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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » National Germplasm Resources Laboratory » Research » Publications at this Location » Publication #377531

Research Project: Characterizing and Detecting Pathogens to Ensure Safe Exchange of Plant Germplasm

Location: National Germplasm Resources Laboratory

Title: Discovery and genome characterization of a new Nepovirus infecting grapevine

item AL RWAHNIH, MAHER - University Of California, Davis
item ALABI, OLUFEMI - Texas A&M Agricultural Experiment Station
item HWANG, MINSOOK - University Of California, Davis
item TIAN, TONGYAN - California Department Of Food And Agriculture
item Mollov, Dimitre
item GOLINO, DEBORAH - University Of California, Davis

Submitted to: Plant Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/7/2020
Publication Date: 4/4/2021
Citation: Al Rwahnih, M., Alabi, O., Hwang, M., Tian, T., Mollov, D.S., Golino, D. 2021. Discovery and genome characterization of a new Nepovirus infecting grapevine. Plant Disease.

Interpretive Summary: Grape is an important crop in the U.S used for fresh and processed products consumption, and winemaking. A proprietary foreign grape accession was imported to the U.S. as a germplasm introduction. Such foreign plant material is tested for pathogens before being released to U.S. research and production systems. As part of the routine screening, symptoms on inoculated bioindicator hosts revealed a potential infection in this grape introduction. The original grape plant was subjected to sequencing analysis and a new virus was discovered. We named the new virus grapevine nepovirus A. The complete genome sequence of this virus was determined and detection protocols were developed. This research characterized the new virus and developed detection methods that will allow testing of future importations, thereby helping to reduce the risks of spreading this virus in propagative plant material.

Technical Abstract: In 2012, dormant canes of a proprietary wine grape (Vitis vinifera L.) accession were included in the collection of the University of California-Davis Foundation Plant Services. No virus-like symptoms were elicited when bud chips from propagated own-rooted canes of the accession were graft-inoculated onto a panel of biological index grape varieties. However, chlorotic ring symptoms were observed on sap inoculated Chenopodium amaranticolor and C. quinoa plants, indicating the presence of a mechanically transmissible virus. Transmission electron microscopy of virus preps from symptomatic C. quinoa revealed spherical, non-enveloped virions of ~27 nm in diameter. Nepovirus-like haplotypes of sequence contigs were detected in both the source grape accession and recipient C. quinoa plants using high throughput sequencing analysis. A novel bipartite nepovirus-like genome was assembled from these contigs and the termini of each RNA segment were verified by RACE assays. The RNA1 (7,186-nt) of the virus encode a large polyprotein P1 of 231.1 kDa while the RNA2 (4,460-nt) also encode a large polyprotein P2 of 148.9 kDa. Each of the polyadenylated RNA segment is flanked by 5'- (RNA1=156-nt; RNA2=170-nt) and 3'- (RNA1=834-nt; RNA2=261-nt) untranslated region sequences that shared >90% identities between their corresponding sequences. Maximum-likelihood phylogenetic analyses of the conserved Pro-Pol amino acid sequences of Secoviridae species revealed the clustering of the new virus within the nepovirus clade. Considering its biological and molecular characteristics, and based on current criteria, we propose that the novel virus, named as grapevine nepovirus A (GNVA), be assigned as a member of the genus Nepovirus.