Overview

• Polymerase chain reaction (PCR) involves the sequential amplification of target sequences of DNA by repeated cycles of oligonucleotide primer-driven DNA synthesis.
• It is traditionally qualitative but is often now more quantitative which has revolutionized the investigation and diagnosis of health and disease at the molecular level.

Sampling

Tests

Methodologies

• Many laboratories now offer PCR testing. They require a good ‘uniflow’ design to avoid problems with contamination so the end result is accurate.
• The sample is first processed using commercially available extraction kits to obtain high quality DNA/RNA from a number of different sample types, whilst minimizing the presence of inhibitors that could interfere with the subsequent amplification process.
• PCR uses a pair of synthetic oligonucleotide sequences (primers) which are designed to anneal (bind) to a target region of DNA, both the 5 and 3 regions of the target organism.
• Primers, purified sample DNA and Taq DNA polymerase are combined in a suitable buffer and placed in a thermocycler.
• Thermocycling comprises typically a melting step (c. 95°) where the DNA strands separate. This is followed by an annealing/extension step (c. 60°C) when the primers attach/affix to their target sequence (if present). The polymerase then extends the primers sequentially using the single DNA strand template up to a certain size.
• When heated again, four DNA strands are now created for again affixing and extension. This doubling occurs on each heating and cooling cycle.
• This coupled cycle repeated 40-45 times, such that there is an exponential increase in the amount of DNA. This can then be measured via the increase in fluorescence measured at each cycle.
• The amount of target DNA in the original sample is related to the point at which the fluorescence value crosses a threshold detection value. This is commonly reported as the Ct value.
• In qPCR lower Ct values then indicate more target DNA was present as fewer cycles were needed to cross the threshold. If there was very little material there, more cycles would be required to cross this threshold. In this way if only minimal material is present (Ct 40), the significance of this result clinically can change and may be questioned.
• A final feature is reproducibility as both gel and qPCR are typically done in duplicate but with qPCR, only more than 10 copies of DNA per PCR are required for almost identical fluorescence graphs.

Further Reading

Publications

Refereed papers

• Recent references from VetMedResource and PubMed.
• Sykes J E, Allen J L, Studdert V P & Browning G F (2001) Detection of feline calicivirus, feline herpesvirus 1 and Chlamydia psittaci mucosal swabs by multiplex RT-PCR/PCR. Vet Microbiol 81, 95-108.
• He X, Li C M, Simonaro C M, Wan Q, Haskins M E, Desnick RJ & Schuchman E H (1999) Identification and characterization of the molecular lesion causing mucopolysaccharidosis type I in cats. Mol Genet Metab 67, 106-112
• McDonald M, Willett B J, Jarrett O & Addie D D (1998) A comparison of DNA amplification, isolation and serology for the detection of Chlamydia psittaci infection in cats. Vet Rec 143, 97-101.
• Sykes J E, Studdert V P & Browning G F (1998) Detection and strain differentiation of feline calicivirus in conjunctival swabs by RT-PCR of the hypervariable region of the capsid protein gene. Arch Viro l143, 1321-1334.
• Nasisse M P, Glover T L, Moore C P & Weigler B J (1998) Detection of  feline herpesvirus 1 DNA in corneas of cats with eosinophilic keratitis or corneal sequestration.  Am J Vet Res 59, 856-858.
• Radford A D, Bennett M, McArdle F, Dawson S, Turner P C, Glenn M A & Gaskell R M (1997) The use of sequence analysis of a feline calicivirus (FCV) hypervariable region in the epidemiological investigation of FCV related disease and vaccine failures. Vaccine 15, 1451-1458.
• Mochizuki M, San Gabriel M C, Nakatani H & Yoshida M (1993) Comparison of polymerase chain reaction with virus isolation and haemagglutination assays for the detection of canine parvovirus in faecal specimens.  Res Vet Sci 55, 60-63

Organisation(s)

• SYNLAB-VPG.
• Idexx.
• Rossdales/Beaufort.
• Langford.
• Biobest.
• Envigo.