Identification of novel tick-associated RNA virus sequences from questing ticks collected in Ishikawa and Ehime Prefectures, Japan

The emergence of tick-borne viral diseases has significantly led to intensified efforts to identify viruses harbored by ticks. In this study, we employed next-generation sequencing to analyze RNA viral sequences present in 1360 questing ticks collected from the Ishikawa and Ehime Prefectures, Japan. Phylogenetic analysis of these viral sequences suggested that these viruses may not be affiliated with vertebrate-infecting groups but instead, show close relationships with previously reported tick-specific viruses. A novel iflavirus has been detected in Ixodes turdus tentatively named Ixodes turdus iflavirus, displaying less than 52% similarity to the amino acid sequence of its closest known virus. Two new strains of Hubei tick virus 3 belonging to the Iflaviridae family, were detected in Haemaphysalis formosensis. Furthermore, Ehime tick reovirus (EhTRV), identified in Haemaphysalis flava, shares approximately 89% pairwise amino acid identity of the largest polymerase protein with Zoersel tick virus, suggesting a close relationship. Lastly, two different segments of an unclassified sobemo-like virus were identified as putative novel species. The findings of this study offer new insights into the presence of viruses in questing ticks, particularly in specific regions of Japan.