Abstract
To characterize their virome, double stranded RNAs extracted from scrapings of two Iranian grapevine varieties held in the Vassal-Montpellier Grapevine Biological Resources Center were analysed by high-throughput sequencing. In addition to several well-known grapevine viruses, divergent isolates of the newly described grapevine Kizil Sapak virus were identified in both accessions. Four complete genome sequences were determined, as well as two additional partial sequences (1,580 and 3,849 nucleotides long). These genomic sequences highlight the molecular diversity of this poorly known virus. In view of the absence of amplification of the GKSV isolates characterized here using the published primer pair, novel degenerate, polyvalent primers were designed, providing a more robust diagnosis.
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Acknowledgements
The authors would like to thank Sandrine Dedet and Cécile Marchal (CRB Vigne de Vassal-Montpellier) and Thierry Mauduit (UMR BFP) for taking care of experimental plants, and the Platform GenoToul (INRAE, Toulouse, France) for Illumina sequencing.
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The nucleotide sequences reported in this manuscript have been deposited in the GenBank database under accession numbers MK204652-5 and MK775527-8.
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Fig. S1
Detection of GKSV in Askeri and Sahami samples by RT-PCR using isolate-specific and broad-spectrum primer pairs. Lanes 1 and 2, amplification with the NT20-MPF1/CPR1 primer pair; lanes 3 and 4, amplification with the NT28-MPF1/CPR1 primer pair; lanes 5 and 6, amplification with the NT177-MPF1/CPR2 primer pair; lanes 7 and 8, amplification with the NT200-MPF1/CPR1 primer pair; lanes 9 and 10, amplification with the NT41-MPF1/CPR1 primer pair; lanes 11 and 12, amplification with the NT87-MPF1/CPR1 primer pair; lanes 13-15, amplification with the ViniF1/R1 primer pair. Lanes 1, 3, 5, 7, 9, 11 and 13, healthy controls; lanes 2, 4, 6, 8 and 14, Askeri extract; lanes 10, 12 and 15, Sahami extract. L, molecular weight markers. Horizontal bars on the right side of the figure indicate the size of representative marker bands. Nucleotide sequences of the isolate-specific primer pairs are listed in Table 1. (PDF 295 kb)
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Marais, A., Faure, C., Lefebvre, M. et al. Molecular diversity of grapevine Kizil Sapak virus and implications for its detection. Arch Virol 165, 1849–1853 (2020). https://doi.org/10.1007/s00705-020-04673-9
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DOI: https://doi.org/10.1007/s00705-020-04673-9