The complete nucleotide sequence and genome organization of lychnis mottle virus

Abstract

The complete genomic sequence of lychnis mottle virus (LycMoV) from a Lychnis cognata plant was determined. LycMoV has a bipartite genome consisting of RNA1 (7,428 nt) and RNA2 (3,734 nt). Species in the family Secoviridae are demarcated based on their amino acid similarities in the protease-polymerase and coat protein. In LycMoV, these proteins share 90% and 63% sequence similarity, respectively, with the most closely related virus, strawberry latent ringspot virus, which is a member of the family Secoviridae but has not been assigned to a genus. Therefore, LycMoV is a tentative new virus of the family Secoviridae.

Creation of a new genus in the family Secoviridae substantiated by sequence variation of newly identified strawberry latent ringspot virus isolates

“…Based on the current genus demarcation criteria described in the 10th Report of the International Committee on Taxonomy of Viruses (ICTV), which include the number of genomic RNA segments, the number of CPs, and the clustering in phylogenetic trees based on aa sequence alignments of the conserved Pro-Pol region [21], SLRSV cannot be assigned to any of the genera within the family Secoviridae. The same holds for two tentative new members of the family Secoviridae that were recently reported in the Republic of Korea, i.e., lychnis mottle virus (LycMoV) from Lychnis cognate [28] and cnidium vein yellowing virus (CnVYV) from Cnidium officinale [27]. Phylogenetic analysis of both the Pro-Pol region and the CPs of these viruses revealed their close relationship to SLRSV, and these viruses are distinct from all other members of the family Secoviridae.…”

“…Group B includes the Bioreba antiserum isolate 15-07_Prunus_persica and the 14-023_Fragaria isolate. Group C includes the six lily isolates 14-001, 14-002, 14-034, 14-035, 5875017 and 17-007 and the isolates LycMoV, LycMoV-J, CnVYV1 and CnVYV2 [6,27,28]. The grouping shown in the CP phylogenetic trees (Figs.…”

“…In the first phylogenetic analysis of the Pro-Pol region, the amino acid (aa) sequence of the conserved domains between the CG motif of the 3C-like proteinase and the GDD motif of the polymerase [10,21] of the five full-length RNA1 sequences of SLRSV and selected members of the family Secoviridae were used. In addition, a phylogenetic analysis was performed for both the Pro-Pol region and the CPs (large and small CP together), using all available SLRSV nt and aa sequences in the NCBI GenBank database, and also including the SLRSV-related isolates of LycMoV and CnVYV [6,27,28].…”

“…Based on aa sequence comparisons of the Pro-Pol region of the full-length sequences of the SLRSV isolates and a selection of other members of different genera within the family Secoviridae, all of the newly generated SLRSV sequences grouped together with NCGR MEN 454.001 and isolates of the recently described viruses LycMoV, and CnVYV [6,27,28], which together formed a distinct clade (Fig. 1).…”

“…For this family, species demarcation is mainly based on the aa sequence of the Pro-Pol region (< 80% identity) and the aa sequence of the CPs (large and small CP together, < 75% identity) [21]. The recently described LycMoV and CnVYV [27,28] show the highest sequence similarity to SLRSV within the family Secoviridae. Lyc-MoV and CnVYV have been proposed as tentative members of the family Secoviridae solely based on the % aa sequence identity of the CPs to SLRSV sequences available in the NCBI GenBank database (LycMoV, 63%; CnVYV1, 64%; CnVYV2, 63%).…”