Identification and Characterization of a Pear Chlorotic Leaf Spot-Associated Virus, a Novel Emaravirus Associated with a Severe Disease of Pear Trees in China

Abstract

Pear chlorotic leaf spot (PCLS) is a recently emerged disease of commercially cultivated sandy pear (Pyrus pyrifolia) trees in central and southern China. By integrating high-throughput sequencing (HTS) and conventional Sanger sequencing of RT-PCR products, a novel emaravirus infecting pear trees is identified and molecularly characterized. The virus is provisionally named pear chlorotic leaf spot-associated virus (PCLSaV). PCLSaV shows the typical molecular features of members of the genus Emaravirus in the family Fimoviridae. It has a genome composed of at least five negative-sense RNA segments, with each containing a single open reading frame (ORF) and two complementary 13-nt stretches at the 5′ and 3′ termini. PCLSaV shows a close phylogenetic relationship with recognized emaraviruses but forms a separate clade. Moreover, double-membrane-bound bodies were observed in PCLSaV-infected tissues and in extracts of PCLSaV-infected leaves. For the first time, our study reveals the profile distribution of viral RNA reads from the RNA-seq libraries of three samples along the RNAs 1-5 of an emaravirus. Field surveys combined with specific RT-PCR assays reveal the presence of PCLSaV in almost all PCLS-diseased pear samples, strongly supporting the association of the virus with the PCLS disease. This study reveals the first emaravirus infecting pear trees and its association with a severe pear chlorotic leaf disease.