Date of Award

January 2024

Document Type

Open Access Thesis

Degree Name

Master of Public Health (MPH)


School of Public Health

First Advisor

Nathan Grubaugh

Second Advisor

Philip Armstrong


Jamestown Canyon virus (JCV) is a re-emerging arthropod-borne virus in the midwest and northeast United States, infecting mosquitoes and white-tailed deer in a seasonal transmission cycle. Its spread may contribute to thousands of asymptomatic human infections, with 194 total cases of neuroinvasive disease diagnosed. However, very little is known about the virus’s evolutionary history, transmission patterns, and lineage distribution. For this project, we sequenced 689 JCV samples collected from mosquito pools in the northern U.S., increasing the availability of this species’ genomes. Using maximum likelihood estimation on surveillance data, we found that JCV is maintained through the overwintering of single-brood mosquitoes, with peaks in percent infection rate and vector index corresponding with their emergence in the early summer. To corroborate these results, we coupled the surveillance data with phylogenetic analysis of our sequenced genomes. JCV’s genomic diversity can be divided into 2 lineages, A and B, which are made up of 6 and 2 sub-lineages respectively. These lineages demonstrate significant geographic clustering, suggesting that ecological factors, such as white-tailed deer distribution, may restrict the virus’s movement within and between U.S. states. After comparing lineage designations across the genome, 0.73% of sequences exhibited segment reassortment. It is therefore likely that JCV primarily evolves through genetic drift, with shift occurring at a rate of 0.18 events per year. Incorporating both genomic and surveillance data, this project significantly expands our understanding of JCV, untangling a complex viral transmission cycle to identify future areas for public health intervention.


This is an Open Access Thesis.

Open Access

This Article is Open Access