Editing Polymerase chain reaction (section)

===Infectious disease applications===
PCR allows for rapid and highly specific diagnosis of infectious diseases, including those caused by bacteria or viruses.<ref name=Cai2014>{{cite journal | vauthors = Cai HY, Caswell JL, Prescott JF | title = Nonculture molecular techniques for diagnosis of bacterial disease in animals: a diagnostic laboratory perspective | journal = Veterinary Pathology | volume = 51 | issue = 2 | pages = 341–50 | date = March 2014 | pmid = 24569613 | doi = 10.1177/0300985813511132 | doi-access = free }}</ref> PCR also permits identification of non-cultivatable or slow-growing microorganisms such as [[mycobacterium|mycobacteria]], [[anaerobic organism|anaerobic bacteria]], or [[virus]]es from [[tissue culture]] assays and [[animal model]]s. The basis for PCR diagnostic applications in microbiology is the detection of infectious agents and the discrimination of non-pathogenic from pathogenic strains by virtue of specific genes.<ref name= "Cai2014" /><ref>{{cite book |author=Salis AD|year=2009|chapter= Applications in Clinical Microbiology|title=Real-Time PCR: Current Technology and Applications|publisher= Caister Academic Press |isbn= 978-1-904455-39-4}}</ref>

Characterization and detection of infectious disease organisms have been revolutionized by PCR in the following ways:
* The ''human immunodeficiency virus'' (or ''[[HIV]]''), is a difficult target to find and eradicate. The earliest tests for infection relied on the presence of antibodies to the virus circulating in the bloodstream.  However, antibodies don't appear until many weeks after infection, maternal antibodies mask the infection of a newborn, and therapeutic agents to fight the infection don't affect the antibodies.  PCR [[HIV test|tests]] have been developed that can detect as little as one viral genome among the DNA of over 50,000 host cells.<ref>{{cite journal | vauthors = Kwok S, Mack DH, Mullis KB, Poiesz B, Ehrlich G, Blair D, Friedman-Kien A, Sninsky JJ | title = Identification of human immunodeficiency virus sequences by using in vitro enzymatic amplification and oligomer cleavage detection | journal = Journal of Virology | volume = 61 | issue = 5 | pages = 1690–94 | date = May 1987 | pmid = 2437321 | pmc = 254157 | doi = 10.1128/jvi.61.5.1690-1694.1987 }}</ref> Infections can be detected earlier, donated blood can be screened directly for the virus, newborns can be immediately tested for infection, and the effects of antiviral treatments can be [[Viral load|quantified]].
* Some disease organisms, such as that for ''[[tuberculosis]]'', are difficult to sample from patients and slow to be [[Tuberculosis diagnosis|grown]] in the laboratory.  PCR-based tests have allowed detection of small numbers of disease organisms (both live or dead), in convenient [[Sputum|samples]].  Detailed genetic analysis can also be used to detect antibiotic resistance, allowing immediate and effective therapy.  The effects of therapy can also be immediately evaluated.
* The spread of a [[pathogen|disease organism]] through populations of [[Domestication#Animals|domestic]] or [[Wildlife|wild]] animals can be monitored by PCR testing.  In many cases, the appearance of new virulent sub-types can be detected and monitored.  The sub-types of an organism that were responsible for [[List of epidemics|earlier epidemics]] can also be determined by PCR analysis.
* Viral DNA can be detected by PCR. The primers used must be specific to the targeted sequences in the DNA of a virus, and PCR can be used for diagnostic analyses or DNA sequencing of the viral genome. The high sensitivity of PCR permits virus detection soon after infection and even before the onset of disease.<ref name="Cai2014"/> Such early detection may give physicians a significant lead time in treatment. The amount of virus ("[[viral load]]") in a patient can also be quantified by PCR-based DNA quantitation techniques (see below). A variant of PCR ([[Reverse transcription polymerase chain reaction|RT-PCR]]) is used for detecting viral RNA rather than DNA: in this test the enzyme reverse transcriptase is used to generate a DNA sequence which matches the viral RNA; this DNA is then amplified as per the usual PCR method. RT-PCR is widely used to detect the SARS-CoV-2 viral genome.<ref>{{cite web |title=Coronavirus: il viaggio dei test |url= https://www.iss.it/web/guest/primo-piano/-/asset_publisher/o4oGR9qmvUz9/content/id/5269706 |website=Istituto Superiore di Sanità}}</ref>
* Diseases such as pertussis (or [[whooping cough]]) are caused by the bacteria ''[[Bordetella pertussis]]''. This bacteria is marked by a serious acute respiratory infection that affects various animals and humans and has led to the deaths of many young children. The pertussis toxin is a protein exotoxin that binds to cell receptors by two [[Dimer (chemistry)|dimers]] and reacts with different cell types such as T lymphocytes which play a role in cell immunity.<ref>{{Cite book|url= https://www.ncbi.nlm.nih.gov/books/NBK7813/ |title=Medical Microbiology|last1= Finger|first1=Horst|last2=von Koenig|first2= Carl Heinz Wirsing|date=1996|publisher=University of Texas Medical Branch at Galveston |isbn= 978-0-9631172-1-2 |editor-last=Baron|editor-first= Samuel|edition=4th |location= Galveston, TX |pmid= 21413270}}</ref> PCR is an important testing tool that can detect sequences within the gene for the pertussis toxin.  Because PCR has a high sensitivity for the toxin and a rapid turnaround time, it is very efficient for diagnosing pertussis when compared to culture.<ref>{{Cite book |last1= Yeh|first1= Sylvia H.|last2=Mink|first2= ChrisAnna M.|title= Netter's Infectious Diseases|year=2012 |pages= 11–14 |doi= 10.1016/B978-1-4377-0126-5.00003-3 |chapter= Bordetella pertussis and Pertussis (Whooping Cough) |isbn= 978-1-4377-0126-5}}</ref>