Metatranscriptomic analysis reveals the virome and viral genomic evolution of medically important mites

Mites are notorious for being vectors transmitting infectious pathogens and a source of allergens causing allergic conditions in animals and humans. However, despite their huge impact on public health, the virome of mites remains unknown. Here, we characterized the virus diversity and abundance of 14 species of medically important mites based on total RNA sequencing data sets generated in this study, as well as those deposited in the Sequence Read Archive (SRA) database. A total of 47 genetically distinct viruses were identified and classified into 17 virus families or virus supergroups, and the viral sequences accounted for as much as 29.67% of the total non-rRNA transcriptome in one mite library. The most commonly identified viruses are members of Picornavirales, among which we revealed more than one type of viruses that are evolutionarily related to dicistronic viruses but contain a single open reading frame, thus likely representing a recent example of host (i.e., mite)-related parallel evolution from the dicistronic to monocistronic genomic form within the family Dicistroviridae. To our best knowledge, this is the first time a comprehensive and systematic screening of the RNA virome in medically important mites, including house dust mites (HDM), has been performed. Overall, the RNA virome identified here provides not only significant insights into the diversity and evolution of RNA viruses in mites, but also a solid knowledge base for studying their roles in human diseases. IMPORTANCE Mites are an important group of arthropods that are associated with a variety of human diseases, including scrub typhus and asthma. However, it remains unclear whether or not mites carry viruses that might play a role in human infections or allergic disease. In this study, we used a total transcriptomics approach to characterize and compare the complete RNA virome within mites that are relevant to human health and diseases. Specifically, our data revealed a large diversity, a high abundance, and a flexible genomic evolution for these viruses. Although most of the viruses identified here are not known to be associated with human infectious disease, the abundant presence of viral RNAs may play an immunomodulatory role in the development of allergic reactions, such as asthma, during environmental exposure to mite allergens and therefore may provide important insights into the mite-induced allergy and preparation of mite allergen vaccines.