Seasonal dynamics of the wild rodent faecal virome

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.
Utilizing noninvasive faecal samples from a long‐term wild rodent study,
we characterized viral communities of three common European rodent species
(Apodemus sylvaticus, A. flavicollis and Myodes 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.