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

A.M. Dullemans, M. Botermans, M.J.D. de Kock, C.E. de Krom, T.A.J. van der Lee, J.W. Roenhorst, I.J.E. Stulemeijer, M. Verbeek, M. Westenberg, R.A.A. van der Vlugt

Research output: Contribution to journalArticleAcademicpeer-review

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.
Original languageEnglish
Pages (from-to)21-31
Number of pages11
JournalArchives of Virology
Volume165
Issue number1
Early online date17 Oct 2019
DOIs
Publication statusPublished - Jan 2020

Fingerprint

Fragaria
Viruses
Capsid Proteins
Genome
Lychnis
Amino Acid Sequence
Peptide Hydrolases
Cercopithecine Herpesvirus 1
Nucleic Acid Databases
Immune Sera
Databases

Cite this

Dullemans, A.M. ; Botermans, M. ; de Kock, M.J.D. ; de Krom, C.E. ; van der Lee, T.A.J. ; Roenhorst, J.W. ; Stulemeijer, I.J.E. ; Verbeek, M. ; Westenberg, M. ; van der Vlugt, R.A.A. / Creation of a new genus in the family Secoviridae substantiated by sequence variation of newly identified strawberry latent ringspot. In: Archives of Virology. 2020 ; Vol. 165, No. 1. pp. 21-31.
@article{029edb619ae64f9c9e382bf9c40c39ca,
title = "Creation of a new genus in the family Secoviridae substantiated by sequence variation of newly identified strawberry latent ringspot",
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.",
author = "A.M. Dullemans and M. Botermans and {de Kock}, M.J.D. and {de Krom}, C.E. and {van der Lee}, T.A.J. and J.W. Roenhorst and I.J.E. Stulemeijer and M. Verbeek and M. Westenberg and {van der Vlugt}, R.A.A.",
year = "2020",
month = "1",
doi = "10.1007/s00705-019-04437-0",
language = "English",
volume = "165",
pages = "21--31",
journal = "Archives of Virology",
issn = "0304-8608",
publisher = "Springer Verlag",
number = "1",

}

Creation of a new genus in the family Secoviridae substantiated by sequence variation of newly identified strawberry latent ringspot. / Dullemans, A.M.; Botermans, M.; de Kock, M.J.D.; de Krom, C.E.; van der Lee, T.A.J.; Roenhorst, J.W.; Stulemeijer, I.J.E.; Verbeek, M.; Westenberg, M.; van der Vlugt, R.A.A.

In: Archives of Virology, Vol. 165, No. 1, 01.2020, p. 21-31.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - Creation of a new genus in the family Secoviridae substantiated by sequence variation of newly identified strawberry latent ringspot

AU - Dullemans, A.M.

AU - Botermans, M.

AU - de Kock, M.J.D.

AU - de Krom, C.E.

AU - van der Lee, T.A.J.

AU - Roenhorst, J.W.

AU - Stulemeijer, I.J.E.

AU - Verbeek, M.

AU - Westenberg, M.

AU - van der Vlugt, R.A.A.

PY - 2020/1

Y1 - 2020/1

N2 - 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.

AB - 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.

U2 - 10.1007/s00705-019-04437-0

DO - 10.1007/s00705-019-04437-0

M3 - Article

VL - 165

SP - 21

EP - 31

JO - Archives of Virology

JF - Archives of Virology

SN - 0304-8608

IS - 1

ER -