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Strawberry vein banding virus isolates in eastern Canada are molecularly divergent from other isolates

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Abstract

The complete sequence of a strawberry vein banding virus (SVBV) isolate collected in Nova Scotia, Canada, and designated NS8, was determined. The 7,856-nucleotide circular double-stranded DNA genome contains seven open-reading frames (ORFs), which is consistent with other SVBV isolates and other members of the genus Caulimovirus. Comparison of NS8 with other whole-genome sequences retrieved from databases revealed that NS8 shares the highest sequence similarity (96.5% identity) with isolate China (accession number HE681085) and the lowest (88.3% identity) with clone pSVBV-E3 (accession number X97304). Despite the overall high sequence similarity between NS8 and China, the coat protein encoding ORF IV of NS8 shares only 90.9% sequence identity with the China isolate. Phylogenetic analysis at the complete-genome level placed NS8 and all Chinese isolates in one clade and clone pSVBV-E3 in a separate clade. Interestingly, phylogenetic analysis of all available ORF IV sequences, including those retrieved from databases and newly sequenced samples in this study from Canada, revealed three distinct clades. All Canadian isolates grouped together as one clade, pSVBV-E3 and several others from Europe, Egypt and the USA grouped as a second clade, and isolates from China formed a third clade. These results demonstrate that SVBV is more divergent than previously reported.

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Acknowledgements

We thank Dr. Pervaiz Abbasi for providing strawberry plants, and Darcy Sutherland for technical assistance. We also acknowledge the participation and contribution of Dylan Woodcock at the early stage of this research.

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Authors and Affiliations

  1. Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, P.O. Box 20280, 850 Lincoln Road, Fredericton, NB, E3B 4Z7, Canada

    Virginia Dickison & Xianzhou Nie

  2. Agricultural Certification Services Inc., 1030 Lincoln Road, Fredericton, NB, E3B 8B7, Canada

    Tyler D. B. MacKenzie & Mathuresh Singh

  3. Department of Biology, University of New Brunswick, P.O. Box 4400, Fredericton, NB, E3B 5A3, Canada

    Janice Lawrence

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  1. Virginia Dickison
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  2. Tyler D. B. MacKenzie
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  3. Mathuresh Singh
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  4. Janice Lawrence
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  5. Xianzhou Nie
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Correspondence to Xianzhou Nie.

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This study was funded by Agriculture and Agri-Food Canada under the project J-000051. All authors declare that they have no conflict of interest. This article does not contain any studies with human participants or animals performed by any of the authors.

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Supplementary material 1 (DOC 84 kb)

705_2017_3252_MOESM2_ESM.jpg

Supplementary Figure 1 Analysis of sequence identities between the query sequence (A. pSVBV-E3; B. BJ; C. Shenyang; D. China) and other isolates (reference sequences) using SimPlot [9]. Similarities (y-axis, 0.5-1) are plotted along the nucleotide sequence (x-axis, nt 1-ca. 7,800). The window covered 200 nucleotides and moved along the alignment in 20-nucleotide steps (JPEG 2843 kb)

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Dickison, V., MacKenzie, T.D.B., Singh, M. et al. Strawberry vein banding virus isolates in eastern Canada are molecularly divergent from other isolates. Arch Virol 162, 1777–1781 (2017). https://doi.org/10.1007/s00705-017-3252-1

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  • DOI: https://doi.org/10.1007/s00705-017-3252-1

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