Many viruses that cause serious and often fatal disease in humans have spilled over from bats. Recent evidence suggests that stress may enhance virus shedding by bats increasing the possibility of transmission to other species. To understand the reasons for spillover is therefore important to determine the molecular pathways that link stress to virus reactivation and shedding in bats. We recently isolated and characterized a gammaherpesvirus (Eptesicus fuscus herpesvirus, EfHV) autochthonous to North American big brown bats. Since herpesviruses are known to reactivate from latent infections in response to a wide variety of stressors, EfHV presents us with an opportunity to study how physiological, behavioural or environmental changes may influence the big brown bats' relationship with EfHV. To understand the biology of the virus and how the extended periods of torpor experienced by these bats during hibernation along with the stress of arousal might influence the virus-host relationship, we attempted to detect the virus in the blood of wild-caught non-hibernating bats as well as captive bats arising from hibernation. We compared the prevalence of EfHV in the blood (using PCR) and EfHV-specific antibodies (using ELISA) between captive hibernating bats and wild-caught non-hibernating bats. We detected EfHV only in the blood of captive hibernating bats (27.8% = 10/36) and not in wild-caught non-hibernating bats (0.0% = 0/43). In contrast, the EfHV-specific antibody titres were higher in the non-hibernating bats compared to the hibernating bats. Our study suggests that: (a) viral DNA in blood indicates reactivation from latency, (b) long periods of hibernation lead to suppression of immunity, (c) stress of arousal from hibernation reactivates the virus in bats with lower levels of anti-viral immunity (indicated by humoral immune response), and (d) levels of anti-viral immunity increase in non-hibernating bats following reactivation.