In this study, an extensive virome investigation was performed on a germplasm collection ofpear trees (Pyrus communis L.) from the Walloon Agricultural Research Centre (Gembloux,Belgium). In total,128 pear trees samples were analyzed as pools using high-throughputsequencing (HTS) techniques, and/or tested individually for targeted viruses by RT-PCR.During the virome survey, a novel velarivirus was identified in several asymptomatic treeswhile four known viruses were detected. Bioinformatics tools were used to assemble thegenome of the new virus. The pear germplasm collection from Kozjanski Park (Slovenia) anda viral collection from Agroscope (Nyon, Switzerland) were also surveyed for the new pearvirus and for three known viruses (CiVA, ARWV-1, and ARWV-2) to study their prevalenceand geographic distribution. In Belgium, the new velarivirus was detected by RT-PCR in sixof the 99 sampled trees (6%) and citrus virus A (CiVA) in 49 (49%) of them; in Slovenia fourof the six trees sampled (67%) were positive for CiVA; and in Switzerland four of the ninetrees sampled (44%) were positive for CiVA and 1 (11%) for apple rubbery wood virus 1 and2 (ARWV-1 and -2). This study, combined pooled HTS analyses to maximize the number ofgermplasm tested and targeted RT-PCR tests on individual samples for accurate detection. Itreports and describes a new velarivirus discovered in pear trees and first detections of CiVA inBelgium, Switzerland and Slovenia, and ARWV-1 and -2 in Switzerland.
