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Detection of a New Luteovirus in Imported Nectarine Trees: A Case Study to Propose Adoption of Metagenomics in Post-entry Quarantine
S. BAG (1), M. Al Rwahnih (1), A. Li (2), A. Gonzalez (2), A. Rowhani (1), J. K. Uyemoto (2), M. R. Sudarshana (2). (1) University of California-Davis, Davis, CA, U.S.A.; (2) USDA-ARS, Davis, CA, U.S.A.

In spring 2013, five year-old nectarine (<i>Prunus persica</i>) trees, grafted on Nemaguard rootstock were found stunted in an orchard in California. These trees had been propagated from budwood of three nectarine varieties imported from France cleared through post-entry quarantine procedure. Examination of the canopy failed to reveal any obvious symptoms, but the examination of the trunks, after stripping the bark, revealed extensive pitting on the woody cylinder. To investigate the etiological agent, a cDNA library was prepared from dsRNA extracted from bark scrapings from the scion and rootstock portions, and sequenced using Illumina platform. BLAST analysis of the contigs generated by the <i>de novo</i> assembly of sequence reads indicated the presence of a novel luteovirus. Complete sequence of the viral genome was obtained by sequencing of three overlapping cDNA clones generated by RT-PCR and amplification of 5'- and 3'- termini. The virus genome was 4,991 nucleotides long with a gene organization similar to members of the genus <i>Luteovirus</i> (family <i>Luteoviridae</i>). The presence of the virus, named ‘Nectarine stem pitting-associated virus’, was confirmed in symptomatic trees by RT-PCR. Discovery of a new virus in nectarine trees after post-entry quarantine indicates the importance of including (i) metagenomic analysis as an essential tool to assess the plant health status, and (ii) examination of the woody cylinders as part of the indexing process.

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