Gene from a novel plant virus satellite from grapevine identifies a viral satellite lineage

Abstract

We have identified the genome of a novel viral satellite in deep sequence analysis of double-stranded RNA from grapevine. The genome was 1,060 bases in length, and encoded two open reading frames. Neither frame was related to any known plant virus gene. But translation of the longer frame showed a protein sequence similar to those of other plant virus satellites. Other than in commonalities they shared in this gene sequence, members of that group were extensively divergent. The reading frame in this gene from the novel satellite could be translationally coupled to an adjacent reading frame in the -1 register, through overlapping start/stop codons. These overlapping AUGA start/stop codons were adjacent to a sequence that could be folded into a pseudoknot structure. Field surveys with PCR probes specific for the novel satellite revealed its presence in 3% of the grapevines (n = 346) sampled.

A classification system for virophages and satellite viruses

“…SSADV is 95 % identical to SPMV over the entire genome length (36 nt changes, 5 aa changes) and can be considered a different strain of SPMV. The second putative satellite virus, satellite grapevine virus (SGVV), was discovered by deep sequencing of total intracellular RNA from grapevine [2]. However, neither the viral particles nor the associated helper virus have been characterized.…”

Complete Genome Sequence of a Novel Satellite Virus Associated with Cassava Plants

“…The second ORF starts at nucleotide 646, overlapping the last four nucleotides of the first ORF, and finishes at nucleotide 918, probably encoding a protein with 90 amino acids. This protein showed 38% of amino acid identity with ORF2 of grapevine satellite virus (4). A second start codon is present at nucleotide 709.…”

“…Just one of the total contigs obtained showed similarity with viral genomes. This contig was generated by 10 reads and had 946 nt in length, presenting two putative ORFs, both with their highest amino acid identities with grapevine satellite virus proteins (4). …”

“…The first ORF starts at nucleotide 179 and finishes at nucleotide 649. This ORF probably encodes a protein with 156 amino acids and has 57% of amino acid identity with ORF1 of grapevine satellite virus (4). This protein also presents a conserved domain from the Potexvirus coat superfamily.…”

Complete Nucleotide Sequence of an Isolate of Grapevine Satellite Virus and Evidence for the Presence of Multimeric Forms in an Infected Grapevine

“…Grapevine satellite virus (GV-Sat) is a recently discovered agent with a reported prevalence of about 3% in two grapevine collections in the United States (1). Its genome (KC149510) harbors two open reading frames (ORFs) that may be translationally coupled through frameshifting.…”