Discovery and Diagnosis of a New Sobemovirus Infecting Cyperus esculentus Showing Leaf Yellow Mosaic and Dwarfism Using Small-RNA High Throughput Sequencing

C. esculentus is a profitable crop in Valencia, Spain, but the emergence of a disease causing of leaf yellow mosaic, dwarfism, and a drastic decrease in tuber production has become a problem. The small-RNA high-throughput sequencing (HTS) of a diseased C. esculentus plant identified only one virus, which could be the causal agent of this disease. The amino-acid comparison with viral sequences from GenBank and phylogenetic analyses indicated that this was a new species of genus Sobemovirus, and the name Xufa yellow dwarf virus was proposed. Completion with Sanger sequencing yielded a contig of 3072 nt corresponding to about 75% of the typical genome of sobemoviruses, including ORFs 2a (polyprotein-containing protease, VPG, and other proteins), 2b (RNA-dependent RNA polymerase), and 3 (coat protein). The nucleotide sequence was used to develop fast and accurate methods for the detection and quantification of xufa yellow dwarf virus (XYDV) based on reverse transcription (RT) and DNA amplification. XYDV was detected in leaves and tubers and showed a high incidence in the field in both symptomatic (almost 100%) and asymptomatic (70%) plants, but its accumulation was much higher in symptomatic plants. The relevance of these results for disease control was discussed.