The Molecular Diagnostics Laboratory is equipped with state-of-the-art equipment and facilities including high-throughput automated extraction and liquid handling systems and a variety of platforms for PCR and next-generation sequencing. We operate within a Quality Assurance System that complies with the American Association of Veterinary Laboratory Diagnosticians. The lab also undergoes proficiency testing conducted by the National Veterinary Services Laboratory and the US Food and Drug Administration.

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Diagnostic Testing

Polymerase chain reaction (PCR) results will now be reported as "Detected" or "Not Detected" by the molecular diagnostics laboratory.

Starting April 9, 2024, polymerase chain reaction (PCR) results reported by the molecular diagnostics laboratory at the AHDC will be resulted as "detected" or "not detected," and a Ct (Cycle threshold) value will be reported with the "detected" results. A "not detected" result is the equivalent of a negative result, and a "detected" result is the equivalent of a positive result. This is a shift from the previous reporting of low, moderate, or high positive results, without the inclusion of the Ct value.

PCR assays at the AHDC undergo initial validation/verification and are periodically monitored for their suitability for intended testing needs, which is to detect the "target nucleic acid" (DNA or RNA depending on the target). 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 determines analytical sensitivity. The linearity of the standard curve, the repeatability and the reproducibility are determined. The Ct limit of reproducibility (LOR) is determined for each target or pathogen. Any Ct value ≤ the LOR is reported as "detected" and any Ct value > the LOR is reported as "not detected." If no Ct is observed in the run, we report the sample as "not detected." When interpreting Ct values, the lower the Ct, the more target present in the sample, and the reverse is true as well. Samples with Ct values meeting quality criteria are reported as "detected." However, samples with Ct values > the LOR will include a comment that states 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 result of testing is reported. As an American Association of Veterinary Laboratory Diagnosticians (AAVLD) accredited lab, we strive to maintain our accreditation standards and offer clients the quality service they look for.

This change in result reporting does not apply to the following PCR tests:

1. Johnes (Mycobacterium avium subspecies paratuberculosis) fecal PCR testing will still include low, moderate, or heavy in the results for all species tested.
2. Bovine viral diarrhea (BVD) genotyping PCR tests will still be resulted as type (1a, 1b, 2a, or 2b).
3. Equine herpes virus-1 neuropathogenic genotyping PCR will be resulted as ORF 30- G2254, ORF 30-A2254 or both.
4. 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 (ex: Foot and Mouth disease and Highly Pathogenic Avian Influenza) will be resulted as “non-negative” or “detected” with a CT value, as they have been previously. 
6. Conventional PCR assays (unless otherwise indicated) will be reported as “detected” (with no Ct values) or as “not detected”.

Please note that some PCR testing is performed in our virology laboratory, which has been reporting results this way historically.

STAT Testing Procedures

Results for most infectious disease PCR tests are reported 1 or 2 business days after the sample is received. Specific information for each test is provided in our test catalog. Please also refer to our list of STAT-eligible molecular tests, turnaround times, and instructions.

Formalin-fixed samples may be submitted for most PCR tests and will incur a $20 surcharge. These are not eligible for STAT testing

Surveillance Testing

As a level I NAHLN lab, we perform surveillance testing for avian influenza virus, avian paramyxovirus-1/Exotic Newcastle Disease, foot and mouth disease virus and classical swine fever virus. We also participate in the FDA Vet-LIRN and GenomeTrakr networks to improve pet food safety and outbreak response capacity.

In cooperation with our Bacteriology section, we perform Johne's direct fecal PCR testing for the New York State Cattle Health Assurance Program (NYSCHAP) and Salmonella Environmental Surveillance for animal facilities.

People

Please direct all molecular testing queries to ahdc_mol_mgmt@cornell.edu or (607) 253-3900.

Research

Research and development is part of the mission of the AHDC at Cornell. The Molecular Diagnostics Section is available to collaborate with you to develop new or improve existing test methods and reagents, investigate specific problems or provide customized testing to meet your needs. As an academic lab, we are eager to form collaborations with other researchers and provide support for a wide variety of projects. Please contact us to discuss the specific needs for your project.

Several recent publications highlighting work that we have contributed to include:

• McDonagh et al. Frequent human-poultry interactions and low prevalence of Salmonella in backyard chicken flocks in Massachusetts. Zoonoses and Public Health 2019
• Voorhees et al. Multiple Incursions and Recurrent Epidemic Fade-Out of H3N2 Canine Influenza A Virus in the United States. Journal of Virology 2018
• Goodman et al. Detection of Salmonella spp. in veterinary samples by combining selective enrichment and real-time PCR. Journal of Veterinary Diagnostic Investigation 2017
• Manjunatha et al. A Cryptosporidium PI(4)K inhibitor is a drug candidate for cryptosporidiosis. Nature 2017
• Wagner et al. Neonatal Immunization with a Single IL-4/Antigen Dose Induces Increased Antibody Responses after Challenge Infection with Equine Herpesvirus Type 1 (EHV-1) at Weanling Age. PLoS One 2017
• Goodman et al. High-throughput Detection of Respiratory Pathogens in Animal Specimens by Nanoscale PCR. Journal of Visualized Experiments 2016