West Nile virus genomic data from California

Summary: Genomic epidemiology of West Nile virus in California. Data here.

We are sequencing West Nile virus from California, with an emphasis on San Diego, Kern, and Sacramento/Yolo counties, to understand how 1) the virus spreads between regions, 2) is maintained locally between seasons, and 3) the factors that promote local outbreaks. Our goal is to generate 600-700 new West Nile virus genomes from infected birds and mosquitoes collected from 2004-2017.

To date, we have sequenced 90 West Nile virus genomes from San Diego county. The samples were provided by Nikos Garfield and Saran Grewal from the San Diego County Vector Control Program. In the coming weeks, we plan to sequence an additional ~100 West Nile virus genomes from San Diego as well as ~200 genomes from each of Kern and Sacramento/Yolo counties from samples provided by Chris Barker and Ying Fang (University of California, Davis).

Stay tuned for new data uploads and preliminary analysis.

Disclaimer. Please note that this data is still based on work in progress 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 – we’ll buy beers for #ResearchParasites that spot flaws and faults in the data and come up with improvements!

Andersen Lab
The Scripps Research Institute
La Jolla, CA, USA
[email protected]

GitHub Commits


GitHub Repo
By: Andersen Lab

West Nile virus

West Nile virus