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United States Department of Agriculture

Agricultural Research Service

Research Project: Physiology and Genetic Improvement of Small Fruit Crops

Location: Horticultural Crops Research

Title: Genetic characterization of Blueberry necrotic ring blotch virus, a novel RNA virus with unique genetic features

Authors
item Quito-Avila, D -
item Brannen, P -
item Cline, W -
item Harmon, P -
item Martin, Robert

Submitted to: Journal of General Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: March 11, 2013
Publication Date: June 14, 2013
Citation: Quito-Avila, D.F., Brannen, P.M., Cline, W.O., Harmon, P.F., Martin, R.R. 2013. Genetic characterization of Blueberry necrotic ring blotch virus, a novel RNA virus with unique genetic features. Journal of General Virology. 94:1426-1434.

Interpretive Summary: A new disease was observed on southern highbush blueberry (Vaccinium corymbosum interspecific hybrids) in several southeastern states. Symptoms included irregularly shaped circular spots or blotches with green centers on the top and bottom of leaves. The disease was reported initially in the state of Georgia in 2006 and 2007, but in 2008 it was found in production areas in the states of Florida, Mississippi, South Carolina, and North Carolina. The perfect correlation between the virus and symptoms in plants from across several states suggests that the virus, for which we propose the name Blueberry necrotic ring blotch virus (BNRBV), is the causal agent of the disease. The vector of the virus has not been identified, but sequence information would suggest an eriophyid mite the likely vector.

Technical Abstract: A new disorder was observed on southern highbush blueberries in several southeastern states in the United States. Symptoms included irregularly shaped circular spots or blotches with green centers on the top and bottoms of leaves. Double-stranded RNA (dsRNA) was extracted from symptomatic leaves, suggesting the presence of virus(es) possibly involved in the disease. Deep sequencing revealed the presence of a novel virus with a genome composed of ~14 kb divided in 4 positive-sense RNA segments. Sequence analyses showed that the virus, for which we propose the name Blueberry necrotic ring blotch virus (BNRBV), possess protein domains conserved across RNA viruses in the alpha-virus like super group. Phylogenetic inferences using different genes placed BNRBV in a clade that includes the Bromoviridae, the genus Cilevirus, and the recently characterized Hibiscus green spot virus (HGSV). Despite the strong genetic relationships found among BNRBV, CiLV and HGSV, the genome of BNRBV contains three features that distinguish it significantly from its closest relatives: i) the presence of two Helicase (HEL) domains with different evolutionary pathways; ii) the existence of three conserved nucleotide stretches located at the 3’ non-coding regions (NCRs) of each RNA segment; and iii) the conservation of terminal nucleotide motifs (5’-29 CACAAAT) and (CG-3’) across each segment, with RNA 1 and RNA 2 sharing two additional bases at the 3’ terminus (-ATCG-3’). Furthermore, CiLV and HGSV possess poly (A)-tailed bipartite and tripartite genomes, respectively; whereas, BNRBV has a quadra-partite genome lacking a poly (A) tail. Based on these 32 genetic features a new genus is proposed for the classification of BNRBV.

Last Modified: 9/22/2014
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