Molecular characterization of sweet potato leaf curl virus isolate from China (SPLCV-CN) and its phylogenetic relationship with other members of the Geminiviridae

A Sweet potato-infecting sweet potato leaf curl virus (SPLCV) isolated in China was detected by Polymerase Chain Reaction (PCR). PCR products amplified from DNA-A were cloned and sequenced. The isolates of SPLCV from China(SPLCV-CN) has a genome organization similar to that of monopartite begomoviruses. The DNA-A had two ORFs (AV1 and AV2) in the virion sense and four ORFs (AC1, AC2, AC3, and AC4) in the complementary sense, separated by an intergenic region (IR) containing a conserved stem-loop motif. Three incomplete direct repeat iterons were also found within the IR. The presence of AV2 ORF supports the relationship of SPLCV-CN to the Old World gemimiviruses. Sequence comparisons showed that the DNA-A sequence of SPLCV-CN were closely related to those of sweet potato leaf curl Georgia virus-[16] (SPLCGV-[16]), Ipomoea yellow vein virus (IYVV-SI), and sweet potato leaf curl virus (SPLCV) with nucleotide sequence identity ranging from 88% to 91%. Comparison of individual encoded proteins between SPLCV-CN and that of three other SPLCV isolates showed the coat protein (AV1) shared the highest amino acid sequence identity (93%-96%), suggesting the coat protein of these viruses may have identical ancestor. The relationships between SPLCVCN and other whitefly-transmitted geminiviruses were investigated by using phylogeny of derived AV1, AC1, and AV2 amino acid sequences. In all phylogenetic trees, SPLCV-CN clustered with three other isolates of SPLCV. The analyses revealed that the four isolates of SPLCV have coat proteins which are unique from its counterparts from both the Old World and New World. The present of AV2 and phylogenic analysis of AC1 suggest that SPLCV is more close to begomoviruses from the Old World but isolates of this virus seems to form a separate subset.