Viruses in marine animals: Discovery, detection, and characterizarion

• Main Author: Fahsbender, Elizabeth
• Format: Doctoral or Postdoctoral Thesis
• Language: unknown
• Published: Digital Commons @ University of South Florida 2017
• Subjects: Animal virus; Viral metagenomics; Whole-genome sequencing; Serology; Other Oceanography and Atmospheric Sciences and Meteorology; Antarctic; Weddell; Antarc*; Antarctica; Weddell Seal; Weddell Seals
• Online Access: https://digitalcommons.usf.edu/etd/6832; https://digitalcommons.usf.edu/context/etd/article/8029/viewcontent/Fahsbender_usf_0206D_14311.pdf

Diseases in marine animals are emerging at an increasing rate. Disease forecasting enabled by virus surveillance presents a proactive solution for managing emerging diseases. Broad viral surveys aid in disease forecasting by providing baseline data on viral diversity associated with various hosts, including many that are not associated with disease. However, these viruses can become pathogens due to expansion in host or geographic range, as well as when changing conditions shift the balance between commensal viruses and the host immune system. Therefore, it is extremely valuable to identify and characterize viruses present in many different hosts in a variety of environments, regardless of whether the hosts are symptomatic or not. The lack of a universal gene shared by all viruses makes virus surveillance difficult, because no single assay exists that can detect the enormous diversity of viruses. Viral metagenomics circumvents this issue by purifying viral particles directly from host tissues and sequencing the nucleic acids, allowing for virus identification. However, virus identification is only the first step, which should ideally be followed by complete sequencing of the viral genome to identify genes of interest and develop assays to reveal viral prevalence, tropism, ecology, and pathogenicity. This dissertation focuses on the discovery of novel viruses in marine animals, characterization of complete viral genomes, and the development of subsequent diagnostic assays for further analysis of virus ecology. First, viral metagenomics was used to explore the viruses present in the healthy Weddell seal (Leptonychotes weddellii) population in Antarctica, which led to the discovery of highly prevalent small, circular single-stranded DNA (ssDNA) viruses. The lack of knowledge regarding the viruses of Antarctic wildlife warrants this study to determine baseline viral communities in healthy animals that can be used to survey changes over time. From the healthy Weddell seals, viral metagenomics led to the discovery of ...