Discovery of rodent-borne viruses over a biodiversity gradient in Morogoro, Tanzania

To mitigate and prevent zoonotic disease to humans, it is necessary to understand how pathogens are transmitted in populations of their wildlife reservoir. In fact, most wildlife pathogens circulate endemically within communities of multiple host species that differ in density, susceptibility, infectiousness and behaviour. One of the main questions within this one-health perspective is whether increasing biodiversity will lead to a decrease or increase in infection prevalence, termed the dilution and amplification effects, respectively. In this project, we will investigate these mechanisms focusing on viruses in rodent communities using a unique combination of empirical data, existing sample sets, and state-of the art metagenomic sequencing and modelling. More specifically we will integrate a CRISPR-Cas-based host depletion technique into existing metagenomic sequencing pipeline that will allow us to deplete any target (e.g. host gene, adapters) of any type (DNA or RNA), in any sample (acellular vs cellular), and in any species. This will greatly expand the diagnostic range for human and wildlife samples at ITM and UAntwerp and more importantly provide a more in-depth understanding of the ecology and evolution of zoonotic viruses.

To mitigate and prevent zoonotic disease to humans, it is necessary to understand how pathogens are transmitted in populations of their wildlife reservoir. In fact, most wildlife pathogens circulate endemically within communities of multiple host species that differ in density, susceptibility, infectiousness and behaviour. One of the main questions within this one-health perspective is whether increasing biodiversity will lead to a decrease or increase in infection prevalence, termed the dilution and amplification effects, respectively. In this project, we will investigate these mechanisms focusing on viruses in rodent communities using a unique combination of empirical data, existing sample sets, and state-of the art metagenomic sequencing and modelling. More specifically we will integrate a CRISPR-Cas-based host depletion technique into existing metagenomic sequencing pipeline that will allow us to deplete any target (e.g. host gene, adapters) of any type (DNA or RNA), in any sample (acellular vs cellular), and in any species. This will greatly expand the diagnostic range for human and wildlife samples at ITM and UAntwerp and more importantly provide a more in-depth understanding of the ecology and evolution of zoonotic viruses.