What is PCR (or qPCR)?
PCR stands for Polymerase Chain Reaction. PCR has been a long-used molecular diagnostic testing technique used to identify, or target, a genetic sequence of DNA or RNA (e.g., bacteria, viruses) in a sample.
Typically, the ‘chain reaction’ refers to amplifying or photocopying the amount of DNA in the sample 40 times, a process that generally takes 40 – 85 min.
If a single strand of targeted DNA is present (a positive result) and every strand is photocopied during each of the 40 cycles of PCR, then a single strand of DNA should turn into > 1 trillion copies at the conclusion of PCR (assuming a 100% efficient reaction (=2^40)). This is what makes PCR so amazingly sensitive. Also, if proper care is taken in developing a pathogen-specific test, then the test should rarely—if ever—generate a false positive test. This is called specificity.
Because the sensitivity and specificity of PCR is so high, PCR is widely regarded as a ‘gold standard’. In layman’s terms, it is very accurate.
SARS-CoV-2 (the pathogen that causes COVID-19) is an RNA pathogen. In order to successfully detect this pathogen using PCR, it is first necessary to convert the RNA into DNA, and this is done by reverse transcribing the RNA into DNA. When scientists combine reverse transcription (RT) and PCR to amplify RNA targets, it is abbreviated as RT-PCR. The RT step takes 5 – 15 minutes. Due to its accuracy, RT-PCR is the main method used by reference laboratories to identify the presence of SARS-CoV-2 (COVID-19) and many other pathogens.
Despite the reliability of PCR, there are many competing chemistries that can be used to detect pathogens. Isothermal amplification and antigen-based tests are two examples. These chemistries are generally faster and less technical to perform. However, these technologies are widely considered as inferior to RT-PCR in terms of sensitivity. Because of this, they are not the choice of most reference labs, as most reference laboratories would prefer to take a bit more time and get the answer right, than rush with an inferior technology and be at higher risk of a misdiagnosis.
PCR-based tests take about one hour and generate extremely accurate test results. There are other chemistries (isothermal amplification and antigen tests) that can offer faster test results, but they miss a percentage of cases that would be detected using PCR.
PCR is traditionally performed in a reference laboratory, which typically returns results within 24 hours of receiving a sample. Shipping samples to reference laboratories can significantly add to the delay in receiving results. LexaGene helps solve the ‘time’ problem by automating PCR at the point of need – and returning results ~ 1 hour after initiating sample processing.