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

Arch Virol. 2020 Jan;165(1):21-31. doi: 10.1007/s00705-019-04437-0. Epub 2019 Oct 17.

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.

MeSH terms

  • Capsid Proteins / genetics
  • DNA-Directed RNA Polymerases / genetics
  • Fragaria / virology*
  • Genetic Variation
  • High-Throughput Nucleotide Sequencing / methods*
  • Molecular Sequence Annotation
  • Peptide Hydrolases / genetics
  • Phylogeny
  • Plant Viruses / classification
  • Plant Viruses / genetics
  • Plant Viruses / isolation & purification
  • RNA, Viral / genetics
  • Secoviridae / classification*
  • Secoviridae / genetics
  • Secoviridae / isolation & purification
  • Sequence Analysis, RNA / methods*

Substances

  • Capsid Proteins
  • RNA, Viral
  • DNA-Directed RNA Polymerases
  • Peptide Hydrolases