Genomic Analysis of Viral Outbreaks

Abstract

Due to recent advances in sequencing technologies, genomics has emerged as a powerful tool for combating viral outbreaks. In this dissertation, I show how genomic data can be used to understand the transmission, as well as the origin and evolution, of three different viruses. In Chapter 2, I describe Ebola virus (EBOV) sequences from the 2014–2016 outbreak in Sierra Leone, and what they tell us about cross-border and individual transmission, as well as evolution of the virus. In Chapter 3, we apply these findings to the 2014 EBOV outbreak in Nigeria. I present a direct comparison between genomic data and contact tracing performed during the outbreak, and show that these methods suggest similar transmission patterns, but that viral sequences provide additional information about the origins of the outbreak. In Chapter 4, I describe our efforts to characterize the movement of Zika virus (ZIKV) throughout the Americas in 2016, and I explain how we dealt with challenges related to low viral content in ZIKV samples. In Chapter 5, I explain how mumps virus (MuV) sequences from 2016–2017 informed our understanding of disease spread at multiple geographic scales. I explain the evidence for ongoing MuV transmission in the United States, and show that pairing genomic and detailed epidemiological data reveals transmission within a local community. Taken together, these chapters demonstrate the emerging capabilities of genomics, including how genomic analysis can inform our understanding of viral transmission, and show how viral sequence data can influence public health at local, national, and international scales.