Elucidating the sweet potato virome in Greece with the aid of high-throughput sequencing technology

In 2018, typical symptoms of sweet potato virus disease (SPVD) such as purple ringspots, distortion and crinkling of the leaves appeared on a sweet potato crop located in southern Greece. High-throughput sequencing (HTS) analysis revealed the presence of seven viruses, sweet potato feathery mottle virus (SPFMV), sweet potato chlorotic stunt virus (SPCSV), sweet potato virus C (SPVC), sweet potato virus G (SPVG), sweet potato virus 2 (SPV2), sweet potato leaf curl virus (SPLCV) and sweet potato pakakuy virus (SPPV). In silico analysis of the HTS data in combination with Sanger sequencing succeeded in obtaining the complete genome sequences of all seven viruses. Nucleotide sequence comparisons of complete viral genomes showed high similarity of all detected potyviruses and SPLCV with homologous sequences retrieved from Gen Beta ank, whereas a new variant of SPCSV RNA1 was characterized and successfully transmitted onto Nicotiana benthamiana plants with the whitefly species Bemisia tabaci MED and MEAM1. Moreover, the Greek strain of SPPV showed higher similarity with SPPV strain B, even though it possesses a variable RT-RNase H domain. Further phylogenetic analysis clustered Greek sweet potato virus isolates into various phylogenetic groups, whereas few new clades were formed in the cases of SPFMV, SPVG and SPCSV RNA1. Small-scale surveys on three different sweet potato crops exhibiting typical, mild or no symptoms also indicated the close association of SPCSV with SPVD. Taken together, this study characterizes for the first time the virome of sweet potato crops in Greece and provides a glimpse into the evolutionary relationships of the identified viruses.