The genetic diversity of eukaryotic RNA viruses is poorly described, due to sparse sampling and biases towards pathogens that impact human health or commercial agriculture. Positive single-stranded RNA viruses exhibit a distinct ability to restructure the endomembranes of host cells to facilitate their propagation. Mitochondria in particular are attractive targets for viral replication, given their central roles in amino acid synthesis, nucleoside synthesis, and host defense mechanisms. We searched publicly available metatranscriptomic datasets for signs of mitochondria-associated (+)ssRNA viruses, identifying hundreds of candidate genomes and genomic fragments encoding ORFs adhering to mitochondrial, as opposed to cytosolic, translational codes. These findings raise the possibility that the cloister of viral gene expression inside the mitochondrion itself may provide an opportunity to evade immune activation pathways at the outer mitochondrial membrane surface
