Molecular Characterization of a Sweet Potato Leaf Curl Virus Isolate from Egypt and Its Phylogenetic Relationship with Other Members of the Begomovirus

Abstract

The present study was undertaken to isolate and molecularly and phylogenetically characterize a Sweet potato leaf curl virus isolate infecting sweet potato plants in Giza governorate in Egypt. The virus was isolated from infected plants showing leaf curl symptoms using non-viruliferous Bemisia tabaci insects. Total extracted DNA was amplified with polymerase chain reaction (PCR) using the degenerate AV/AC core primers and produced 580 bp of the DNA-A core coat protein in agarose gel. PCR conditions of 6 mM MgCl2, combinatorial enhancer solution, and a 53°C/40s annealing temperature facilitated coat protein amplification. Recovered virus amplicon was ligated into pGEM T-Easy vector and cloned into Eschericia coli, strain DH5α. Purified plasmid DNA was submitted to GenBank and given an accession number FJ455517. Sequence comparisons with 13 sweepoviruses indicated that the SPLCV-Giza isolate has the highest nucleotide sequence identity (97%) with the SPLCV-US (KC253238). According to the current taxonomic criteria for Begomovirus classification, the Giza isolate of SPLCV in Egypt would be considered as a variant of the SPLCV-US. Phylogenic study using amino acid substitution showed the clustering of the 13 studied sweepoviruses in one major clade and one minor clade.  The SPLCV-Giza isolate clustered with SPLCV-US in a monophyletic branch within the large clade circumventing nine sweepoviruses, viz. SPLCV isolates from: Korea, Brazil, Japan, USA, China, India, and Ipomoea yellow vein virus (IYVV) from Italy and Spain. The second minor clade involved the clustering of SPLCV isolates from Uganda and Spain in a monophyletic branch apart from the rest of the studied sweepoviruses.  Phylogenic analysis of SPLCV-Egypt with five other mono and bipartite begomomoviruses showed its distinctive clustering nature from these viruses. In conclusion, the present study confirms the presence of an isolate SPLCV in Egypt as a variant of the SPLCV-US. The study also illustrates the high worldwide diversity of SPLCV isolates and signifies the economic importance of this newly introduced virus into Egypt.