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

Abstract

A new disorder was observed on southern highbush blueberries in several south-eastern states in the USA. Symptoms included irregularly shaped circular spots or blotches with green centres on the upper and lower surfaces of leaves. Double-stranded RNA was extracted from symptomatic leaves suggesting the presence of virus(es) possibly involved in the disease. Sequencing revealed the presence of a novel RNA virus with a~14 kb genome divided into four RNA segments. Sequence analyses showed that the virus, for which we propose the name Blueberry necrotic ring blotch virus (BNRBV), possesses protein domains conserved across RNA viruses in the alphavirus-like supergroup. Phylogenetic inferences using different genes placed BNRBV in a clade that includes the Bromoviridae, the genus Cilevirus (CiLV) and the recently characterized Hibiscus green spot virus (HGSV). Despite the strong genetic relationships found among BNRBV, Cilevirus and HGSV, the genome of BNRBV contains three features that distinguish it significantly from its closest relatives: (i) the presence of two helicase domains with different evolutionary pathways, (ii) the existence of three conserved nucleotide stretches located at the 39 non-coding regions of each RNA segment and (iii) the conservation of terminal nucleotide motifs across each segment. 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 genetic features a new genus is proposed for the classification of BNRBV.

Genetic characterization, molecular epidemiology, and phylogenetic relationships of insect-specific viruses in the taxon Negevirus

“…In this work, we observed the presence of two insect-restricted negevirus groups ( Nelorpivirus and Sandewavirus genera) that are genetically related to plant viruses from the genera Blunevirus, Higrevirus and Cilevirus (Pascon et al, 2006; Melzer et al, 2013; Quito-Avila et al, 2013; Carapeta et al, 2015) (Fig. 3).…”

“…The Nelorpivirus clade clustered eight well-supported genetic subclades (bootstrap value >98%) which includes five previously described negeviruses (PIUV, BREV, NEGV, NWTV, and LORV) as well as three new viruses designated as SBDV, CDBV, and BCPV, which are more closely related genetically to two arthropod-borne plant viruses, HGSV ( Higrevirus genus) (Pascon et al, 2006) and CiLV ( Cilevirus genus) (Melzer et al, 2013). The Sandewavirus group also includes six well-supported subclades (100% bootstrap values) represented by WALV, GANV, DEZV, SANTV, TANV and the newly described BIRV, which are more closely related to the plant virus Blueberry necrotic ring blotch virus (BNRBV) ( Blunevirus genus) (Quito-Avila et al, 2013). (Fig.…”

“…Based on their genomic organization and phylogeny, the negeviruses are most closely related to plant viruses in the genera Cilevirus, Higrevirus and Blunervirus (Pascon et al, 2006; Melzer et al, 2013; Quito-Avila et al, 2013; Carapeta el al., 2015). Viruses in these genera and the related family Virgaviridae (Adams et al, 2009) are transmitted to plants by a variety of modes, including mites, soil nematodes, seeds and protozoa ( Polymyxa ) (King et al, 2012).…”

Powerful Sequence Similarity Search Methods and In-Depth Manual Analyses Can Identify Remote Homologs in Many Apparently “Orphan” Viral Proteins

“…aProposed genus (P. Blanchard, personal communication).bProposed genus (this study).cProposed genus (89). …”

New Report ofBrevipalpus yothersi(Prostigmata: Tenuipalpidae) on Blueberry in Florida

“…Blueberry necrotic ring blotch virus (BNRBV) was reported from Florida by Quito-Avila et al (2013). It is closely related to the viral plant diseases citrus leprosis virus and Hibiscus green spot virus (HGSV), which are transmitted by Brevipalpus species (Robinson 2013).…”