title: Flying-fox ecology and transmission dynamics of Hendra virus
Creators: name: Lunn, Tamika J
Publisher: name: Griffith University
Year: 2021
Subjects: subject: Hendra virus
subject: infection
subject: flying-fox

description: Emerging zoonoses from wildlife present an increasing threat to global public health. Bats, in particular, host some of the most significant viral families to have emerged in recent decades, including coronaviruses, henipaviruses and filoviruses. Hendra virus (Genus: Henipavirus) is one such virus, which emerged in 1994 to cause lethal disease in horses and humans in eastern Australia. Increased incidence of spillover in recent decades has been concurrent with observations of dramatic ecological shifts in host flying-fox (Family: Pteropodidae) populations. Wide-spread land clearing in south-eastern Australia has compounded the effects of inter-annual climate cycles on flying-fox food availability, resulting in large-scale fragmentation and fissioning of flying-fox roosts. This has manifest as an increasing transition from a nomadic ecology, where individuals move across the landscape and form large roosts in response to ephemeral foraging opportunities, to residency, where individuals continuously occupy a single roost in an area with predictable (often exotic) food sources. Typical roosting habitat has shifted as a result, moving from forest remnants with dense roosting habitat, to urban areas with more sparse roosting habitat. Incidence of Hendra virus spillover has been correlated with the formation of these urban, continuously occupied population groups, suggesting that recent changes in host ecology may play a role in spillover dynamics. In order to predict and manage pathogen spillover from bats, we require a detailed understanding of infection dynamics within host bat populations. In this thesis, I employ a multidisciplinary approach to investigate patterns and mechanistic drivers of Hendra virus infection dynamics in flying-fox populations, focusing on bat roosting structure as a driver of virus transmission. In Chapter 1, I describe the spillover process, and outline Hendra virus as a model to understanding spillover of bat-borne viruses. In Chapter 2, I present a spatio-temporal analysis of Hendra virus infection prevalence and excreted viral load from flying-fox populations, to estimate the dynamics of pathogen pressure over space and time, and to elaborate on possible drivers contributing to differences between roosts. This chapter presents a new longitudinal dataset of Hendra virus excretion dynamics, collected over 2.5 years (June 2017- December 2019), and comprising 4,343 samples from five main roost sites. A key finding of this chapter is that infection intensity is variable between roosts within the same regional area, suggesting that spillover risk is more nuanced than previously identified variation between broader regions. To understand the ecological context for transmission in aggregative bat populations, I then assess spatio-temporal patterns of flying-fox density and distribution within roosts in Chapter 3. I present insights from detailed roost structure surveys, comprising a 13-month dataset from 2,522 spatially referenced roost trees across eight roost sites. A key finding is that tree structure density drives patterns of bat abundance within trees, with implications for transmission in emerging, urban roost types. I then integrate this ecological context into mathematical models of infection in Chapter 4, where I develop spatially explicit, compartmental models of bat roosts, and explore dynamics of infection invasion and spread. I utilise empirical data on roost tree structure and flying-fox aggregation from Chapter 3 to capture the spatial structure of roosts, and contrast scenarios of tree structure density that are representative of observed ecological shifts with urbanisation. In my last research chapter (Chapter 5), I propose a modelling framework to holistically integrate between-host and within-host contexts into these transmission dynamics. Specifically, I propose an alternative transmission model structure to allow the integration of dose-response relationships into epidemiological models. I also demonstrate how changes in the design and accessibility of dose-response experiments would facilitate integration into epidemiological modelling, to ultimately enable more realistic predictions of zoonotic transmission outcomes. Collectively, insights from this thesis further our understanding of Hendra virus infection dynamics and spillover risk in a situation of changing host ecology. Beyond Hendra virus, the information presented highlights how aggregative spatial structuring of bats within roosts can add substantial heterogeneity to the contact structure of roost populations, with implications for models of bat-virus interactions. I present compelling evidence that spatial structure and flying-fox aggregation may be a missing piece to understanding differences in shedding intensity and spillover risk from roost sites across eastern Australia, particularly in the context of urbanisation and shifting roost structure. These insights will be relevant for modelling studies of other communally roosting species of zoonotic interest, as well as other emerging diseases linked with habitat modification and changing populations, including coronaviruses like SARS-CoV-2.