Molecular characterization and phylogenetic analysis of Citrus viroid I-LSS variants from citrus in Pakistan and China reveals their possible geographic origin

CVd-I-LSS (low sequence similarity), a variant of Citrus bent leaf viroid (CBLVd), was first discovered in Japan, and its distribution is currently limited to Japan and Iran. In the present study, seven CVd-I-LSS isolates were detected from different citrus hosts (Citrus sinensis, C. reticulata and C. limettioides) in Pakistan and China. Genetic diversity analysis of 49 cDNAs of CVd-I-LSS isolates showed that the Pakistan population was more diverse than that tested from Japan or China. Phylogenetic analysis clustered the predominant sequences examined into three main clades. Only sequences from the Pakistan isolates were found in all three clades, suggesting Pakistan may be the original source of CVd-I-LSS. Cultivar import records and the close phylogenetic relationship found between CVd-I-LSS from China and Japan suggested that the viroid isolated from China might have originated from Japan.