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Animal Health Diagnostic Center

Improving the health of animals, animal populations and wildlife

Interpretation of PCR results

Polymerase chain reaction (PCR) assays detect the "target nucleic acid" (DNA or RNA depending on the organism).

PCR assays, either conventional or real-time, in general (unless otherwise specified), will be reported as 'detected' or 'not detected' by the AHDC Molecular Diagnostics Laboratory.

A Ct (Cycle threshold) value will also be reported for real-time PCR assays with the ‘detected’ results. The Ct value ranges between 0 and the total number of PCR cycles (40 or 45) performed for that assay. A ‘not detected’ report corresponds to Ct=0 and is equivalent to a negative result. A Ct >0 means the target was ‘detected’ in the sample and is equivalent to a positive result. The Ct is inversely proportional to the amount of target nucleic acid present in the sample. The lower the Ct, the more target is present in the tested sample, and the reverse is true as well. If a sample results with a Ct value ≥ the limit of reproducibility (LOR) for that assay, it will be reported as ‘detected’ and include a comment that states that the result may not be reproducible.

The PCR assays are always run with a negative amplification control, a positive amplification control, and a DNA or RNA extraction control. A list of quality criteria must be met before the testing result is finalized or otherwise reported as 'inconclusive.'

PCR assays at the AHDC molecular diagnostic lab have undergone validation/verification and are periodically monitored for their suitability for intended purpose. Real-time probe-based PCR ensures high diagnostic specificity. The validation/verification process involves generating a standard curve using a serial dilution of a known positive, run under standard PCR cycling conditions that determine analytical sensitivity and the linearity of the standard curve. The repeatability and the reproducibility (including the LOR) are determined for each assay.

List of Real-time probe-based PCR assays with Ct ranges 1 to 40

Alpha Coronavirus PCR - (ACOR)

Anaplasma marginale PCR - (AMAR)

Anaplasma phagocytophilum (Ehrlichia equi) PCR - (EHRE)

Avian H5 Influenza Virus PCR - (AIH5PCR)

Avian H7 Influenza Virus PCR - (AIH7PCR)

Avian Influenza Virus PCR - (AIPCR)

Avian Influenza Virus PCR, LBM - (AILBPCR)

Avian Metapneumovirus Subgroup A - (AMPA)

Avian Metapneumovirus Subgroup B - (AMPB)

Avian Metapneumovirus Subgroup C - (AMPC)

Avian Mycoplasma synoviae PCR - (MSYN)

Avian Mycoplasmosis gallisepticum PCR - (MGAL)

Avian Paramyxovirus-1 PCR - (APMPCR)

Babesia microti PCR (Dev) - (BMICT)

Batrachochytrium dendrobatidis PCR - (BDEN)

Batrachochytrium salamandrivorans PCR - (BSAL)

Beta Coronavirus PCR - (BCOR)

Bluetongue Virus PCR - (BTT)

Bordetella PCR - (BORD)

Borrelia miyamotoi PCR (Dev) - (BMT)

Bovine Avian Influenza Virus PCR - (BAIPCR)

Bovine Herpesvirus-1 PCR - (BHV1)

Bovine Parainfluenza-3 Virus PCR - (PI3)

Bovine Respiratory Syncytial Virus PCR - (BRS)

Bovine Rotavirus PCR - (BRV)

Bovine Viral Diarrhea Virus PCR - (BVDPCR, BVDMPCR)

Canine Adenovirus PCR - (CADEN)

Canine Distemper PCR - (DIS)

Canine Herpesvirus-1 PCR - (CHV1PCR)

Canine Parainfluenzavirus PCR - (PINF)

Chlamydia PCR - (CHPCR)

Chlamydia abortus PCR - (CABO)

Chlamydia felis PCR - (CFEL)

Chlamydia pecorum PCR - (CPEC)

Chlamydia psittaci PCR - (CPSI)

Coxiella burnetii (Q-Fever) PCR - (COXPCR)

Cryptosporidium PCR - (CRYPCR)

Cytauxzoon felis PCR - (CYF)

E. coli: CNF - (CNF)

E. coli: EAE - (EAE)

E. coli: F17A - (F17A)

E. coli: F41 - (F41)

E. coli: F5 (K99) - (F5(K99))

E. coli: Sta - (Sta)

E. coli: STX1 - (STX1)

E. coli: STX2 - (STX2)

Ehrlichia chaffeensis PCR (Dev) - (ECHT)

Epizootic Hemorrhagic Disease Virus PCR - (EHD)

Equine Adenovirus-1 PCR - (EAD1)

Equine Adenovirus-2 PCR - (EAD2)

