Diversity of Sweepoviruses Infecting Sweet Potato in China

Sweepoviruses (a group of begomoviruses that infect plants in the family Convolvulaceae) have monopartite genomes that consist of a circular, single-stranded DNA molecule. Seventy-three complete genomic sequences of sweepoviruses were characterized from the sweet potato samples collected in China. Eight sweepovirus species, including two novel species with proposed names of Sweet potato leaf curl China virus 2 and Sweet potato leaf curl Sichuan virus 2, were identified among these samples. One species, Sweet potato leaf curl Canary virus, was first identified in China. Among the 13 identified strains of Chinese sweepoviruses, 4 were newly discovered. Sweet potato leaf curl virus had the highest frequency (53.4%) of occurrence in the sweet potato samples from China. The similarities among the 73 sweepovirus genomic sequences were between 77.6 and 100.0%. Multiple recombination events were identified, and 16 recombinant sequences were determined. Recombination was observed between different species and between different strains of the same species. Recombination breakpoints were mainly localized on the intergenic region and in three open reading frames (AC1, AV1, and AV2). This study is the first comprehensive report on the genetic diversity of sweepoviruses in China.