Virome scanning of pear germplasm collections identifies a new Velarivirus and extends the geographical spread of three other pear viruses

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