The WestNile 4K Project is a partnership between West Nile virus surveillance laboratories and academic institutions across the United States. Our main goal is to provide real-time high definition reconstructions of the micro- (e.g., city/county) and macro-level (e.g., state/country) spread and evolution of West Nile virus by sequencing more than 8,000 virus genomes from infected birds, mosquitoes, and patients.
The data generated as part of this project will be immediately released to the public, and along with other entomological data, will be used to uncover local transmission dynamics. Analyses and visualizations will also be made publicly available in real-time as data are produced. As little progress has been made in effectively controlling West Nile virus outbreaks since its emergence in the United States two decades ago, our goal is to use fine-scale genomics-based transmission networks and extensive experimental studies to inform public health responses and help design future targeted control measures.
To learn more about the first twenty years of West Nile virus spread and evolution in the Americas and some of the background behind the WestNile 4K Project, read our recent review in PLOS Pathogens.
1108
Genomes
1
Countries
33
States
48
Institutions
105
Collaborators
Recent Data Releases
Colorado
Collaboration and Data Sources We received 626 samples of RNA extracted from mosquito pools that tested positive for West Nile virus from Greg Ebel, Reyes Murrieta, Joseph Fauver, and Michael C. Young from Colorado State University. 94 samples were selected and had suitable genome coverage after sequencing for phylogenetic analysis. Samples came from Larimer County between the years 2013 and…
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Minnesota
Collaboration and Data Sources We received 120 samples of RNA extracted from birds that tested positive for West Nile virus from David Neitzel from the Minnesota Department of Health. 113 samples were selected and had suitable genome coverage after sequencing for phylogenetic analysis. Samples came from 39 counties and the years 2002-2005. In this update, we highlight the sequencing results…
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Illinois
Collaboration and data sources We received 212 samples of RNA extracted from mosquito pools that tested positive for West Nile virus from Alex Westrich, Claudia Blanco, and Raed Mansour from the City of Chicago Department of Public Health. Samples were selected for sequencing from each trap location within the city that we had samples from. 26 samples were ultimately selected…
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Leadership
Nathan D. Grubaugh, M.S., Ph.D. is an Assistant Professor at the Yale School of Public Health in the department of Epidemiology of Microbial Diseases. He spent ~7 years working in the biotech sector before earning a M.S. in biotechnology from Johns Hopkins University in 2011 and a Ph.D. in microbiology from Colorado State University in 2016. Nate did his postdoctoral training in pathogen genomics under the guidance of Kristian Andersen at Scripps Research before joining the faculty at Yale in 2018.
Nate is trained as an arbovirologist, and has used his diverse background in private, government, and academic research to develop molecular strategies to detect, track, and understand mosquito-borne virus outbreaks. Having studied the ecology and evolution of West Nile virus during his Ph.D., a primary objective in his lab is to expand this work into using genomic epidemiology to inform targeted control measures.
Nate Grubaugh
Assistant Professor
Yale School of Public Health
Ryan C. Smith, Ph.D. is an Assistant Professor in the Department of Entomology at Iowa State University. He earned his degree in molecular biology at the University of California Riverside working on mosquito genetics, then did his post-doctoral training at the Johns Hopkins Bloomberg School of Public Health focusing on mosquito host-pathogen interactions. Ryan joined the faculty at Iowa State in 2015 establishing a research program with both lab- and field-based components to better understand mosquito-borne disease transmission.
These experiences have led Ryan to explore how mosquitoes transmit diseases like malaria and Zika virus. Ryan also oversees mosquito and West Nile virus surveillance in the state of Iowa, working closely with local and state public health partners to monitor potential disease outbreaks and to investigate the epidemiological factors that contribute to West Nile virus transmission. Ryan is a member of the Midwest Regional Center for Vector-borne disease, leading efforts to enhance the capacity to anticipate, prevent, and control vector-borne diseases.
Ryan Smith
Assistant Professor
Iowa State University
Professor
University of California, Los Angeles
University of California, Los Angeles
Marc A. Suchard, M.D./Ph.D is a Professor at the University of California in Los Angeles (UCLA). He received a bachelor’s degree in biophysics from the University of California, Berkeley in 1995 and spent two years at Oxford University as a British Marshall Scholar. He then earned his Ph.D in biomathematics from the UCLA in 2002 and continued for a M.D. degree, which he received in 2004, also from UCLA.
His research is on the forefront of high-performance statistical computing. He is a leading Bayesian statistician who focuses on inference of stochastic processes in biomedical research and in the clinical application of statistics. His training in both Medicine and Applied Probability help bridge the gap of understanding between statistical theory and clinical practicality.
He has been awarded several prestigious statistical awards such as the 2003 Savage Award, the 2006 Mitchell Prize, as well as a 2007 Alfred P. Sloan Research Fellowship in computational and molecular evolutionary biology and a 2008 Guggenheim Fellowship to further computational statistics. Recently, he received the 2011 Raymond J. Carroll Young Investigator Award for a leading statistician within 10 years post-Ph.D. He is an elected Fellow of the American Statistical Association.
