Viruses of imported Andean root and tuber crops and their plant health risk to the UK

Abstract

Andean root and tuber crops (ARTCs) are a group of diverse crops belonging to a variety of families, that all originate from the Andean region of South America. From a UK perspective, these plants often enter the country for planting via internet trade, which is frequently a phytosanitary risk, and the CIP Genebank has identified developing tools for phytosanitary diagnostics of ARTCs as an area of concern. This PhD followed on from a High Throughput Sequencing (HTS) study of ulluco (Ullucus tuberosus) plants grown in the UK. Its aim was to determine the virome of ARTCs imported through internet trade and determine the potential risk of this commodity to UK plant health. This project used HTS to study the viruses present in oca (Oxalis tuberosa) plants purchased from several European countries via eBay as well as oca, ulluco, yacón (Smallanthus sonchifolius) and mashua (Tropaeolum tuberosum) plants from a commercial supplier in Ireland. An Illumina MiSeq was used to sequence two bulks of these plants uncovered multiple novel virus candidates from different genera in three ARTCs. Following in silico molecular characterisation based on genome sequence, RT-PCR and qRT-PCR assays were designed to these viruses. A survey was conducted on further oca plants purchased from online sellers in Europe. Three novel viruses (OAV1, OCV1 and OVX) were detected in plants from several European countries, including samples of naturalised Oxalis species growing in the UK. In addition, the quarantine virus potato yellowing virus (PYV), known to infect yacón, was found again in European plants sourced from European nurseries. The sequence of the viruses detected in these plants was closely related but not identical to sequences from a 2019 study of PYV infecting yacón, confirming that PYV continues to circulate in yacón grown in Europe and that yacón presents a plant health risk in Europe