Complete genomic characterization of a reassortment isolate of Sophora yellow stunt virus from Sophora alopecuroides in China

Sophora alopecuroides is an important shrub widely distributed in arid and semi-arid regions of Asia. Recently, S. alopecuroides plants with symptoms of severe stunting, yellowing and small sized leaves were observed in Wuhai, Inner Mongolia, of China. In this work, the infection of Sophora yellow stunt virus (SYSV), a virus belonging to the genus Nanovirus , was confirmed by next-generation sequencing of small RNAs. The complete genome of the SYSV CH isolate, including eight circular single-stranded DNA components, was amplified by PCR and sequenced. SYSV-CH shared 87.0% identity in overall nucleotide sequence with SYSV-IR:Har:H13:Soph:17 isolate. Both of phylogenetic analysis based on individual DNA components and recombination analysis based on concatenated components supported the hypothesis that SYSV-CH might be a reassortment isolate whose DNA-R originated from faba bean necrotic yellows virus. In addition, an alphasatellite was identified and sequenced. To our knowledge, this is the first report of occurrence and complete genome sequence of SYSV from China.