Owen, Christopher J.; (2022) Global genomic diversity of a major wildlife pathogen: Ranavirus, past and present. Doctoral thesis (Ph.D), UCL (University College London).

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Abstract

Ranavirus is a genus of large double-stranded DNA viruses (family Iridoviridae) that parasitise three taxonomic classes of poikilothermic vertebrates. They are important wildlife pathogens of conservation and economic concern, posing significant threat to amphibian biodiversity and aquaculture commerce. Despite substantial advances since their discovery in the 1960s, the evolutionary history of ranaviruses remains poorly characterised. The aim of this thesis is to advance the characterisation of Ranavirus evolutionary dynamics to contemporary standards. A large whole-genome dataset was collated and scrutinised, combining all publicly available material with a novel collection of isolate genomes. Cutting-edge microbial genomics tools were applied to gain insight into ranavirus genetic diversity, phylogeography, and genome evolution. Delineation of the Ranavirus pan-genome served as a foundation to conduct phylogenetic and population genetic analyses. Where the limitations of alignment-based methodologies were met, alignment-free techniques were employed to make full use of all genomic information. Phylogenetic reconstructions uncovered unique genetic diversity incompatible with current taxonomic demarcations amongst several lineages of Ranavirus. Pervasive genetic recombination was detected across the genus, and certain lineages contained a high degree of ancestral polyphyly. Recurrent patterns linked to animal trade and aquaculture were detected. Extensively polyphyletic viruses were isolated from captive animals, and population genetic analysis revealed ancestry components shared by ranaviruses isolated from farmed animals on separate continents. Finally, phylodynamic analysis suggests human-mediated translocation of FV3-like ranaviruses began more than a century before present. The inadequacies of current Ranavirus taxonomy are highlighted by this work, and suggests a substantial diversity remains to be characterised. The processes by which ranaviral genetic diversity is generated appears particularly dynamic, with significant contributions made via recombination between distinct linages. Altogether, this thesis underscores the vital impact trade and captive rearing of fish and herpetofauna have had on the global spread of ranaviruses and their processes of genetic diversification. Finally, these results suggest that anthropogenic influences commenced decades earlier than previously thought, likely upon the acceleration of modern globalisation.

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