Seasonal dynamics of the wild rodent faecal virome

Raghwani, Jayna; Faust, Christina L.; François, Sarah; Nguyen, Dung; Marsh, Kirsty; Raulo, Aura; Hill, Sarah C.; Parag, Kris V.; Simmonds, Peter; Knowle1, Sarah C.L.; Pybus, Oliver G.

Abstract

Viral discovery studies in wild animals often rely on cross-sectional surveys at a single time point. As a result, our understanding of the temporal stability of wild animal viromes remains poorly resolved. While studies of single host-virus systems indicate that host and environmental factors influence seasonal virus transmission dynamics, comparable insights for whole viral communities in multiple hosts are lacking. Leveraging non-invasive faecal samples from a long-term wild rodent study, we characterised viral communities of three common European rodent species (Apodemus sylvaticus, A. flavicollis, and M. glareolus) living in temperate woodland over a single year. Our findings indicate that a substantial fraction of the rodent virome is seasonally transient and associated with vertebrate or bacteria hosts. Further analyses of one of the most common virus families, Picornaviridae, show pronounced temporal changes in viral richness and evenness, which were associated with concurrent and up to ~3-month lags in host density, ambient temperature, rainfall and humidity, suggesting complex feedbacks from the host and environmental factors on virus transmission and shedding in seasonal habitats. Overall, this study emphasizes the importance of understanding the seasonal dynamics of wild animal viromes in order to better predict and mitigate zoonotic risks.

Citation

Raghwani, J., Faust, C. L., François, S., Nguyen, D., Marsh, K., Raulo, A., Hill, S. C., Parag, K. V., Simmonds, P., Knowle1, S. C., & Pybus, O. G. (2023). Seasonal dynamics of the wild rodent faecal virome. Molecular Ecology, https://doi.org/10.1111/mec.16778

• Journal Article Type: Article
• Acceptance Date: Nov 3, 2022
• Online Publication Date: Nov 11, 2022
• Publication Date: Jan 23, 2023
• Deposit Date: Nov 7, 2022
• Publicly Available Date: Jan 23, 2023
• Journal: Molecular Ecology
• Print ISSN: 0962-1083
• Electronic ISSN: 1365-294X
• Publisher: Wiley
• Peer Reviewed: Peer Reviewed
• DOI: https://doi.org/10.1111/mec.16778
• Publisher URL: https://onlinelibrary.wiley.com/doi/10.1111/mec.16778