Fall 2025

Molecular Diagnostics Section

Driving Innovation in Pathogen Detection and Genomic Surveillance

In today’s fast-moving world of veterinary diagnostics, the Molecular Diagnostics Section at the Nebraska Veterinary Diagnostic Center (NVDC) stands at the forefront of disease detection and surveillance. Our dedicated team of molecular scientists combines expertise with cutting-edge technology to deliver rapid, precise, accurate, and actionable results—protecting animal health, safeguarding public health, and supporting Nebraska’s agricultural economy.

What We Do

The Molecular Diagnostics Section specializes in detecting, identifying, and characterizing pathogens at the genetic level. This work is vital for:

• Rapid disease results to support diagnosis, guide treatment decisions, and assist in testing for regulatory diseases.
• Outbreak tracking and surveillance for endemic and foreign animal threats such as African Swine Fever (ASF), Classical Swine Fever (CSF), and Foot and Mouth Disease (FMD).
• Pathogen typing and characterization, including rotaviruses and BVD typing and bacterial toxinotyping to support disease mitigation strategies.
• Next-generation sequencing (NGS) for identifying unknown pathogens and monitoring pathogen evolution and diversity.
• Advanced applications of digital PCR, enabling ultra-sensitive detection in low target samples (for research).

FY 2024–25 Testing Highlights

This year, the molecular diagnostic section processed 11,418 PCR tests, underscoring its role as a cornerstone of Nebraska’s animal health infrastructure. Highlights include:

• 4,500+ tests for reproductive and enteric pathogens, including Trichomoniasis and Johne’s disease.
• 1,300 tests for Bovine Viral Diarrhea (BVD) and 800+ test panels for Bovine Respiratory Disease (BRD).
• 1,820 Influenza A tests, supporting Nebraska’s poultry and dairy industries and wild bird surveillance.

Expanded multiplex PCR testing for vector-borne diseases such as Anaplasma and Theileria.

Technology That Powers Our Work

The strength of this section lies in both expertise and advanced instrumentation, enabling fast, accurate, and high-quality results:

• Automated Nucleic Acid Extraction and Real-Time PCR Systems. automated nucleic acid extraction and Realtime PCR streamlines PCR testing by reducing manual handling and ensuring consistent, high-quality sample preparation. This leads to faster turnaround times and more reliable results for clients, especially during high-volume testing scenarios.
• Absolute Q digital PCR (dPCR). Used in research applications, dPCR provides ultra-sensitive absolute quantification of genetic targets, supporting the detection of low level of genetic materials. We have developed an assay to detect low levels of genetic material and to test for Bovine Viral Diarrhea (BVD) in ear notch samples. Read the reference article in the Journal of Microbiological Methods.
• Next-Generation Sequencing (NGS)—Illumina iSeq100 for high-throughput genomic sequencing and Oxford Nanopore MinION for rapid, portable sequencing of emerging or unknown pathogens. We use the Illumina iSeq100 for whole genome sequencing (WGS) of bacterial pathogens to identify antimicrobial resistance (AMR) genes. This work is conducted in collaboration with the National Animal Health Laboratory Network (NAHLN).

Discoveries That Matter

• In 2023, our section identified a raccoon variant rabies virus (RRV) in a cat, the first time this strain has been detected in the western U.S. This finding immediately alerted state officials to a new risk, reinforcing the critical role of our molecular surveillance in protecting both animals and people. (Read the reference articles in the AVMA Journal and the CDC Morbidity and Mortality Weekly Report.)
• An outbreak of Highly Pathogenic Avian Influenza (HPAI) started in 2023 in Nebraska, and since then our molecular team has been at the forefront of diagnostic testing. We’ve maintained a rapid turnaround time—delivering results within 24 hours of sample receipt at NVDC—to help control and prevent the spread of this serious disease and have expanded to milk testing to support Nebraska’s dairy producers.
• In response to the SARS-CoV-2 pandemic, our department, with the support of NVDC faculty and staff, conducted over 300,000 Real-Time PCR tests using the SalivaDirect assay from 2020 to 2022. This integration of human diagnostic testing within a veterinary diagnostic laboratory highlights our adaptability and commitment to public health during critical times.

