Human Clinical Isolates of Pathogenic Fungi Are Host to Diverse Mycoviruses.

Fungi host viruses from many families, and next-generation sequencing can be used to discover previously unknown genomes. Some fungus-infecting viruses (mycoviruses) confer hypovirulence on their pathogenic hosts, raising the possibility of therapeutic application in the treatment of fungal diseases. Though all fungi probably host mycoviruses, many human pathogens have none documented, implying the mycoviral catalogue remains at an early stage. Here, we carried out virus discovery on 61 cultures of pathogenic fungi covering 27 genera and at least 56 species. Using next-generation sequencing of total nucleic acids, we found no DNA viruses but did find a surprising RNA virus diversity of 11 genomes from six classified families and two unclassified lineages, including eight genomes likely representing new species. Among these was the first jivivirus detected in a fungal host (Aspergillus lentulus). We separately utilized rolling circle amplification and next-generation sequencing to identify ssDNA viruses specifically. We identified 13 new cressdnaviruses across all libraries, but unlike the RNA viruses, they could not be confirmed by PCR in either the original unamplified samples or freshly amplified nucleic acids. Their distributions among sequencing libraries and inconsistent detection suggest low-level contamination of reagents. This highlights both the importance of validation assays and the risks of viral host prediction on the basis of highly amplified sequencing libraries. Meanwhile, the detected RNA viruses provide a basis for experimentation to characterize possible hypovirulent effects, and hint at a wealth of uncharted viral diversity currently frozen in biobanks.