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Characterization of RNA viruses from the coastal waters of British Columbia Culley, Alexander Ian

Abstract

RNA viruses are major pathogens o f animals and plants and include viruses that are of enormous economic and public-health concern. In the ocean, RNA viruses infect organisms from bacteria to whales, but RNA virus communities in the sea remain essentially unknown. Although what we know of marine RNA viruses is restricted to a limited number of isolates, emerging data suggest that RNA viruses might be more abundant, and are more ecologically important, than has been suggested. Therefore the hypothesis of this dissertation is that RNA viruses comprise a detectable and diverse fraction of the marine virus community. Towards testing this premise, the research objectives were to sequence a marine RNA virus isolate, Heterosigma akashiwo RNA virus (HaRNAV) , evaluate the diversity of picorna-like viruses, a superfamily of positive-sense single-stranded (ss) RNA viruses, and construct whole-genome shotgun libraries to characterize two complete RNA virus assemblages. The results of all three studies underline the novelty of the marine RNA virus community. For example, HaRNAV is related to picorna-like viruses, but does not belong within any currently defined virus family and has therefore been classified in the Marnaviridae, a newly established virus family. Furthermore, on the basis of analysis of RNA-dependent RNA polymerase sequences amplified from marine virus communities from the Strait of Georgia, a diverse array of picorna-like viruses exists in the ocean. All of the sequences amplified were divergent from known picorna-like viruses, and fell within four monophyletic groups. Finally, analysis of reverse transcribed whole-genome shotgun libraries revealed a diverse assemblage of RNA viruses, including a broad group of marine picorna-like viruses and distant relatives of viruses infecting arthropods and higher plants. Moreover, the genomes of several hitherto undiscovered viruses were completely assembled. These data are among the first characterizations of the in situ marine RNA virus community and represent a preliminary step in the elucidation of their role in the marine environment. The discovery of novel groups of viruses that are significantly divergent from established taxa should be of interest to virologists, oceanographers, and microbial ecologists.

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