Longitudinal surveillance of synanthropic molossid bats reveals viral diversity and temporal patterns at the human–bat interface

Bats host several emerging viruses, including filoviruses, coronaviruses, and paramyxoviruses. Land-use change and urbanisation increasingly bring bat species into closer contact with humans, thereby potentially increasing opportunities for viral exposure at the human-bat interface. Understanding viral dynamics in natural bat hosts is essential for assessing emergence risks. This study spanned 12 months of longitudinal virus surveillance in two molossid bat species (genus Mops ) that roosted in close association with humans within two contrasting land-use systems in northeastern Eswatini. Bats were tested for filovirus, coronavirus, and paramyxovirus viral RNA with additional serosurveillance for filoviruses. In addition to identifying novel paramyxovirus diversity, the ongoing circulation of molossid-associated alphacoronaviruses was also confirmed. Coronavirus peak shedding was observed during spring (July-September), with shedding adults consistently displaying lower forearm-mass indices as compared to non-shedding bats. Recapture analysis showed that alphacoronavirus RNA was no longer detectable in most bats within a month, although a small number of individuals remained PCR-positive after several months, consistent with intermittent shedding or reinfection. While no filovirus RNA was detected, 29.5% (95% CI: 26.1–33.1%) of bats were sero-reactive with Bombali virus glycoprotein. These findings demonstrate the value of longitudinal wildlife surveillance for understanding seasonal viral dynamics, identifying periods of increased opportunities for human exposure and informing evidence-based surveillance at the human-bat interface.