Description of interactions of Ebola virus with a putative reservoir species using next-generation sequencing

Ebola virus (EBOV) causes a severe, often fatal disease in humans and nonhuman primates. Recently, EBOV has caused two very large outbreaks, one of which is ongoing in the Democratic Republic of the Congo. Bats are the likely reservoir of EBOV, but little is known of their relationship with the virus. Next-generation sequencing has become an extremely powerful and flexible tool in virology over the past decade as new library preparation techniques have been developed that permit the selective sequencing of small RNAs, and the characterization of entire viral populations at incredible levels of detail. For this work, I exploited this technology to explore two aspects of the bat/virus nexus; namely the small RNA profile of infection, and the evolution of the virus in bat cells. The biology of the virus in human cells was used for comparison. Here I describe a new class of small noncoding RNAs produced by EBOV during infection of bat and human cells that resemble microRNAs, but are not associated with the microRNA machinery, and lack any discernable RNAi function. I also describe the evolution of EBOV in an experimental passage series in bat and human cells. This work led to the discovery of a potential role for host RNA editing enzymes in the evolution of EBOV in bats, and identified loci within the viral genome that appear to be associated with adaptation to human cells.