Animal genomics in natural reservoirs of infectious diseases

Natural virus reservoirs such as wild bats, birds, rodents and non-human primates are generally non-model organisms that have, until recently, presented limited opportunities for in-depth study. Next-generation sequencing provides a way to partially circumvent this limitation, since the methods required for data acquisition and analysis are largely species-independent. Comparative genomics and other 'omics' provide new opportunities to study the structure and function of various biological systems of wild species that are otherwise out of reach. Genomes of natural reservoir hosts can help to identify dominant pathways of virus-host interaction and to reveal differences between susceptible and resistant organisms, populations and species. This is of great scientific interest and may also provide a resource for the rational design of treatments for viral diseases in humans and livestock. In this way, we will 'learn from nature' and one day apply this knowledge to create disease-resistant livestock or develop novel therapeutic and prevention strategies. Reservoir host genomics will also open up possibilities for developing novel vaccines for wildlife, aid in the development of new diagnostic platforms, and have broad implications for developmental and evolutionary biology. In this review, the authors focus on natural reservoir hosts of viral pathogens, although most of the discussion points should be equally applicable to natural reservoirs of pathogenic bacteria, fungi or other parasites.