Revealing the determinants of virus ecology, evolution and emergence in fish

Abstract

Viral diseases emerge when a virus jumps from a donor to a recipient host species. Revealing the determinants of how viruses jump between animals is a question of fundamental importance in infectious disease ecology and evolution. With over 34,000 species, representing some 50% of all extant vertebrates with evolutionary origins dating back over 500 million years, fish constitute a powerful model system to reveal the determinants of cross-species virus transmission and the factors that shape vertebrate viromes. I utilised unbiased metatranscriptomic sequencing to reveal the viruses that exist in iconic ecosystems such as the Great Barrier Reef, Lake Tanganyika, and Murray-Darling Basin that are characterised by high levels of species connectivity. This led to the discovery of 185 novel fish viruses, spanning 24 viral families. A key finding of this thesis was that varying levels of host genetic relatedness among species had a significant impact on the viruses that infect them. The African cichlids of Lake Tanganyika, that are characterised by some of the lowest pairwise genetic differences observed among vertebrate groups, exhibited high levels of cross-species transmission. In marked contrast, reef fishes, composed of high levels of genetic divergence between several fish families, experienced low levels of virus transmission among species, despite high contact rates on coral reefs. While revealing patterns of virus ecology and evolution in aquatic ecosystems, I also discovered notable pathogens in asymptomatic hosts, including iridoviruses and nodaviruses as well as the opportunistic bacterial pathogen Photobacterium damselae. These discoveries are of particular importance given the severe impact of emerging infectious diseases in one of the most rapidly growing industries worldwide – aquaculture. Overall, this thesis provides a detailed analysis of the fish virome and offers a new perspective for the study of virus ecology and evolution in aquatic ecosystems.