First report of shallot virus X in shallot in New Zealand

In January 2005, mild mosaic and chlorosis were observed on leaves of shallot (Allium cepa var. aggregatum) ‘Red Prisma’ growing in Marlborough, New Zealand. Leaves from 100 plants were collected and bulked into groups of ten. Three composite samples tested positive for Shallot mite-borne latent virus (ShMbLV) using polyclonal antiserum (supplied by Dr. E. Barg, Biologische Bundesanstalt, Germany) in an antigen-coated plate enzyme-linked immunosorbent assay (ACP-ELISA). Similar symptoms were seen in shallot ‘Jermor’ in the same region in December 2007. Leaves from these plants also tested positive for ShMbLV by ACP-ELISA. To confirm the identification of the samples from 2007, dried tissue of the type isolate of ShMbLV was obtained (Van Dijk & van der Vlugt, 1994). RNA was extracted from diseased shallot samples and the ShMbLV type isolate and tested by RT-PCR using primers that amplify a ca. 750 bp fragment between the coat protein (CP) and ORF6 region of allexiviruses (Chen et al., 2004). For both samples, amplicons of the expected size were obtained and sequenced directly. Analysis showed a 93 to 95% nucleotide identity with Shallot virus X (ShVX) (GenBank Accession No. M97264). RT-PCR was then done using specific primers designed to amplify a 912 bp fragment of ShVX including the CP gene (ShVX-CPF: 5'-ATTTAGGGGTGAAGGTCTGT-3'; ShVX-CPR: 5'-GAGTTTTGAGGTCGTTGG-3'). Amplicons of the correct size were obtained from both diseased shallot samples and the ShMbLV type isolate. Subsequently, one-step immunocapture RT-PCR was performed using the ShMbLV antiserum and the ShVX-specific primers, and bands of the correct size were obtained for both samples. The amplicons were cloned and sequenced. A BLAST search showed that the sequence from shallot (EU835197) and that of the type isolate of ShMbLV (EU835196) showed 93% and 95% nucleotide identity, respectively, with ShVX (M97264). According to the criteria demarcating species in the genus (Adams et al., 2004), we suggest that ShMbLV should be considered a synonym of ShVX as previously proposed (Van Dijk & van der Vlugt, 1994). This is the first report of ShVX in New Zealand and until these findings it was considered a regulated pest. However, no phytosanitary measures will be imposed to eradicate the virus and it is likely to spread in the future, especially as the vector, Aceria tulipae, is present in New Zealand. Allexiviruses, including ShVX, often infect allium crops in combination with carlaviruses and/or potyviruses and cause significant yield losses (Chen et al., 2004; Van Dijk & van der Vlugt, 1994