A novel mycovirus identified in clinical isolates of Cryptococcus neoformans

Mycoviruses are widespread throughout the fungal kingdom and are known to infect diverse fungal taxa, including fungal species that are important plant and human pathogens. Although many mycoviruses have been found to have minimal effects on their host, several viruses have been found to modulate fungal physiology, and, as a result, impact fungal virulence. Screens for mycoviruses in clinically relevant fungi have identified numerous mycoviruses within several important human pathogens, but mycoviruses remain uncharacterized in the clinically relevant human pathogen Cryptococcus neoformans. C. neoformans is an opportunistic encapsulated yeast responsible for life-threatening cryptococcal meningitis, a leading cause of mortality among immunocompromised individuals, particularly those with HIV/AIDS. We performed a search for viral RNA-dependent RNA polymerase (RdRP) signatures in publicly available C. neoformans transcriptomic data. This search identified Totiviridae viral genomes within six clinical isolates of C. neoformans from Botswana. All six isolates originated from the cerebrospinal fluid (CSF) of HIV-positive individuals with cryptococcal meningitis. Reverse transcription PCR (RT-PCR) independently validated the continued presence of the virus in three of these clinical isolates. Subsequent analysis of the viral genome identified two genotypes of a single species of Totivirus. This new species possesses canonical features of the Totiviridae family, including a slippery heptamer and a predicted RNA pseudoknot structure involved in programmed −1 ribosomal frameshifting for RdRP expression. Taken together, these results provide evidence of a mycovirus capable of infecting C. neoformans .