Development and comparison of a quantitative TaqMan-MGB real-time PCR assay to three other methods of quantifying vaccinia virions

J Virol Methods. 2014 Feb:196:126-32. doi: 10.1016/j.jviromet.2013.10.026. Epub 2013 Nov 8.


Plaque assays are a widely used method to quantify stocks of viruses. Although this method is well established for titrating viral stocks, it is time consuming and can take several days to complete. In this study, the creation and validation of a quantitative real-time PCR (qPCR) assay for enumerating virions of vaccinia virus is reported. PCR primers and a minor groove-binding probe were designed to hybridize to the DNA polymerase gene (E9L) from a number of different orthopoxviruses. The number of viral genomes determined using qPCR was approximately similar to results obtained using OD260 measurements and a direct count of fluorescent virions by microscopy indicating that all three methods are comparable in their ability to quantify virions from a purified stock. In addition, this report describes methodologies to harvest and quantify, using the qPCR assay, three of the four types of vaccinia virions produced during morphogenesis: intracellular mature virions, cell-associated enveloped virions, and extracellular enveloped virions. Using these procedures a particle to plaque forming unit of 61:1, 14:1 and 6:1 was calculated for IMV, CEV and EEV, respectively. These results show that qPCR can be used as a fast and accurate assay to quantify stocks of vaccinia virus over several orders of magnitude from both purified and unpurified stocks and should be applicable to other members of the orthopoxvirus genera.

Keywords: Orthopoxvirus; Particle to PFU ratio; Vaccinia virus; qPCR.

Publication types

  • Evaluation Study
  • Research Support, N.I.H., Extramural

MeSH terms

  • DNA Primers / genetics
  • DNA, Viral / genetics
  • Oligonucleotide Probes / genetics
  • Real-Time Polymerase Chain Reaction
  • Vaccinia virus / isolation & purification*
  • Viral Load / methods*
  • Virion / genetics
  • Virion / isolation & purification*


  • DNA Primers
  • DNA, Viral
  • Oligonucleotide Probes