Ancient and current association of the Trichinella complex with negative-sense and double-stranded RNA viruses

The earliest records of Trichinellosis might be found in bibles that recommend against pork consumption due to the spread of a disease that resembles what is now identified as Trichinellosis. Parasitic nematodes (round worms) of the genus Trichinella form a complex of at least 13 species with a broad geographic range. Herein, through data mining of transcriptomic data, and re-sequencing of the transcriptome of representative isolates, we demonstrate the presence of viruses within 10 recognized Trichinella species. We provide genome sequences of four viral species of negative sense RNA viruses that belong to the Family Lispiviridae , Order Mononegavirales, and of eight novel viruses of double-stranded RNA viruses that belong to a novel sub-order within the order Ghabrivirales . The integration of viral genome fragments within encapsulated Trichinella genomes demonstrates that these parasite-virus associations are ancient. Overall, viruses show co-diversification with their parasitic hosts. Yet the phylogenetic position of viruses revealed past host jump from an ancestral encapsulated Trichinella species to the ancestral T. pseudospiralis and challenges previous dogma on the phylogeny and biogeography of Trichinella species in North America. IMPORTANCE We are witnessing the emergence of a novel field of research focusing on viruses of parasites and their role in parasite pathogenicity. Herein, we describe the characterization of viruses within 10 recognized species of Trichinella . The viruses were distantly related to known viruses which led us to propose the creation of a novel genera and a novel sub-order. We demonstrated the integration of viral genome fragments within the genome of Trichinella species and an on-going process of birth and death of viral integration. Finally, we showed that virus phylogenetic analyses can provide fine-tuned information about their parasitic host evolutionary history. This study demonstrates the ancient and close association between Trichinella and viruses and strong species specificity. Further studies are now needed to determine whether the newly discovered viruses could be targeted for the development of novel diagnostic approaches.