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Recent studies have shown the superiority of high-throughput sequencing (HTS) technology over many standard protocols for pathogen detection. HTS was initiated on fruit tree accessions from disparate sources to improve and advance virus-testing procedures. A virus with genomic features resembling most closely that of the recently described Nectarine stem-pitting-associated virus, putative member of genus Luteovirus, was found in three nectarine trees (Prunus persica cv. nectarina), each exhibiting stem-pitting symptoms on the woody cylinder above the graft union. In these samples, HTS also revealed the presence of a coinfecting virus with genome characteristics typical of members of the genus Marafivirus. The same marafivirus- and luteovirus-like viruses were detected in nonsymptomatic nectarine and peach selections, indicating only a loose relationship between these two viruses with nectarine stem-pitting disease symptoms. Two selections infected with each of these viruses had previously tested free of known virus or virus-like agents using the current biological, serological, and molecular tests employed at the Clean Plant Center Northwest. Overall, this study presents the characterization by HTS of novel marafivirus- and luteovirus-like viruses of nectarine, and provides further insights into the etiology of nectarine stem-pitting disease. The discovery of these new viruses emphasizes the ability of HTS to reveal viruses that are not detected by existing protocols.

High-Throughput Sequencing Identifies Novel Viruses in Nectarine: Insights to the Etiology of Stem-Pitting Disease