Show simple item record Noune, Christopher 2020-09-29T04:13:38Z 2020-09-29T04:13:38Z 2017-07-30
dc.description.abstract The Nucleopolyhedroviruses (NPV) are dsDNA invertebrate-specific obligate pathogens of the insect orders Lepidoptera, Hymenopteran and Dipteran belonging to the family Baculoviridae (Baculovirus). An NPV consists of a genome with lengths between 80 and 180 kbp and a community of phenotypically and genetically diverse virus strains that are co-occluded within a protein body. NPVs are widely used in biological control of Lepidopteran pests, and understanding isolate dynamics, diversity and evolution is important in resistance management strategies and developing next generation biopesticides with desired phenotypic traits. The aim of this study was to apply next generation sequencing and develop bioinformatic techniques to expand and accelerate current knowledge of baculoviruses by studying the dynamics, diversity and evolution. This included the development of a new bioinformatic pipeline to analyse the within-isolate and within-strain diversity, applying this pipeline to monitor the change in genotype abundance during the infection cycle and derivatisation of in vitro and in vivo selected strains from a wild type isolate of commercial importance, Helicoverpa armigera Single Nucleopolyhedrovirus (HaSNPV) isolate AC53 (AC53). Derived genomes were analysed to identify trait or isolation technique specific mutations, and the global relationships of these strains to all known HaSNPV isolates. Phylogenetic analysis of all known HaSNPV and H. zea SNPV isolates with the addition of AC53 and some of its derivatives supported the claim that these viruses are the same viral species, and suggests that the HaSNPV species may have originated in Australia. The use of whole genomes in phylogenetic analysis gave greater resolution than the more commonly used analysis using selected open reading frames. Five strain derivatisation approaches were applied: two in vitro (in tissue culture) and three in vivo. Analysis of both in vitro and in vivo -derived strains genomes identified selection specific mutations, with fast speed of kill, slow speed of kill and maximum virus production strains containing trait specific mutations. Biological characterisation of these trait-specific strains identified significant virulence-transmission trade-offs such as enhanced speed of kill but reduced efficacy which implicates commercial optimisation of strains. A new software pipeline called the ‘Meta-barcoding Genotyping and Abundance Pipeline’ (MetaGaAP) was developed to identify genotypes and their relative abundance within the AC53 isolate. This was validated by Sanger sequencing and comparison to the AC53-T2 strain. The pipeline was applied to monitor AC53 during the infection cycle and identified two evolutionary effects occurring within the population; weak-negative selection with mutation bias and a ‘drift barrier’ to limit the effects of genetic drift. Furthermore, time-course assays revealed a significant reduction in dominant genotype abundance with an increase in minor genotype abundance when the initial viral stock is compared to the final viral product. This implicates commercial production as the starting material and the produced material contain different genotype abundance profiles, however, both products contain the same genotype composition. In addition, results presented throughout this study suggested that NPVs fit the viral quasispecies model as mutations that arose were the result of mutational robustness and genotype cooperation. Limitations observed with current NGS and bioinformatic techniques partially impacted the described results but may eventually resolve with advent of third-generation sequencing en_US
dc.description.sponsorship CRDC en_US
dc.publisher Queensland University of Technology en_US
dc.relation.ispartofseries QUT1402;
dc.title PhD: Evolution of viral diversity and virus ecology in the management of resistance to bipesticides en_US
dc.title.alternative Dynamics, Diversity and Evolution of Baculoviruses en_US
dc.type Thesis en_US

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