The information below is to help explain guidelines, policies, and deadlines for PCR submissions coming into the Molecular Diagnostics section. As always, please call the NDSU-VDL if you have any questions.
- We will always do our best to get Molecular (PCR) results back in a timely manner; however, due to the SARS-CoV-2 pandemic, many general supplies and reagents are in short supply and unexpected/lengthy absences in a small lab will impact processing and reporting.
- Samples must be received by the business day prior to the scheduled test day to make sure it gets on the run. It takes time to process samples to prepare them for DNA/RNA extraction, and we start extractions by 8am. Therefore, samples dropped off the night before a run may not make it on the run.
- The length of processing varies considerably between specimen type and number of samples. For example, 5 Trichs will take ~15 minutes to process and 5 BVD ear notches will take over an hour. One hundred (20 pools) for Johne’s can take an hour to lay out and weigh if properly labeled and clean, or closer to three hours if samples are contaminated on the outside and we have to relabel them.
Important Johne’s Test Notes:
- It is essential to have consecutive Sample ID numbers (starting with 1, 2, 3, etc.) on the fecal samples. Correctly labeling will avoid extra processing fees and get your results turned around faster.
- Please fill out and send the Sample Identification Form electronically. This allows for the case to be entered quickly and without transcription errors.
- DO NOT send fecal samples in whirl packs, exam gloves, or glass containers. These usually leak and can contaminate other samples. They also take a great deal of extra time to process.
Johne’s submission case study: Last year, a particular case took over 8 hours across two days to label and organize a case of ~350 fecals with only animal IDs that were thrown randomly into 5 boxes. After feedback from the NDSU-VDL, the latest submission was labelled with consecutive Sample ID numbers starting with 1, and forms were typed and submitted electronically. It only took 30 minutes to organize before we could weigh and pool the samples, and we were able to test and report results within 5 days.
Important molecular test limitations:
Failure to include a collection date may cause delays in your results because we cannot postpone a run and delay other clients’ results while waiting for a collection date.
It is very important to send samples quickly after collection. Always include the collection date and case history/reason for testing on every submission.
- Send samples to the VDL as soon as possible. Fresh samples yield the best results. PCR, like many other diagnostics tests, is susceptible to effects of sample degradation, particularly those caused by inhibitors. Inhibitors include (but are not limited to) proteases, EDTA, heme, urea, formalin, gel, and overgrowth. In addition, DNA and RNA can degrade rapidly due to DNases, RNases, and suboptimal temperatures. For these reasons, there are timelines for sample submissions on specific tests such as urines (Leptospirosis), blood (Bovine Leukosis) and preputial washes (Tritrichomonas). Inhibitors do not have the same effect on all assays, and we do processing steps upon receiving specimens to remove/wash inhibitors so they can be frozen until DNA/RNA extraction.
- In general, “negative” or “not detected” PCR results on any specimen that does not arrive at the VDL within 5 days should be interpreted with caution. Inhibitors and degradation of target DNA/RNA may result in false negatives.
- Please collect a sample before antibiotic or antiviral treatment, as prior treatment(s) may have cleared up the infection.
- PCR will detect the DNA/RNA of the pathogen, if it is present. Please keep in mind that the pathogen could be dead or alive, actively infecting the host, just passing through, or a vaccine strain (see below). Therefore, it is important to also look at case history and symptomology for a diagnosis.
- It is helpful to include vaccination history on submission forms. In many cases, PCR assays can detect vaccine strains so it is recommended that you wait a minimum of two weeks, preferably at least four weeks, between vaccination and testing. Bovine viral diarrhea virus and canine distemper are the most common tests where we can detect vaccine strains. These can cause a false positive or suspect result because our assays cannot differentiate between vaccine and wild type strains.
- It is very helpful if you let us know when you are sending more than 50 individuals for the majority of our PCR tests, and more than 250 individuals for Johne’s. This gives us time to make sure we have enough reagents and plastics available or prepped, and streamline testing for a given day.
- We are always looking to improve our test offerings based on client needs. Please let us know if there are any tests or pathogens you would like us to add into the Molecular Diagnostics PCR test list and we would be happy to look into it.
Brianna Stenger, PhD
Molecular Diagnostics Section Head