Molecular characterization of an Apple stem grooving virus isolate from kiwifruit (Actinidia chinensis) in China

Apple stem grooving virus (ASGV) is the type species of the genus Capillovirus in the family Betaflexiviridae. The virus naturally infects several important horticultural crops. Although many ASGV isolates from apple (Malus spp.), pear (Pyrus spp.), citrus (Citrus spp.) and lily (Lilium spp.) have been characterized, the occurrence status and molecular characteristics of the virus from kiwifruit trees are still largely unknown. In this study, by employing the strategy of small RNA deep sequencing coupled with conventional RT-PCR, we provide the first complete genome sequence of an ASGV isolate (named ASGV-Ac) infecting a kiwifruit plant (Actinidia chinensis) grown in China. The complete genome of ASGV-Ac consisted of 6496 nucleotides, excluding poly (A) tail at its 3ʹ end. ASGV-Ac shared high nucleotide sequence identities of 96.9% and 93.5% with a kiwifruit ASGV isolate reported from New Zealand (accession no. AF522459) for their CP and MP coding regions. However, the isolate was phylogenetically distal to ASGV isolates from all other hosts by sharing 79.5–82.4% genome sequence identity, and likely represented a novel variant. RT-PCR detection revealed the presence of ASGV-infected kiwifruit in two provinces in China. The partial CP gene of nine ASGV isolates determined in this study shared 87.8–99.6% nucleotide sequence identity with the corresponding sequences of other reported ASGV isolates from kiwifruit, indicating molecular diversity of ASGV isolates from kiwifruit plants. This study provides important evidence for monitoring the viral disease and novel molecular information for developing efficient detection techniques to prevent virus spread.