Reexamination of the Sida Micrantha Mosaic Virus and Sida Mottle Virus Complexes: Classification Status, Diversity, Cognate DNA–B Components, and Host Spectrum

Sida mottle virus (SiMoV) and Sida micrantha mosaic virus (SiMMV) are major Brazilian begomoviruses (<i>Geminiviridae</i>). However, the range of DNA-A identity of isolates of these viruses (81-100%) is not in agreement with the current criteria for <i>Begomovirus</i> species demarcation (<91%). To clarify this putative classification problem, we performed a comprehensive set of molecular analyses with all 53 publicly available isolates (with complete DNA-A genomes) designated as either SiMoV or SiMMV (including novel isolates obtained herein from nationwide metagenomics-based studies). Two well-defined phylogenetic clusters were identified. The SiMMV complex (<i>n</i> = 47) comprises a wide range of strains (with a continuum variation of 88.8-100% identity) infecting members of five botanical families (Malvaceae, Solanaceae, Fabaceae, Oxalidaceae, and Passifloraceae). The SiMoV group now comprises eight isolates (90-100% identity) restricted to Malvaceae hosts, including one former reference SiMMV isolate (gb|NC_077711) and SP77 (gb|FN557522; erroneously named as "true SiMMV"). Iteron analyses of metagenomics-derived information allowed for the discovery of the missing DNA-B cognate of SiMoV (93.5% intergenic region identity), confirming its bipartite nature. Henceforth, the correct identification of SiMoV and SiMMV isolates will be a crucial element for effective classical and biotech resistance breeding of the viral host species.