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Polymerase Chain Reaction, PCR, Generally



Polymerase Chain Reaction (PCR) is a gene amplification tool that allows detection of tiny pieces of infectious agent genetic material (DNA) in a sample. It is a fast, sensitive and specific way of diagnosing infectious agents. The inventor of the PCR procedure received the Nobel Prize in 1993.

In basic terms, the procedure involves repetitive splitting and rejoining of chains of DNA through heating and cooling cycles. The process encourages the replication of segments of recognizable DNA, which can then be detected.

The most common indications for this test are horses with diarrhea or evidence of respiratory disease.

Samples are taken from the manure or rectum, or the respiratory tract, respectively. Swabs are taken of particular locations within the respiratory tract. Swabs or manure samples are provided to the lab in the case of diarrhea.

The EHV-1 PCR has recently been improved (Gluck Center) and is more reliable for differentiating the mutated strain of EHV-1, which causes neurologic disease from non-neuropathogenic EHV-1

A Strep equi equi PCR has been developed which is highly sensitive and specific in the identification of Strangles. This can be helpful for a quick differentiation in respiratory outbreaks.


The benefits of PCR include great sensitivity, the test can detect tiny amounts of DNA. In most cases, the test result is available rapidly, another great advantage. Finally, most PCR testing is relatively inexpensive.

Because the test looks for infectious agent DNA and does not rely on the horse's antibody, it can be performed as a one-time test for the presence of the organism.


The test only detects infectious organism DNA, not live organisms. In the case of the Strep equi PCR, sometimes this can be significant. For example, the DNA can persist in the guttural pouch of horses even when there are no live bacteria. In this case, a positive test would suggest a false conclusion. For this reason, in certain cases an appropriate culture should also be used in order to confirm the diagnosis.

This process can rarely go awry, leading to aberrant binding of DNA and false positives.

Helpful Terms & Topics in HSVGWritten, Reviewed or Shared by Experts in Equine Health


  • What does a positive test tell us?
  • What does a negative test tell us?
  • What is the likelihood of an erroneous conclusion one way or the other?
  • Should you also perform a culture to confirm the diagnosis?
  • Author: Doug Thal DVM Dipl. ABVP


    Sigsgaard S. Gluck Center Develops New PCR Assay for EHV-1. Bluegrass Equine Digest July 2012: 5.North SE, Wakeley PR, Mayo N, et al. Development of a real-time PCR to detect Streptococcus equi subspecies equi. Eq Vet J 2014;46:56-59.


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