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

<i>Apple stem grooving virus</i> (ASGV) is the type species of the genus <i>Capillovirus</i> in the family <i>Betaflexiviridae</i>. The virus naturally infects several important horticultural crops. Although many ASGV isolates from apple (<i>Malus</i> spp.), pear (<i>Pyrus</i> spp.), citrus (<i>Citrus</i> spp.) and lily (<i>Lilium</i> 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 (<i>Actinidia chinensis</i>) 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.苹果茎沟病毒（Apple stem grooving virus, ASGV）是柔丝病毒科（Betaflexiviridae）毛形病毒属（Capillovirus）的模式种。该病毒可自然侵染多种重要园艺作物。尽管已有诸多分离自苹果属（Malus spp.）、梨属（Pyrus spp.）、柑橘属（Citrus spp.）及百合属（Lilium spp.）的ASGV分离物得到鉴定，但猕猴桃树上该病毒的发生现状与分子特征仍鲜为人知。本研究结合小RNA深度测序与常规逆转录聚合酶链反应（RT-PCR）策略，首次报道了一株侵染中国境内种植的中华猕猴桃（Actinidia chinensis）的ASGV分离物（命名为ASGV-Ac）的完整基因组序列。ASGV-Ac的完整基因组全长6496个核苷酸，不含3'端poly(A)尾。ASGV-Ac的外壳蛋白（CP）与运动蛋白（MP）编码区，与新西兰报道的一株猕猴桃来源ASGV分离物（登录号AF522459）分别具有96.9%和93.5%的高核苷酸序列同源性。然而，该分离物的全基因组序列与其他寄主来源的ASGV分离物仅具有79.5%~82.4%的同源性，系统发育上也与它们亲缘关系较远，大概率代表一个新的变异株。RT-PCR检测显示，中国两个省份的猕猴桃植株中存在ASGV侵染情况。本研究中测定的9株ASGV分离物的部分CP基因序列，与其他已报道的猕猴桃来源ASGV分离物的对应序列具有87.8%~99.6%的核苷酸同源性，表明猕猴桃来源的ASGV分离物存在分子多样性。本研究为该病毒病害的监测提供了重要依据，也为开发高效检测技术以阻断病毒传播提供了全新的分子信息。