Aquatic turtles, many of which are threatened or endangered, face numerous threats, including anthropogenic interaction, ocean pollution, climate change, and infectious agents. Viruses have been implicated in severe disease outbreaks in other endangered wildlife, such as outbreaks of canine distemper virus in black-footed ferrets and ranavirus-induced mass mortality events in multiple amphibian species. However, the threat of viruses on freshwater and marine turtle populations is unknown, largely due to the limited knowledge regarding viruses found in aquatic turtles. Notably, the aquatic environment, both freshwater and marine, is rich in viral diversity, most of which remains to be discovered and characterized. Thus, there is a need to fill this knowledge gap.

Metagenomic sequencing has revolutionized viral detection and characterization. Metagenomic sequencing has been used as a surveillance tool for unveiling novel viral taxa in diverse ecosystems and as an agnostic diagnostic test for the identification of pathologic viral infections in a wide array of species. Third-generation sequencing makes metagenomic sequencing more accessible due to reduced costs, methodologic flexibility, and simplified bioinformatic analysis. This allows for metagenomic sequencing to be applied to research fields that are historically less funded, but are ecologically important, such as endangered reptiles.

This dissertation has two aims. First to use efficient third-generation sequencing technology to survey for known and unknown viruses in aquatic turtles (Chapter 1). This data can then be used in the future for determining their impact on the health of endangered aquatic turtles and improve the understanding of viral evolution, genetics, and ecology. In the second aim, molecular Koch’s postulates are applied to aquatic turtle meningoencephalitis to discover the likely cause of that disease (Chapter 2). This work collectively identified and characterized twelve novel viral species in this study (eleven in the gastrointestinal tract and one in the central nervous system with spatial localization of mRNA within the affected tissues).

The foundational insight of viral discovery and diversity presented in this dissertation will lay a groundwork for future hypothesis-driven research and underline the imperative need to comprehend viral diversity in understudied species such as endangered aquatic turtles.