Using high‐throughput sequencing in support of a plant health outbreak reveals novel viruses in <i>Ullucus tuberosus</i> (Basellaceae)

Abstract

Ullucus tuberosus (ulluco) is a tuber‐forming species that has become a novel crop in highland and temperate maritime climates. Eight viruses have been previously reported infecting Ullucus , including Andean potato latent virus ( APLV ), a quarantine virus within the European Union. No reference sequences have been published for the viruses previously described from U . tuberosus . Plants grown in the UK for the internet trade were tested for the presence of quarantine viruses using ELISA and real‐time RT ‐ PCR . ELISA positive results were obtained for APLV and multiple other viruses. A similar suite of viruses was detected at a second outbreak site linked to horticultural trade. Virus identification was by high‐throughput sequencing ( HTS ) using a ribosomal RNA ( rRNA )‐depleted total RNA approach. Analysis of viral contigs indicated the presence of several novel viruses closely related to, but not consistent with, the viruses indicated by ELISA . Further confirmatory testing by real‐time RT ‐ PCR indicated that two tymoviruses, tentatively named Ullucus tymovirus 1 and Ullucus tymovirus 2, were more closely related to each other (85% identity), than to APLV or Andean potato mild mosaic virus (63–66% identity). APLV could not be confirmed from either site by either HTS or PCR . A novel tobamovirus (Ullucus tobamovirus 1) was only detected at the initial outbreak site. A novel polerovirus (Ullucus polerovirus 1) and a distinct genotype of Papaya mosaic virus were detected from both outbreak sites. Deploying HTS during a plant health outbreak demonstrates the potential of this approach to give rapid, accurate diagnosis.