Equine Arteritis Virus (EAV) PCR - (EAR)

Equine Herpes Virus-1 Neuropathogenic Genotype PCR - (EHVN)

Equine Herpesvirus-1 PCR - (EHV1PCR)

Equine Herpesvirus-2 PCR- (EHV2PCR)

Equine Herpesvirus-4 PCR- (EHV4PCR)

Equine Herpesvirus-5 PCR- (EHV5PCR)

Equine Rhinitis Virus A PCR - (ERHA)

Equine Rhinitis Virus B PCR - (ERHB)

Infectious Laryngotracheitis Virus PCR - (ILT)

Influenza Virus Matrix PCR - (IVMPCR)

Johne's fecal PCR -(JPCRD, JPCRI, JPCRN, JPCRO, JGPCR, JCPCR)

Lawsonia intracellularis PCR - (LAWPCR)

Leptospira PCR - (LEPTPCR)

Lyme Disease PCR - (LYMPCR)

Mycobacterium avium avium PCR - (MAAPCR)

Mycobacterium avium complex PCR - (MACPCR)

Mycoplasma cynos PCR - (MCYN)

Mycoplasma felis PCR - (MFEL)

Pneumovirus PCR - (PNVPCR)

Potomac Horse Fever PCR - (EHRR)

Powassan Virus PCR (Dev) - (POWT)

Rickettsia rickettsii PCR - (RRT)

Rickettsia spp. PCR (Dev) - (RICT)

Salmonella PCR - (SPCR)

Streptococcus equi equi PCR - (SEQUPCR)

Streptococcus zooepidemicus PCR - (SZT)

Theileria orientalis PCR - (THOR)

Virulent Newcastle Disease Virus PCR - (VNDVPCR)

White-Nose Syndrome PCR - (WNST)

List of Real-time probe-based PCR assays with Ct ranges 1 to 45:

African Swine Fever PCR - (ASFPCR)

Avian H2 Influenza Virus PCR - (AIH2N2)

Campylobacter jejuni PCR - (CJPCR)

Classical Swine Fever PCR - (CSFPCR)

Environmental Avian Influenza PCR - (EAIPCR)

Foot and Mouth Disease PCR -(FMDPCR)

SARS CoV-2 PCR - (COV2)

Swine Influenza Virus Matrix PCR - (SIPCR)

List of conventional PCR assays (no Ct values):

Ehrlichia canis PCR - (EHRC)

Avian Infectious Bronchitis Virus PCR - (IBVPCR)

Bovine Viral Diarrhea Virus Genotype -(BVDG)

Canine Scott Syndrome Mutation Detection - (CSS)

Clostridium perfringens Genotype PCR - (CPGPCR)

Listeria monocytogenes PCR - (LSTPCR)

Ophidiomyces ophiodiicola PCR - (OOPCR)

Rhodococcus equi Virulence PCR - (REQUPCR)

For the following PCR tests, results will be reported as per the specific needs of the assay:

  1. Johne's fecal PCR (JPCRD, JPCRI, JPCRN, JPCRO, JGPCR) testing will include low, moderate, heavy, or inconclusive as a result for all species tested.
  2. Bovine viral diarrhea genotyping PCR (BVDG) tests will result as type (1a, 1b, 2a, or 2b).
  3. Equine herpes virus-1 neuropathogenic genotyping PCR (EHVN) will be resulted as 'ORF 30- G2254', 'ORF 30-A2254', or as 'inconclusive.' No Ct will be provided.
  4. The Shar-Pei Auto-Inflammatory Disease Genetic Test (SPAID) will be resulted as 'single carrier', 'double carrier', or 'no carrier' for allele 5.
  5. National Animal Health Laboratory Network (NAHLN) foreign animal disease PCR testing [African Swine fever-(ASFPCR), Classical Swine Fever-(CSFPCR), Foot and Mouth disease-(FMDPCR), Avian Influenza and related subtests (AIPCR, AILBPCR, EAIPCR, AIH2N2, AIH7PCR, BAIPCR, AIH5PCR), Avian Paramyxovirus-1 (APMPCR, vNDVPCR), and Swine Influenza Virus Matrix PCR - (SIPCR)] will be resulted as 'non-negative' or 'not detected' with a Ct value.
  6. Conventional PCR assays (unless otherwise indicated) will be reported as 'detected' or as 'not detected.'
  7. Canine Scott Syndrome Mutation Detection (CSS) will be reported as 'mutation present (2 copies)', 'mutation present (1 copy)', or 'mutation absent.'

Note: AHDC Virology Laboratory also offers PCR testing and reports results per its reporting procedures.