Enhancing Understanding of CRESS Viral Diversity through Development of a Computational Tool for Replication-associated Structure Identification
Alyssa A. Pratt, Westview High School; Ignacio de la Higuera, Ellis Lynn Torrance, George Kasun, Kenneth M. Stedman, Biology Department, Portland State University
Single-stranded DNA (ssDNA) viruses are abundant units of our biosphere, characterized by uniquely high mutation rates and diversity. A grouping of ssDNA viruses, CRESS - circular replication protein-encoding ssDNA viruses - has compact genomes, characterized by a capsid gene, replication protein gene, and a stem-loop secondary structure, at which the replication protein nicks and initiates viral replication. These stem-loop structures are considered highly-conserved, each including similar nonanucleotide sequences that vary by family. Within CRESS, a novel proposed family of viruses, cruciviruses, has been identified, that contains a unique feature: their putative capsid gene has greater homology to RNA viruses than DNA viruses, indicating their genome may be the product of a recombination event. The goal of this project to develop a tool that detects putative stem-loop regions from CRESS viruses, which can then be applied to both detection and analysis of diversity in Cruciviridae. To do so, algorithms were designed to first detect the conserved nonanucleotide sequence within the loop, with optimizations for known viral families. In the region surrounding these nucleotides, predicted DNA folds are examined for potential stem-loop structures, compared to those known, and scored against ideal attributes. The resultant software tool, “StemLoop-Finder”, finds that putative cruciviral stem-loop sequences, like the rest of their genome, tend to be more diverse than those in comparable families. The development of this software as an easily-accessible computational tool may aid researchers in understanding viral evolution and the origin of features in these unusual genomes.