The family Filoviridae includes Ebola virus and Marburg virus, which are associated with sporadic outbreaks and high case fatality rates. A maximum containment laboratory (Biosafety Level-4) is required to study infectious forms of these viruses. Our laboratory is interested in multiple aspects of filovirus biology with a view to exploiting this knowledge to further the development of vaccines and therapeutics.
Typically, RNA viruses have high spontaneous mutation rates due to error prone RNA-dependent RNA polymerases. The consequences of high spontaneous mutation and replication rates are populations composed of heterogeneous swarms of related variant sequences, sometimes called quasispecies. We are investigating the importance of this diversity to filovirus replication and pathogenesis in vitro and in vivo and are particularly interested in exploiting the mutation rate as a therapeutic mechanism. Specifically, we work to understand the roles of the individual genotype populations in virus infection; for example, in any Ebola virus population there is a mixture of genotypes that appear to control the expression of different forms of the virus glycoprotein (GP). The ratios of the genotypes is dynamic and changes dependent on the origin species of cells used to propagate virus, and even in an infected animal. These changes are certainly important for the development of vaccines and therapeutic – that require animal models – but also for viral pathogenesis.
Many of these studies exploit recent advances in sequencing. We have several Illumina sequencing machines on our campus and a miSeq in our laboratory. This system permits quantification of the individual viral genotypes in a sample and we have developed techniques to rapidly sequence whole viral genomes, including the 5’ and 3’ termini. We are expanding the use of these machines into other areas including gene expression and ribosome profiling of cells and tissues infected with BSL-4 pathogens.