title: The Current Status, Evolution and Spread of Arboviruses Circulating in Australia
Creators: name: Madzokere, Eugene T
Publisher: name: Griffith University
Year: 2022
Subjects: subject: Arboviruses
subject: Public health
subject: Infection control

description: Arboviruses circulating in Australia are of clinical importance as they cause painful, often chronic musculoskeletal arthritic or fatal dengue disease. They include Ross River virus (RRV), Barmah Forest virus (BFV), chikungunya virus (CHIKV) and dengue virus (DENV). This dissertation assessed the seroprevalence, diversity, evolution, spread and strategies for controlling infection caused by these arboviruses. The overall aim of research presented in this dissertation was to improve public health responses such as nationwide surveillance, diagnosis, and infection control. Research undertaken in chapter 2 achieved this through systematic review and statistical synthesis of human seroprevalence data for RRV, BFV and DENV. I have shown that many factors influence the reporting of human seroprevalences for these three arboviruses. Among these factors is the choice of assay method, timeframe, and sampling strategy. I have also presented findings showing that the spatiotemporal range and median seroprevalences reported for DENV and RRV are wider and higher than those for BFV. This indicates that the risk of exposure to DENV and RRV is significantly higher and extends overseas, however this risk relates to the distribution of the transmitting vectors. My analysis highlighted that DENV presents the highest risk of exposure but its incidence in Australia is declining due to successful implementation of Wolbachia-DENV control programs which have restricted the distribution of Aedes aegypti. Most serosurveys reviewed reported a positive association between age and seroprevalence, and increasing seroprevalence with gender. However, studies reporting gender-seroprevalence data did not do statistical analysis to show the significance of outcomes. This dissertation therefore recommends streamlining, standardization and statistical synthesis of serosurveys data to better quantify risk of exposure, identify risk factors, at-risk groups/populations, associations between seroprevalence and risk factors and at-risk groups/populations. In chapter 3, I characterised the phylogenetic relationship among 193 RRV near whole genomes sourced from multiple hosts, nationwide and the Pacific, in-between 1959-2018. Eight-six of these genomes were generated in this dissertation. My assessment revealed that the four RRV genotypes display high levels of intra-genomic diversity, as I was able to characterise the virus into eight additional sublineages within genotypes G1 (n = 2), G3 (n = 5) and G4 (n = 1). This characterisation brings the total number of known RRV sublineages to 13. Only three of these sublineages (G3D, G4A and G4B) contain viruses that have circulated in Australia within the last decade. The last sampling of genotype 1 and 2 (G1 and G2) viruses was in 1976 and 1995 from Queensland and Western Australia. These viruses may no longer be in circulation within Australia. Sublineages G4A and G4B the most dominant circulating variants of RRV in recent times but they are spatially restricted to Eastern and Western Australia. My phylogenetic analysis suggests that a human traveller likely introduced RRV into the PICTs from northern rather than eastern Australia causing the explosive 1979-80 epidemic. This hypothesis builds upon the one postulated by authors of previous studies who used genomic datasets for RRV isolates sampled from a few locations and not nationwide as I did. Future studies are required to determine differences between RRV sublineages, factors driving lineage replacement, and understand the role of positively selected codon site to RRV evolution. For chapter 4, I studied the evolution, dissemination and phylogenetic relation between 87 BFV near whole genomes sourced nationwide and from Papua New Guinea from three hosts; humans, mosquitoes and a macropod, during 1974-2018. Fifty-four of these genomes were generated in this dissertation and were sampled throughout Australia. Despite the addition of these new genomes to the BFV phylogeny, results obtained indicate that BFV still consists of three genotypes with most new genomes generated from isolates sampled from northern, eastern, and Western Australia grouping in genotype G3. This dissertation reconstructed the most plausible and statistically supported dissemination pathways for BFV and identified the PNG as the most likely source of the virus. The impacts of nucleotide variation within repeat sequence elements and positive selection with the nsP1 Mtase-Gtase domain on virus replication and host range need to be investigated further. For Chapter 4 and 5, I showed that BFV and RRV have a synonymous codon usage bias toward A or C at the 3rd codon position; an abundance of CA and UG, and suppression of CG and UA dinucleotides; display coincidental and antagonistic synonymous codon usage bias with their respective mosquito and vertebrate hosts. In chapter 7, I also showed that amino acid coevolution and compositional biases are prevalent within protein coding regions belonging to RRV and BFV. I found translational selection to be the most influential evolutionary force driving RRV codon usage patterns (chapter 5). Mutational pressure was a close second. I also identified host motifs associated with RRV and BFV coevolving sites. Altogether these results indicate that many factors drive RRV and BFV evolution, among them virus and host related influences. Investigation of the clinical relevance of these findings (chapters 4, 5, and 7) is required. In chapters 6 of this dissertation, I identified five drugs [Anidulafungin (an antifungal), Fondaparinux (an anticoagulant), Rifabutin (an antibiotic), Deslanoside (a cardiac glycoside), and Temsirolimus (an antineoplastic agent)] that bind with high affinity, potency and efficiency to the RRV, BFV and CHIKV capsid. Their role as capsid inhibitors and potential treatments for RRV, BFV and CHIKV infection needs validating through functional and preclinical studies. In chapter 8, I proposed a strategy for generating integrated species distribution modelling frameworks to improve prediction of mosquito-vector habitat shifts in the future. Such modelling frameworks do not currently exist and so their generation and evaluation as an additional component to existing vector and arbovirus surveillance initiatives in Australia is required. This dissertation has addressed its research aims and hypothesis. It has demonstrated that robust nationwide surveillance, review and synthesis of seroprevalence, genomic, host, and environmental data for RRV, BFV and DENV enhances the understanding and management of arbovirus epidemics, virus characterisation and discovery, and infection control in Australia. This research has also shown that some of the factors driving alphavirus evolution, can be exploited for vaccine development. In addition, this dissertation has also presented five approved medicines with potential for repurposing as anti-alphaviral treatments. More broadly, this dissertation has generated new strategies and concepts for improving arbovirus surveillance and infection control in Australia.