Bat things come in threes: within-host dynamics of herpesvirus triple infection in bats

Understanding viral community ecology in bats is essential for elucidating shedding patterns and the drivers of co-infections. 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 three consecutive years, we collected saliva samples from seven roosts, including repeated 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 with different subfamilies appeared random, our results suggested a negative influence of gamma-HSV occurrence of the probability of co-shedding alpha-HSV. We also demonstrated a lower HSV diversity in juveniles as compared to adult bats, while pregnancy appeared to increase viral diversity-although this requires further confirmation. Longitudinal recaptures of bats 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 showing fluctuations in strain diversity over time-either gaining or losing strains-consistent with latency and reactivation mechanisms. These findings provide new insights into the ecological and evolutionary dynamics of herpesviruses in wild bat populations.