Characterizing Ebola virus mutation and selection between and within hosts

Abstract

Ebola virus (EBOV), a causative agent of Ebola virus disease (EVD), has re-emerged as a serious threat to human health. The recent 2013–2016 EVD epidemic in Western Africa and the ongoing outbreak in the Democratic Republic of the Congo (DRC) have resulted in more than 30,000 cases combined, with case fatality rates exceeding 40%. Recently developed vaccines offer effective prophylaxis prior to infection, but therapeutics provide only modest efficacy for infected individuals. Moreover, there is precedent for EBOV evolving drug resistance during a non-human primate trial, highlighting the need to better understand both EBOV biology and evolution to combat this deadly pathogen. Here, I develop and apply genomic tools to investigate viral mutation and selection between and within individuals during the 2013–2016 EVD epidemic. In Chapter 2, I identify viral genomic mutations that emerged during the epidemic and rose to high frequency by spreading rapidly between individuals. I characterize two key mutations by developing reporter assays and find that these mutations may have altered essential viral functions. In Chapter 3, I present a case study of EVD persistence within an individual over the course of 110 days. I observe fewer viral mutations than expected based on evolutionary rate estimates between acutely diseased individuals, suggesting that selective forces are altered during persistent infection. In Chapter 4, I explore a potential cause behind unexplained patterns of T-to-C mutations observed during the epidemic. I map the EBOV genome's RNA structure and find these T-to-C mutations have nucleotide context and structural profiles consistent with the human enzyme ADAR's RNA editing preferences, suggesting that ADAR can directly cause EBOV mutations. In Chapter 5, I perform transcriptome profiling to identify host genes that are differential expressed during EVD, down to the single-cell level. I show that, though EBOV-infected cells fail to trigger antiviral responses, uninfected bystander cells promote these responses in vivo, resolving a longstanding disparity between cell culture and animal studies studies of EBOV infection. In total, this dissertation presents a multi-scale view of EBOV replication, leading to a clearer understanding of viral evolution, host-mediated mutational mechanisms, and potential pro- and antiviral host factors.