Date of Award


Document Type


Degree Name

Doctor of Philosophy (PhD)


Biomedical Sciences


Microbiology, Immunology, and Biochemistry

Research Advisor

Colleen B. Jonsson, PhD


Lorraine M. Albritton, PhD Kui Li, PhD P. David Rogers, PharmD, PhD Michael A. Whitt, PhD


Antiviral resistance, Venezuelan equine encephalitis virus, Virus evolution


Venezuelan equine encephalitis virus (VEEV) is a New World Alphavirus that causes Venezuelan equine encephalitis (VEE), which is characterized by a febrile illness that can progress to neurological disease and death. While no major outbreaks of VEE have occurred since 1995, VEEV is a virus of concern as, in addition to its spread through mosquitos, it can be aerosolized and used as a bioweapon. Unfortunately, there are currently no FDA-approved vaccines or antivirals against VEEV. Efforts have been made to discover small molecules with an inhibitory effect on VEEV, but the potential for emergence of antiviral resistance to these compounds will remain a concern because VEEV is an RNA virus with a high mutation rate and grows to high titers. To examine the evolutionary trajectory of antiviral resistance in VEEV, we developed a next-generation sequencing pipeline to examine single-nucleotide polymorphisms that emerged after repeated passaging of the virus with increasing concentrations of antiviral compounds. In addition, we examined the effect of the microenvironment on the evolution of antiviral resistance, both in cell culture and mouse models. We found that VEEV evolves resistance to the compound ML336 and its derivatives through mutations in the nsP2 and nsP4 genes, but the number, timing of emergence, and the extent of penetrance of these SNPs depend on the compound. These mutations emerged more slowly when infecting an astrocyte cell line. We also found that neurons in the mouse brain did not impose a selective pressure on VEEV during an infection. These results demonstrate how the population dynamics of RNA viruses can be tracked over time and the extent to which they are affected by selective pressures, as well as opening questions about how viruses can mutate and adapt at the molecular level.

Declaration of Authorship

Declaration of Authorship is included in the supplemental files.




2021-030-Lee-DOA.pdf (172 kB)
Declaration of Authorship