First Report of Nectarine stem pitting-associated virus Infecting Prunus mume in Japan

Nectarine stem pitting-associated virus (NSPaV) is a recently described member of the genus Luteovirus in the family Luteoviridae on which very limited information is available. Initially described in the United States on post-quarantine imported nectarine (Prunus persica) trees (Bag et al. 2015), it was later detected on peach and nectarine plants from California (Villamor et al. 2016). Although it was initially described as tentatively associated with severe stem-pitting symptoms (Bag et al. 2015), NSPaV association with disease remains uncertain because it has been detected in some symptomless trees (Villamor et al. 2016). During a survey in 2015, five Japanese apricot (P. mume) samples collected in Japan and showing various virus-like symptoms such as discolorations and spotting on their leaves were individually analyzed by Illumina deep sequencing of cDNA libraries prepared from purified double-stranded RNAs (Candresse et al. 2013). Analysis of the sequence data showed that in one sample, collected in a park in Morioka, seven contigs showed high nucleotide identity values (90 to 98%) with the closely related NSPaV sequences available in GenBank (accession nos. KP638562, KT273409, and KT273410). These contigs totaled 3.4 kb or about 68% of NSPaV genome (NC_027211; Bag et al. 2015) and corresponded to about 0.37% of the total sequencing reads obtained for the sample. The presence of NSPaV in the sample was confirmed by RT-PCR using the NSPaV-F mod 5′-AGACTMAAATTCAATGARAAGA-3′ and NSPaV-R 5′-TTTCACAAATGATAACACAAT-3′ primer pair modified from Bag et al. (2015). The expected 460-bp fragment, corresponding to positions 1646 to 2106 of the genome (RdRp gene), was obtained and, upon direct sequencing (KX853093), shown to share 96.2 to 96.7% nucleotide identity with the NSPaV isolates present in GenBank. To the best of our knowledge, this is the first report of NSPaV presence in Japan and in P. mume, extending the information on both its host range and geographical distribution. The analysis of the high-throughput sequence data obtained on the NSPaV-infected sample showed it to be also infected by Asian prunus virus 1 and thus, no clear conclusion can be drawn on whether NSPaV may be responsible for any specific symptoms in P. mume