Abstract
To obtain insight into the sequence diversity of strawberry latent ringspot virus (SLRSV), isolates from collections and diagnostic samples were sequenced by high-throughput sequencing. For five SLRSV isolates, the complete genome sequences were determined, and for 18 other isolates nearly complete genome sequences were determined. The sequence data were analysed in relation to sequences of SLRSV and related virus isolates available in the NCBI GenBank database. The genome sequences were annotated, and sequences of the protease-polymerase (Pro-Pol) region and coat proteins (CPs) (large and small CP together) were used for phylogenetic analysis. The amino acid sequences of the Pro-Pol region were very similar, whereas the nucleotide sequences of this region were more variable. The amino acid sequences of the CPs were less similar, which was corroborated by the results of a serological comparison performed using antisera raised against different isolates of SLRSV. Based on these results, we propose that SLRSV and related unassigned viruses be assigned to a new genus within the family Secoviridae, named “Stralarivirus”. Based on the phylogenetic analysis, this genus should include at least three viruses, i.e., SLRSV-A, SLRSV-B and lychnis mottle virus. The newly generated sequence data provide a basis for designing molecular tests to screen for SLRSV.
Highlights
Strawberry latent ringspot virus (SLRSV), an unassigned member of the family Secoviridae [21], was first identified in rosaceous plants by Lister in Scotland more than 50 years ago [11]
RNA1 codes for proteins involved in replication, i.e., protease cofactor (Pro-C), helicase (Hel), protease (Pro) and RNA-dependent RNA polymerase (Pol), whereas RNA2 codes for the movement protein (MP) and the large and small coat proteins (CPs)
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], strawberry latent ringspot virus (SLRSV) cannot be assigned to any of the genera within the family Secoviridae
Summary
Strawberry latent ringspot virus (SLRSV), an unassigned member of the family Secoviridae [21], was first identified in rosaceous plants by Lister in Scotland more than 50 years ago [11]. The genome comprises two positive-sense ssRNA molecules with an approximate size of 7.5 kb for RNA1 and 3.8 kb for RNA2 Both have a 3’-terminal poly(A) tail and a genomelinked virus protein (VPg) covalently bound at the 5’ end. 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. Including two tentative members of this family, LycMoV and CnVYV, in the phylogenetic analysis supported the assignment of all three of these viruses to a new genus in the family Secoviridae, for which the name “Stralarivirus” is proposed
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