Abstract
Co-infections are a common feature of wildlife systems, yet the factors influencing within-host viral dynamics remain largely unclear. In bats, understanding viral community ecology is essential for elucidating shedding patterns and potential drivers of zoonotic spillover risk. In this study, we explore the genetic diversity and within-host dynamics of herpesviruses (HSV) in Mormopterus francoismoutoui, a tropical insectivorous bat endemic to Reunion Island. Over 3 consecutive years, we collected saliva samples from seven roosts, including samples from recaptured individuals. Illumina sequencing of HSV PCR-positive samples revealed a high diversity of strains (n = 20), belonging to alpha, beta, and gamma-HSV subfamilies. Co-infection was frequent, with 44% of bats shedding strains from all three subfamilies. While most shedding patterns appeared random across subfamilies, our results suggest that gamma-HSV negatively affects the probability of alpha-HSV co-shedding. We also demonstrated a lower HSV diversity in juveniles as compared to adults, while pregnancy appeared to increase viral diversity-although this requires further confirmation. Longitudinal recaptures revealed an accumulation of multiple HSV latent infections over life, as the probability to be infected with a new subfamily increased with time interval between recaptures. Within-host strain dynamics were highly variable, with 79% of bats either gaining or losing strains, consistent with latency and reactivation mechanisms. This study provides rare empirical insight into the within-host viral ecology of a natural reservoir host and can help uncover complex pathways by which viruses interact.IMPORTANCEUnderstanding viral dynamics in bats is critical for anticipating and mitigating zoonotic emergence. This study provides rare, longitudinal insight into herpesvirus co-shedding patterns in Mormopterus francoismoutoui, an endemic bat species on Reunion Island. Here, we revealed high strain diversity and frequent multi-subfamily shedding, highlighting complex within-host viral ecology, shaped by host age, reproductive status, and infection history. Interactions between viral subfamilies suggest competitive dynamics that may influence shedding. These findings deepen our understanding of viral persistence and reactivation in bats and underscore the need to investigate how environmental and anthropogenic stressors may modulate co-shedding and increase the likelihood of spillover events.