Functional Genomics for Emerging Infectious Diseases

The focus of my proposed research is on the ecology of emerging zoonotic viruses, both in their natural and dead-end host context. I propose to investigate these viruses’ clinical relevance for and the genetic susceptibility of their host, and to explore and predict the mechanisms that determine the capability of these reservoir-borne viruses to switch hosts as well as their pathogenic potential. To achieve these goals, I am finalizing an optimized protocol to isolate complete DNA and RNA virus genomes from different sample types in order to use both the Illumina and Oxford Nanopore MinION sequencing platforms.

This procedure will be used to (i) study the virosphere in rodents, insectivores and hematophagous arthropods and to (ii) perform DNA profiling of infected patients with different clinical outcomes. I will use filovirus- and hantavirus-infected patients as case study. Additionally, I aim to (iii) perform functional genomics on newly discovered viruses to grade possible pathogenicity and to (iv) develop and optimize specific antiviral screening assays that can be used for high-throughput screening.