Genomes of Small RNA Viruses: Amendments, Discoveries, and Characterizations

Abstract

RNA viruses make up a disproportionate amount of emerging human diseases, largely contribute to agriculture, and are recognized for their important roles in shaping the evolution of life. Metagenomics datasets have emphasized the importance of viral genomics in virus discovery. The International Committee on Taxonomy of Viruses (ICTV) has endorsed use of metagenomics data alone in identifying new viruses. One immediate question the ICTV will have to address is how to sort through these data. The works presented here are broken into three sections and are aimed at identifying general rules that can be applied to classification and extracting further utility of metagenomics data. In Section I, I describe general rules that have been successfully applied retroactively to hypothesize potential errors or incompleteness in previously reported RNA viral sequences. In Section II, I present newly discovered small RNA viruses and subviral agents of such identified from metagenomics data and the information they contribute to an understanding of evolutionary history and virus biology. In Section III, I present development of a virus-mediated reverse genetics system that can be used to understand the biological function of viral sequences at the nucleotide level, thus providing a biological means to assess confidence in sequence differences between closely-related and concurrent infection of multiple virus species. Thus, Section I will cover amendments to previously reported RNA viral sequences have been proposed, Section II will provide how metagenomics data provide insights into virus evolution and virus biology, and Section III will provide a biological means of improving confidence in sequencing results from metagenomics data. I conclude by presenting thoughts on how the data from the three sections and their implications may shape future discussions in the age of viral metagenomics.