Development of universal primers for detection of potato carlaviruses by RT-PCR

J Virol Methods. 2008 May;149(2):209-16. doi: 10.1016/j.jviromet.2008.02.004. Epub 2008 Mar 18.

Abstract

To facilitate efficient and accurate detection of potato-infecting carlaviruses, degenerated universal primers were designed based on conserved amino acid and nucleotide sequences. Two sense primers, Car-F1 and Car-F2, were based on the amino acid sequences "SNNMA" and "GLGVPTE", respectively, in the coat protein. The reverse primer, Car-R, which was located at the border of the nucleic acid binding protein gene and the 3' untranslated region, and dT-B, which was derived from the oligo-dT targeting the poly(A) tail, were selected. Successful application of fragments within the predicted size range of carlaviruses was obtained using Car-F1 paired with either Car-R or dT-B from tested carlaviruses (Potato virus S, M and latent) by RT-PCR. The Car-F2 failed to yield clear-cut fragments within the predicted size range when paired with either Car-R or dT-B in RT-PCR. However, a less degenerated version of the primer, Car-F2b, resulted in amplicons within the predicted size range when paired with either Car-R or dT-B. Sequencing of the tentative carlavirus-fragments resulting from Car-F1/Car-R and Car-F2b/dT-B proved their carlavirus-origin, thus indicating the high specificity of these primers. The sensitivity of Car-F1/Car-R or Car-F2b/Car-R mediated RT-PCR for the detection of carlavirus-infected potato tubers were assessed using composite samples containing one carlavirus-infected-potato-tuber RNA sample with up to 49 virus-free-potato-tuber RNA samples under the optimal annealing temperature. The target carlaviruses were detected readily from all composites, demonstrating a high sensitivity. The method was further evaluated using presumed virus-free or carlavirus-infected potatoes of several cultivars, and reliable results were obtained.

Publication types

  • Evaluation Study

MeSH terms

  • 3' Untranslated Regions / genetics
  • Capsid Proteins / genetics
  • Carlavirus / genetics
  • Carlavirus / isolation & purification*
  • DNA Primers / genetics
  • Molecular Sequence Data
  • Plant Diseases / virology*
  • RNA, Viral / genetics
  • Reverse Transcriptase Polymerase Chain Reaction / methods*
  • Sensitivity and Specificity
  • Sequence Analysis, DNA
  • Solanum tuberosum / virology*

Substances

  • 3' Untranslated Regions
  • Capsid Proteins
  • DNA Primers
  • RNA, Viral

Associated data

  • GENBANK/EU433397
  • GENBANK/EU433398
  • GENBANK/EU433399