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PCR Defined

Diagnoses of Specific Diseases

Future Role of PCR in Clinical Diagnostics

Questions to Ask Your PCR LAB

 

A. PCR Defined

A1. What is PCR?
PCR--Polymerase Chain Reaction is a DNA-based method that amplifies a precisely defined segment of target DNA. Target DNA is specified by design of two primers. The DNA undergoes logarithmic amplification resulting in a single copy being multiplied into billions.

A2. How is PCR detected?
Electrophoresis on an agarose gel stained with Ethidium Bromide and observed under UV light.

B.  Diagnoses of Specific Diseases

B1.  What are the current PCR methods?
There are three (3) PCR Methods:

1) Single PCR Method:

  • Used for Toxoplasma, Ehrlichia, Bartonella, FeLV, Mycobacterium, Feline Herpes, Equine Herpes.
  • Difficulty interpreting results because PCR indicates organisms present but not causing disease. For example, Toxoplasma PCR on cats with uveitis: 19% PCR Positive compared with cats without uveitis 9% positive

2) Nested PCR Method:

  • Used to detect target organisms at low concentrations
  • Utilizes a second round of amplification
  • Main disadvantage is turnover time--requires two runs

3) Reverse Transcription PCR (RT-PCR) Method

  • Used for FIP, Canine Distemper
  • Amplifies an RNA template (i.e. RNA must be converted to DNA)

B2. What specific diseases can be diagnosed with PCR testing?
FeLV (Feline Leukemia Virus)

  • Single PCR method.
  • Synbiotics research: 62 feline blood samples from Antech Labs were analyzed by ELISA, IFA and Synbiotics FeLV PCR. PCR had good correlation with strong positive IFA and strong positive ELISA. However, weak positive IFA conflicted with PCR.
  • 45 samples strong positive ELISA/42 PCR Positive/93% correlation.
    5 samples weak positive ELISA/2 PCR Positive/40% correlation
  • PCR is helpful in resolving conflicts between antibody based tests.

FIV (Feline Immunodeficiency Virus)

  • Double PCR Method.
  • Single PCR results with 12 antibody positive cats: 7 FIV PCR positive.
  • Double PCR on the same 12 cats: 12 PCR positive.
  • Note: Some cats fail to produce antibodies after infection, i.e., False Negative ELISA & Western Blots. False positive ELISA in kittens less than 6 months.
  • PCR is more sensitive for FIV detection--patent restrictions prohibit its commercial application.

FIP (Feline Infectious Peritonitis)

  • RT-PCR (Reverse Transcription Polymerase Chain Reaction).
  • RNA must be converted to DNA in two-step procedure.
  • Test detects small amounts of virus in effusions, plasma, and feces. Symbiotics
  • Study: 40 cases from Antech Laboratories analyzed by the Synbiotics PCR Assay. All 40 cases presented with effusive e fluid. Results: 18 cases PCR Negative: 14-not FIP, 3 FIP, 1 Uncertain.
    22 Cases Positive FIP PCR: 20-FIP positive, 1-Negative, and 1-Uncertain. All confirmed FIP Positive cats Died (Necropsy, cytology, histology, clinical outcome). All FIP Negative Cats are alive.
  • Accuracy: 87% for sensitivity and 93% for specificity.
  • Considerations: Cats with dry FIP or a localized lesion may not have virus in the blood that may result in false negative results. FIP-PCR is specific and works well on effusions but lacks sensitivity when performed on whole blood. RNA is very fragile and may degrade if the sample is stored incorrectly or is too old. Keep it cold but not frozen in an EDTA (lavender top) tube.

Haemobartonella felis (FIA)

  • Single PCR. PCR more sensitive than cytology, e.g., cat with profound FIA-induced anemia was cytology positive and PCR positive.
  • Treated with antibiotics.
  • After treatment, cat became cytology negative and PCR positive for several weeks. (Symbiotics Data).
    20 suspect FIA cats were PCR positive
    10 known negative FIA cats PCR negative (Synbiotics data)

B3.  Are there other single step PCR Tests are available?

  • Bartonella henselae (Cat Scratch)
  • Canine parvovirus
  • Chlamydia psittaci
  • Cryptosporidium
  • Ehrlichia canis
  • Ehrlichia risticci (Potomac Fever)
  • Ehrlichia ewingii
  • Equine herpes
  • Feline herpes
  • Giardia
  • Mycobacterum spp (M. avium, M. bovix, M. tuberculosis)
  • Tick multiplex (Ehrlichia canis, Rocky Mountain Spotted Fever, Lymes)
  • Yersinia pestis

B4.  Are there other RT-PCR Tests available?

Canine Distemper (very sensitive as a research issue is whether Distemper PCR tests will detect vaccine virus in recently vaccinated dogs)

C.  Future Role of PCR in Clinical Diagnostics

C1.  What is the biggest challenge to PCR?
It is contamination, which can generate billions of copies of PCR product and thus produces false positive results.

C2.  What is the remedy to contamination?

  • Separate rooms for DNA/RNA extractions and PCR preparation.
  • PCR preps in a sterile environment (e.g. laminar flow or "PCR" Hood")
  • Decontaminate with special chemicals such as RNA-ASE Away, DNA-ASE Away
  • Ozone decontamination (Alpine ozonators)

D.  Questions to Ask Your PCR Lab

D1.  Does your PCR lab quantitative the DNA?
Samples vary in the amount of DNA that is successfully extracted. In some samples recovery may be too high or too low. Too much DNA or too little has an effect on results. Was an adequate amount of DNA recovered from the extraction? Quantification allows the technician to make proper adjustments from the sample for optimum sensitivity.

D2. Does your Laboratory archive and photodocument results?
In cases where there may be a legal action or complaint filed against a practitioner, photos of the electrophoresis gels are acceptable as definitive proof.

D3.  Does your laboratory prepare their reactions in a sterile environment, such as a laminar flow hood or a special PCR Hood that is equipped with UV light?
This is extremely important to avoid contamination.

D4. Is your PCR laboratory equipped with an autoclave and a microwave?
This may seem to be a rather silly question, but in order to prevent contamination laboratory equipment and consumables need sterilization often and routinely. There are PCR laboratories in business that do not have these essentials.

D5. What is your PCR Lab's policy with regard to when results are released?
A reputable laboratory may choose to release results with appropriate positive and negative controls included with the test sample. Our laboratory chooses to hold results and rerun the tests if there is a discrepancy in the controls.

D6.  Does your PCR lab run positive and negative controls?
Positive control to confirm that the PCR is working properly.
Negative controls to confirm positives are true positive results.

 For a consultation contact DyNAgenics Veterinary Diagnostics today!

 

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Last updated July 20, 2006