Discovery and characterization of a novel dsRNA virus infecting the human parasite Trichomonas vaginalis

Abstract

Trichomonas vaginalis is the most common non-viral cause of sexually transmitted infections around the world. Infection by this protozoan parasite results in trichomoniasis, a clinical inflammatory disease with acute and chronic consequences. These parasites, in turn, can be infected by up to four known dsRNA viruses, Trichomonas vaginalis virus 1 through 4 (TVVs). These viruses can exacerbate the inflammatory syndrome incited by their protozoan host, underscoring their significance. Despite the global prevalence of these viruses, few coding-complete genome sequences have been determined. We hypothesized that transcriptome mining of publicly available RNA-seq datasets of T. vaginalis would enable characterization of coding-complete viral genomes, expand the number of known TVV strains, and enable the discovery of divergent viruses in T. vaginalis. We used this transcriptome mining approach to examine 60 RNA-seq datasets representing 13 distinct isolates of T. vaginalis. The results led to sequence assemblies for 27 novel trichomonasvirus strains across all four recognized species. Using a strategy of de novo sequence assembly followed by taxonomic classification, we additionally discovered six strains of a newly identified fifth species, for which we propose the name Trichomonas vaginalis virus 5, also in genus Trichomonasvirus. These TVV5 sequences exhibit high sequence identity to each other but low identity to strains of the four other species. Phylogenetic analysis corroborates the species-level designations. We next employed high-throughput sequencing of RNA isolated from T. vaginalis and enriched for dsRNA molecules (dsRNA-seq) to characterize the viral infections of all available T. vaginalis isolates from the American Type Culture Collection (ATCC). Of the 32 available isolates, 16 isolates were found to be infected with one or more species of TVV. Excitingly, five of these commercially available isolates were found to harbor TVV5. A subset of these isolates was subjected to 3' Rapid Amplification of cDNA Ends (3’RACE), resulting in the determination of the full-length TVV5 genome. Taken together, these results vastly expand the number of coding-complete trichomonasvirus genomes and present the discovery and genomic characterization of a new dsRNA virus infecting a critical human pathogen. These studies contribute to a robust framework for systematic virus characterization and discovery in protozoan parasites. Early evidence for additional viruses infecting T. vaginalis is discussed.