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A degenerate pair of primers for simultaneous detection of four alpha- and betanecroviruses

Varanda, C.M.R., Cardoso, J.M.S., Oliveira, M.D.M., Oliveira, S., Clara, M.I.E., Félix, M.R.F.
Journal of virological methods 2014 v.208 pp. 63-65
DNA primers, European Union, Olive latent virus 1, Olive mild mosaic virus, RNA-directed RNA polymerase, Tobacco necrosis virus A, Tobacco necrosis virus D, coat proteins, compliance, double-stranded RNA, genes, marketing, olives, orchards, reverse transcriptase polymerase chain reaction, trees, virus-free plants, viruses
The high infection levels due to Olive latent virus 1 (OLV-1), Olive mild mosaic virus (OMMV) (alphanecrovirus) and Tobacco necrosis virus D (TNV-D) (betanecrovirus) in Portuguese olive orchards prompted us to develop a rapid PCR-based assay for the simultaneous detection of these viruses aimed at the sanitary selection and marketing of plant material in compliance with European Union regulations. A pair of degenerate oligonucleotide primers, parRdRp5′ and parCoat3′ was designed based on conserved regions located in the RNA-dependent RNA polymerase (RdRp) and coat protein (CP) genes of these viruses and one other alphanecrovirus, Tobacco necrosis virus A. Its use in RT-PCR assays generated a product of ca. 2000bp for the 4 viral species tested. These primers were compared with virus specific primers in multiplex RT-PCR, and identical results were obtained. Its application to dsRNA extracted from 54 olive field growing trees originated the expected ca. 2000bp amplicon in 17 trees. The virus identity was determined by sequencing the cloned RT-PCR products. No TNV-A was found.The RT-PCR assay using the degenerate primers described in this study were shown to be reliable in detecting any of the above-mentioned alpha- and betanecroviruses, and it is as sensitive as that which uses virus specific primers in multiplex assays. Therefore, this assay is well suited for the rapid screen of virus-free plant material in selection and improvement crop programmes. Additionally, it has the potential to reveal virus diversity and the presence of new viruses, provided the RT-PCR generated amplicon is further sequenced.