Biological and molecular characterization of sweet potato chlorotic stunt virus (SPCSV) in some sweet potato (Ipomoea batatas (L) Lam.) growing areas in the Philippines

Sweetpotato virus disease (SPVD), the most important virus disease of sweetpotato (Ipomoea batatas (L) Lam.), is caused by the synergistic interaction of whitefly-transmitted crinivirus Sweet Potato Chlorotic Stunt (SPCSV), and the aphid-transmitted potyvirus Sweet Potato Feathery Mottle Virus (SPFMV). The presence of SPFMV, SPCSV and Sweet Potato Chlorotic Fleck Virus (SPCFV) using CIP (International Potato Center)-developed NCM ELISA kit was detected in some sweetpotato commercial growing areas in the country. Double infection of SPFMV and SPCSV was found to be the most prevalent, causing the SPVD in these areas. The SPCSV was isolated from the complex virus using whitefly-transmission into propagation hosts (I. setosa and I. nil) and typical symptoms of vein clearing and sunken vein were observed on the diseased susceptible plants. Reverse-transcriptase polymerase chain reaction (RT-PCR) resulted to the positive amplification of the 460bp heat shock protein 70 homologue (HSP70h) fragment for the Ablang (Tarlac), Rang-ayan (Tarlac), Saysain (Bataan), Tranca (Laguna), Tanato (Bataan), ViSCA (Leyte) and Nagbunga (Zambales) isolates using primers specific to non-East African strains. Nucleic acid from the partial Hsp70h gene of Ablang (Tarlac), Rang-ayan (Tarlac), Saysain (Bataan), Tranca (Laguna) and Tanato (Bataan) isolates were sequenced with 99.3-100 percent and 97.2-100 percent homology based on nucleotide (nt) and derived amino acid sequences, respectively. All isolates obtained from Central Luzon were found to be 100 percent similar based on the deduced amino acid sequence. The Tranca isolate had variation of 99.1-99.5 percent on nt and 98.6 percent on deduced amino acid as compared to the other Philippine isolates. Phylogenetic analysis of the partial Hsp70h gene indicated that all the Philippine SPCSV isolates obtained belongs to the non-East African (NEA) strain group of SPCSV that confirmed the presence of SPCSV NEA strains in the Philippines. Comparison of the partial Hsp70h sequence of the four isolates to previously described sequences of Hsp70h of East Africa (EA) and NEA strains generated nt homology between 74.2-77.8 percent and derived amino acid similarity of 89.1-92.5 percent. The high sequence variation of EA and NEA SPCSV strains is not only relevant in the improvement of indexing methods of planting materials for quarantine measure but should also be considered in planning sustainable control strategies against SPVD, and for deploying various forms of resistance in sweetpotato breeding program.