Figure 1, Bands or "ladder" like steps of PCR produced DNA of Mycobacterium (courtesy of the CDC)
Polymerase chain reaction (PCR) is a chemical reaction harnessed to detect and identify trace bits of DNA, whether from a virus or bacteria to study the organism or diagnose an infection, or for forensic examination in criminal justice and archaeology. As of June, 2020, this type of test is the standard for detecting the presence of the SARS CoV-2 coronavirus responsible for the deadly COVID-19 pandemic.
PCR is a technique that is used to amplify trace amounts of DNA (and in some instances, RNA) located in or on almost any liquid or surface where DNA strands may be deposited. The key to understanding PCR is to know that every human, animal, plant, parasite, bacterium, or virus contains genetic material such as DNA (or RNA) sequences (nucleotide sequences or pieces of DNA or RNA) that are unique to their species, and to the individual member of that species. Consequently, if a sample contains segments of DNA or RNA, PCR is a method used to amplify (make many more identical copies) of these unique sequences so they can then be used to determine with a very high probability the identity of the source (a specific person, animal, or pathogenic organism) of the trace DNA or RNA found in or on almost any sample of material.
PCR amplification is only part of the identifying test, however. Once the amplification is done (see below), the amplified segments need to be compared to other nucleotide segments from a known source (for example, a specific person, animal, or pathogenic organism). This comparison of unique segments is often done by placing PCR-generated nucleotide sequences next to known nucleotide sequences from humans, pathogens, or other sources in a separating gel. Electrical current is run through the gel and the various nucleotide sequences form bands that resemble a "ladder" according to their electrical charge and molecular size. This is termed gel electrophoresis. Bands or "ladder" like steps that migrate to the same levels in the gel show identity of nucleotide sequences. This method is one of the most popular ways PCR tests are completed (See Fig 1).
Figure. Repetitive element (Rep)–PCR (A) and pulsed-field gel electrophoresis (PFGE) (B) patterns of Mycobacterium cosmeticum isolates from 2 patients in Ohio and 1 patient in Venezuela. Rep-PCR was performed by using BOXA1R primer (3), and PFGE was performed with restriction enzyme AseI. Lanes 1, 2, Ohio isolates OH1 and OH2; lanes 3, 4, control strains ATCC BAA-878T and ATCC BAA-879; lane 5, Venezuelan isolate VZ1. DNA size standards are 100-bp (S1) and 48.5-kb marker (S2).