Development and validation of a multiplex quantitative PCR assay for the rapid detection of Grapevine virus A, B and D

Fatima Osman, Emir Hodzic, Alicja Omanska-Klusek, Tammi Olineka, Adib Rowhani

Research output: Contribution to journalArticle

19 Citations (Scopus)

Abstract

A single real-time multiplex quantitative PCR (qPCR) assay for the simultaneous detection of Grapevine virus A, B and D (GVA, GVB and GVD) was developed, using three different fluorescently labeled minor groove binding probes. This multiplex RT-qPCR was compared to singleplex RT-qPCR designed specifically for each virus and a conventional multiplex RT-PCR. The capacity of the multiplex RT-qPCR assay in detecting the three vitiviruses in mixed infections from a range of virus concentrations in the host was assessed. A series of cDNA derived from 48 different grapevine cultivars obtained from diverse geographical regions infected with various isolates and strains of GVA, GVB and GVD were subjected to singleplex, multiplex RT-qPCR, and conventional multiplex RT-PCR testing. The results showed that the developed multiplex RT-qPCR assay was a cost-effective diagnostic tool that could streamline the testing of grapevine vitiviruses, and replace the singleplex RT-qPCR assays, thus reducing time and labor while retaining the same sensitivity and specificity. In particular, no significant differences in detection limits were found between singleplex and multiplex RT-qPCR and specificity was not affected by the inclusion of the three primer/probe combinations within a multiplex RT-qPCR. Comparing the viral load for each virus using singleplex and multiplex RT-qPCR assays revealed no significant differences between the two assays in detecting GVB and GVD. However, while in detecting GVA using singleplex RT-qPCR assay, viral load was higher. Finally, the multiplex RT-qPCR assay was also more sensitive and time efficient than the conventional multiplex RT-PCR that was designed using degenerate primers to detect GVA, GVB and GVD. This multiplex RT-qPCR method could detect viruses in 95.83% of mixed infected samples as compared to 77.08% for multiplex RT-PCR.

Original languageEnglish (US)
Pages (from-to)138-145
Number of pages8
JournalJournal of Virological Methods
Volume194
Issue number1-2
DOIs
StatePublished - Dec 2013

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Cercopithecine Herpesvirus 1
Multiplex Polymerase Chain Reaction
Polymerase Chain Reaction
Flexiviridae
Viruses
Viral Load
Coinfection
Limit of Detection
Real-Time Polymerase Chain Reaction

Keywords

  • Detection
  • Grapevine vitiviruses
  • Multiplex RT-qPCR

ASJC Scopus subject areas

  • Virology

Cite this

Development and validation of a multiplex quantitative PCR assay for the rapid detection of Grapevine virus A, B and D. / Osman, Fatima; Hodzic, Emir; Omanska-Klusek, Alicja; Olineka, Tammi; Rowhani, Adib.

In: Journal of Virological Methods, Vol. 194, No. 1-2, 12.2013, p. 138-145.

Research output: Contribution to journalArticle

Osman, Fatima ; Hodzic, Emir ; Omanska-Klusek, Alicja ; Olineka, Tammi ; Rowhani, Adib. / Development and validation of a multiplex quantitative PCR assay for the rapid detection of Grapevine virus A, B and D. In: Journal of Virological Methods. 2013 ; Vol. 194, No. 1-2. pp. 138-145.
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