Case report: Pregnancy toxemia

By Dr. Matt Hille

Routine fresh and fixed tissues from a single doe were submitted to the NVDC after several pregnant Boer goats died unexpectedly within a week of kidding. The submission form indicated the does displayed respiratory distress shortly before death in each case. Based on the history and clinical suspicions described on the submission form, the diagnostic workup consisted of histology, aerobic culture of lung, and copper analysis of liver and kidney.

Grossly, the liver was subjectively pale with a pronounced lobular pattern and rounded margins (Figure 1). The most significant histologic finding was severe, diffuse, microvesicular and macrovesicular hepatic lipidosis with multifocal aggregates of neutrophils throughout the liver parenchyma (Figure 2). Other findings included; 1) mild to moderate, multifocal, suppurative inflammation in the heart and kidneys, and 2) aggregates of neutrophils and necrotic debris within the lumina of smaller airways. Corynebacterium pseudotuberculosis was also isolated on lung culture.

The clinical history and hepatocellular accumulation of lipid in this case supported a presumptive diagnosis of pregnancy toxemia. This disease process is well described and is the result of inadequate nutrition in pregnant dams that are in late gestation, especially in those carrying more than one fetus. Ewes and does that are either too thin or overconditioned are at increased risk. The negative energy balance is often the result of a combination of the increased demands of carrying multiple late-term fetuses, inadequate energy content of the feed, and/or the fact that multiple late-term fetuses limit the volume capacity of the rumen which physically limits feed intake. The negative energy balance causes mobilization of fat stores and increased uptake of lipid by hepatocytes. Hepatocellular uptake of lipid is a passive process, but the synthesis and secretion of lipoproteins from hepatocytes is an energy dependent process and is therefore impaired due to the negative energy balance, leading to hepatic lipidosis.

Initially, affected dams will most often present with depression and anorexia that can progress to death in a relatively short period of time. Since the fetuses tend to die in utero prior to death of the dam, it is not uncommon to see evidence of acute septicemia in affected dams postmortem, which is consistent with the acute inflammation in other organs and isolation of Corynebacterium pseudotuberculosis in this case. The most reliable diagnostic test for confirming pregnancy toxemia is evaluation of beta-hydroxybutyrate levels in serum. This method can be used to confirm the diagnosis in clinical animals as well as gauge the risk of individual animals as they approach late gestation, which can help guide management strategies to prevent clinical disease in those deemed more susceptible. Elevated ketones in urine, hypoglycemia, and hypocalcemia are sometimes observed as well, but these tend to be less reliable from a diagnostic standpoint when compared to serum beta-hydroxybutyrate levels.

The Merck Veterinary Manual provides an excellent and more detailed review of pregnancy toxemia in sheep and goats. For clients who are interested in learning more about raising goats as a hobby or a 4-H project, Nebraska Extension has published a NebGuide available online which provides an overview of the basics of goat production in Nebraska.

Maize is a two-year-old half German Shepherd, half Anatolian Shepherd with a personality as big as her heart. She has an endless love for other dogs, instantly lighting up whenever she meets a new four-legged friend. Water is another of her greatest joys. Like many shepherds, she has a watchful streak, staying cautious and suspicious around people unless they’re with dogs and then they are automatically declared safe. Loud noises, especially fireworks, can unsettle her, causing an instant retreat under the bed.

Despite her wariness with strangers, Maize is all heart when it comes to the people she loves. She greets her favorite humans with unreserved joy, bounding in with full enthusiasm, tail wagging, and energy that fills the room. Her blend of loyalty, playfulness, and protectiveness makes her a remarkable companion—equal parts spirited playmate and devoted guardian. 

With her unique mix of German and Anatolian Shepherd traits, Maize is both gentle and bold, a dog who brings a special kind of love and adventure to every day. She is histology manager Kristen Reynolds' companion.