UC San Diego

Human history has been marked by viral epidemics of zoonotic origin which have evolved and spread through the human population with devastating effect. In this dissertation, I explore the origins of zoonosis, adaptation, and spread of viruses in heterogeneous human populations. To understand how viral epidemics can circulate in the human population, I first investigate how the first wave of SARS-CoV-2 in New York City impacted different areas and with this context I explore the dynamics of how different variants circulate in these areas during the second wave. Then, I examine the context in which SARS-CoV-2 variants arose, using a synonymous molecular clock to characterize evolution in different environments. I expand on understanding selection, by examining the selection regime in viral host reservoirs, selection preceding human outbreaks, and selection after zoonosis during human outbreaks for viruses including Ebola virus, Marburg virus, influenza A virus, SARS-CoV, and SARS-CoV-2. Finally, I explore how herpes simplex virus 2 migrated globally and characterize the uncertainty by developing a simulation framework. By understanding the path and evolutionary history of viruses, I hope to contribute to the fundamental understanding of epidemics which is needed to make informed and effective plans to mitigate harm, and perhaps even prevent viral outbreaks in the future.