Understanding the ecology of Ross River virus; novel approaches and insights into non-human reservoirs Author Stephenson, Eloise Published 2019-11-19 Thesis Type Thesis (PhD Doctorate) School School of Environment and Sc DOI https://doi.org/10.25904/1912/570 Copyright Statement The author owns the copyright in this thesis, unless stated otherwise. Downloaded from http://hdl.handle.net/10072/389694 Griffith Research Online https://research-repository.griffith.edu.au Understanding the ecology of Ross River virus; novel approaches and insights into non-human reservoirs. by Eloise Birgitta Stephenson BSc, MSc Submitted in fulfilment of the requirements of the degree Doctor of Philosophy School of Environment and Science Griffith University August 2019 Acknowledgements This dissertation does not represent the work of a sole individual; instead it is the product of generous support, guidance and inspiration from many people whom have woven into the fabric of my life. I would like to start off by thanking my supervisors, Prof. Hamish McCallum, Dr. Alison Peel, Dr. Cassie Jansen, Dr. Lara Herrero, and Ass. Prof. Simon Reid, who have been incredibly supportive of both my research and my overall growth throughout my PhD. I have a large supervisory team and have been very fortunate to receive advice, guidance and support from each of them in many shapes and forms. Very special thanks to Hamish, not just for sharing his vast knowledge on R, analyses and models with me, but for his quick wit and willingness to expand my networks through introductions. I owe a large thank you also to Ali, who has inspired and challenged me throughout my PhD. Ali is an incredible researcher who taught me to formulate and present my research questions clearly, and broadened my critical analysis skills. Ali is also a great mentor, and I am inspired by her work, her family and her fabulous earrings. I am also very grateful to Cassie, whose faith in me over the years has been unflappable! Thank you to Lara for her laboratory supervision and willingness to think outside the box across the multiple disciplines covered in this project, and to Simon who helped guide this project. Amanda Murphy has been a shining light during this PhD; and together we have tackled fieldwork, RRV notification data and many wines across Brisbane. Amanda is a fabulous sounding board and is always bubbling with ideas and enthusiasm for the disease system we both work on. She has kept me motivated, sane and excited about my research. I thank her, and her colleagues, for all of this. I am very lucky to work among two research groups at Griffith and am grateful for the support, laughter and feedback from the members of these groups; Lara Herreros’ group (Penny, Joyce, Aroon, Elina, Elisa, Eugene and Julie), and Hamish McCallums’ group (Doug, Laura, Tamika, Thais, Will, Mandy, Manuel, Remy and the bat catching team!). Griffith has taught me much about research, but in particular, the importance of a good support team. So I would also like to thank Dian, Isaac and Christina at EFRI for their assistance with much of the paperwork and applications that are required throughout a PhD. ii My project has led me to meet, and collaborate with many other researchers and institutions all over the world. I have had the great pleasure of discussing this project and ideas with many people, and ultimately sometimes these have led to my best analyses or interpretations. My family is a big part of my life, and throughout this PhD they offered to proof read sections, cook dinners, or just simply distract me. My family have been with me for all the moments of triumph and angst along the way. I am so fortunate to be able to speak with my Mum, Dad, sisters, grandparents and parents-in-law almost every week, and am always offered support, empathy and encouragement. The love and support of my family extends far beyond the duration of this project, and I wouldn’t have committed to a PhD without their encouragement to pursue my passions. To my friends, whether in academia or not, I am grateful for being able to share ideas, beers and tears with you along the way. I am inspired and motivated by so many of my friendships. My PhD friends, Jenna, Pat and Steph have been especially empathetic to the process and I can only wish that my future colleagues are as supportive and inspirational as you have been. Finally, I would like to thank my husband and best friend, Tim. Somewhere in between the lines of these pages we managed to travel, move house, get married and start a family. You have kept me grounded during all of this, recognising the little moments – like tea to keep going, a break to stop working, or even just space – as well as the big moments. Thank you for not just for supporting me to follow my dreams, but for being a part of them too. I am just as much excited about our future, as I am when I look back on our past. iii This work has not previously been submitted for a degree or diploma in any university. To the best of my knowledge and belief, the dissertation contains no material previously published or written by another person except where due reference is made in the dissertation itself. --- Eloise B. Stephenson iv Abstract Arboviruses contribute a significant burden to human and animal health. Circulation of arboviruses comprises three components; blood-sucking arthropods, vertebrate hosts, and viruses that can infect vertebrates and invertebrates. Interaction of these components is dependent on ecological factors (such as species distributions and climate), epidemiological factors (including vector and host immunity) and behavioural determinants (such as vector feeding host preference or host defensive behaviours). Identifying these drivers of disease emergence can be complicated but informs efforts to mitigate on-going circulation. This dissertation generates new perspectives on the transmission dynamics of Australia’s most common arbovirus, Ross River virus (RRV), with a particular focus on non-human reservoirs. Specifically, I (a) critically analysed current and historic knowledge for non-human reservoirs and vector feeding patterns, (b) examined the natural exposure of RRV in human, free-living and domestic vertebrate populations, and (c) assessed the vertebrate and vector community ecology across areas of varying human notification rates. I began by undertaking a systematic literature review (Chapter 2) assessing evidence for non- human reservoirs of RRV. This chapter synthesised published serological, virus isolation and experimental infection studies in light of the long-held dogma that marsupials are the primary reservoir of RRV. A key finding of this chapter was emerging evidence that placental mammals and birds were also capable of transmitting RRV to mosquito vectors, suggesting a broader reservoir potential than marsupials alone. To further assess the current and historic knowledge, a meta-analysis was performed on mosquito blood meal analysis studies (Chapter 3). It was evident from this chapter that Australian mosquitoes have highly varied feeding patterns which did not reflect their taxonomic classification or larval ecology. To understand the natural exposure of RRV in vertebrate populations I used both existing literature and performed serological surveys. Although humans are largely thought to be RRV dead-end hosts (species which are incapable of pathogen amplification), circulation of the virus in human populations is well documented and provides insights into spatial-temporal patterns of transmission relevant to the understanding of non-human reservoirs. In Chapter 4, I assessed spatial-temporal patterns of seroprevalence in human populations reported from across the natural distribution of RRV in Australia and the Pacific Island Countries from 1958 to present day. A key finding was that RRV circulated in human populations at least since 1975 when v human seropositivity between 20 and 34% was reported in Indonesia and Papua New Guinea. This is important because these countries have different vertebrate fauna to Australia, suggesting different transmission cycles. I then assessed RRV exposure in non-human vertebrate species, focussing on South East Queensland, a RRV endemic area (Chapter 5). Samples were collected through a network of veterinary clinics over a 12-month period, and a total 595 samples from 31 species were obtained. The results showed that taxonomic relatedness is not an important determinant for seropositivity, but rather the ecology and physiology of a species including diet, body size and longevity is most important for exposure to RRV. This study not only tests the greatest diversity of vertebrate species in a single RRV seroprevalence study, but is also novel because it provides methodological advances for analysing seroprevalence data for other zoonotic pathogens. In my last data chapter (Chapter 6), I assessed the vertebrate-vector communities across sites with varied RRV human notification rates. Field surveys assessing ‘abundance’ and ‘diversity’ in light of human notifications were undertaken for six months. Human notifications were positively correlated with vertebrate biomass and total mosquito abundance. Although informative in highlighting variables for ongoing investigations, the data from this chapter was insufficient to determine whether this pattern was unique to the specific habitats in which the data was collected, or a true relationship between disease in humans and non-human reservoirs. Nevertheless, this result lends support to the complex