Overview

Summary

By partnering with West Nile virus surveillance labs across the country, the WestNile 4K Project is planning to sequence more than 4,000 virus genomes to reconstruct a high definition picture of West Nile virus spread and evolution during the last 20 years in the United States. The data that they generate will be immediately released and, along with other entomological data, will be used to uncover local transmission dynamics. As little progress has been made in effectively controlling West Nile virus outbreaks since its emergence, their goal is to use fine-scale transmission networks revealed through virus genomics to better design targeted control measures.

Collaborators

RegionCollaborators
San Diego county, CaliforniaNikos Garfield and Saran Grewal from the San Diego County Vector Control Program
All the other counties in California, including Sacramento-Yolo and KernYing Fang and Chris Barker from the Barker Lab, University of California, Davis and Sarah Wheeler from Sacramento-Yolo Mosquito and Vector Control Program.
Iowa, Idaho, and the US Virgin IslandsWashington Animal Disease Diagnostic Laboratory (WADDL)
OregonOregon Veterinary Diagnostic Laboratory
WashingtonKrisztian Magori from the Eastern Washington University, Amy Salamone, Wayne Clifford, David Kangiser from the Washington State Department of Health, the Washington Animal Disease Diagnostic Laboratory (WADDL), and the Oregon Veterinary Diagnostic Laboratory
New HampshireDenise Bolton, Abigail Mathewson, Carolyn Fredett, Amy Kutschke and Rebecca Lovell at the New Hampshire Division of Public Health Services, Department of Health and Human Services
LouisianaUdeni Balasuriya, Rebecca Christofferson, Tarra Harden, Zelalem Mekuria, Laura Peak, Alma Roy, and Keith Strother from the Louisiana Animal Disease Diagnostic Laboratory at Louisiana State University
MinnesotaDavid Neitzel from the Minnesota Department of Health

Raw Data

The BAM files are available on Google Cloud.

The sequencing is being performed using an amplicon-based sequencing scheme using PrimalSeq. Our full protocol is available online here. Sequencing data is aligned using bwa and processed using iVar (Grubaguh et al. Genome Biology 2019).

Below is a table showing the number of sequenced genomes by state.

StateCount
CA740
IA1
ID2
LA46
MN85
NH41
OR10
WA7
Other1
Total933

Disclaimer. Please note that this data is released as work in progress by the WestNile 4K Project and should be considered preliminary. If you intend to include any of these data in publications, please let us know – otherwise please feel free to download and use without restrictions. We have shared this data with the hope that people will download and use it, as well as scrutinize it so we can improve our methods and analyses. Please contact us if you have any questions or comments.


Andersen Lab
The Scripps Research Institute
La Jolla, CA, USA
data@andersen-lab.com

People

GitHub Commits

Data

Resources

Collaborators

Nate Grubaugh
Yale School of Public Health

Ryan Smith
Iowa State University

WestNile 4K Collaborators

Funding

NIH_CTSA
PEW