US-UK Collab: Integrating metaviromics with epidemiological dynamics: understanding virus transmission in the Anthropocene

This project will develop and test new methods for tracking RNA viruses in wild rodent populations, which are important viral reservoirs worldwide because many species live in close proximity to human populations and are highly responsive to environmental change. Most emerging infectious diseases affecting humans, including AIDS, influenza, and COVID-19, are caused by RNA viruses originating from non-human animals. In recent years, these diseases have become more common and widespread, a pattern frequently attributed to increasing environmental change, notably the conversion of natural landscapes into agricultural and urban environments. These changes have dramatically altered wild animal communities, influencing how viruses circulate within these communities and simultaneously increasing human exposure to new animal viruses. Seasonal variation and climate change can also alter pathogen prevalence in wild animal populations and influence disease risk. A critical barrier to controlling future viral outbreaks is a lack of knowledge about how environmental change affects virus transmission within wild animal populations and how, in turn, that affects human risk. This project will investigate these gaps using established field studies in England and Uganda that monitor wild rodent communities. Additionally, this project will involve researchers in the United Kingdom and Uganda, and provide training for undergraduates, graduate students, and post-doctoral scholars. To tackle the practical challenges of studying viral transmission, researchers will develop new tools to infer epidemiological dynamics and zoonotic risk from increasingly accessible and low-cost host virome data. This flexible approach will allow rapid discovery and monitoring of zoonotic viruses by enabling epidemiological inferences from cross-sectional samples and guidance for appropriate sampling strategies to interpret metaviromic data in new host systems. Researchers will use a long-term capture-mark-recapture wild study in Oxfordshire, UK, to determine how seasonal environmental change influences rodent viral communities. Lastly, researchers will use field sites along land cover gradient in Uganda to understand how physical environmental change influences the risk of zoonotics in rodent communities. This fieldwork will identify local and landscape drivers of zoonotic hazards and how humans change behaviour to affect zoonotic risk across this gradient. Together, this research will substantially improve our understanding of viral pathogens within key reservoir hosts and identify important environmental drivers that increase zoonotic risk. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.