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

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.Publisher's Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Known and Potential Invertebrate Vectors of Raspberry Viruses

“…Besides this, one species from the genus Cheravirus (cherry rasp leaf virus [CRLV]) and another unassigned species in the family of Secoviridae (strawberry latent ringspot virus [SLRSV]) have also been reported [ 9 , 33 ]. The SLRSV was recently proposed to a new genus “ Stralarivirus ” within the family of Secoviridae [ 51 ]. Raspberry is infected by eight nematode-transmitted viruses and all these viruses are from the Secoviridae family ( Table 1 ).…”

Genome Sequence of Pineapple Secovirus B, a Second Sadwavirus Reported Infecting Ananas Comosus

“…The cleavage sites recognized by the RNA-1-encoded 3C-like protease (3CL-Pro) likely cleave P1 at ve sites, de ning six domains; while 3CL-Pro likely cleaves P2 at one site, de ning two domains (Fig. 1) [1,6,7].…”

“…1). Like other secovirids, both PSV-B RNAs are expected to possess a genomelinked viral protein termed "VPg" bound at the 5' end and a poly(A) tail at the 3' end, respectively [1,7].…”

Genome sequence of pineapple secovirus B, a second sadwavirus reported infecting Ananas comosus

“…1 ). Similar to other secovirids, both PSV-B RNAs are expected to possess a VPg bound at the 5’end and a poly(A) tail at the 3’end, respectively [ 1 , 8 ]. Analysis of conserved domains using the NCBI Conserved Domain Search Tool ( https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi ) showed the presence of conserved motifs in the Pol and Hel of P1, whereas a conserved MP motif was predicted for P2.…”

“…The cleavage sites recognized by the RNA1-encoded 3C-like protease (3CL-Pro) likely cleave P1 at four sites, defining five domains, while 3CL-Pro likely cleaves P2 at one site, defining two domains (Fig. 1 ) [ 1 , 7 , 8 ].…”