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Here, we examined 25 clinical strains of\n              <jats:italic>R. microsporus<\/jats:italic>\n              for viral infection with a conventional double-stranded RNA (dsRNA) assay using agarose gel electrophoresis (AGE) and the recently established fragmented and primer-ligated dsRNA sequencing (FLDS) protocol. By AGE, five virus-infected strains were detected. Then, full-length genomic sequences of 12 novel RNA viruses were revealed by FLDS, which were related to the families\n              <jats:italic>Mitoviridae, Narnaviridae,<\/jats:italic>\n              and\n              <jats:italic>Endornaviridae,<\/jats:italic>\n              ill-defined groups of single-stranded RNA (ssRNA) viruses with similarity to the established families\n              <jats:italic>Virgaviridae<\/jats:italic>\n              and\n              <jats:italic>Phasmaviridae,<\/jats:italic>\n              and the proposed family \u201cAmbiguiviridae.\u201d All the characterized viruses, except a potential phasmavirid with a negative-sense RNA genome, had positive-sense RNA genomes. One virus belonged to a previously established species within the family\n              <jats:italic>Mitoviridae<\/jats:italic>\n              , whereas the other 11 viruses represented new species or even new genera. These results show that the fungal pathogen\n              <jats:italic>R. microsporus<\/jats:italic>\n              harbors diverse RNA viruses and extend our understanding of the diversity of RNA viruses in the fungal order Mucorales, division Mucoromycota. Identifying RNA viruses from clinical isolates of\n              <jats:italic>R. microsporus<\/jats:italic>\n              may expand the repertoire of natural therapeutic agents for mucormycosis in the future.\n            <\/jats:p>\n            <jats:sec>\n              <jats:title>IMPORTANCE<\/jats:title>\n              <jats:p>\n                The diversity of mycoviruses in fungal hosts in the division Mucoromycota has been underestimated, mainly within the species\n                <jats:italic>Rhizopus microsporus<\/jats:italic>\n                . Only five positive-sense RNA genomes had previously been discovered in this species. Because current sequencing methods poorly complete the termini of genomes, we used fragmented and primer-ligated double-stranded RNA sequencing to acquire the full-length genomes. Eleven novel mycoviruses were detected in this study, including the first negative-sense RNA genome reported in\n                <jats:italic>R. microsporus<\/jats:italic>\n                . Our findings extend the understanding of the viral diversity in clinical strains of Mucoromycota, may provide insights into the pathogenesis and ecology of this fungus, and may offer therapeutic options.\n              <\/jats:p>\n            <\/jats:sec>\n          <\/jats:sec>","DOI":"10.1128\/msphere.00345-24","type":"journal-article","created":{"date-parts":[[2024,7,29]],"date-time":"2024-07-29T13:11:18Z","timestamp":1722258678000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":2,"title":["New lineages of RNA viruses from clinical isolates of\n            <i>Rhizopus microsporus<\/i>\n            revealed by fragmented and primer-ligated dsRNA sequencing (FLDS) analysis"],"prefix":"10.1128","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0009-0006-3301-8575","authenticated-orcid":true,"given":"Wasiatus","family":"Sa'diyah","sequence":"first","affiliation":[{"name":"Department of Life and Environmental 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