Molecular characterization of an unusual new plant RNA virus reveals an evolutionary link between two different virus families

Abstract

An unusual novel plant virus provisionally named goji berry chlorosis virus (GBCV) was isolated from goji berry plants (Lycium chinense Miller) showing chlorosis symptoms and its complete genome sequence was determined. The viral genome consists of a positive-sense single-stranded RNA of 10,100 ribonucleotides and contains six open reading frames (ORFs). Electron microscopy showed that the viral genome is packaged as a filamentous particle with an average length of approximately 850 nm. Phylogenetic analysis and amino acid similarity analysis of the encoded ORFs revealed that this new virus could be classified in an intermediate position between the families Benyviridae and Virgaviridae. The GBCV 200-kDa replicase (ORF1) is more similar to benyvirus replicases than to virgavirus replicases, while its 17-kDa coat protein (CP, ORF2) is more closely related with virgavirus CPs than benyvirus CPs. ORF3 was predicted to produce a C-terminally extended protein from ORF2 via frameshifting. While ORF4 (45-kDa), ORF5 (44-kDa), and ORF6 (16-kDa) have no apparent sequence homology with other known viruses, ORF5 is predicted to encode a movement protein (MP) that is phylogenetically related to the furovirus MP and ORF6 was experimentally proven to encode a viral suppressor of RNA silencing. These unusual characteristics suggest that GBCV may represent an evolutionary link between the families Benyviridae and Virgaviridae and indicate the existence of a novel, unidentified virus group.

Characterization and complete genome sequences of two novel variants of the family Closteroviridae from Chinese kiwifruit

“…High-throughput sequencing is not only used to analyze the expression levels of known genes from multiple organisms, it can also be used to detect new genes and new variants [24][25][26]. Compared with Sanger sequencing, transcriptome sequencing using next-generation sequencing (NGS) technology provides greater throughput and broader coverage [27].…”

Identification and characterization of a novel Cytorhabdovirus associated with goji berry (Lycium barbarum L.) crinkle disease

“…It can also be used as food, and many people avidly use the berries in soups. To our knowledge, almost no viruses have been reported in goji, except for goji berry chlorosis virus (GBCV), which was chlorotic identified in another species of goji berry plant ( L. chinense Miller) ( Kwon et al, 2018 ).…”

Predicted Membrane-Associated Domains in Proteins Encoded by Novel Monopartite Plant RNA Viruses Related to Members of the Family Benyviridae

“…[2,7] (Figure 1). The latter branch contains exclusively monopartite viruses and, in particular, includes Goji berry chlorosis virus (GBCV), which encodes six polypeptides and has no close relatives with similar genome organization [8]. Four additional benyvirus-like members of this brunch are predicted to encode a binary movement block (BMB), which is also found in multipartite viruses of the family Kitaviridae [7,[9][10][11] (Figure 1).…”