Ecological Drivers of Viral Persistence in Malagasy Fruit Bats

In the wake of Hendra/Nipah outbreaks, SARS-CoV, and the COVID-19 pandemic, there has been a growing interest in describing bat-borne viruses of zoonotic concern prior to cross-species emergence. Much current work in this field focuses on massive metagenomic sequencing efforts by screening bat-derived samples cross-sectionally for viral genomes. However, the literature on how these viruses are maintained in their natural reservoir hosts is still catching up. Deciphering the transmission dynamics of viruses in bat reservoir host systems remains a priority in pandemic prevention and disease ecology. By leveraging an extensive collection of longitudinal samples from Malagasy fruit bats, I first metagenomically describe multiple new coronaviruses, picornaviruses, and henipaviruses. Then, I use phylogenetic methods to determine evolutionary relatedness and history of these viruses in the context of African bat-hosted viruses – an area which is critically under-sampled. I use full genomes of coronaviruses and henipaviruses to further design system-specific molecular assays to investigate viral shedding (corresponding to real time infection or the “I” class of a classic SIR model) and serological profiles (corresponding to antibody response after an infection or the “R” class of a classic SIR model) in Malagasy fruit bats. I use both active molecular prevalence data and serological data which signifies past infection, combined with individual-level metadata to jointly infer the virus population dynamics, a novel approach in the field of bat-hosted viruses. The reproductive stress of gestation has been thought to contribute to immune tradeoffs with viral maintenance, but other studies lack the individual-level data to support this. Here, we directly address this research gap by showing that reproductive stress does correlate to peaks in viral shedding of henipaviruses, while peaks in viral shedding of coronaviruses are either also linked to reproductive stress or to nutritional stress in the dry season.