temporal dynamics of West Nile virus between Africa and Europe. Nat Commun 14, 6440 (2023). https://doi.org/10.1038/s41467-023-42185-7

The Washington focused WNV build uses the sequence AF481864 as this is the sequence that is most closely related to the sequences isolated from New York in 1999. Hadfield J, Brito AF, Swetnam DM, Vogels CBF, Tokarz RE, Andersen KG, Smith RC, Bedford T, Grubaugh ND. Twenty years of West Nile virus spread and evolution in the Americas visualized by Nextstrain. PLoS Pathog. 2019 Oct 31;15(10):e1008042. doi: 10.1371/journal.ppat.1008042. PMID: 31671157; PMCID: PMC6822705.

Subsampling

The Washington focused WNV build pulls all the WNV sequences available in NCBI and filters the data in the phylogenetic workflow based on criteria defined in the config.yml file that is located inside the build-configs/washington-state folder. The subsampling criteria focuses on geographic location selecting all sequences from Washington, neighboring states, and region but up to a maximum of 5,000 sequences; and up to 300 sequences selected randomly from the rest of the states. All sequences have to meet a minimum genome length that is also specified as part of the subsampling criteria. There is more information about how to subsample data in Nextstrain here Filter and Subsampling

Lineage Designation

For global lineage designations, we query pathoplexus

Host mapping to Host Genus and Host Type

We further refined the information in the NCBI Host column by categorizing it into Host_Genus and Host_Type, creating broader groupings for more effective data analysis. For example, the Host Homo sapiens is classified under Host_Genus as Homo and Host_Type as Human. This broader categorization is particularly useful for visualizing the phylogenetic tree. Instead of distinguishing between individual mosquito species, you can use the broader categories like Host_Genus Culex or the higher-level category Host_Type Mosquito to color the tips of the tree.