Complete genome sequence of a new virga-like virus identified in Viburnum opulus in China

Abstract

A virga-like virus, provisionally named “Viburnum opulus virus 1” (VoV1), was identified by RNA-seq in a Viburnum opulus plant. The monopartite genome of VoV1 is 12,538 nucleotides (nt) in length, excluding the poly(A) tail, and contains seven open reading frames (ORF1–7). The genome organization most closely resembles those of two unclassified plant-infecting virga-like viruses (rubber tree latent virus 1 and 2), which also have seven ORFs but show sequence similarity to VoV1 in only three ORFs. ORF1 is the largest ORF and is predicted to encode a large protein containing six conserved structural domains, including one for the viral replicase. Putative proteins of ORF3 and ORF4 both contain CP-like motifs, while putative proteins encoded by the other ORFs were not identified. Sequence comparisons showed that VoV1 shared the highest nucleotide and amino acid (aa) sequence similarity in ORF1 with rose latent virus 1 (45.0/28.7 identity). Phylogenetic analysis based on the amino acid sequence of the protein encoded by ORF1 showed that VoV1 grouped with some other virga-like viruses in a distinct clade. Analysis of the sequence of VoV1 suggested that it should be classified as a member of a new species within the family Virgaviridae, for which we propose the name “Virgavirus viburnii”.