Molecular characterization of the coat protein gene of Prunus necrotic ringspot virus infecting sweet cherry in China Shandong

Abstract

Shandong Province (SD) is the largest area of sweet cherry production in China. It also holds the dominant position in terms of nursery stock exports to the rest of the country. Several surveys on viral infections of sweet cherry in this district have been carried out. The rate of infection with Prunus necrotic ringspot virus (PNRSV), which causes serious economic losses in most Prunus species, is higher than that with other viruses in SD. The rate of PNRSV infection increased from 38.00% in 2011 to 66.67% in 2016. To better understand the genetic variation in PNRSV at a molecular level, 33 full-length PNRSV coat protein (CP) sequences from 23 PNRSV-infected samples were acquired. Compared with other PNRSV isolates obtained from GenBank, CP sequences from SD isolates shared 96.67-100 and 96.70-100% nucleotide sequence and amino acid sequence identity, respectively. Phylogenetic reconstruction confirmed the clustering of the isolates into three molecular groups (PV-96, PV-32, and PE-5), whereby SD isolates were separated into two phylogroups (PV-96 and PV-32). However, 10 of 23 samples exhibited mixed infection with PV-96-type and PV-32-type PNRSV. In mixed-infection samples, PV-96-type PNRSV (66.28%) was more likely to be detected than PV-32-type PNRSV (33.72%); and PV-96-type PNRSV (2.22%) was more likely to be mutated than PV-32-type PNRSV (1.65%). Furthermore, those mutations were often concentrated at specific positions. Therefore, analysis of nucleotide sequence 'hot spots' can provide information on the molecular mechanisms of viral mutagenesis.