Marc Suchard
Professor
UCLA
Kristian Andersen, PhD is an associate professor in the Department of Immunology and Microbiology at Scripps Research, with joint appointments in the Department of Integrative Structural and Computational Biology, and at the Scripps Research Translational Institute. Over the past decade, his research has focused on the complex relationship between host and pathogen. Using a combination of next-generation sequencing, field work, experimentation, and computational biology he has spearheaded large international collaborations investigating the spread and evolution of deadly pathogens, including Zika virus, Ebola virus, West Nile virus, and Lassa virus. His work is highly cross-disciplinary and exceptionally collaborative.
Kristian earned his doctoral degree from the University of Cambridge in immunology and performed postdoctoral work in Pardis Sabeti's group at Harvard University and the Broad Institute. He has received several awards, including the Max Perutz Prize in 2008, a Carlsberg Foundation Fellowship in 2009, and was chosen as a PEW Biomedical Scholar in 2016.
Kristian Andersen
Professor
Scripps Research
Team
Karthik Gangavarapu
Graduate Student
Scripps Research
Nate Matteson
Graduate Student
Scripps Research
Refugio Robles
Lab Manager
Scripps Research
Chantal Vogels
Postdoc
Yale School of Public Health
Anderson Brito
Postdoc
Yale School of Public Health
Mary Petrone
Graduate Student
Yale School of Public Health
Analysis Partners
Katholieke Universiteit Leuven
Philippe Lemey
Simon Dellicour
Bram Vrancken
NextStrain
Trevor Bedford
James Hadfield
Sample Partners
City of Chicago / CDPH Vector Control Program
Alex Westrich
Claudia Blanco
Raed Mansour
City of Sioux Falls Health
Denise Patton
Champaign-Urbana Public Health District
Jeff Blackford
Colorado State University
Greg Ebel
Reyes Murrieta
Joseph Fauver
Michael C. Young
Connecticut Agricultural Experiment Station
Phil Armstrong
John Shepard
Ted Andreadis
John Anderson
Eastern Washington University
Krisztian Magori
Florida Department of Health
Andrea Morrison
Grand Forks Public Health Department
Todd Hanson
Idaho Department of Health and Welfare
Vonnita Barton
Indiana State Department of Health
Bryan Price
Iowa Department of Public Health
Ann Garvey
Julie Coughlin
Kansas Biological Survey / The University of Kansas
Christopher Rogers
Kansas Department of Health and Environment
Ingrid Garrison
Amie Cook
Louisiana Animal Disease Diagnostic Laboratory / Louisiana State University
Udeni Balasuriya
Rebecca Christofferson
Tarra Harden
Zelalem Mekuria
Laura Peak
Alma Roy
Keith Strother
Maine Medical Center Research Institute
Chuck Lubelczyk
Metropolitan Mosquito Control District
Kirk Johnson
Michigan State University
Michael Kaufman
Ned Walker
Trisha Dubie
Minnesota Department of Health
David Neitzel
Mississippi State Department of Health
Wendy Varnado
Nebraska Department of Health and Human Services
Jeff Hamik
Nebraska Public Health Laboratory / University of Nebraska Medical Center
Pete Iwen
Vicki Herrera
Emily McCutchen
New Hampshire Public Health Laboratories
Denise Bolton
Abigail Mathewson
Carolyn Fredette
Rebecca Lovell
Amy Kutschke
North Shore Mosquito Abatement District
Mark Clifton
Ohio Department of Health
Leeanne Garrett
Kevin Sohner
Jim Scott
Oregon Veterinary Diagnostic Laboratory / Oregon State University
Donna Mulrooney
Manoj Pastey
Justin Sanders
Andree Hunkapiller
Noah Lawler
Sarah Greene
Pennsylvania Department of Agriculture
Michael Hutchinson
Pennsylvania Department of Environmental Protection
Keith Price
San Diego Vector Control
Nikos Gurfield
Saran Grewal
Jorell Tuncap
South Dakota Public Health Laboratory
Chris Carlson
Southern Nazarene University
Caio França
St. Louis County Vector Control
Tony Patullo
Texas Department of State Health Services
Bethany Bolling
University of California, Davis
Chris Barker
Sarah Wheeler
Ying Fang
Lark Coffey
William Reisen
University of Georgia
Daniel Mead
Isabel Ott
University of Illinois at Urbana-Champaign
Chris Stone
University of Iowa / State Hygienic Laboratory
Lucy Desjardin
Jeff Benfer
University of South Alabama
Jonathan Rayner
Ryan Wood
John McCreadie
University of Tennessee
Becky Trout-Fryxell
University of Wisconsin-Madison
Lyric Bartholomay
Susan Paskewitz
Vermont Department of Health Laboratory
Christine Matusevich
Patti Casey
Eliza Doncaster
Washington State Department of Health
Amy Salamone
Elizabeth Dykstra
Erin Knutson
Anne Duffy
Washington State University
Dan Bradway
Becca Wolking
Marla Francis
Managing Partners
